[ { "question":"How many subunits make up the RNA polymerase I complex in Arabidopsis thaliana?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis, RNA Pol I consists of 12 protein subunits common to RNA Pol II and Pol III the two others being RNA Pol I-specific subunits.", "In Arabidopsis, RNA Pol I consists of 14 protein subunits: 12 are RNA Pol I-specific protein subunits and two others are common to RNA Pol II and Pol III.", "In Arabidopsis, RNA Pol I consists of 12 subunits common to those of all nuclear RNA polymerases (RNA Pol I\u2013Pol V). 5 are common to RNA Pol II and Pol III and the others are RNA Pol I-specific subunits." ], "source":"10.1093\/nar\/gkv247", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1093\/nar\/gkv247", "Year":2015.0, "Citations":20.0, "answer":2, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"What is in an RNA polymerase I holoenzyme?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "RNA Pol I holoenzyme is the RNA Pol I complex that associates with additional General Transcription Factor (GFTs) to form larger RNA Pol I complexes which are competent for RNA pol I elongation", "RNA Pol I holoenzyme is the RNA Pol I \u201ccore\u201d complex competent to specifically initiate rDNA transcription", "The RNA Pol I holoenzyme is the RNA Pol I complex associated to General Transcription Factors (GFTs) to form larger RNA Pol I complexes capable of specifically initiating rDNA transcription" ], "source":"10.1073\/pnas.94.22.11869", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1073\/pnas.94.22.11869", "Year":1997.0, "Citations":48.0, "answer":2, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"Can the activity of RNA polymerase I complex be regulated by casein kinase 2 (CK2)?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "CK2 interacts with the RNA Pol I holoenzyme and it can phosphorylate transcription factors, thereby increasing rDNA transcription", "CK2-like protein (CASEIN KINASE2) interacts with the RNA Pol I holoenzyme and can desphosphorylate transcription factors, thereby increasing rDNA transcription.", "CK2-like protein (CASEIN KINASE2) interacts with the RNA Pol I holoenzyme and can phosphorylate transcription factors, thereby decreasing rDNA transcription." ], "source":"10.1023\/a:1011619413393", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1023\/a:1011619413393", "Year":2001.0, "Citations":16.0, "answer":0, "source_journal":"Plant Molecular Biology", "is_expert":true }, { "question":"Which genes are transcribed by RNA polymerase I in Arabidopsis plants?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The RNA Pol I transcribes a single 45S rDNA copy gene encoding the rRNA 18S, 5.8S and 25S.", "The RNA Pol I transcribes the rRNA 18S, 5.8S, 5S and 25S ", "The RNA Pol I transcribes the tandemly organised 45S rDNA encoding the rRNA 18S, 5.8S and 25S. " ], "source":"10.1105\/tpc.18.00874", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1105\/tpc.18.00874", "Year":2019.0, "Citations":124.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"Where does RNA polymerase I transcriptional activity take place?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "The RNA Pol I transcription takes place in the nucleolus and more precisely in the dense fibrillary centres (DFC).", "The RNA Pol I transcription takes place in the nucleolus and more precisely in the dense fibrillary component (DFC).", "The RNA Pol I transcription takes place in the nucleoplasm and more precisely in the dense fibrillary component (DFC)." ], "source":"10.1038\/s41580-020-0272-6", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41580-020-0272-6", "Year":2020.0, "Citations":708.0, "answer":1, "source_journal":"Nature Reviews Molecular Cell Biology", "is_expert":true }, { "question":"Can plant microRNA (miRNA) precursors be shortened to express artificial microRNAs (amiRNAs) from viral vectors?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "non-specific" ], "options":[ "Yes, plant miRNA precursors can be shortened to express amiRNAs from viral vectors, as such minimal precursors retain the essential structural features necessary for accurate processing and function.", "No, plant miRNA precursors cannot be shortened to express amiRNAs from viral vectors, as such minimal precursors do not retain the essential structural features necessary for accurate processing and function.", "Yes, plant miRNA precursors can be shortened to express artificial miRNAs from viral vectors, but the shortening removes essential structural features required for proper processing, resulting in non-functional amiRNAs." ], "source":"https:\/\/doi.org\/10.1093\/nar\/gkad747", "normalized_plant_species":"Non-specific", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1093\/nar\/gkad747", "Year":2023.0, "Citations":16.0, "answer":0, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"Can TAS1c-based synthetic trans acting small interfering RNAs (syn-tasiRNAs) move throughout Nicotiana benthamiana and induce the systemic silencing of the SULPHUR gene?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "non-specific" ], "options":[ "No, TAS1c-based syn-tasiRNAs can move throughout Nicotiana benthamiana, but they are unable to induce systemic silencing of the SULPHUR gene because their movement is restricted to the local tissue where they are produced and do not enter the phloem for long-distance movement.", "Yes, TAS1c-based syn-tasiRNAs can move throughout Nicotiana benthamiana and induce the systemic silencing of the SULPHUR gene. Syn-tasiRNAs are processed from TAS1c precursors and move as duplexes though the phloem to reach apical tissues where they are incorporated into ARGONAUTE1 proteins to degrade SULPHUR mRNAs.", "Yes, TAS1c-based syn-tasiRNAs can move throughout Nicotiana benthamiana and induce the systemic silencing of the SULPHUR gene. TAS1c precursors move through the phloem to reach apical tissues where they are processed into syn-tasiRNA duplexes, and are incorporated into ARGONAUTE1 proteins to degrade SULPHUR mRNAs." ], "source":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/tpj.15730", "normalized_plant_species":"Non-specific", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1111\/tpj.15730", "Year":2022.0, "Citations":10.0, "answer":1, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"Under which molecular form do artificial microRNAs (amiRNAs) and synthetic trans acting small interfering RNAs (syn-tasiRNAs) move throughout Nicotiana benthamiana to induce systemic silencing of endogenous genes?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Nicotiana benthamiana" ], "options":[ "AmiRNAs and syn-tasiRNAs move throughout the plant to induce systemic silencing, typically in the form of ARGONAUTE 1-small RNA complexes that are ready for target-specific silencing.", "AmiRNAs and syn-tasiRNAs move throughout the plant to induce systemic silencing, typically in the form of small RNA precursors that, in distal tissues, are processed into small RNA duplexes that are loaded into ARGONAUTE 1 for target-specific silencing.", "AmiRNAs and syn-tasiRNAs move throughout Nicotiana benthamiana to induce systemic silencing, typically in the form of small RNA duplexes that are loaded into ARGONAUTE 1 for target-specific silencing." ], "source":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/tpj.15730", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1111\/tpj.15730", "Year":2022.0, "Citations":10.0, "answer":2, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"Does multi-targeting of viral RNAs with synthetic trans-acting small interfering RNAs (syn-tasiRNAs) enhance plant antiviral resistance?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "non-specific" ], "options":[ "Yes, multi-targeting of viral RNAs with syn-tasiRNAs enhances plant antiviral resistance. By expressing multiple syn-tasiRNAs from a single precursor, plants can simultaneously target several regions of a viral genome or even multiple viral genomes, minimizing the likelihood of viral escape mutants, as the virus would need to mutate multiple target sites simultaneously to overcome the resistance.", "No, multi-targeting of viral RNAs with syn-tasiRNAs fails to enhance plant antiviral resistance. Expressing multiple syn-tasiRNAs from a single precursor results in competition among the syn-tasiRNAs, reducing their overall efficiency and allowing viruses to evade silencing more easily.", "Yes, multi-targeting of viral RNAs syn-tasiRNAs enhances plant antiviral resistance. By expressing multiple syn-tasiRNAs from a single precursor, plants can simultaneously target several regions of a viral genome or even multiple viral genomes, maximizing the likelihood of viral escape mutants, as the virus would not need to mutate multiple target sites simultaneously to overcome the resistance." ], "source":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/tpj.14466", "normalized_plant_species":"Non-specific", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1111\/tpj.14466", "Year":2019.0, "Citations":44.0, "answer":0, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"How is it possible to fine-tune control target RNAi efficacy in Arabidopsis thaliana using syn-tasiRNAs?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "It is possible to fine-tune target gene expression with syn-tasiRNAs in Arabidopsis thaliana through two strategies: i) by modulating the level of accumulation of a syn-tasiRNA if changing its precursor position, and ii) by modifying the degree of base-pairing between the 3' end of the syn-tasiRNA and the 5' end of the target RNA.", "It is possible to fine-tune target gene expression with syn-tasiRNAs in Arabidopsis thaliana through two strategies: i) by modulating the level of accumulation of a syn-tasiRNA if changing its precursor position, and ii) by modifying the degree of base-pairing between the 5' end of the syn-tasiRNA and the 3' end of the target RNA.", "It is possible to fine-tune target gene expression with syn-tasiRNAs in Arabidopsis thaliana through two strategies: i) by modulating the level of accumulation of a syn-tasiRNA if maintaining its precursor position, and ii) by maintaining the degree of base-pairing between the 3' end of the syn-tasiRNA and the 5' end of the target RNA." ], "source":"https:\/\/doi.org\/10.1093\/nar\/gkaa343", "normalized_plant_species":"Model Organisms", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1093\/nar\/gkaa343", "Year":2020.0, "Citations":20.0, "answer":0, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"Do you find rna polymerase ii transcription start sites only in annotated gene promoter regions?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "No, there are two places where rna polymerase ii can start transcription. 1.) in gene promoters, 2.) in some regions between annotated genes. ", "Yes, the only location where transcription starts are gene promoters. ", "No, it is possible to detect transcription start sites in additional regions without annotated promoters, for example some intergenic regions. In addition, transcription can start within annotated genes on the sense and antisense strand. " ], "source":"10.1371\/journal.pgen.1007969", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1371\/journal.pgen.1007969", "Year":2019.0, "Citations":72.0, "answer":2, "source_journal":"PLOS Genetics", "is_expert":true }, { "question":"Are plant genes are only transcribed in one direction?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "Yes, the only way plant genes can be transcribed is in the direction that results in sense mRNA. ", "No, but the only type of antisense transcription from genes starts in the 3\u00b4-UTR of plant genes. ", "No, antisense transcription is common. It can either be antisense transcription initiating in the 3\u00b4-UTR, or initiation of antisense transcription intragenically. " ], "source":"10.1093\/nar\/gkz1189", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1093\/nar\/gkz1189", "Year":2019.0, "Citations":91.0, "answer":2, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"When transcription starts in gene promoters, are only possible outcomes the production of mRNA isoforms?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "No, rna polymerase ii can continue transcription of a different chromosome due to the 3-dimensional genome architecture of plants. ", "Yes, once rna polymerase ii initiates transcription from a plant gene promoter the only outcome is the production of mRNA isoforms. ", "No, initiation of rna polymerase ii transcription from gene promoters often results in the production of short promoter-proximal RNAs. " ], "source":"10.1038\/s41467-020-16390-7", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41467-020-16390-7", "Year":2020.0, "Citations":49.0, "answer":2, "source_journal":"Nature Communications", "is_expert":true }, { "question":"Are there methylation signatures of histone H3 tails that correlate positively with rna polymerase ii transcriptional activity?", "area":"GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS", "plant_species":[ "non-specific" ], "options":[ "Yes, in particular tri-methylation and di-methylation of histone 3 lysine 4, and histone 3 lysine 36. ", "Yes, histone 3 lysine 27 tri-methylation.", "No, only acetylation of histone H3 tails correlates positively with rna polymerase ii transcription. " ], "source":"10.1016\/j.tplants.2020.03.005", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.tplants.2020.03.005", "Year":2020.0, "Citations":33.0, "answer":0, "source_journal":"Trends in Plant Science", "is_expert":true }, { "question":"Is the transcript resulting from the torpedo-mechanism of transcriptional termination is incorporated into standard genome annotations?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "No, standard methods such as RNA-seq usually rely on 3\u00b4- poly-adenylated and 5\u00b4-m7G capped RNA species. The transcript associated with torpedo termination lacks both of these features and is therefore usually missing in genome annotations unless the information from suitable methods is used. ", "No, the reason is that these transcripts do not really exist because RNA-seq cannot detect them. ", "Yes, these transcripts are generated when an mRNA is produced and are therefor also part of genome annotations. " ], "source":"10.1186\/s12859-021-04259-5.", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1186\/s12859-021-04259-5", "Year":2021.0, "Citations":1.0, "answer":0, "source_journal":"BMC Bioinformatics", "is_expert":true }, { "question":"How does the UV-B photoreceptor UVR8 regulate gene expression changes in Arabidopsis thaliana plants?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "After UV-B absorption, the homodimeric UVR8 induces its monomerization, and monomeric UVR8 interacts with the E3 ubiquitin ligases RUP1 and RUP2, leading to gene expression changes. UVR8 is then inactivated through redimerization, facilitated by COP1.", "After UV-B absorption, the monomeric UVR8 induces its dimerization, and UVR8 dimers interact with the E3 ubiquitin ligase COP1, leading to gene expression changes. UVR8 is then inactivated through remonomerization, facilitated by RUP1 and RUP2.", "After UV-B absorption, the homodimeric UVR8 induces its monomerization, and monomeric UVR8 interacts with the E3 ubiquitin ligase COP1, leading to gene expression changes. UVR8 is then inactivated through redimerization, facilitated by RUP1 and RUP2." ], "source":"https:\/\/doi.org\/10.1073\/pnas.2017284118", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1073\/pnas.2017284118", "Year":2021.0, "Citations":34.0, "answer":2, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"Which are the similitudes and differences between palisade and other photosynthetic cells from Arabidopsis leaves exposed to UV radiation?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Palisade cells have a unique morphology, but are transcriptionally similar to other photosynthetic cell types. However, some genes in the phenylpropanoid biosynthesis pathway, which are required for production of the ultraviolet protectant sinapoylmalate, have palisade-enriched expression. ", "Palisade cells have a similar morphology, but are transcriptionally different to other photosynthetic cell types. Moreover, some genes in the phenylpropanoid biosynthesis pathway, which are required for production of the ultraviolet protectant sinapoylmalate, have palisade-enriched expression. ", "Palisade cells have a unique morphology, and are transcriptionally different to other photosynthetic cell types. Moreover, some genes in the phenylpropanoid biosynthesis pathway, which are required for production of the ultraviolet protectant sinapoylmalate, have palisade-enriched expression. " ], "source":"doi: 10.1093\/plcell\/koac167.", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1093\/plcell\/koac167", "Year":2022.0, "Citations":60.0, "answer":0, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"Which proteins physically interact in the regulation of UV-B tolerance depending on the jasmonic acid signaling pathway in A. thaliana?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "UV RESISTANCE LOCUS 8 (UVR8), TEOSINTE BRANCHED1, Cycloidea and PCF 4 (TCP4) and LIPOXYGENASE2 (LOX2) physically interacts in the nuclei to increase the DNA binding activity of TCP4 and upregulate the JA biosynthesis.", "UV RESISTANCE LOCUS 8 (UVR8) and TEOSINTE BRANCHED1, Cycloidea and PCF 4 (TCP4) physically interacts in the nuclei to increase the DNA binding activity of TCP4 and upregulate the JA biosynthesis gene LOX2.", "UV RESISTANCE LOCUS 8 (UVR8), TEOSINTE BRANCHED1, Cycloidea and PCF 4 (TCP4) and LIPOXYGENASE2 (LOX2) physically interacts in the nuclei to increase the DNA binding activity of TCP4 and downregulate the JA biosynthesis." ], "source":"https:\/\/doi.org\/10.1111\/jipb.13648", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/jipb.13648", "Year":2024.0, "Citations":9.0, "answer":1, "source_journal":"Journal of Integrative Plant Biology", "is_expert":true }, { "question":"Which plant photoreceptors participate in the induction of FERULIC ACID 5-HYDROXYLASE 1 (FAH1), leading to the accumulation of UV-absorbing sinapate esters in Arabidopsis?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Both UV RESISTANCE LOCUS 8 (UVR8) UV-B and phytochrome red, but not cryptochrome blue-light photoreceptors, converge on the induction of FERULIC ACID 5-HYDROXYLASE 1 (FAH1), which encodes a key enzyme in the phenylpropanoid biosynthesis pathway. This induction leads to the accumulation of UV-absorbing sinapate esters in Arabidopsis.", "Both UV RESISTANCE LOCUS 8 (UVR8) UV-B and cryptochrome blue, but not phytochrome red light photoreceptors, converge on the induction of FERULIC ACID 5-HYDROXYLASE 1 (FAH1), which encodes a key enzyme in the phenylpropanoid biosynthesis pathway. This induction leads to the accumulation of UV-absorbing sinapate esters in Arabidopsis.", "UV RESISTANCE LOCUS 8 (UVR8) UV-B, phytochrome red, and cryptochrome blue-light photoreceptors converge on the induction of FERULIC ACID 5-HYDROXYLASE 1 (FAH1), which encodes a key enzyme in the phenylpropanoid biosynthesis pathway. This induction leads to the accumulation of UV-absorbing sinapate esters in Arabidopsis." ], "source":"https:\/\/doi.org\/10.1093\/plphys\/kiae352", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1093\/plphys\/kiae352", "Year":2024.0, "Citations":1.0, "answer":2, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"What is the role of the Jumonji27 (JMJ27) protein during the UV-induced DNA damage in Arabidopsis thaliana plants?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "JMJ27 is responsible for the UV-induced reduction of H3K9me2 content at chromocenters. In addition, JMJ27 forms a complex with the photodamage recognition factor, DNA Damage Binding protein 2 (DDB2). The fine tuning of H3K9me2 contents orchestrates DDB2 dynamics on chromatin in response to UV-C exposure.", "JMJ27 is responsible for the UV-induced increase in H3K9me2 content at chromocenters. In addition, JMJ27 forms a complex with the photodamage recognition factor, DNA Damage Binding protein 1 (DDB1). The fine tuning of H3K9me2 contents orchestrates DDB1 dynamics on chromatin in response to UV-C exposure.", "JMJ27 is responsible for the UV-induced reduction in H3K9me2 content at chromocenters. In addition, JMJ27 forms a complex with the photodamage recognition factor, DNA Damage Binding protein 1 (DDB1). The fine tuning of H3K9me2 contents orchestrates DDB1 dynamics on chromatin in response to UV-C exposure." ], "source":"https:\/\/doi.org\/10.1038\/s41477-024-01814-9", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/s41477-024-01814-9", "Year":2024.0, "Citations":1.0, "answer":0, "source_journal":"Nature Plants", "is_expert":true }, { "question":"Which proteins have been identified as physical interactors of the C subunit of the Nuclear Factor Y 1 (NF-YC1) from common bean (Phaseolus vulgaris)?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Phaseolus vulgaris" ], "options":[ "SIN1 and NF-YA1 have been identified by bimolecular fluorescence complementation using an NF-YC1-gfp fusion. Both proteins are involved in nodule development. ", "SIN1 and NIPK have been identified by a yeast two hybrid screening using NF-YC1 as a bait. Both proteins are involved in nodule development. ", "SIN1 and NF-YA1 have been identified by a yeast two hybrid screening using NF-YC1 as a bait. Only NF-YA1 is involved in nodule development. " ], "source":"10.3389\/fpls.2022.992543 10.1104\/pp.113.230896", "normalized_plant_species":"Legumes", "normalized_area":"ENVIRONMENT", "doi":"10.1104\/pp.113.230896", "Year":2014.0, "Citations":53.0, "answer":1, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"The promotor of which gene is recognized by the complex that contains NF-YC1 from common bean (Phaseolus vulgaris) and what is its function?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Phaseolus vulgaris" ], "options":[ "NF-YC1 binds to the promoter of Aurora, a cyclin protein that controls the cell cycle and is involved in root hair development", "NF-YC1 binds to the promoter of the cyclin P3;1, a cyclin protein that controls the DNA repair and is involved in root hair development", "NF-YC1 binds to the promoter of the cyclin P4;1,a cyclin protein that controls the cell cycle and is involved in nodule organogenesis" ], "source":"https:\/\/doi.org\/10.1111\/nph.19419", "normalized_plant_species":"Legumes", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/nph.19419", "Year":2023.0, "Citations":0.0, "answer":2, "source_journal":"New Phytologist", "is_expert":true }, { "question":"How small GTPases from the Rab subfamily have been associated to nodulation in common bean (Phaseolus vulgaris)?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Phaseolus vulgaris" ], "options":[ "RabA2a from common bean was identified by its differential expression in response to two different strains of Rhizobium leguminosarum. It is expressed in roots, particularly in athrichoblasts and the protein is located in vesicles. Genetic studies have shown that RabA2a is required for root growth, early infection events and nodule development.", "RabA2a from common bean was identified by its differential expression in response to two different strains of Rhizobium etli. It is expressed in roots, particularly in thrichoblasts and the protein is located in vesicles. Genetic studies have shown that RabA2a is required for root hair growth, early infection events and nodule development.", "RabA2a from common bean was identified by its differential expression in response to two different strains of Rhizobium tropici. It is expressed in roots, particularly in athrichoblasts and the protein is located in the nucleus. Genetic studies have shown that RabA2a is required for lateral root growth, early infection events and nodule development." ], "source":"10.1094\/MPMI, 10.1105\/tpc.108.063420", "normalized_plant_species":"Legumes", "normalized_area":"ENVIRONMENT", "doi":"10.1105\/tpc.108.063420", "Year":2009.0, "Citations":51.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How the trimer of NF-YC that acts during symbiosis was identified in common bean (Phaseolus vulgaris)?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Phaseolus vulgaris" ], "options":[ "The subunits of the trimer formed by NF-YA1, NF-YB1 and NF-YC1 were selected according to their expression pattern in root hairs and tested by coimmunoprecipitation assays", "The subunits of the trimer formed by NF-YA1, NF-YB7 and NF-YC1 were selected according to their expression pattern at early stages of the symbiotic interaction and tested by coimmunoprecipitation assays", "The subunits of the trimer formed by NF-YA1, NF-YB1 and NF-YC1 were selected according to their expression pattern at early stages of the symbiotic interaction and tested by bimolecular fluorescence complementation" ], "source":"10.1104\/pp.15.01144", "normalized_plant_species":"Legumes", "normalized_area":"ENVIRONMENT", "doi":"10.1104\/pp.15.01144", "Year":2015.0, "Citations":25.0, "answer":1, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"How RNAs produced by Bradyrhizobium japonicum can modulate soybean (Glycine max) genes to promote nodulation?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Glycine max" ], "options":[ "Small fragments of RNA are produced in Bradyrhizobium japonicum by degradation of tRNAs (tRFs) and transported to soybean cells, where postranscriptionally regulate mRNA targets using ARGONAUTE 1 and the host RNAi machinery. tRFs are positive regulators of nodulation since their mRNA targets repress nodule formation.", "Small fragments of RNA are produced in Bradyrhizobium japonicum by degradation of mRNAs (tRFs) and transported to soybean cells, where postranscriptionally regulate mRNA targets using ARGONAUTE 2 and the host RNAi machinery. tRFs are positive regulators of nodulation since their mRNA targets repress nodule formation.", "Small fragments of RNA are produced in Bradyrhizobium japonicum by degradation of rRNAs (tRFs) and transported to soybean cells, where postranscriptionally regulate mRNA targets using ARGONAUTE 4 and the host RNAi machinery. tRFs are negative regulators of nodulation since their mRNA targets promote nodule formation." ], "source":"10.1126\/science.aav8907", "normalized_plant_species":"Legumes", "normalized_area":"ENVIRONMENT", "doi":"10.1126\/science.aav8907", "Year":2019.0, "Citations":221.0, "answer":0, "source_journal":"Science", "is_expert":true }, { "question":"What is the impact of the presence of an IR inserted near the sunflower HaWRKY6 locus?", "area":"GENE REGULATION - PTGS", "plant_species":[ "Helianthus annuus" ], "options":[ "The presence of an IR inserted near the sunflower HaWRKY6 locus regulates the expression of the HaWRKY6 gene by altering the chromatin structure. The IR is transcribed, and its transcript gives rise to 21-nt siRNAs, which trigger posttranscriptional silencing. This epigenetic mark stabilizes the formation of two alternative chromatin loops: one loop forms in cotyledons, enhancing HaWRKY6 transcription, while an alternative intragenic loop forms in leaves, repressing HaWRKY6 transcription.", "The presence of an IR inserted near the sunflower HaWRKY6 locus regulates the expression of the HaWRKY6 gene by altering the chromatin structure. The IR is transcribed, and its transcript gives rise to 24-nt siRNAs, which trigger DNA methylation. This epigenetic mark stabilizes the formation of two alternative chromatin loops: one loop forms in cotyledons, enhancing HaWRKY6 transcription, while an alternative intragenic loop forms in leaves, repressing HaWRKY6 transcription.", "The presence of an IR inserted near the sunflower HaWRKY6 locus regulates the expression of the HaWRKY6 gene by altering the promoter efficiency. The IR is transcribed, and its transcript gives rise to 24-nt siRNAs, which trigger DNA methylation. This epigenetic mark stabilizes the formation of two alternative chromatin loops: one loop forms in cotyledons, repressing HaWRKY6 transcription, while an alternative intragenic loop forms in leaves, activating HaWRKY6 transcription." ], "source":"https:\/\/doi.org\/10.1073\/pnas.1903131116", "normalized_plant_species":"Other Herbaceous Crops, Spices, Fibers & Weeds", "normalized_area":"GENE REGULATION", "doi":"10.1073\/pnas.1903131116", "Year":2019.0, "Citations":41.0, "answer":1, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"How can the insertion of transposon-derived inverted repeats (IRs) impact transcription in Arabidopsis thaliana?", "area":"GENE REGULATION - PTGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The presence of transposon-derived inverted repeats (IRs), particularly near coding genes can cause chromatin rearrangements. These rearrangements often lead to the formation of short-range chromatin loops, which are associated with either the activation or repression of transcription in neighboring genes.", "The presence of transposon-derived inverted repeats (IRs), particularly in non-coding regions can cause chromatin rearrangements. These rearrangements often lead to the formation of long-range chromatin loops, which are associated with either the activation or repression of transcription in neighboring genes.", "The presence of transposon-derived inverted repeats (IRs), anywhere in the genome can cause chromatin rearrangements. These rearrangements often lead to the formation of short-range chromatin loops, which are associated with the activation of transcription in neighboring genes." ], "source":"https:\/\/doi.org\/10.1016\/j.celrep.2023.112029", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.celrep.2023.112029", "Year":2023.0, "Citations":12.0, "answer":0, "source_journal":"Cell Reports", "is_expert":true }, { "question":"How do transposon-derived inverted repeats (IRs) impact the adaptation of Arabidopsis thaliana?", "area":"GENE REGULATION - PTGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The natural variation in the presence of transposon-derived inverted repeats (IRs) among Arabidopsis thaliana accessions and their correlation with variations in gene expression can explain the differential phenotypes observed among these accessions. Therefore, IRs represent powerful elements in adaptive evolution.", "The lack of variation in the presence of transposon-derived inverted repeats (IRs) among Arabidopsis thaliana accessions and their correlation with similar gene expression can explain the lack of differential phenotypes observed among these accessions. Therefore, IRs represent powerful elements in adaptive evolution.", "The natural variation in the presence of transposon-derived inverted repeats (IRs) among Arabidopsis thaliana accessions and their lack of correlation with variations in gene expression cannot explain the differential phenotypes observed among these accessions. Therefore, IRs do not represent significant elements in adaptive evolution." ], "source":"https:\/\/doi.org\/10.1016\/j.celrep.2023.112029", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.celrep.2023.112029", "Year":2023.0, "Citations":12.0, "answer":0, "source_journal":"Cell Reports", "is_expert":true }, { "question":"Is RdDM-dependent silencing of transposable elements always associated with the transcriptional repression of the TEs and their surrounding regions in Arabidopsis?", "area":"GENE REGULATION - PTGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In the case of transposon-derived inverted repeats (IRs), non-canonical RdDM, triggered by the production of 24-nt siRNAs from the single-stranded secondary structure formed by Pol IV-driven IR transcription, and the resulting DNA condensation, appears to function differently. For example, it can alter chromatin topology, always increasing transcription of neighboring genes.", "In the case of transposon-derived inverted repeats (IRs), non-canonical RdDM, triggered by the production of 24-nt siRNAs from the double-stranded secondary structure formed by Pol II-driven IR transcription, and the resulting DNA methylation, appears to function differently. For example, it can alter chromatin topology, either increasing or decreasing transcription of neighboring genes.", "In the case of transposon-derived inverted repeats (IRs), canonical RdDM, triggered by the production of 21-nt siRNAs from the double-stranded secondary structure formed by Pol II-driven IR transcription, and the resulting DNA methylation, appears to function conservatively. For example, it can alter chromatin condensation causing IR silencing." ], "source":"https:\/\/doi.org\/10.1016\/j.celrep.2023.112029", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.celrep.2023.112029", "Year":2023.0, "Citations":12.0, "answer":1, "source_journal":"Cell Reports", "is_expert":true }, { "question":"Which transposable elements have been identified as capable of regulating the expression of the EFR gene in Arabidopsis thaliana?", "area":"GENE REGULATION - PTGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "A transposon-derived inverted repeat (IR) element located downstream of the EFR gene in Arabidopsis thaliana, named Ea-IR, has the capacity to regulate EFR gene expression. Depending on its methylation state, the Ea-IR can rearrange chromatin topology, creating a short-range chromatin loop that enhance EFR gene expression, ultimately affecting pathogen responses.", "A transposon-derived inverted repeat (IR) element located upstream of the EFR gene in Arabidopsis thaliana, named Ea-IR, has the capacity to regulate EFR gene expression. Depending on its methylation state, the Ea-IR can rearrange chromatin topology, creating a short-range chromatin loop that inhibiting EFR gene expression, ultimately affecting pathogen responses.", "A transposon-derived inverted repeat (IR) element located in the second exon of the EFR gene in Arabidopsis thaliana, named Ea-IR, has the capacity to regulate EFR gene expression. Depending on its orientation, the Ea-IR can rearrange itself, enhancing EFR gene expression, ultimately affecting pathogen responses." ], "source":"https:\/\/doi.org\/10.1101\/2023.10.06.561201", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1101\/2023.10.06.561201", "Year":2023.0, "Citations":0.0, "answer":0, "source_journal":null, "is_expert":true }, { "question":"What are the two main molecular mechanisms for the co-regulation of hypocotyl growth by auxin and gibberellin (GA) in Arabidopsis?", "area":"HORMONES", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The two primary mechanisms are: (1) Auxin-induced gibberellin catabolism: Auxin stimulates the ARF-dependent transcriptional upregulation of genes encoding GA 2-oxidases, which are key enzymes in gibberellin inactivation. This leads to decreased local GA production in hypocotyl tissues, driving cell elongation. (2) DELLA protein interaction with ARF transcription factors: ARF transcription factors repress cell elongation but are suppressed by their interaction with DELLA proteins. Gibberellins counteract this inhibition by promoting the degradation of DELLA proteins, thereby freeing ARF transcription factors to repress elongation-related processes.", "The two primary mechanisms are: (1) Auxin-induced gibberellin biosynthesis: Auxin stimulates the ARF-dependent transcriptional upregulation of genes encoding GA 20-oxidases and GA 3-oxidases, which are key enzymes in gibberellin biosynthesis. This leads to increased local GA production in hypocotyl tissues, repressing cell elongation. (2) DELLA protein interaction with ARF transcription factors: ARF transcription factors facilitate cell elongation and are enhanced by their interaction with DELLA proteins. Gibberellins counteract this stimulation by promoting the degradation of DELLA proteins, thereby impairing the promotion by ARF transcription factors of elongation-related processes.", "The two primary mechanisms are: (1) Auxin-induced gibberellin biosynthesis: Auxin stimulates the ARF-dependent transcriptional upregulation of genes encoding GA 20-oxidases and GA 3-oxidases, which are key enzymes in gibberellin biosynthesis. This leads to increased local GA production in hypocotyl tissues, driving cell elongation. (2) DELLA protein interaction with ARF transcription factors: ARF transcription factors facilitate cell elongation but are suppressed by their interaction with DELLA proteins. Gibberellins counteract this inhibition by promoting the degradation of DELLA proteins, thereby freeing ARF transcription factors to activate elongation-related processes." ], "source":"https:\/\/doi.org\/10.1104\/pp.106.084871 https:\/\/doi.org\/10.7554\/eLife.03031", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.7554\/eLife.03031", "Year":2014.0, "Citations":459.0, "answer":2, "source_journal":"eLife", "is_expert":true }, { "question":"What three molecular changes explain the conversion of an ancestral carboxylesterase into a gibberellin receptor?", "area":"HORMONES", "plant_species":[ "non-specific" ], "options":[ "The conversion of an ancestral carboxylesterase into a gibberellin (GA) receptor is explained by the following three molecular changes: (1) Loss of enzymatic activity: The carboxylesterase's enzymatic function was reduced or eliminated, permitting the protein to specialize as a receptor. This loss enabled the focus on gibberellin recognition without interference from the original carboxylesterase activity. (2) Loss of the ligand binding capacity: The ancestral carboxylesterase lost a specific pocket or binding site capable of recognizing gibberellin molecules. (3) Signal transduction adaptation: the ancestral protein developed the ability to phosphorylate DELLA proteins through a newly developed protein kinase domain.", "The conversion of an ancestral carboxylesterase into a gibberellin (GA) receptor is explained by the following three molecular changes: (1) Gain of enzymatic activity: The carboxylesterase's enzymatic function was enhanced, permitting the protein to specialize as a receptor. This loss enabled the focus on gibberellin recognition in addition to maintaining the original carboxylesterase activity. (2) Structural modification for ligand binding: The ancestral carboxylesterase acquired a specific pocket or binding site capable of recognizing gibberellin molecules. (3) Signal transduction adaptation: the ancestral protein developed the ability to interact with the F-box protein SLEEPY\/GID2 through a dedicated surface region.", "The conversion of an ancestral carboxylesterase into a gibberellin (GA) receptor is explained by the following three molecular changes: (1) Loss of enzymatic activity: The carboxylesterase's enzymatic function was reduced or eliminated, permitting the protein to specialize as a receptor. This loss enabled the focus on gibberellin recognition without interference from the original carboxylesterase activity. (2) Structural modification for ligand binding: The ancestral carboxylesterase acquired a specific pocket or binding site capable of recognizing gibberellin molecules. (3) Signal transduction adaptation: the ancestral protein developed the ability to interact with DELLA proteins through a dedicated surface region." ], "source":"DOI: 10.1073\/pnas.1806040115", "normalized_plant_species":"Non-specific", "normalized_area":"HORMONES", "doi":"10.1073\/pnas.1806040115", "Year":2018.0, "Citations":56.0, "answer":2, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"What is the impact of gibberellins in the control of flowering time in Arabidopsis and what are the main flowering-time genes involved?", "area":"HORMONES", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Gibberellins are essential to repress flowering under non-inductive short-day conditions. They do it by decreasing the expression of key flowering-time genes, such as LEAFY and SUPPRESSOR OF CONSTANS OVEREXPRESSION (SOC1). ", "Gibberellins are essential to promote flowering under non-inductive short-day conditions. They do it by enhancing the expression of key flowering-time genes, such as LEAFY and SUPPRESSOR OF CONSTANS OVEREXPRESSION (SOC1). ", "Gibberellins are essential to promote flowering under long day conditions. They do it by enhancing the expression of key flowering-time genes, such as FLOWERING LOCUS C (FLC) and SUPPRESSOR OF CONSTANS OVEREXPRESSION (SOC1). " ], "source":"DOI: 10.1105\/tpc.10.5.791. doi: 10.1046\/j.1365-313x.2003.01833.x", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1046\/j.1365-313x.2003.01833.x", "Year":2003.0, "Citations":463.0, "answer":1, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"What molecular mechanisms regulate DELLA activity in Arabidopsis, beyond the control of cellular DELLA levels?", "area":"HORMONES", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "DELLA activity, defined by the interaction with transcription factors and other transcriptional regulators, is regulated by postranslational modifications that alter DELLA\u2019s capacity to establish these interactions. Among them, three are the best studied ones: In Arabidopsis, O-fucosylation catalyzed by SPINDLY (SPY) stimulates the interaction with PIF transcription factors, while O-GlcNAcylation catalyzed by SECRET AGENT (SEC) impairs this interaction. Finally, SUMOylation has been described in rice to differentially affect the interaction with distinct transcription factors, leading to salt stress tolerance.", "DELLA activity, defined by the interaction with transcription factors and other transcriptional regulators, is regulated by postranslational modifications that alter DELLA\u2019s capacity to establish these interactions. Among them, three are the best studied ones: In Arabidopsis, O-fucosylation catalyzed by SECRET AGENT (SEC) impairs the interaction with PIF transcription factors, while O-GlcNAcylation catalyzed by SPINDLY (SPY) promotes this interaction. Finally, SUMOylation has been described in rice to differentially affect the interaction with distinct transcription factors, leading to salt stress tolerance.", "DELLA activity, defined by the interaction with transcription factors and other transcriptional regulators, is regulated by postranslational modifications that alter DELLA\u2019s capacity to establish these interactions. Among them, three are the best studied ones: In Arabidopsis, O-fucosylation catalyzed by SPINDLY (SPY) represses the interaction with PIF transcription factors, while O-GlcNAcylation catalyzed by SECRET AGENT (SEC) stimulates this interaction. Finally, phosphorylation has been described in rice to differentially affect the interaction with distinct transcription factors, leading to salt stress sensitivity." ], "source":"doi: 10.1101\/gad.270587.115. doi: 10.1038\/nchembio.2320. doi: 10.1007\/s00425-024-04565-1", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1007\/s00425-024-04565-1", "Year":2024.0, "Citations":0.0, "answer":0, "source_journal":"Planta", "is_expert":true }, { "question":"What is the experimental evidence for the involvement of NPF3 in gibberellin-dependent regulation of Arabidopsis root growth?", "area":"HORMONES", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "NPF3 is a gibberellin influx carrier expressed in the root endodermis. Gibberellin accumulation in the endodermis drives cell expansion in this cell type, from which growth of the whole organ is coordinated. Overexpression of NPF3 causes a phenotype associated to gibberellin hypersensitivity in roots.", "NPF3 is a gibberellin influx carrier expressed everywhere in the root except in the endodermis. Gibberellin deprivation in the root endodermis promotes cell expansion in this cell type, from which growth of the whole organ is coordinated. Overexpression of NPF3 causes a phenotype associated to gibberellin deficiency in roots.", "NPF3 is a gibberellin efflux carrier expressed in the root endodermis. Gibberellin accumulation in the endodermis prevents cell expansion in this cell type, from which growth of the whole organ is coordinated. Overexpression of NPF3 causes a phenotype associated to gibberellin deficiency in roots." ], "source":"doi: 10.1038\/ncomms11486", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1038\/ncomms11486", "Year":2016.0, "Citations":181.0, "answer":0, "source_journal":"Nature Communications", "is_expert":true }, { "question":"Does the alfalfa dwarf cytorebdovirus P protein exhibit activity as a suppressor of local and\/or systemic RNA silencing?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ " The phosphoprotein (P) encoded by alfalfa dwarf virus (ADV) is a suppressor of RNA silencing. ADV P has a very strong local suppressor activity and prevents RNAi accumulation, but weakly suppresses systemic RNA silencing. Protein-protein interaction assays determined that the suppression mechanism appears to involve the binding of ADV P to the RNA-induced silencing complex protein AGO2 and probably works by inhibiting miRNA-guided AGO2 cleavage and prevents transitive amplification by repressing secondary RNAi production.", "The phosphoprotein (P) encoded by alfalfa dwarf virus (ADV) is not a suppressor of RNA silencing. P from ADV has no local or systemic suppressor activity on RNA silencing. Protein-protein interaction assays have shown that it does not present a suppression mechanism since it does not bind to any of the secondary RNA silencing complex proteins.", " The phosphoprotein (P) encoded by alfalfa dwarf virus (ADV) is a suppressor of RNA silencing. ADV P has relatively weak local suppressor activity but strongly suppresses systemic RNA silencing. Protein-protein interaction assays determined that the suppression mechanism appears to involve binding of ADV P to the RNA-induced silencing complex proteins AGO1 and AGO4. ADV P likely functions by inhibiting miRNA-guided cleavage of AGO1 and prevents transitive amplification by repressing secondary siRNA production." ], "source":"http:\/\/dx.doi.org\/10.1016\/j.virusres.2016.08.008", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.virusres.2016.08.008", "Year":2016.0, "Citations":16.0, "answer":2, "source_journal":"Virus Research", "is_expert":true }, { "question":"Is the transmission of CMV through seeds possible in pepper, and if so, what is the estimated rate of such transmission?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Capsicum annuum" ], "options":[ " When CMV seed growth tests were performed in pepper pots, no transmission was detected in either the seed coat or the embryo. The final transmission rate of the seeds was 0%.", " When CMV seed growth tests were performed in pots on peppers, transmission was detected only in seed coat. CMV infection in seeds ranged from 10 to 15% for the coat. While the final transmission rate from seeds was approximately 82 to 84%.", "When CMV seed growth tests were performed in pots on peppers, transmission was detected in both the seed coat and the embryo. CMV infection in seeds ranged from 53 to 83% for the coat and from 10 to 46% for the embryo. While the final transmission rate from seeds was approximately 10 to 14%." ], "source":"doi:10.1016\/j.jviromet.2009.09.026", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.jviromet.2009.09.026", "Year":2010.0, "Citations":60.0, "answer":2, "source_journal":"Journal of Virological Methods", "is_expert":true }, { "question":"What is the relationship between the efficiency of PVY inhibition across multiple strains (PVYN, PVYO, and PVYNTN) and the expression of Cas13 with specific gRNA cassettes in transgenic potato lines?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Solanum tuberosum" ], "options":[ "Efficiency of PVY inhibition against multiple strains of PVYN, PVYO, and PVYNTN does not correlate with Cas13 with specific gRNA cassette expression in transgenic potato lines.", " Efficiency of PVY inhibition against multiple strains of PVYN, PVYO, and PVYNTN positively correlated with Cas13 with specific gRNA cassette expression in transgenic potato lines.", "Efficiency of PVY inhibition against multiple strains of PVYN, PVYO, and PVYNTN negatively correlated with Cas13 with specific gRNA cassette expression in transgenic potato lines." ], "source":"https:\/\/doi.org\/10.1080\/21645698.2022.2080481", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"ENVIRONMENT", "doi":"10.1080\/21645698.2022.2080481", "Year":2022.0, "Citations":13.0, "answer":1, "source_journal":"GM Crops & Food", "is_expert":true }, { "question":"What is the effect of silencing the stress-induced gene encoding Kunitz peptidase inhibitor-like protein on the death rate of TMV-infected Nicotiana benthamiana plants ?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Nicotiana benthamiana" ], "options":[ "Compared to both the control group and plants with elevated KPILP levels in Nicotiana benthamiana, silencing the stress-induced gene encoding Kunitz peptidase inhibitor-like protein (KPILP) increases the death rate of TMV-infected plants. Systemic infection of N. benthamiana plants with tobacco mosaic virus (TMV) induces a reduction in KPILP mRNA accumulation. KPILP knockdown significantly reduces the efficiency of TMV and or the closely related crucifer-infecting tobamovirus (crTMV) intercellular transport but not in the reproduction rate.", "Compared to both the control group and plants with elevated KPILP levels in Nicotiana benthamiana, silencing the stress-induced gene encoding Kunitz peptidase inhibitor-like protein (KPILP) reduces the death rate of TMV-infected plants. Systemic infection of N. benthamiana plants with tobacco mosaic virus (TMV) induces a drastic increase in KPILP mRNA accumulation. KPILP knockdown significantly reduces the efficiency of TMV and or the closely related crucifer-infecting tobamovirus (crTMV) intercellular transport and reproduction", "Compared with the control group and plants with elevated levels of KPILP in Nicotiana benthamiana, stress-induced silencing of the gene encoding Kunitz inhibitor peptidase-like protein (KPILP) does not produce any change in the death rate of TMV-infected plants. KPILP mRNA accumulation does not change by an systemic infection of N. benthamiana plants with tobacco mosaic virus (TMV). KPILP knockdown significantly reduces the efficiency of TMV intercellular transport and reproduction but do not alter the ffeciency of the closely related crucifer-infecting tobamovirus (crTMV)." ], "source":"https:\/\/doi.org\/10.3389\/fpls.2023.1224958", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"ENVIRONMENT", "doi":"10.3389\/fpls.2023.1224958", "Year":2023.0, "Citations":5.0, "answer":1, "source_journal":"Frontiers in Plant Science", "is_expert":true }, { "question":"Considering emerging studies, what are the critical factors contributing to the manifestation of virus-induced symptoms in plants through the manipulation of plant cellular processes by viruses?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ " Key factors involved in the mechanisms by which viruses manipulate plant cellular processes inducing symptoms have been identified as hormonal manipulation and gene expression changes.", "Key factors involved in the mechanisms by which viruses manipulate plant cellular processes inducing symptoms have been identified as chloroplast protein dysfunction, and hormonal manipulation, metabolic disorder.", "Key factors involved in the mechanisms by which viruses manipulate plant cellular processes inducing symptoms have been identified as chloroplast protein dysfunction, hormonal manipulation, ROS accumulation and cell cycle control." ], "source":"https:\/\/doi.org\/10.3390\/plants12152830", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.3390\/plants12152830", "Year":2023.0, "Citations":26.0, "answer":2, "source_journal":"Plants", "is_expert":true }, { "question":"Which gene was targeted using CRISPR\/Cas9 to delay flowering time in Medicago sativa (alfalfa)?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Medicago sativa" ], "options":[ "The polyester synthase-like gene At1g73750 has been disrupted using CRISPR\/Cas9 to delay flowering time in Medicago sativa.", "The FT1 gene has been disrupted using CRISPR\/Cas9 to delay flowering time in Medicago sativa.", "The polyester synthase-like gene MSAD_264347 has been disrupted using CRISPR\/Cas9 to delay flowering time in Medicago sativa." ], "source":"https:\/\/doi.org\/10.1007\/s00299-023-02997-9", "normalized_plant_species":"Legumes", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1007\/s00299-023-02997-9", "Year":2023.0, "Citations":2.0, "answer":2, "source_journal":"Plant Cell Reports", "is_expert":true }, { "question":"What is one of the main challenges in applying CRISPR\/Cas9 technology to crop genomes?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "non-specific" ], "options":[ "Efficient delivery of CRISPR\/Cas9 components into plant cells and successful regeneration of edited plants.", "CRISPR\/Cas9 cannot target coding regions of plant genomes due to polyploidy.", "CRISPR\/Cas9 requires the presence of specific RNA polymerases unique to animals, making it less efficient in plants." ], "source":"https:\/\/doi.org\/10.1016\/j.plantsci.2023.111809", "normalized_plant_species":"Non-specific", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1016\/j.plantsci.2023.111809", "Year":2023.0, "Citations":0.0, "answer":0, "source_journal":"Plant Science", "is_expert":true }, { "question":"How does the Protospacer Adjacent Motif (PAM) influence the CRISPR\/Cas9 genome editing process?", "area":"GENOME AND GENOMICS", "plant_species":[ "non-specific" ], "options":[ "The PAM sequence determines the efficiency of DNA repair after Cas9 introduces a double-strand break.", "The PAM sequence is incorporated into the guide RNA to enhance its stability during the editing process.", "The PAM sequence is required for Cas9 to identify and bind the target DNA site, enabling precise cleavage." ], "source":"https:\/\/doi.org\/10.1093\/aob\/mcae191", "normalized_plant_species":"Non-specific", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1093\/aob\/mcae191", "Year":2024.0, "Citations":0.0, "answer":2, "source_journal":"Annals of Botany", "is_expert":true }, { "question":"What is the impact of disrupting the SPL13 gene in lettuce via genome editing, and why could this strategy be useful for developing a commercial variety?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Lactuca sativa" ], "options":[ "Disrupting the SPL13 gene in lettuce via genome editing delays flowering, increases biomass, and enhances leaf production. This strategy is useful for developing a commercial variety as it extends the vegetative growth phase, resulting in higher yields and improved agronomic traits that are desirable for market production.", "Disrupting the SPL13 gene in lettuce via genome editing accelerates flowering, decreases biomass, and reduces leaf production. This strategy is not ideal for developing a commercial variety as it shortens the vegetative phase, limiting yield potential and agronomic value.", "Disrupting the SPL13 gene in lettuce via genome editing enhances drought tolerance, increases water-use efficiency, and improves photosynthesis rates. This strategy is useful for developing a commercial variety in water-scarce environments but does not directly affect flowering time or biomass production." ], "source":"https:\/\/doi.org\/10.1007\/s00299-022-02952-0", "normalized_plant_species":"Other Herbaceous Crops, Spices, Fibers & Weeds", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1007\/s00299-022-02952-0", "Year":2022.0, "Citations":6.0, "answer":0, "source_journal":"Plant Cell Reports", "is_expert":true }, { "question":"Which genes were successfully modified using cytosine base editing (CBE) in alfalfa to confer herbicide tolerance, and why was a dead Cas9 (dCas9) used in this process?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Medicago sativa" ], "options":[ "The ALSI and ALSII genes were successfully modified using CBE to confer herbicide tolerance. A dead Cas9 (dCas9), fused to a cytosine deaminase, was used to cleave the DNA at specific sites, enabling the integration of a resistance gene into the target locus.", "The ALS1 and ALS2 genes were successfully modified using CBE to confer herbicide tolerance. A dead Cas9 (dCas9), fused to a cytosine deaminase, was used to facilitate precise base substitutions without creating double-strand breaks, generating a new allele with a single nucleotide change.", "The ALSI and ALSII genes were successfully modified using CBE to confer herbicide tolerance. A dead Cas9 (dCas9), fused to a cytosine deaminase, was used to alter the target site by introducing insertions and deletions that disrupt gene function." ], "source":"https:\/\/doi.org\/10.1007\/s00299-021-02827-w", "normalized_plant_species":"Legumes", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1007\/s00299-021-02827-w", "Year":2022.0, "Citations":15.0, "answer":1, "source_journal":"Plant Cell Reports", "is_expert":true }, { "question":"Which is the master regulator gene involved in branching regulation in Arabidopsis thaliana? And how is it expression regulated?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis thaliana, the master regulator of branching is BRANCHED1 (BRC1), a transcription factor from the TCP class II family. This gene is regulated by numerous environmental and endogenous conditions. Regarding environmental conditions, being shaded by neighbor plants or increasing far red light promote BRC1 expression. As to endogenous conditions, there is a regulation mediated by hormones. Cytokinins down regulate BRC1 while strigolactones increase its transcription levels. Also sucrose down regulates BRC1 expression. ", "The master regulator gene of branching in Arabidopsis thaliana is FLC, a MADS-domains transcription factor. This gene is repressed after a prolonged period of low temperatures. Also FRIGIDA (FRI) increases the FLC protein production, while VERNALIZATION INSENSITIVE3 (VIN3) reduces FLC transcriptional activity during vernalization. ", "BRANCHED1 is the master regulator of branching in Arabidopsis. This gene promotes axillary bud outgrowth integrating different signals as cold or blue light. Also its transcription level increase with high levels of sucrose." ], "source":"doi: 10.3389\/fpls.2014.00741", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.3389\/fpls.2014.00741", "Year":2015.0, "Citations":222.0, "answer":0, "source_journal":"Frontiers in Plant Science", "is_expert":true }, { "question":"How is the long noncoding RNA APOLO involved in the regulation of branching in Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The long non coding RNA APOLO participates in branching regulation through the epigenetic modulation of BRC1expression. This regulation occurs in the context of shade or under high levels of far red light. Different levels of APOLO modulate a chromatin loop opening or formation. This chromatin loop encompasses BRC1 and its neighbor gene\u2019s promoters so, when it is open it allows the transcription of both genes but, when it is formed, the transcription levels of both decrease. ", "The long non coding RNA APOLO participates in branching regulation by increasing strigolactones levels. ", "The long non coding RNA APOLO participates in branching regulation by modulating FLC expression. This regulation occurs in the context of low temperatures. " ], "source":"DOI 10.15252\/embj.2023113941", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.15252\/embj.2023113941", "Year":2023.0, "Citations":3.0, "answer":0, "source_journal":"The EMBO Journal", "is_expert":true }, { "question":"In which context does the long noncoding RNA APOLO participate in BRC1 expression modulation in Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The long non coding RNA APOLO modulates BRC1 expression in the context of shade or under high far red light levels.", "The long non coding RNA APOLO modulates BRC1 expression in the context of low far red levels.", "The long non coding RNA APOLO modulates BRC1 expression in the context of high temperatures" ], "source":"DOI 10.15252\/embj.2023113941", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.15252\/embj.2023113941", "Year":2023.0, "Citations":3.0, "answer":0, "source_journal":"The EMBO Journal", "is_expert":true }, { "question":"Which are the most important responses of Arabidopsis thaliana plants to the shade avoidance syndrome?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis thaliana, shade light signals delay flowering and promote branching. ", "In Arabidopsis thaliana, the shade avoidance syndrome induces seeds germination and suppresses hypocotyl and petiole elongation.", "In Arabidopsis thaliana, the shade avoidance syndrome presents different responses depending on the plant developmental stage. In seeds, shade light signals repress germination. At seedling stage, promote hypocotyl elongation. At the rosette stage, promote petiole elongation, reduce leaf lamina expansion and induce hyponasty. Also, accelerate flowering and reduce branching. " ], "source":"doi: 10.1199\/tab.0157", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1199\/tab.0157", "Year":2012.0, "Citations":311.0, "answer":2, "source_journal":"The Arabidopsis Book", "is_expert":true }, { "question":"How is hyponasty regulated in Arabidopsis thaliana?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The hyponasty response is the leaf upward movement driven by a higher rate of cell expansion on de abaxial side compared with the adaxial. This difference in cell expansion depends on auxin biosynthesis, transport and distribution, which is regulated by R\/FR light. Low R\/FR inactivates phyB, allowing PIFs to accumulate and become active to control transcription of target genes including YUCs which are involved in auxin biosynthesis. Also there are some evidences that the long non coding RNA APOLO has a role in the hyponastic response to a low R\/FR through the modulation of some genes. APOLO is induced by auxin, regulates genes involved in auxin biosynthesis like YUC2 and participates in auxin redistribution modulating PID and WAG2 expression. ", "The hyponasty response is the leaf upward movement driven by a higher rate of cell expansion on de adaxial side compared with the abaxial. This difference in cell expansion depends on gibberellin biosynthesis and distribution, which is regulated by R\/FR light. Low R\/FR inactivates phyB, allowing PIFs to accumulate and become active to control transcription of target genes including YUCs which are involved in ethylene biosynthesis. ", "The hyponasty response is regulated by cold temperatures through the long non coding RNA CIL1 action." ], "source":"DOI 10.15252\/embj.2023113941", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.15252\/embj.2023113941", "Year":2023.0, "Citations":3.0, "answer":0, "source_journal":"The EMBO Journal", "is_expert":true }, { "question":"Which genes (AGI) encode structural proteins of cytochrome c oxidase in Arabidopsis thaliana? Mention whether there is homology with any yeast and\/or mammalian genes?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Cytochrome c Oxidase is composed of several subunits in Arabidopsis thaliana. The enzymatic core is highly conserved between plants, mammals and yeasts and the genes are normally encoded by the mitochondrial genome. The Arabidopsis genes are COX1 (ATMG01360), COX2 (ATMG00160) and COX3 (ATMG01520). The rest of the subunits are encoded in the nuclear genome and only some of them are conserved, including COX10 (AT2G44520), COX11 (AT1G02410), COX15, (AT5G56090), COX17 (AT3G15352 and AT1G53030) and COX19 (AT1G66590 and AT1G52710), and all of them have the same name in mammals and yeast. There are also other genes found in proteomic analysis, but without a clear function, such as COX6b-1 to 4, COX6a whose mammalian counterparts have the same name and are COX12 and Cox13 in yeast. Finally, there are other genes exclusive to plants such as COX5c-1 to 3 and COX-X1 to 6", "The Arabidosis Cytochrome c Oxidase CcO catalytic core is encoded by 3 mitochondrial gene, COX1 (ATMG00460), COX2 (ATMG00760) and COX2 (ATMG00550), all of them present conserved homologous in mammals and yeast. The rest of the subunits are also encoded in the mitochondrial genome and only some of them are conserved, including COX5b-1 to 3 (ATMG00455, ATMG00410, ATMG01160), homologous to COX5b of mammals and Cox4 of yeast. Also, other proteins are part of the enzyme and act as regulatory modules, among them we can find COX10 (AT2G44520), COX11 (AT1G02410), COX15, (AT5G56090), COX17 (AT3G15352 and AT1G53030) and COX19 (AT1G66590 and AT1G52710), and all of the have the same name in mammals and yeast. ", "ytochrome c Oxidase is composed of several subunits in Arabidopsis thaliana. The enzymatic core is highly conserved between plants, mammals and yeasts and the genes are normally encoded by the mitochondrial genome. The Arabidopsis genes are COX1 (ATMG01360), COX2 (ATMG00160) and COX3 (ATMG00730). The rest of the subunits are encoded in the nuclear genome and only some of them are conserved, including COX5b-1 to 3 (AT3G15640, AT1G80230, AT1G52710), homologous to COX5b of mammals and Cox4 of yeast. All of these subunits are necessary for the correct assembly and function of the enzyme. There are also other genes found in proteomic analysis, but without a clear function, such as COX6b-1 to 4, COX6a whose mammalian counterparts have the same name and are COX12 and Cox13 in yeast. Finally, there are other genes exclusive to plants such as COX5c-1 to 3 and COX-X1 to 6.\n" ], "source":"https:\/\/doi.org\/10.3390\/ijms19030662", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.3390\/ijms19030662", "Year":2018.0, "Citations":97.0, "answer":2, "source_journal":"International Journal of Molecular Sciences", "is_expert":true }, { "question":"Describe the main phenotypes of the Cytochrome c mutants in Arabidopsis thaliana and the associated molecular pathways that are affected", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ " Arabidopsis thaliana has 2 genes that encode for the heme protein Cytochrome c, CYTC-1 and CYTC-2. This protein is involved in the electron transfer between complex III and complex IV of the mitochondrial electron transport chain. The mutation in the CYTC genes in Arabidopsis generates different phenotypes depending on the mutant analyzed. Double knock-out mutants are embryo lethal. The mutants knock-down in CYTC-1 and knock-out in CYTC-2 that have very low levels of CYTC protein present a reduced growth rate and early flowering. These phenotypes are mostly associated with the CYTC-2 gene. The reduced growth rate is associated with a lower level of ATP, which generates a lower activation of the SnRK2-pathway and reduces the autophagy to adjust growth and cellular energy production. On the other hand, the CYTC-1 gene presents redundancy with CYTC-2 in all the phenotypes and this could be explained due to both genes have almost identical protein sequence and very similar expression pattern but the CYT-C2 expression is stronger, masking CYT-C1 mutations effects.\n", "Arabidopsis thaliana has 2 genes that encode for the heme protein Cytochrome c, CYTC-1 and CYTC-2. This protein is involved in the electron transfer between complex III and complex IV of the mitochondrial electron transport chain. The mutation in the CYTC genes in Arabidopsis generates different phenotypes depending on the mutant analyzed. Double knock-out mutants are embryo lethal. The mutants knock-down in CYTC-1 and knock-out in CYTC-2 that have very low levels of CYTC protein present a reduced growth rate and late flowering. These phenotypes are mostly associated with the CYTC-1 gene. The reduced growth rate is associated with a higher level of NADH, which generates a lower activation of the TOR-pathway and reduces the autophagy to adjust growth and cellular energy production. On the other hand, the CYTC-2 gene presents redundancy with CYTC-1 in most of the phenotypes with the only exception found during the germination process. During germination, CYTC-2 is repressed due to the decrease in ABI4, and it decreases the sensitivity to ABA stimulating the germination.", "Arabidopsis thaliana has 2 genes that encode for the heme protein Cytochrome c, CYTC-1 and CYTC-2. This protein is involved in the electron transfer between complex III and complex IV of the mitochondrial electron transport chain. The mutation in the CYTC genes in Arabidopsis generates different phenotypes depending on the mutant analyzed. Double knock-out mutants are embryo lethal. The mutants knock-down in CYTC-1 and knock-out in CYTC-2 that have very low levels of CYTC protein present a reduced growth rate and late flowering. These phenotypes are mostly associated with the CYTC-1 gene. The reduced growth rate is associated with a lower synthesis of ATP, which generates a lower activation of the TOR-pathway and an increase in autophagy to adjust growth and cellular energy production. On the other hand, the CYTC-2 gene presents redundancy with CYTC-1 in most of the phenotypes with the only exception found during the germination process. During germination, CYTC-2 is de-repressed due to the decrease in ABI4, stimulating the synthesis of the ATP required for this process, in addition the increase in CYTC-2 decreases the sensitivity to ABA." ], "source":"https:\/\/doi.org\/10.1111\/tpj.13845, https:\/\/doi.org\/10.1111\/nph.18287, https:\/\/doi.org\/10.1111\/nph.19506, ", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1111\/nph.19506", "Year":2024.0, "Citations":6.0, "answer":2, "source_journal":"New Phytologist", "is_expert":true }, { "question":"Does the Arabidopsis cytochrome CYT-C2 gene have any function that is not redundant with the CYT-C1 gene? If there is any molecular mechanism described, please explain it.", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Both CYT-C genes present redundancy in most biological processes. This is because both are the result of a recent duplication. However, beyond the fact that at the protein sequence level they are practically identical, their promoters have different expression patterns. During germination, a repression of the CYT-C2 gene occurs caused by the decrease in ABA levels and less activation of the transcription factors of the ABI family, particularly ABI4. The decrease in CYT-C2 reduces the synthesis of ATP at the mitochondrial level increasing the Reactive oxygen species that are crucial in this process. In addition, this decrease in CYT-C2 reduces the sensitivity to ABA in seeds, stimulating germination.", "Both CYT-C genes present redundancy in most biological processes. This is because both are the result of a recent duplication. However, beyond the fact that at the protein sequence level they are practically identical, their promoters have different expression patterns. During germination, a de-repression of the CYT-C2 gene occurs caused by the decrease in ABA levels and less activation of the transcription repressor factors of the ABI family, particularly ABI4, which bind the G-BOX sites present in the CYT-C2 promoter. The increase in CYT-C2 during germination stimulates the synthesis of ATP at the mitochondrial level, which is essential for this process. Furthermore, this increase in CYT-C2 decreases the sensitivity to ABA in seeds, stimulating germination", "Both CYT-C genes present redundancy in most biological processes. This is because both are the result of a recent duplication. However, beyond the fact that at the protein sequence level they are practically identical, their promoters have different expression patterns. During germination, a de-repression of the CYT-C2 gene occurs caused by the decrease in ABA levels and less activation of the transcription repressor factors of the HD-zip family, particularly HB40, which bind the G-BOX sites present in the CYT-C2 promoter. The increase in CYT-C2 during germination stimulates the synthesis of ATP at the mitochondrial level, which is essential for this process. Furthermore, this rise in CYT-C2 increase the gibberellin synthesis in seeds, stimulating germination." ], "source":"https:\/\/nph.onlinelibrary.wiley.com\/doi\/10.1111\/nph.18287", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1111\/nph.18287", "Year":2022.0, "Citations":9.0, "answer":1, "source_journal":"New Phytologist", "is_expert":true }, { "question":"In the aerial tissue of plant organisms, both chloroplasts and mitochondria have the capacity to synthesize ATP. In Arabidopsis, do cytoplasmic and nuclear metabolism directly use ATP from both sources equally?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Currently, very few studies have delved into this topic. However, the use of fluorescent ATP sensors has allowed the evaluation of the level of ATP in the cytoplasm of different Arabidopsis tissues, under light and dark conditions. In addition, the evolution of ATP was evaluated by inhibiting the mitochondrial electron transport chain with antimycin A. According to what was reported by this sensor, in light condition, the level of cytoplasmic ATP drops around 60% when mitochondrial production is blocked. The same does not happen when the measurement is made in darkness where chloroplast ATP synthesis is stopped. Due to this, the authors of this work conclude that probably around half of the ATP used in cytoplasmic metabolism is generated in the mitochondria, in light. In darkness the ATP is provided almost exclusively by the mitochondria.", "Currently, very few studies have delved into this topic. However, the use of fluorescent ATP sensors has allowed the evaluation of the level of ATP in the cytoplasm of different Arabidopsis tissues, under light and dark conditions. In addition, the evolution of ATP was evaluated by inhibiting the mitochondrial electron transport chain with antimycin A. According to what was reported by this sensor, the level of cytoplasmic ATP drops abruptly when mitochondrial production is blocked in darkness. The same does not happen when the measurement is made in light where chloroplast ATP synthesis is active. Due to this, the authors of this work conclude that probably most of the ATP used in cytoplasmic metabolism is generated in chloroplast under light conditions, and by the mitochondria in darkness.", "Currently, very few studies have delved into this topic. However, the use of fluorescent ATP sensors has allowed the evaluation of the level of ATP in the cytoplasm of different Arabidopsis tissues, under light and dark conditions. In addition, the evolution of ATP was evaluated by inhibiting the mitochondrial electron transport chain with antimycin A. According to what was reported by this sensor, the level of cytoplasmic ATP drops abruptly when mitochondrial production is blocked. The same does not happen when the measurement is made in darkness where chloroplast ATP synthesis is stopped. Due to this, the authors of this work conclude that probably most of the ATP used in cytoplasmic metabolism is generated in the mitochondria, both in light and in darkness.\n" ], "source":"https:\/\/doi.org\/10.7554\/eLife.26770", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.7554\/eLife.26770", "Year":2017.0, "Citations":130.0, "answer":2, "source_journal":"eLife", "is_expert":true }, { "question":"The COX10 and COX15 genes are involved in the biosynthesis of the heme a group, which is essential for the assembly of cytochrome c oxidase (CcO) in humans and yeasts. Are there homologs of these genes in Arabidopsis? Is their function conserved? Is there a molecular mechanism that describes its participation in the biosynthesis of the heme a and assembly of CcO in Arabidopsis?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Both genes have homologs encoded in the Arabidopsis genome. COX10 is encoded in the locus AT2G44520, while COX15 is encoded in AT5G56090. The function of both genes in the assembly of CcO would be conserved, since these Arabidopsis thaliana genes are able to rescue mitochondrial respiration in mutants of its homologs in Saccharomyces cerevisiae. Furthermore, the Arabidopsis null mutant of both genes are embryo lethal, displaying very low histochemical CcO activity staining. Heterozygous COX10 mutant plants show reduced respiration rates in leaves and seeds, probably caused by a decrease in assembled and functional CcO. A similar observation was made in a heterozygous mutant of COX15. These observations are similar to those found in yeast or mammals, and it is attributed to the fact that both proteins catalyze consecutive biochemical steps and both are necessary for the heme a biosynthesis. In line with this, these plants accumulate the precursor heme b and have lower levels of heme o and a.", " Both genes have homologs encoded in the Arabidopsis genome. COX10 is encoded in the locus AT1G24720, while COX15 is encoded in AT2G43090. The function of the COX10 gene in the assembly of CcO would be conserved, since this Arabidopsis thaliana gene is able to rescue mitochondrial respiration in mutants of its homolog in Saccharomyces cerevisiae. Furthermore, Heterozygous mutant plants show reduced respiration rates in leaves and seeds, probably caused by a decrease in assembled and functional CcO. Also these plants accumulate the precursor heme b and have lower levels of heme o and a. This is explained because it is not converted by the absence of COX10. On the other hand, there are no studies on the function of the Arabidopsis COX15 gene.", "Both genes have homologs encoded in the Arabidopsis genome. COX10 is encoded in the locus AT2G44520, while COX15 is encoded in AT5G56090. The function of the COX10 gene in the assembly of CcO might be conserved, since this Arabidopsis thaliana gene is able to rescue mitochondrial respiration in mutants of its homolog in Saccharomyces cerevisiae. Furthermore, the Arabidopsis null mutant is embryo lethal, displaying very low histochemical CcO activity staining. Heterozygous mutant plants show reduced respiration rates in leaves and seeds, probably caused by a decrease in assembled and functional CcO. However, there is no direct evidence associating this protein with heme a biosynthesis in Arabidopsis. On the other hand, there are no studies on the function of the Arabidopsis COX15 gene." ], "source":"https:\/\/doi.org\/10.1093\/jxb\/erv381, https:\/\/doi.org\/10.3390\/ijms19030662", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.3390\/ijms19030662", "Year":2018.0, "Citations":97.0, "answer":2, "source_journal":"International Journal of Molecular Sciences", "is_expert":true }, { "question":"How LncRNA MSTRG.13420 formed R-loop functions in cold response of rice?", "area":"GENOME AND GENOMICS", "plant_species":[ "Oryza sativa" ], "options":[ "LncRNA MSTRG.13420 located in downstream region of OsDof16 was transcribed from antisense strand and significantly downregulated in cold treatment. LncRNA MSTRG.13420 formed R-loop to negatively regulate OsDof16, and act as posstive regulator in cold response in rice.", "LncRNA MSTRG.13420 located in promoter of OsDof16 was transcribed from antisense strand and significantly downregulated in cold treatment. LncRNA MSTRG.13420 formed R-loop to positively regulate OsDof16, and act as negative regulator in cold response in rice.", "LncRNA MSTRG.13420 located in promoter of OsDof16 was transcribed from sense strand and significantly upregulated in cold treatment. LncRNA MSTRG.13420 formed R-loop to negatively regulate OsDof16, and act as posstive regulator in cold response in rice." ], "source":"10.1111\/nph.19315.", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1111\/nph.19315", "Year":2023.0, "Citations":2.0, "answer":1, "source_journal":"New Phytologist", "is_expert":true }, { "question":"What\u2019s the relationship between DNA G4 intensity and expression levels of G4-overlapping genes in rice genome?", "area":"GENOME AND GENOMICS", "plant_species":[ "Oryza sativa" ], "options":[ "G4s intensity exhibited a negative association with expression levels of G4-overlapping genes at transcript end sites (TTSs), while G4s in gene bodies was positively corresponded with expression levels.", "G4s intensity exhibited a positive association with expression levels of G4-overlapping genes at transcript start sites (TSSs), while G4s at transcript end sites (TTSs) was negatively corresponded with expression levels.", "G4s intensity exhibited a positive association with expression levels of G4-overlapping genes at transcript start sites (TSSs), while G4s in gene bodies was negatively corresponded with expression levels." ], "source":"doi: 10.1093\/plphys\/kiab566.", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1093\/plphys\/kiab566", "Year":2021.0, "Citations":28.0, "answer":2, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"How 5mC DNA methylation affect i-motif formation under different pH condition in rice genome?", "area":"GENOME AND GENOMICS", "plant_species":[ "Oryza sativa" ], "options":[ "Subset of i-motif folded at pH 5.5 show high methylation levels than those folded at pH 7.0, and core regions of i-motifs trend to be higher methylated than flank regions.", "Subset of i-motif folded at pH 7.0 show high methylation levels than those folded at pH 5.5, and flank regions of i-motifs trend to be higher methylated than core regions.", "Subset of i-motif folded at pH 7.0 show high methylation levels than those folded at pH 5.5, and core regions of i-motifs trend to be higher methylated than flank regions." ], "source":"10.1093\/nar\/gkad1245.", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1093\/nar\/gkad1245", "Year":2024.0, "Citations":8.0, "answer":2, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"In which genomic regions the i-motif structure trend to be present or depleted?", "area":"GENOME AND GENOMICS", "plant_species":[ "Oryza sativa" ], "options":[ "The rice genome was divided into seven genomic subregions, including 5\u2032UTRs, 3\u2032UTRs, exons, introns, downstream and distal intergenic regions. The i-motif structure trend to present in promoters and 5\u2032UTRs, and depleted in exons and distal intergenic regions.", "The rice genome was divided into seven genomic subregions, including 5\u2032UTRs, 3\u2032UTRs, exons, introns, downstream and distal intergenic regions. The i-motif structure trend to present in downstream and 3\u2032UTRs, and depleted in exons and introns regions.", "The rice genome was divided into seven genomic subregions, including 5\u2032UTRs, 3\u2032UTRs, exons, introns, downstream and distal intergenic regions. The i-motif structure trend to present in exons and 5\u2032UTRs, and depleted in introns and distal intergenic regions." ], "source":"10.1093\/nar\/gkac121.", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1093\/nar\/gkac121", "Year":2022.0, "Citations":34.0, "answer":0, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"What are the intrinsic sequence feature for Cold-induced R-loop regions.", "area":"GENOME AND GENOMICS", "plant_species":[ "Oryza sativa" ], "options":[ "Cold-induced R-loops have highest GC content compare to other genomic regions, GCGGC and CCTCC binding motifs of C2H2 family were enriched in Cold-induced R-loops, which were reported to be involved in plant stress response.", "Cold-induced R-loops have highest GC content compare to other genomic regions, CCGCC and CCTCC binding motifs of AP2-EREBP family were enriched in Cold-induced R-loops, which were reported to be involved in plant stress response.", "Cold-induced R-loops have lowest GC content compare to other genomic regions, CGCC and CCTCC binding motifs of AP2-EREBP family were enriched in Cold-induced R-loops, which were reported to be involved in rice root development ." ], "source":"10.1111\/nph.19315.", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1111\/nph.19315", "Year":2023.0, "Citations":2.0, "answer":1, "source_journal":"New Phytologist", "is_expert":true }, { "question":"In what ways has the functional characterization of BBX proteins in crop species, such as BBX32 in soybean, BBX21 in potato, or BBX24 in Chrysanthemum, advanced our understanding of their potential applications in improving agronomic traits?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Solanum tuberosum", "Glycine max", "Chrysanthemum" ], "options":[ "Functional characterization of BBX proteins indicates they only affect flowering time and have no relevance to traits like photosynthesis or yield improvement.", "The studies have shown that BBX proteins are primarily involved in promoting vegetative growth, with no significant impact on yield or stress tolerance.", "Research on BBX proteins has demonstrated their role in enhancing stress resilience, yield potential, and improving phenological traits in crops, leading to applications in breeding programs that can increase crop productivity." ], "source":"https:\/\/doi.org\/10.1104\/pp.17.01417", "normalized_plant_species":"Other Herbaceous Crops, Spices, Fibers & Weeds", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1104\/pp.17.01417", "Year":2018.0, "Citations":31.0, "answer":2, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"How does BBX24 influence the interaction between DELLAs and PIF4 in the context of shade avoidance?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "BBX24 has no effect on the interaction between DELLAs and PIF4, regardless of light conditions.", "BBX24 promotes the interaction between DELLAs and PIF4, leading to reduced growth in shaded environments.", "BBX24 sequesters DELLAs, preventing them from inhibiting PIF4, which enhances cell elongation and growth in response to shade." ], "source":"https:\/\/doi.org\/10.1038\/ncomms7202", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1038\/ncomms7202", "Year":2015.0, "Citations":89.0, "answer":2, "source_journal":"Nature Communications", "is_expert":true }, { "question":"How does UV-B radiation impact Arabidopsis BBX29 expression and its role in plant defense?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "UV-B radiation strongly induces AtBBX29 expression in a UVR8-dependent manner, enhancing the accumulation of phenolic compounds that boost plant resistance to pathogens.", "UV-B radiation decreases AtBBX29 expression, leading to reduced accumulation of phenolic compounds and increased susceptibility to pathogens.", "UV-B radiation has no effect on AtBBX29 expression, and it does not influence plant defense mechanisms." ], "source":"https:\/\/link.springer.com\/article\/10.1007\/s43630-023-00391-8", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1007\/s43630-023-00391-8", "Year":2023.0, "Citations":6.0, "answer":0, "source_journal":"Photochemical & Photobiological Sciences", "is_expert":true }, { "question":"In what ways do photoreceptors, such as phytochromes and cryptochromes, interact with light-regulated transcription factors like HY5, BBXs and PIFs to regulate the developmental processes in crops, and how can these interactions be targeted for crop improvement?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "non-specific" ], "options":[ "Interactions between photoreceptors and light-regulated transcription factors like HY5, BBXs and PIFs play a crucial role in regulating key developmental processes, such as flowering time and leaf expansion, and can be targeted in breeding programs to enhance crop performance.", "Photoreceptors and light-regulated transcription factors operate independently of each other, so their interactions do not influence developmental processes in crops.", "The primary role of photoreceptors is to inhibit light-regulated transcription factors, which leads to decreased growth rates and reduced crop yield across all species." ], "source":"https:\/\/doi.org\/10.1104\/pp.17.01417", "normalized_plant_species":"Non-specific", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1104\/pp.17.01417", "Year":2018.0, "Citations":31.0, "answer":0, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"How do ABA sensitivity and stomatal responses differ between BBX21-OE lines and wild-type potato plants?", "area":"HORMONES", "plant_species":[ "Solanum tuberosum" ], "options":[ "BBX21-OE lines exhibit increased sensitivity to ABA, resulting in reduced stomatal openings compared to wild-type plants when both are exposed to ABA.", "BBX21-OE lines show improved tolerance to ABA, maintaining stomatal openings under lower ABA concentrations, whereas wild-type plants exhibit reduced stomatal apertures when exposed to ABA.", "There is no difference in ABA sensitivity or stomatal responses between BBX21-OE lines and wild-type plants under ABA treatment." ], "source":"https:\/\/doi.org\/10.1111\/tpj.15499", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"HORMONES", "doi":"10.1111\/tpj.15499", "Year":2021.0, "Citations":18.0, "answer":1, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"What role does the trans-acting small interfering RNA (tasiRNA) pathway play in lateral root development in Arabidopsis thaliana and what are the components involved?", "area":"GENE REGULATION - PTGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis thaliana, cytokinins, miR390, TAS3, and their ARFs targets define a regulatory network quantitatively controlling lateral root growth. Mutations affecting the abundance of TAS3-derived tasiRNAs lead to inhibition of lateral root growth. miR390 is induced in response to cytokinins during lateral root initiation and triggers the local production of tasiRNAs. In the lateral root primordium, the tasiARFs enhance the activity of the auxin response factors ARF2, ARF3, and ARF4, thereby inhibiting lateral root initiation. In addition, ARF2, ARF3, and ARF4 are required for proper miR390 expression through negative feedback mechanisms.", "In Arabidopsis thaliana, auxin, miR173, TAS1, and their targets define a regulatory network quantitatively controlling lateral root initiation. Mutations affecting the abundance of TAS1-derived tasiRNAs lead to quantitative changes in the number of lateral root initiation events. miR173 is induced in response to auxin during lateral root initiation and triggers the local production of tasiRNAs. In the lateral root primordium, the tasiARFs reduce the activity of the auxin response factors ARF2, ARF3, and ARF4, thereby promoting lateral root initiation. In addition, ARF2, ARF3, and ARF4 repress miR173 expression.", "In Arabidopsis thaliana, auxin, miR390, TAS3, and their ARFs targets define a regulatory network quantitatively controlling lateral root growth. Mutations affecting the abundance of TAS3-derived tasiRNAs lead to quantitative changes in the rate of lateral root growth. miR390 is induced in response to auxin during lateral root initiation and triggers the local production of tasiRNAs. In the lateral root primordium, the tasiARFs reduce the activity of the auxin response factors ARF2, ARF3, and ARF4, thereby promoting lateral root growth. In addition, ARF2, ARF3, and ARF4 are required for proper miR390 expression through positive and negative feedback mechanisms. \n" ], "source":"https:\/\/doi.org\/10.1105\/tpc.109.072553", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1105\/tpc.109.072553", "Year":2010.0, "Citations":486.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"By which mechanism has the function of the transcription factor LEAFY evolved in land plants?", "area":"EVOLUTION", "plant_species":[ "Arabidopsis thaliana", "Physcomitrella patens" ], "options":[ "The plant-specific transcription factor LEAFY is found in all land plants, usually as a single copy gene. While it controls general aspects of the life cycle in the basal plant Physcomitrella patens, it has more specialized functions in flowering plants, where it specifically induces floral fate during the reproductive phase. Changes in the mode of DNA binding of the conserved DNA binding domain of LEAFY underpin this change in function. Structural analyses show that Hornworts have preserved a promiscuous intermediary form able to bind DNA in all conformations, suggesting that this promiscuous intermediate could have smoothed the evolutionary transitions, thereby allowing LEAFY to evolve new binding specificities while remaining a single-copy gene.", "The plant-specific transcription factor LEAFY is found in all land plants, usually as a small gene family. While it controls general aspects of the life cycle in flowering plants, it has more specialised functions in basal plants, where it specifically induces floral fate during the reproductive phase. Changes in the mode of DNA binding of the variable DNA binding domain of LEAFY underpin this change in function. Structural analyses show that the evolutionary transitions have occurred progressively through the accumulation of several changes.", "The plant-specific transcription factor LEAFY is found in flowering plants, usually as a single copy gene that controls general aspects of the life cycle. Changes in the variable domains of LEAFY underpin changes in the mode of transcriptional activation." ], "source":"https:\/\/doi.org\/10.1126\/science.1108229 https:\/\/doi.org\/10.1126\/science.1248229", "normalized_plant_species":"Model Organisms", "normalized_area":"EVOLUTION", "doi":"10.1126\/science.1248229", "Year":2014.0, "Citations":121.0, "answer":0, "source_journal":"Science", "is_expert":true }, { "question":"Where is the biogenesis of trans-acting siRNA taking place in plant cells?", "area":"GENE REGULATION - PTGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Trans-acting small interfering RNAs (ta-siRNAs) from the TAS3 precursor are produced by cleavage of the TAS3 precursor by the AGO1\/miR173 complex, priming it for conversion into single-stranded RNA by the DICER LIKE 4 (DCL4). AGO7 and DCL4 accumulate in cytoplasmic P-bodies. These foci are membrane-associated sites of accumulation of mRNA primed for degradation. AGO7 congregates with miR390 and DCL4 in the cytoplasm for TAS3 processing.", "Trans-acting small interfering RNAs (ta-siRNAs) from the TAS3 precursor are produced by cleavage of the TAS3 precursor by the AGO7\/miR390 complex, priming it for conversion into double-stranded RNA by the RNA-dependent RNA polymerase RDR6 and SGS3. AGO7, SGS3 and RDR6 accumulate in cytoplasmic foci that are distinct from P-bodies. These foci are membrane-associated sites of accumulation of mRNA stalled during translation. AGO7 congregates with miR390 and SGS3 in membranes and is required in the cytoplasm and membranous siRNA bodies for TAS3 processing.", "Trans-acting small interfering RNAs (ta-siRNAs) from the TAS3 precursor are produced by cleavage of the TAS3 precursor by the AGO1\/miR390 complex, priming it for conversion into double-stranded RNA by the RNA-dependent RNA polymerase RDR2 and SGS3. AGO7, SGS3 and RDR6 accumulate in nuclear foci that are distinct from dicing-bodies. These foci are sites of accumulation of micro-RNA production. AGO7 congregates with miR390 and SGS3 in the nucleus, where it is required for TAS3 processing." ], "source":"https:\/\/doi.org\/10.1038\/emboj.2012.20", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1038\/emboj.2012.20", "Year":2012.0, "Citations":122.0, "answer":1, "source_journal":"The EMBO Journal", "is_expert":true }, { "question":"In Arabidopsis thaliana, what role does the microtubule network play during lateral root initiation and emergence?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The rearrangement of the microtubule (MT) cytoskeleton, alongside changes in cell-wall properties, contributes to the symmetric radial expansion necessary for endodermis thinning. In the endodermis, the organization and response of the cortical microtubule lattice are polarised. On the inner side, in contact with the pericycle, the arrays are more disorganized than those on the outer side of the same cell. Specific disruption of microtubules in endodermal cells overlying a lateral root primodium results in enhanced cellular remodeling and increased radial swelling of the lateral root primodium. Reorganization of endodermal cortical microtubules depends on a SOLITARY ROOT-dependent auxin response. The MICROTUBULE ASSOCIATED PROTEIN 70-5 (MAP70-5) is not required for the organization of the endodermal cortical microtubule lattice, the remodelling of the endodermis, and the morphogenesis of the lateral root primordium. Microtubules and MAP70-5 contribute to the swelling of the lateral root primordium outgrowth and together function as an auxin-regulated integrator of mechanical constraints during organogenesis.", "The rearrangement of the microtubule (MT) cytoskeleton, alongside changes in membrane properties, contributes to the radial expansion necessary for lateral root development. In the endodermis, the organization and response of the cortical microtubule lattice are polarized. On the inner side, in contact with the pericycle, the arrays are disorganized while on the outer side of the same cell, they are organized in parallel arrays. Specific disruption of microtubules in pericycle cells results in delayed cellular remodeling and a flattened lateral root primodium with atypical cell division patterns. Reorganization of pericycle cortical microtubules depends on the MICROTUBULE ASSOCIATED PROTEIN 70-5 (MAP70-5) which is required for the organization of the pericycle cortical microtubule lattice. Microtubules and MAP70-5 contribute to the lateral root primordium outgrowth and together function as an auxin-regulated driver of growth during organogenesis.", "The rearrangement of the microtubule (MT) cytoskeleton, alongside changes in cell-wall properties, contributes to the asymmetric radial expansion necessary for lateral root development. In the endodermis, the organization and response of the cortical microtubule lattice are polarized. On the inner side, in contact with the pericycle, the arrays are more ordered than those on the outer side of the same cell. Specific disruption of microtubules in endodermal cells overlying a lateral root primodium results in delayed cellular remodeling and a flattened lateral root primodium with atypical cell division patterns. Reorganization of endodermal cortical microtubules depends on both the swelling of the underlying pericycle and a SHY2-dependent auxin response. The MICROTUBULE ASSOCIATED PROTEIN 70-5 (MAP70-5) is required for the organization of the endodermal cortical microtubule lattice, the remodelling of the endodermis, and the morphogenesis of the lateral root primordium. Microtubules and MAP70-5 contribute to the perception of lateral root primordium outgrowth by the endodermis and together function as an auxin-regulated integrator of mechanical constraints during organogenesis." ], "source":"https:\/\/doi.org\/10.1016\/j.cub.2019.06.039 https:\/\/doi.org\/10.1126\/sciadv.abm4974", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1126\/sciadv.abm4974", "Year":2022.0, "Citations":28.0, "answer":2, "source_journal":"Science Advances", "is_expert":true }, { "question":"What role does TOR play during lateral root formation in Arabidopsis thaliana, and by which mechanism?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The Target-of-Rapamycin (TOR) kinase plays a crucial role in lateral root (LR) formation in Arabidopsis thaliana by integrating local auxin signaling with systemic metabolic cues. TOR is specifically repressed in the lateral root domain, where it regulates the transcription of key auxin-induced transcription factors, including ARF7, ARF19, and LBD16, all of which are essential for lateral root development. When TOR activity is promoted, LR initiation is enhanced, as the transcription of ARF7, ARF19, and LBD16 is significantly increased. Interestingly, TOR activation induces the translation of WOX11, a factor involved in adventitious root formation and promotes root branching. By coordinating metabolic signals with the transcription of auxin-responsive genes, TOR ensures the proper control of lateral root formation. With TOR, auxin signaling can drive root branching, underscoring its pivotal role in linking metabolism to development.", "The Target-of-Rapamycin (TOR) kinase plays a crucial role in lateral root (LR) formation in Arabidopsis thaliana by integrating local cytokinin signaling with systemic metabolic cues. TOR is specifically repressed in the lateral root domain, where it enhances the translation of key cytokinin-induced transcription factors, including ARF7, ARF19, and LBD16, all of which are essential for lateral root development. When TOR activity is activated, LR initiation is promoted, as the translation of ARF7, ARF19, and LBD16 is significantly attenuated. Interestingly, TOR activation induces the transcription of WOX11, a factor involved in lateral root formation. However, this induction does not lead to root branching, as TOR remains necessary for the translation of LBD16. By coordinating metabolic signals with the translation of cytokinin-responsive genes, TOR ensures the proper initiation and progression of lateral root formation. Without TOR, cytokinin signaling alone cannot drive root branching, underscoring its pivotal role in linking metabolism to development.", "The Target-of-Rapamycin (TOR) kinase plays a crucial role in lateral root (LR) formation in Arabidopsis thaliana by integrating local auxin signaling with systemic metabolic cues. TOR is specifically activated in the lateral root domain, where it regulates the translation of key auxin-induced transcription factors, including ARF7, ARF19, and LBD16, all of which are essential for lateral root development. When TOR activity is inhibited, LR initiation is blocked, as the translation of ARF7, ARF19, and LBD16 is significantly attenuated. Interestingly, TOR inhibition induces the transcription of WOX11, a factor involved in adventitious root formation. However, this induction does not lead to root branching, as TOR remains necessary for the translation of LBD16. By coordinating metabolic signals with the translation of auxin-responsive genes, TOR ensures the proper initiation and progression of lateral root formation. Without TOR, auxin signaling alone cannot drive root branching, underscoring its pivotal role in linking metabolism to development." ], "source":"https:\/\/doi.org\/10.15252\/embj.2022111273", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.15252\/embj.2022111273", "Year":2023.0, "Citations":27.0, "answer":2, "source_journal":"The EMBO Journal", "is_expert":true }, { "question":"What is \u2018state transitions\u2019 and which molecular processes are involved in its regulation in plants?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "non-specific" ], "options":[ "State transitions is the process through which plants rebalance the activity of photosystem I (PSI) and photosystem II (PSII) under fluctuating light quality conditions. Two states were defined, one induced by light preferentially absorbed by PSII (State II), and the other induced by light preferentially absorbed by PSI (State I). The transition from one state to the other is triggered by changes in the redox state of the plastoquinone (PQ) pool. Under conditions where PSII is preferentially excited, reduction of the PQ pool activates the STN7\/STT7 kinase which phosphorylates the membrane-bound light-harvesting complex II (LHCII). Phosphorylation of LHCII results in its detachment from PSII and attachment to PSI, triggering the transition from State I to State II. Conversely, when the PQ pool gets oxidized due to preferential absorption of light by PSI, the STN7\/STT7 kinase is deactivated, and LHCII is dephosphorylated by the TAP38\/PPH1 phosphatase. Dephosphorylation triggers migration of LHCII back to PSII, leading to State I transition.", "State transitions is the process through which plants rebalance the activity of photosystem I (PSI) and photosystem II (PSII) under fluctuating light quality conditions. Two states were defined, one induced by light preferentially absorbed by PSI (State II), and the other induced by light preferentially absorbed by PSII (State I). The transition from one state to the other is triggered by changes in the redox state of the plastoquinone (PQ) pool. Under conditions where PSI is preferentially excited, reduction of the PQ pool activates the STN7\/STT7 kinase which phosphorylates the membrane-bound light-harvesting complex II (LHCII). Phosphorylation of LHCII results in its detachment from PSII and attachment to PSI, triggering the transition from State I to State II. Conversely, when the PQ pool gets oxidized due to preferential absorption of light by PSII, the STN7\/STT7 kinase is deactivated, and LHCII is dephosphorylated by the TAP38\/PPH1 phosphatase. Dephosphorylation triggers migration of LHCII back to PSII, leading to State I transition.", "State transitions is the process through which plants decreases the energy arriving at both photosystem I and II (PSI and PSII) under fluctuating light quality conditions. Two states were defined, one induced by light preferentially absorbed by PSII (State II), and the other induced by light preferentially absorbed by PSI (State I). The transition from one state to the other is triggered by changes in the redox state of the plastoquinone (PQ) pool. Under conditions where PSI is preferentially excited, oxidation of the PQ pool activates the STN7\/STT7 kinase which phosphorylates the membrane-bound light-harvesting complex II (LHCII). Phosphorylation of LHCII results in its detachment from PSII and attachment to PSI, triggering the transition from State I to State II. Conversely, when the PQ pool gets reduced due to preferential absorption of light by PSII, the STN7\/STT7 kinase is deactivated, and LHCII is dephosphorylated by the TAP38\/PPH1 phosphatase. Dephosphorylation triggers migration of LHCII back to PSII, leading to State I transition." ], "source":"https:\/\/doi.org\/10.1016\/j.bbabio.2010.11.005", "normalized_plant_species":"Non-specific", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1016\/j.bbabio.2010.11.005", "Year":2011.0, "Citations":225.0, "answer":0, "source_journal":"Biochimica et Biophysica Acta (BBA) - Bioenergetics", "is_expert":true }, { "question":"How do you explain the rise in transient chlorophyll a fluorescence when leaves are exposed to light based on the QA model?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "non-specific" ], "options":[ "Based on the QA model, the increase in transient fluorescence yield is related to the reduction of electron acceptors and the relaxation of fluorescence quenchers in the photosynthetic electron transport chain. Upon light absorption, photosystem II (PSII) chlorophyll P680 reduces QA (a PSII-bound quinone). Reduced QA cannot accept another electron from P680 until oxidation by the following electron carrier molecule QB. This net reduction of QA is the main contributor to the rise in chlorophyll fluorescence observed after light exposure of leaves. However, further fluorescence emission is released by the relaxation of an unknown quencher due to photosystem I (PSI) oxidation. Therefore, the rise in transient chlorophyll fluorescence reflects the interaction of light-excited PSI and PSII. ", "Based on the QA model, the increase in transient fluorescence yield is related to light-induced conformational changes in the closed photosystem II (PSII) reaction centers. These structural alterations impact the physical and photochemical properties of the PSII core complex, due to charge stabilization at its donor side. This leads to the relaxation of a fluorescence quencher, increasing the chlorophyll fluorescence emission of the photosystem. Therefore, the rise in transient chlorophyll fluorescence reflects structural modifications within PSII.", "Based on the QA model, the increase in transient fluorescence yield is related to the reduction of electron acceptors in the photosynthetic electron transport chain. Upon light absorption, photosystm II (PSII) chlorophyll P680 reduces QA (a PSII-bound quinone). Reduced QA cannot accept another electron from P680 until oxidation by the following electron carrier molecule QB. During this period, the reaction center is defined as \u2018closed\u2019 and cannot drive electron transfer reactions with further excitation energy, being the absorbed energy released as fluorescence. Therefore, the rise in transient chlorophyll fluorescence reflects the QA reduction rates." ], "source":"https:\/\/doi.org\/10.1093\/jxb\/erad252", "normalized_plant_species":"Non-specific", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1093\/jxb\/erad252", "Year":2023.0, "Citations":25.0, "answer":2, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"Which and where reactive oxygen species (ROS) are produced in the chloroplast photosynthetic electron transport chain and what is defined as photoinhibition?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "non-specific" ], "options":[ "The main site of ROS production in the photosynthetic electron transport chain are photosystem I and II (PSI and PSII). Over-excitation of the photosystems mainly generate singlet excited oxygen (1O2*) at the level of PSII and superoxide radicals (O2.-) and hydrogen peroxide (H2O2) at PSI. ROS production in the photosystems can induce oxidative damage and this process is known as photoinhibition.", "The main site of ROS production in the photosynthetic electron transport chain are photosystem I and II (PSI and PSII). Over-excitation of the photosystems mainly generate singlet excited oxygen (1O2*) at the level of PSI and superoxide radicals (O2.-) and hydrogen peroxide (H2O2) at PSII. ROS production in the photosystems can induce oxidative damage and and this process is known as photoinhibition.", "The only site of ROS production in the photosynthetic electron transport chain is photosystem II (PSII). Over-excitation of PSII can trigger triplet excited state chlorophylls (3Chl*) which are highly reactive and transfer the energy to oxygen, thereby generating singlet excited oxygen (1O2*). Singlet excited oxygen can induce oxidative damage of the D1 protein in the reaction center and PSII photoinactivation. This process is known as photoinhibition." ], "source":"https:\/\/doi.org\/10.1042\/BST20211246", "normalized_plant_species":"Non-specific", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1042\/BST20211246", "Year":2022.0, "Citations":24.0, "answer":0, "source_journal":"Biochemical Society Transactions", "is_expert":true }, { "question":"What is the role of the transporters TPT and PHT2;1 in regulating chloroplastic phosphorus (Pi) homeostasis and photosynthesis in Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "TPT and PHT2;1 are molecular transporters that import phosphorus (Pi) to the chloroplast stroma in Arabidopsis thaliana. While TPT couples Pi import with triose phosphate export (produced by photosynthesis) to the cytosol, PHT2;1 imports both Pi and H+\/Na+. Although both transporters contribute to stromal Pi homeostasis, the TPT transporter contributes more to stromal Pi concentration in the adaxial mesophyll, while PHT2; 1 contributes more in the abaxial mesophyll. Maintaining Pi homeostasis is fundamental for photosynthesis since low stromal Pi levels reduce photosynthetic efficiency and trigger photoprotection processes.", "TPT and PHT2;1 are molecular transporters that export phosphorus (Pi) from the chloroplast stroma to the cytosol in Arabidopsis thaliana. While TPT couples Pi and triose phosphate (produced by photosynthesis) export to the cytosol, PHT2;1 exports both Pi and H+\/Na+. Although both transporters contribute to stromal Pi homeostasis, the TPT transporter regulates more stromal Pi concentration in the adaxial mesophyll, while PHT2; 1 contributes more in the abaxial mesophyll. Maintaining Pi homeostasis is fundamental for photosynthesis since low stromal Pi levels reduce photosynthetic efficiency and trigger photoprotection processes.", "TPT and PHT2;1 are molecular transporters that import phosphorus (Pi) to the chloroplast lumen in Arabidopsis thaliana. Although both transporters contribute to stromal Pi homeostasis, the TPT transporter contributes more to the lumen Pi concentration in the abaxial mesophyll, while PHT2; 1 contributes more in the adaxial mesophyll. Maintaining Pi homeostasis in the chloroplast is fundamental for ATP synthesis, which is required for carbon fixation. " ], "source":"https:\/\/doi.org\/10.1093\/plphys\/kiae241", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1093\/plphys\/kiae241", "Year":2024.0, "Citations":4.0, "answer":0, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"How can the activity of the plastid terminal oxidase (PTOX) be explained by the PSII proximity hypothesis in plants?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "non-specific" ], "options":[ "Photosystem II (PSII) and PTOX are located in different sub-compartments of the chloroplast. While PTOX is specifically targeted to the grana, PSII is localized in the stromal lamellae. Since PTOX oxidizes plastoquinol and reduces O2 to produce H2O, its activity will depend on the availability of its substrates. Thus, the distance between PSII and PTOX would preclude a significant electron flow between these two complexes. Decreasing the proximity between PSII and PTOX facilitates electron transport by diffusion of the reduced PQ pool associated with the photosystem.", "Photosystem II (PSII) and PTOX are located in different sub-compartments of the chloroplast. While PSII is specifically targeted to the grana, PTOX is localized to the stromal lamellae. Since PTOX oxidizes plastoquinol and reduces O2 to produce H2O, its activity will depend on the availability of its substrates. Thus, the distance between PSII and PTOX would preclude a significant electron flow between these two complexes. Decreasing the proximity between PSII and PTOX facilitates electron transport by diffusion of the reduced PQ pool associated with the photosystem.", "Photosystem II (PSII) and PTOX are located in different sub-compartments of the chloroplast. While PSII is targeted to the grana, PTOX is localized to the stroma. Since PTOX oxidizes plastoquinol (PQ) and reduces O2 to produce H2O, its activity will depend on the availability of its substrates. Thus, the stromal localization of PTOX would preclude a significant oxidation of the PQ pool. Based on the proximity hypothesis, a pH-dependent activation was proposed in which increasing stromal pH triggers PTOX association with the thylakoid membrane. This membrane binding allows electron transport from PSII through the PQ pool to PTOX. " ], "source":"https:\/\/doi.org\/10.1038\/s41467-023-44454-x", "normalized_plant_species":"Non-specific", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1038\/s41467-023-44454-x", "Year":2024.0, "Citations":6.0, "answer":1, "source_journal":"Nature Communications", "is_expert":true }, { "question":"What is the magnitude of alternative splicing regulation in rice leaves undergoing heat stress?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "Oryza sativa" ], "options":[ "Alternative splicing is widespread in rice leaves undergoing heat stress. For instance, genes coding for key regulators of gene expression can be mispliced in response to heat, suggesting that rice leaves are unable to regulate their transcriptome and proteome diversity in response to heat stress. ", "Alternative splicing regulation is widespread in rice leaves undergoing heat stress. Particularly, genes encoding for key regulators of gene expression undergo heat-stress-induced differential alternative splicing, suggesting that this process helps shape rice leaf transcriptome and proteome diversity in response to heat stress. ", "Alternative splicing regulation is rare in rice leaves undergoing heat stress. Genes encoding for key regulators of gene expression mostly undergo heat-stress-induced differential gene expression, suggesting that alternative splicing has a small role in shaping rice leaf transcriptome diversity in response to heat stress. " ], "source":"https:\/\/doi.org\/10.3390\/plants10081647", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.3390\/plants10081647", "Year":2021.0, "Citations":17.0, "answer":1, "source_journal":"Plants", "is_expert":true }, { "question":"How conserved is the regulation of alternative splicing in circadian clock orthologues from barley and Arabidopsis in response to cold?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "Hordeum vulgare", "Arabidopsis thaliana" ], "options":[ "The regulation of alternative splicing in circadian clock orthologues shows mostly conserved mechanisms and rarely species-specific divergences between barley and Arabidopsis in response to cold. For example, GI, PRR7 and TOC1 orthologues show conservation of alternative splicing events and behaviour in response to cold. Meanwhile, LHY orthologues show conservation of splicing behaviour, where cold-induced changes in species-specific splicing events lead to a decrease in non-productive transcripts and an increase in functional mRNA levels in both species. ", "The regulation of alternative splicing in circadian clock orthologues is rarely conserved between barley and Arabidopsis upon cold. For example, GI and TOC1 orthologues have no conserved alternative splicing behaviour. Meanwhile, LHY orthologues show conservation of splicing events, where cold-induced changes in the splicing lead to an increase in non-productive transcripts and a reduction in functional mRNA levels in both species. In contrast, PRR7 orthologues are considerably similar in terms of alternative splicing regulation, with barley (HvPPD-H1) exhibiting temperature-dependent isoform switching, a response also observed in Arabidopsis.", "The regulation of alternative splicing in circadian clock orthologues shows both conserved mechanisms and species-specific divergences between barley and Arabidopsis upon cold. For example, GI and TOC1 orthologues show conservation of alternative splicing events. Meanwhile, LHY orthologues show conservation of splicing behaviour, where cold-induced changes in species-specific splicing events lead to an increase in non-productive transcripts and a reduction in functional mRNA levels in both species. In contrast, PRR7 orthologues differ markedly, with barley (HvPPD-H1) exhibiting temperature-dependent isoform switching, a response not observed in Arabidopsis" ], "source":"https:\/\/doi.org\/10.1371\/journal.pone.0168028", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1371\/journal.pone.0168028", "Year":2016.0, "Citations":27.0, "answer":2, "source_journal":"PLOS ONE", "is_expert":true }, { "question":"What is the speed of alternative splicing response to cold stress in Arabidopsis leaves?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The alternative splicing response to cold stress in Arabidopsis leaves is rapid. More than half of the genes known to undergo alternative splicing in response to cold show differential gene expression within 9 hours of cold stress. Additionally, over half of the cold-induced isoform switches occurred 6 hours before the cold treatment.", "The alternative splicing response to cold stress in Arabidopsis leaves is rapid. More than half of the genes known to undergo alternative splicing in response to cold show differential alternative splicing within 9 hours of cold stress. Additionally, over half of the cold-induced isoform switches occurs within 6 hours of cold treatment.", "The alternative splicing response to cold stress in Arabidopsis leaves is dynamic. Up to half of the genes known to undergo alternative splicing in response to cold show differential alternative splicing 9 hours before the cold stress. Additionally, less than half of the cold-induced isoform switches occurred within 6 hours of cold treatment." ], "source":"https:\/\/doi.org\/10.1105\/tpc.18.00177", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1105\/tpc.18.00177", "Year":2018.0, "Citations":242.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"Which is the most comprehensive Reference Transcript Dataset for Arabidopsis thaliana to date?", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "AtRTD3 is the most comprehensive and accurate Arabidopsis transcriptome as of 2024. It was constructed from sequencing RNAs from a diverse set of tissues, environmental conditions, and mutants, ensuring transcript diversity. Robust computational methods were used to ensure accuracy of transcript sequences. ", "TAIR10 is the most comprehensive and accurate Arabidopsis transcriptome of all time. It was constructed from sequencing RNAs from a diverse set of tissues, environmental conditions, and mutants, ensuring transcript diversity. Robust computational methods and manual curation were used to ensure accuracy of transcript sequences. ", "AtRTD2 is the most comprehensive and accurate Arabidopsis transcriptome to date. It was constructed from sequencing RNA molecules from Arabidopsis rosettes exposed to different environmental conditions, ensuring transcript diversity. Robust computational methods were used to ensure accuracy of transcript sequences. " ], "source":"https:\/\/doi.org\/10.1186\/s13059-022-02711-0", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1186\/s13059-022-02711-0", "Year":2022.0, "Citations":56.0, "answer":0, "source_journal":"Genome Biology", "is_expert":true }, { "question":"Why is the AtRTD2-QUASI not the most appropriate Reference Transcript Dataset for quantifying Arabidopsis thaliana transcripts with bona fide alternative transcription start site and\/or polyadenylation?", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "AtRTD2-QUASI is unable to properly quantify the expression for the majority of genes because it is built on the assumption that much of the variation in 5\u2019 and 3\u2019 UTR length of transcripts is likely due to transcripts lacking regulatory regions (i.e., not being full-length). Accordingly, modifying the transcripts in AtRTD2-QUASI to have variable start and end coordinates has impacted the quantification of most isoforms compared to AtRTD2, which does not implement such modifications. On the other hand, AtRTD2 has lost all information on endogenous alternative transcription start and polyadenylation sites, making it unsuitable for analysing these mechanisms.", "Although it properly quantifies the expression for the majority of genes, AtRTD2-QUASI is built on the assumption that, for the majority of genes, much of the variation in 5\u2019 and 3\u2019 UTR length of transcripts is likely due to incomplete transcripts lacking terminal regions (i.e., not being full-length). Accordingly, modifying the transcripts in AtRTD2-QUASI to have uniform start and end coordinates has improved quantification for most isoforms compared to AtRTD2, which does not implement such modifications. On the other hand, AtRTD2 has lost all information on alternative transcription start and polyadenylation sites, making it unsuitable for analysing these mechanisms.", "Although it properly quantifies the expression of all Arabidopsis genes, AtRTD2-QUASI is built on the assumption that each and every variation in 5\u2019 and 3\u2019 UTR length of transcripts is likely due to incomplete transcripts lacking intronic regions (i.e., not being full-length). Accordingly, modifying the transcripts in AtRTD2-QUASI to have uniform start and end coordinates has improved quantification of isoforms compared to AtRTD2, which does not implement such modifications. On the other hand, AtRTD2 has included all information on alternative transcription start and polyadenylation sites, making it unsuitable for analysing these mechanisms." ], "source":"https:\/\/doi.org\/10.1093\/nar\/gkx267", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1093\/nar\/gkx267", "Year":2017.0, "Citations":234.0, "answer":1, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"How UV-B radiation impacts in the UVR8 photoreceptor protein structure in Arabidopsis thaliana?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "After UV-B radiation, UVR8 is activated via a structural change from a monomer to dimer. The aminoacids tryptophans Trp- 285 and Trp-233 act as chromophores which absorb UV-B leading to conformational changes generating dimer interactions. ", "After UV-B radiation, UVR8 is activated via a structural change from a dimer to monomer. The aminoacids arginine Arg- 285 and Arg-233, located in the homodimeric interface, act as chromophores which absorb UV-B leading to conformational changes breaking key cross-dimer interactions. ", "After UV-B radiation, UVR8 is activated via a structural change from a dimer to monomer. The aminoacids tryptophans Trp- 285 and Trp-233, located in the homodimeric interface, act as chromophores which absorb UV-B leading to conformational changes breaking key cross-dimer interactions. " ], "source":"https:\/\/doi.org\/10.1146\/annurev-arplant-050718-095946", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1146\/annurev-arplant-050718-095946", "Year":2021.0, "Citations":108.0, "answer":2, "source_journal":"Annual Review of Plant Biology", "is_expert":true }, { "question":"How is the E3 ubiquitin ligase COP1 involved in UV-B perception and signalling in Arabidopsis thaliana?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "COP1 forms an E3 ubiquitin ligase complex together with SPA proteins, and this complex represses photomorphogenesis in the dark by directing promoting factors, such as the UV-B photoreceptor UVR8, to be degraded. After UV-B radiation, the TF HY5 interacts with COP1. This interaction sequesters COP1 from the E3 ubiquitin ligase complex, blocking its degradation function. ", "COP1 forms an E3 ubiquitin ligase complex together with SPA proteins, and this complex represses photomorphogenesis in the dark by directing promoting factors, such as the positive regulator of photomorphogenesis HY5, to be degraded. After UV-B radiation, UVR8 monomer interacts with COP1. This interaction sequesters COP1 from the E3 ubiquitin ligase complex, avoiding HY5 destabilization. ", "COP1 forms an E3 ubiquitin ligase complex together with SPA proteins, and this complex activates photomorphogenesis by promoting the synthesis of transcription factors such as HY5. After UV-B radiation, UVR8 monomer interacts with COP1. This interaction sequesters COP1 from the E3 ubiquitin ligase complex, impairing HY5 synthesis." ], "source":"https:\/\/doi.org\/10.1007\/s44154-022-00076-9", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1007\/s44154-022-00076-9", "Year":2022.0, "Citations":44.0, "answer":1, "source_journal":"Stress Biology", "is_expert":true }, { "question":"Which proteins facilitate UVR8 redimerization in Arabidopsis thaliana?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The proteins are WD40-repeat RUP1 and RUP2 proteins and their transcripts are UV-B inducible in a UVR8 dependent manner. These proteins interact with both UVR8 homodimer and monomers, although they have a stronger affinity for active UVR8 monomers. RUP1 and RUP2 facilitate redimerization of UVR8 in vivo within 2 h to balance the signalling pathway.", "The proteins are RUP1 and RUP2 proteins and their transcripts are UV-B inducible in a UVR8 dependent manner. These proteins have a strong affinity with COP1 sequestering it from the complex UVR8-COP1 and facilitating the consequent redimerization of UVR8 within 2 h of UV-B exposure to balance the signalling pathway.", "The proteins are two TF RUP1 and RUP2 which are UV-B inducible in a UVR8 independent manner. These factors interact with both UVR8 homodimer and monomers, although they have a stronger affinity for active UVR8 monomers. RUP1 and RUP2 facilitate redimerization of UVR8 in vivo within 2 h to balance the signalling pathway." ], "source":"https:\/\/doi.org\/10.1146\/annurev-arplant-050718-095946", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1146\/annurev-arplant-050718-095946", "Year":2021.0, "Citations":108.0, "answer":0, "source_journal":"Annual Review of Plant Biology", "is_expert":true }, { "question":"Which is the subcellular localization and activity of UVR8 in Arabidopsis thaliana?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "UVR8 localizes both in the cytosol and the nucleus. Upon UV-B exposure, UVR8 monomers accumulate in the nucleus, although it does not have a nuclear localization signal (NLS). Intriguingly, COP1 is required for UVR8 nuclear accumulation, and it includes both an NLS and a nuclear export signal. Alternatively, UVR8 may enter the nucleus through either diffusion or its interaction with presently unknown NLS-containing proteins.", "UVR8 localizes both in the cytosol and the nucleus. Upon UV-B exposure, UVR8 monomers accumulate in the cytosol, although it does not have a nuclear export signal. Intriguingly, COP1 is required for UVR8 cytosol accumulation, and it includes a nuclear export signal. ", "UVR8 localizes both in the cytosol and the nucleus. Upon UV-B exposure, UVR8 monomers accumulate in the nucleus. UVR8 may enter the nucleus because of a nuclear localization signal (NLS) present in its structure. " ], "source":"https:\/\/doi.org\/10.1146\/annurev-arplant-050718-095946", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1146\/annurev-arplant-050718-095946", "Year":2021.0, "Citations":108.0, "answer":0, "source_journal":"Annual Review of Plant Biology", "is_expert":true }, { "question":"Which role plays the transcription factor HY5 in UV-B signaling in Arabidopsis thaliana?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "HY5 is a positive regulator of photomorphogenesis, and it directly binds to DNA to regulate expression of numerous genes. HY5 and its homolog HYH, show partially overlapping function in signalling pathways downstream of several photoreceptors; however, HY5 plays the major role under all light conditions. HY5 is also a substrate for the COP1\/SPA E3 ubiquitin ligase complex and due to the UVR8\u2013COP1 interaction, HY5 is rapidly post transcriptionally stabilized under UV-B. ", "HY5 is a repressor of photomorphogenesis, and it directly binds to DNA to block the expression of numerous genes under dark conditions. Upon light + UV-B exposure HY5 is a substrate for the COP1\/SPA E3 ubiquitin ligase complex and due to the UVR8\u2013COP1 interaction, HY5 is rapidly post transcriptionally degraded.", "HY5 is a positive regulator of photomorphogenesis. Under light conditions, it forms a homodimer but after UV-B radiation, HY5 monomerizes and forms a complex with COP1 which binds to DNA to regulate expression of numerous genes, among them, the gene coding for UV-B photoreceptor UVR8. " ], "source":"https:\/\/doi.org\/10.1146\/annurev-arplant-050718-095946", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1146\/annurev-arplant-050718-095946", "Year":2021.0, "Citations":108.0, "answer":0, "source_journal":"Annual Review of Plant Biology", "is_expert":true }, { "question":"In the framework of alternative splicing, what is an exitron?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "non-specific" ], "options":[ "It is a region of an RNA that can be recognized by the spliceosome as an intron but, in opposition to other introns (canonical introns), exitrons have coding capacities and other features that are common for exons. ", "An exitron is a sequence of DNA that is both an intron and an exon, meaning it has characteristics of both: \nIntron: An intron is a noncoding sequence that is removed before a mature mRNA leaves the nucleus.\nExon: An exon is a coding sequence that is used to create proteins.", "It is an intron inside a coding exon." ], "source":"10.1101\/gr.186585.114", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1101\/gr.186585.114", "Year":2015.0, "Citations":137.0, "answer":0, "source_journal":"Genome Research", "is_expert":true }, { "question":"Considering gene expression in eukaryotes, the definition of the term exitron brings to debate more basic questions related to splicing and alternative splicing, in this sense, what is an intron?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "non-specific" ], "options":[ "An intron is a region of an RNA molecule that can be recognized by the spliceosome and spliced out or excised from the RNA molecule forming a lariat. ", "Is an internal non-coding region of an RNA.", "It is a segment of a DNA or RNA molecule which does not code for proteins and interrupts the sequence of genes." ], "source":"non-specific", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":null, "Year":null, "Citations":null, "answer":0, "source_journal":null, "is_expert":true }, { "question":"Considering the kinetic model that explains the coupling between alternative splicing regulation and RNA polymerase II elongation, a \"slower\" elongation would favor or not the inclusion of a cassette exon?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "non-specific" ], "options":[ "Slower elongation rates of RNA polymerase II are linked to higher exclusion of exon cassettes. ", "In general a slower elongation rate would favor the inclusion of alternative exons with weak splice sites in their borders. However, there are specific cases in which there is a competition between splice site selection and the binding of a negative regulator, in those cases, a slow transcription rate could favor the exclusion of the specific exon.", "The kinetic model is not linked to splicing." ], "source":"https:\/\/doi.org\/10.1016\/j.molcel.2014.03.044", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.molcel.2014.03.044", "Year":2014.0, "Citations":199.0, "answer":1, "source_journal":"Molecular Cell", "is_expert":true }, { "question":"What is the most frequent alternative splicing event in plants?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "non-specific" ], "options":[ "In general, the most conspicuous splicing event in plants is intron retention. ", "Exitron splicing is the most frequent event in plants.", "Exon skipping. " ], "source":"https:\/\/doi.org\/10.1016\/j.tplants.2019.02.006", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.tplants.2019.02.006", "Year":2019.0, "Citations":112.0, "answer":0, "source_journal":"Trends in Plant Science", "is_expert":true }, { "question":"There are key differences between plants and animals, also in alternative splicing regulation. In animals the main outcome of alternative splicing of coding genes is the production of proteins with different functions. Would you say that in plants the scenario is the same?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "non-specific" ], "options":[ "There are no differences in this sense, the main outcome of alternative splicing is the generation of different isoforms that can be translated to different proteins.", "The alternative splicing process generates different proteins, in plants as well as in animals.", "In plants intron retention is the most common alternative splicing outcome. This is related to nuclear retention of the corresponding transcripts. Hence, those transcripts cannot be translated. Furthermore, retained introns tend to have stop codons. As a corollary, the general trend of alternative splicing in plants is to produce isoforms that cannot be translated but could regulate the total output (protein levels) of a gene. " ], "source":"https:\/\/doi.org\/10.1016\/j.tplants.2019.02.006", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.tplants.2019.02.006", "Year":2019.0, "Citations":112.0, "answer":2, "source_journal":"Trends in Plant Science", "is_expert":true }, { "question":"How are GRF transcription factors regulated, and how do they control leaf growth in Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "GRFs are transcriptionally regulated by GIF co-regulators and microRNA miR396 through the transcriptional gene silencing pathway. GRFs control leaf longevity and senescence. An increase in microRNA miR396 reduces GRF expression, inducing senescence and decreasing organ size.", "GRFs are post-transcriptionally regulated by microRNA miR396 and form protein complexes with GIF co-regulators. GRFs control the transition from stem cells to transit amplifying cells. An increase in microRNA miR396 reduces GRF expression, increasing stem cell numbers and reducing organ size.", "GRFs are post-transcriptionally regulated by microRNA miR396 and form protein complexes with GIF co-regulators. GRFs control the transition from cell proliferation to cell differentiation in leaves, thereby determining the duration of the proliferative phase. An increase in microRNA miR396 reduces GRF expression, leading to decreased cell proliferation and reduced organ size." ], "source":"10.1242\/dev.043067", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1242\/dev.043067", "Year":2010.0, "Citations":443.0, "answer":2, "source_journal":"Development", "is_expert":true }, { "question":"How is the transcription factor ARF2 involved in the control of cell number in Arabidopsis leaves?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "arf2 mutants have larger leaves with more cells. ARF2 directly activates GRF5, a transcription factor that is not regulated by microRNA miR396. Overexpression of GRF5 in arf2 mutants restores the cell number in leaves to wild-type levels.", "arf2 mutants have larger leaves with more cells. ARF2 directly represses GRF5, a GRF transcription factor that is not regulated by microRNA miR396. A double mutant arf2 grf5 has a similar number of cells as wild-type leaves.", "arf2 mutants produce larger seeds. The increase in seed size triggers a concomitant increase in leaf size, which in turn activates genes involved in cell proliferation and growth, such as the GRF transcription factors." ], "source":"10.1093\/plphys\/kiab014", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1093\/plphys\/kiab014", "Year":2021.0, "Citations":30.0, "answer":1, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"What is the function of miR396 in Arabidopsis roots?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "miR396 has well-known functions in leaves, but its roles in other organs, such as roots, have not yet been studied in detail.", "miR396 controls the transition from cell proliferation to cell differentiation. High levels of miR396 in roots trigger cell differentiation.", "miR396 controls the transition from stem cells to transit-amplifying cells. High levels of miR396 increase the stemness of the root meristem." ], "source":"10.1105\/tpc.15.00452", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1105\/tpc.15.00452", "Year":2015.0, "Citations":141.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How are miRNA precursors recognized by the processing machinery in plant cells?", "area":"GENE REGULATION - PTGS", "plant_species":[ "non-specific" ], "options":[ "All plant miRNA precursors have a 15-nt stem below the miRNA\/miRNA* duplex, which is recognized by the DCL1 complex to make the first cut and release a pre-miRNA. The DCL1 complex makes a second cut 21 nucleotides away from the first cut to release the mature microRNA.", "Plant miRNA precursors can have different structural determinants that guide the DCL1 complex to make the first cut. Precursors may have a 15-nt stem region below the miRNA\/miRNA* duplex or a 15-nt stem above the duplex. This allows processing to initiate either from the base of the stem or from the distal loop, respectively.", "Plant miRNA precursors have an 11-nt stem below the miRNA\/miRNA* duplex, which is recognized by DROSHA to release a pre-miRNA. The pre-miRNA is then exported to the cytoplasm, where Dicer makes a second cut." ], "source":"10.1093\/nar\/gky853", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1093\/nar\/gky853", "Year":2018.0, "Citations":15.0, "answer":1, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"Do mismatches in the miRNA\/miRNA* region of the precursor impact miRNA precursor processing in Arabidopsis Thaliana?", "area":"GENE REGULATION - PTGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "No, the only important factor is the presence of an overall double-stranded RNA region in the precursor.", "Yes, the number and position of mismatches in the miRNA\/miRNA* duplex determine whether the miRNA translationally inhibits its target or guides target cleavage.", "Yes, mismatches can reduce the processing efficiency." ], "source":"10.1093\/nar\/gkae458", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1093\/nar\/gkae458", "Year":2024.0, "Citations":4.0, "answer":2, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"In Arabidopsis, the long non-coding RNA, SVALKA, represses CBF1 via which molecular mechanism?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Transcriptional collision", "Transcriptional regulation", "Epigenetic regulation" ], "source":"10.1038\/s41467-018-07010-6", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41467-018-07010-6", "Year":2018.0, "Citations":177.0, "answer":0, "source_journal":"Nature Communications", "is_expert":true }, { "question":"What is the hallmark of RNAPII collision in Arabidopsis?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "RNAPII stalling on both DNA strands detected by plaNET-seq", "Prematurely terminated mRNA detected by RNA-seq", "Increased occurrence of transcription end sites detected by Direct RNA-seq" ], "source":"10.1038\/s41467-018-07010-6", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41467-018-07010-6", "Year":2018.0, "Citations":177.0, "answer":0, "source_journal":"Nature Communications", "is_expert":true }, { "question":"Why cannot two RNAPII complexes pass each other when transcribing on opposite DNA strands?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "DNA looping", "Formation of R-loops", "Steric hindrance" ], "source":"10.1016\/j.molcel.2012.08.027", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.molcel.2012.08.027", "Year":2012.0, "Citations":151.0, "answer":2, "source_journal":"Molecular Cell", "is_expert":true }, { "question":"What is the prerequisite for transcriptional collision?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "Phosphorylation of serine 2 of the NRPB1 CTD-tail", "Simultaneous transcription of both DNA strands in opposite direction ", "Increased RNAPII stalling on one DNA strand" ], "source":"10.1038\/s41467-018-07010-6", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41467-018-07010-6", "Year":2018.0, "Citations":177.0, "answer":1, "source_journal":"Nature Communications", "is_expert":true }, { "question":"Where is the main stalling site in the 5'-end of genes in Arabidopsis?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The +1 nucleosome", "The transcription start site", "100 bp downstream of the transcription start site" ], "source":"10.1093\/nar\/gkz1189", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1093\/nar\/gkz1189", "Year":2019.0, "Citations":91.0, "answer":0, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"What stages characterize the development of drupes and what are the main processes taking place in each one?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "non-specific" ], "options":[ "The double sigmoid growth rate of drupe development as a function of time is characterized by four stages. The first exponential growth stage is characterized by endocarp cell division and expansion. The second phase, where there is practically no increase in fruit size, is characterized by mesocarp lignification, pit hardening, and stone formation. The third phase is characterized by exponential fruit growth sustained mainly by cell duplication. During the fourth stage, fruit growth is slow; the final fruit size is reached, followed by the ripening process, in which metabolic changes and softening prepare the fruit for consumption.", "The sigmoid growth rate of drupe development as a function of time is characterized by four stages. The first logarithmic growth stage is characterized by cell division and expansion. In the second phase, the increase in fruit size is accompanied by endocarp lignification, pit hardening, and stone formation. The third phase is characterized by the exponential fruit growth sustained mainly by cell expansion. During the fourth stage, fruit growth is fast, the final fruit size is reached, followed by the ripening process, in which metabolic changes and softening prepare the fruit for consumption.", "The double sigmoid growth rate of drupe development as a function of time is characterized by four stages. The first exponential growth stage is characterized by cell division and expansion. The second phase, where there is practically no increase in fruit size, is characterized by endocarp lignification, pit hardening, and stone formation. The third phase is characterized by exponential fruit growth sustained mainly by cell expansion. During the fourth stage, fruit growth is slow; the final fruit size is reached, followed by the ripening process, in which metabolic changes and softening prepare the fruit for consumption. " ], "source":"doi:10.1093\/jxb\/erm213", "normalized_plant_species":"Non-specific", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1093\/jxb\/erm213", "Year":2007.0, "Citations":73.0, "answer":2, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"What are the main physiological and biochemical processes occurring during climacteric fruit ripening?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "non-specific" ], "options":[ "Ripening, which occurs after reaching the fruit maturation stage, is a complex syndrome that transforms the fruit into an edible organ for seed dispersal organisms. Climacteric fruit ripening is characterized by: i) ethylene biosynthesis and respiration increase; ii) loss of flesh firmness and pulp structural changes due to the depolymerization and solubilization of cell wall components and cell turgor decrease; iii) changes in taste and overall flavor due to the increase of mono- and disaccharides and volatile compounds and modification of organic acid levels; iv) changes in flesh and skin color due to chlorophyll degradation and accumulation of carotenoid and\/or flavonoids; v) increase of susceptibility to pathogens.", "Ripening, which occurs after reaching the fruit maturation stage, is a complex syndrome that transforms the fruit into an edible organ for seed dispersal organisms. Climacteric fruit ripening is characterized by: i) ethylene biosynthesis and respiration increase; ii) loss of flesh firmness and pulp structural changes due to the depolymerization and solubilization of cell wall components and cell turgor decrease; iii) changes in taste and overall flavor due to the increase of mono- and disaccharides and volatile compounds and modification of organic acid levels; iv) changes in flesh and skin color due to chlorophyll synthesis and decrease of carotenoid and\/or flavonoids; v) decrease of susceptibility to pathogens.", "Ripening, which occurs after reaching the fruit maturation stage, is a complex syndrome that transforms the fruit into an edible organ for seed dispersal organisms. Climacteric fruit ripening is characterized by: i) ethylene biosynthesis and respiration inhibition; ii) loss of flesh firmness and pulp structural changes due to the polymerization and solubilization of cell wall components and cell turgor increase; iii) changes in taste and overall flavor due to the decrease of mono- and disaccharides and volatile compounds and modification of organic acid levels; iv) changes in flesh and skin color due to chlorophyll degradation and accumulation of carotenoid and\/or flavonoids; v) increase of susceptibility to pathogens." ], "source":"https:\/\/doi.org\/10.1016\/j.pbi.2021.102042", "normalized_plant_species":"Non-specific", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1016\/j.pbi.2021.102042", "Year":2021.0, "Citations":71.0, "answer":0, "source_journal":"Current Opinion in Plant Biology", "is_expert":true }, { "question":"What are the differences between peaches and nectarines and what are the genes involved in these differences?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Prunus persica" ], "options":[ "The absence of skin pubescence fruit trichomes characterizes nectarines. The development of epidermal hairs on fruit peach skin is controlled by a MYB transcription factor (MYB25). In nectarines, the expression of this gene is impaired by the insertion of a LTR retroelement. This unique mutation discriminates between peach and nectarine plants and is used as a tool for seedling selection in peach breeding programs. MYB transcription factors also control the synthesis of anthocyanins, which are important in determining fruit the color peach skin, and other flavonoids, such as flavonols and catechins.", "The presence of skin pubescence fruit trichomes characterizes nectarines. The development of epidermal hairs on fruit peach skin is controlled by a MYB transcription factor (MYB25). In nectarines, the expression of this gene is induced by the insertion of a LTR retroelement. This unique mutation discriminates between peach and nectarine plants and is used as a tool for seedling selection in peach breeding programs. MYB transcription factors also control the synthesis of anthocyanins, which are important in determining the color peach skin, and other flavonoids, such as flavonols and catechins.", "The absence of skin pubescence fruit trichomes characterizes nectarines. The development of epidermal hairs on fruit peach skin is controlled by a MYB transcription factor (MYB25). In nectarines, the expression of this gene is impaired by the insertion of a LTR retroelement. This is one of the mutations that discriminates between peach and nectarine plants and may be used as a tool for seedling selection in peach breeding programs. MYB transcription factors also control the synthesis of anthocyanins, which are important in determining the color peach mesocarp, and other flavonoids, such as flavonols and catechins." ], "source":"e90574. doi:10.1371\/journal.pone.0090574", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1371\/journal.pone.0090574", "Year":2014.0, "Citations":84.0, "answer":0, "source_journal":"PLoS ONE", "is_expert":true }, { "question":"What are the main effects of cold stress in plants, and which genes mediate the plant response to low temperature?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "Cold stress inhibits plant growth and productivity by direct inhibition of enzymatic reactions, decreasing cell membrane fluidity, and altering protein structure, gene expression, and protein biosynthesis. Freezing temperatures (less than 0 \u00b0C) induce cell dehydration and membrane disruption, mainly because of ice crystal formation in the apoplast. To cope with cold stress, plant cells activate a complex defense system, including the induction of reactive oxygen species scavenging systems, the modification of lipid composition to maintain membrane fluidity, and the increase of cryoprotective biomolecules, such as soluble sugars or proline, and antifreeze proteins. These changes are the results of the induction of a set of regulatory networks dependent on the induction of key transcription factors, like C-repeat Binding Factors (CBFs). The cold signaling pathways are integrated with other light signaling, the circadian clock, hormone signaling, and biotic defense.", "Cold stress inhibits plant growth and productivity by direct inhibition of enzymatic reactions, decreasing cell membrane fluidity, and altering protein structure, gene expression, and protein biosynthesis. Freezing temperatures (less than 0 \u00b0C) induce cell dehydration and cell membrane disruption, mainly because of ice crystal formation in the apoplast. To cope with cold stress, plant cells activate a complex defense system, including the decrease of reactive oxygen species scavenging systems, the modification of lipid composition to decrease membrane fluidity, and the decrease of biomolecules, such as soluble sugars or proline, and antifreeze proteins. These changes are the results of the induction of a set of regulatory networks dependent on the induction of key transcription factors, like C-repeat Binding Factors (CBFs). The cold signaling pathways are integrated with other light signaling, the circadian clock, hormone signaling, and biotic defense.", "Cold stress inhibits plant growth and productivity by direct activation of enzymatic reactions, increasing cell membrane fluidity, and altering protein structure, gene expression, and protein biosynthesis. Freezing temperatures (less than 0 \u00b0C) induce cell hydration and membrane disruption, mainly because of ice crystal formation in the cytosol. To cope with cold stress, plant cells activate a complex defense system, including the induction of reactive oxygen species scavenging systems, the modification of lipid composition to maintain membrane fluidity, and the increase of cryoprotective biomolecules, such as soluble sugars or proline, and antifreeze proteins. These changes are the results of the induction of a set of regulatory networks dependent on the induction of key transcription factors, like C-repeat Binding Factors (CBFs). The cold signaling pathways are integrated with other light signaling, the circadian clock, hormone signaling, and biotic defense." ], "source":"doi.org\/10.1146\/annurev-genet-111523-102226", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1146\/annurev-genet-111523-102226", "Year":2024.0, "Citations":24.0, "answer":0, "source_journal":"Annual Review of Genetics", "is_expert":true }, { "question":"What are the advantages and disadvantages of cold storage of fleshy fruits after harvest, and which postharvest treatments prevent cold damage?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "Postharvest cold storage of fleshy fruits is essential for commercialization because it delays ripening, softening, and decay. However, cold storage also induces fruit damage, including symptoms such as surface pitting or discoloration or internal disorders such as browning or mealiness. Besides, cold storage produces several metabolic reconfigurations in the fruit, impairing ripening, organoleptic properties, and overall fruit flavor. The application of chemical compounds after harvest, such as antioxidants or hormones, and pre-conditioned treatments, such as heat treatment or incubation at moderate temperature before cold storage, are successful in preventing fleshy fruits' cold damage. ", "Postharvest cold storage of fleshy fruits is essential for commercialization because it delays ripening, softening, and decay. However, cold storage also induces fruit damage, including symptoms such as surface pitting or discoloration or internal disorders such as browning or mealiness. Besides, cold storage inhibits metabolic reconfigurations in the fruit, increasing organoleptic properties, and overall fruit flavor. The application of chemical compounds after harvest, such as antioxidants or hormones, and pre-conditioned treatments, such as heat treatment or incubation at moderate temperature before cold storage, are not successful in preventing fleshy fruits' cold damage.", "Postharvest cold storage of fleshy fruits is essential for commercialization because it accelerates ripening, softening, and decay. However, cold storage also prevents fruit damage, including symptoms such as surface pitting or discoloration or internal disorders such as browning or mealiness. Besides, cold storage produces several metabolic reconfigurations in the fruit, impairing ripening, organoleptic properties, and overall fruit flavor. The application of chemical compounds after harvest, such as antioxidants or hormones, and pre-conditioned treatments, such as heat treatment or incubation at moderate temperature before cold storage, are successful in preventing fleshy fruits' cold damage." ], "source":"https:\/\/doi.org\/10.1016\/j.fochx.2023.101080", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.fochx.2023.101080", "Year":2024.0, "Citations":8.0, "answer":0, "source_journal":"Food Chemistry: X", "is_expert":true }, { "question":"Which lipid-derived second messengers are produced during the recognition of pathogen-associated molecular patterns (PAMPs)?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "non-specific" ], "options":[ "Nitric Oxide", "AMPc", "Phosphatidic acid" ], "source":"https:\/\/doi.org\/10.1016\/S1369-5266(02)00268-6", "normalized_plant_species":"Non-specific", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1016\/S1369-5266(02)00268-6", "Year":2002.0, "Citations":202.0, "answer":2, "source_journal":"Current Opinion in Plant Biology", "is_expert":true }, { "question":"Which of the following is a lipid-derived signaling molecule involved in plant defense?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "Abscisic acid", "Salicylic acid", "Jasmonic acid" ], "source":"https:\/\/doi.org\/10.1016\/S1369-5266(02)00268-6", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/S1369-5266(02)00268-6", "Year":2002.0, "Citations":202.0, "answer":2, "source_journal":"Current Opinion in Plant Biology", "is_expert":true }, { "question":"The phospholipase C and diacylglycerol kinase pathway produces phosphatidic acid during PAMP perception. Phosphatidic acid has been shown to participate in ROS production by regulating the activity of:", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "Phospholipase D", "NADPH oxidase", "MAPK" ], "source":"10.1016\/j.cell.2023.12.030", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.cell.2023.12.030", "Year":2024.0, "Citations":39.0, "answer":1, "source_journal":"Cell", "is_expert":true }, { "question":"Which of the following enzymes is involved in the jasmonic acid biosynthesis pathway?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "Phospholipase A2", "Phospholipase C", "Phospholipase D" ], "source":"https:\/\/doi.org\/10.1016\/S1369-5266(02)00268-6", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/S1369-5266(02)00268-6", "Year":2002.0, "Citations":202.0, "answer":0, "source_journal":"Current Opinion in Plant Biology", "is_expert":true }, { "question":"Which of the following processes is NOT directly linked to lipid biosynthesis in plants?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "non-specific" ], "options":[ "Cuticle formation", "Cellulose biosynthesis", "Jasmonate signaling" ], "source":"non-specific", "normalized_plant_species":"Non-specific", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":null, "Year":null, "Citations":null, "answer":1, "source_journal":null, "is_expert":true }, { "question":"What structural features make mRNAs more susceptible to translational regulation during rhizobial infection in Medicago truncatula?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "Medicago truncatula" ], "options":[ "Translationally regulated mRNAs exhibit no distinct structural features, relying entirely on transcriptional control.", "mRNAs with shorter coding sequences and UTRs are more susceptible to translational regulation.", "mRNAs with elongated coding sequences and unstructured UTRs are preferentially translated during infection." ], "source":"doi: 10.1105\/tpc.19.00647", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1105\/tpc.19.00647", "Year":2019.0, "Citations":31.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How does the ALT TAS3 transcript affect the miR390\/TAS3 pathway during rhizobial infection in Medicago truncatula?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "Medicago truncatula" ], "options":[ "ALT TAS3 functions as an endogenous target mimic, sequestering miR390 and reducing tasiARF production, thereby modulating nodule formation.", "ALT TAS3 degrades miR390, increasing tasiARF levels and repressing auxin-related pathways critical for nodule formation.", "ALT TAS3 enhances tasiARF production by increasing miR390 stability, leading to suppression of auxin signaling and reduced nodulation." ], "source":"doi: 10.1105\/tpc.19.00647", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1105\/tpc.19.00647", "Year":2019.0, "Citations":31.0, "answer":0, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How does Superkiller3 influence nodule morphology in Medicago truncatula?", "area":"GENE REGULATION - PTGS", "plant_species":[ "Medicago truncatula" ], "options":[ "Superkiller3 promotes the formation of oversized nodules with excessive bacterial growth.", "Superkiller3 prevents nodule formation, prioritizing root growth over symbiotic interactions.", "Superkiller3 ensures the formation of properly structured and functional nodules by regulating mRNA decay pathways during infection." ], "source":"doi: 10.1105\/tpc.19.00647", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1105\/tpc.19.00647", "Year":2019.0, "Citations":31.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"What advantage does TRAP-SEQ offer when studying cell-type-specific translation?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "non-specific" ], "options":[ "It measures protein abundance directly rather than RNA translation.", "It provides a global overview of transcriptional changes across the entire organism.", "It enables the analysis of ribosome-associated RNAs in specific cell types by expressing a tagged ribosomal protein in targeted tissues." ], "source":"doi.org\/10.1007\/978-1-0716-0712-1_26", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1007\/978-1-0716-0712-1_26", "Year":2020.0, "Citations":3.0, "answer":2, "source_journal":"Methods in Molecular Biology", "is_expert":true }, { "question":"How does TRAP-SEQ differ from traditional RNA extraction methods?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "non-specific" ], "options":[ "TRAP-SEQ specifically isolates RNAs associated with actively translating ribosomes, avoiding contamination from other ribonucleoprotein complexes.", "TRAP-SEQ isolates all cellular RNAs indiscriminately, including those not involved in translation", "TRAP-SEQ purifies only small RNAs such as miRNAs and siRNAs." ], "source":"doi.org\/10.1007\/978-1-0716-0712-1_26", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1007\/978-1-0716-0712-1_26", "Year":2020.0, "Citations":3.0, "answer":0, "source_journal":"Methods in Molecular Biology", "is_expert":true }, { "question":"Angiosperms have multiple phytochrome photoreceptors (phyA, phyB, ...). Do their functions differ during seedling de-etiolation?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana", "Solanum lycopersicum" ], "options":[ "phyA and phyB equally contribute to de-etiolation in response to far-red light. They have additive effects.", "phyB is the only phytochrome that significantly contributes to seedling de-etiolation", "phyA is the primary phytochrome triggering de-etiolation in response to far-red light, while phyB is the primary phytochrome triggering de-etiolation in response to red light." ], "source":"https:\/\/doi.org\/10.1093\/jxb\/erp304", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1093\/jxb\/erp304", "Year":2009.0, "Citations":635.0, "answer":2, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"Where is the major site of action of phytochromes in angiosperms?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana", "Marchantia polymorpha" ], "options":[ "Phytochromes primarily act in the cytosol upon light excitation", "Light activated phytochromes act at the cell surface", "The primary site of action of light activated phyA and phyB is in the nucleus" ], "source":"DOI: 10.1016\/j.tplants.2008.08.007", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.tplants.2008.08.007", "Year":2008.0, "Citations":84.0, "answer":2, "source_journal":"Trends in Plant Science", "is_expert":true }, { "question":"Which of the following events is a key for subsequent signalling following cryptochrome light activation?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Cryptochromes dimerise or multimerise following light activation", "Cryptochromes translocate from the cytosol to the nucleus", "Light excitation elicits monomerisation of cryptochromes" ], "source":"DOI: 10.1016\/j.tplants.2011.09.002", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.tplants.2011.09.002", "Year":2011.0, "Citations":250.0, "answer":0, "source_journal":"Trends in Plant Science", "is_expert":true }, { "question":"What is the primary event following light activation of the UVR8 UV-B photoreceptor?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "non-specific" ], "options":[ "UV-B photo-excitation dimerizes UVR8", "UV-B photo-excitation monomerizes UVR8", "UV-B photo-excitation activates an enzymatic activity of UVR8" ], "source":"DOI: 10.1146\/annurev-arplant-050718-095946", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1146\/annurev-arplant-050718-095946", "Year":2021.0, "Citations":108.0, "answer":1, "source_journal":"Annual Review of Plant Biology", "is_expert":true }, { "question":"How do plant phototropins initiate light signalling cascades?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "light activated phototropins interact with transcription factors from the PIF family.", "phototropins are light activated Ser\/Thr protein kinases", "phototropins translocate from the cytosol to the nucleus where they initiate signaling" ], "source":"DOI: 10.1016\/j.cub.2015.03.020", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.cub.2015.03.020", "Year":2015.0, "Citations":133.0, "answer":1, "source_journal":"Current Biology", "is_expert":true }, { "question":"What is the impact of 1\u2009\u03bcM bioactive gibberellin (GA) application on epidermal infection by symbiotic rhizobia in Medicago truncatula?", "area":"HORMONES", "plant_species":[ "Medicago truncatula" ], "options":[ "Application of 1\u2009\u03bcM bioactive GA increases epidermal infection by symbiotic rhizobia in Medicago truncatula", "Application of 1\u00b5M bioactive GA reduces epidermal infection by symbiotic rhizobia in Medicago truncatula", "Application of 1\u2009\u03bcM bioactive GA has no impact on epidermal infection by symbiotic rhizobia in Medicago truncatula " ], "source":"https:\/\/doi.org\/10.1038\/ncomms12636 and https:\/\/doi.org\/10.1038\/ncomms12433", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1038\/ncomms12433", "Year":2016.0, "Citations":192.0, "answer":1, "source_journal":"Nature Communications", "is_expert":true }, { "question":"In Medicago truncatula, GA suppression of infection involves the degradation of which proteins acting in the GA signaling pathway?", "area":"HORMONES", "plant_species":[ "Medicago truncatula" ], "options":[ "In Medicago truncatula, GA suppression of infection involves the degradation of DELLA proteins", "In Medicago truncatula, GA suppression of infection involves the degradation of GID proteins", "In Medicago truncatula, GA suppression of infection involves the degradation of PIF proteins" ], "source":"https:\/\/doi.org\/10.1038\/ncomms12636 and https:\/\/doi.org\/10.1038\/ncomms12433", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1038\/ncomms12433", "Year":2016.0, "Citations":192.0, "answer":0, "source_journal":"Nature Communications", "is_expert":true }, { "question":"In Medicago truncatula, the promoter of which gene encoding an important transcription factor regulating the progression of the infection thread is directly bound by GFP-della1-Delta18 protein?", "area":"HORMONES", "plant_species":[ "Medicago truncatula" ], "options":[ "In Medicago truncatula, GFP-della1-Delta18 directly binds to NF-YA1 promoter", "In Medicago truncatula, GFP-della1-Delta18 directly binds to ENOD11 promoter ", "In Medicago truncatula, GFP-della1-Delta18 directly binds to ERN1 promoter" ], "source":"https:\/\/doi.org\/10.1038\/ncomms12636", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1038\/ncomms12636", "Year":2016.0, "Citations":111.0, "answer":2, "source_journal":"Nature Communications", "is_expert":true }, { "question":"In Lotus japonicus, what is the impact of 1\u2009\u03bcM bioactive gibberellin (GA) application on root hair deformation in response to Nod Factors (NF)?", "area":"HORMONES", "plant_species":[ "Lotus japonicus" ], "options":[ "In Lotus japonicus, with 1\u2009\u03bcM bioactive GA treatment, root hair deformation is increased compared with Nod Factors alone", "In Lotus japonicus, with 1\u2009\u03bcM bioactive GA treatment, root hair deformation is completely abolished, even though Nod Factors were present", "In Lotus japonicus, with 1\u2009\u03bcM bioactive GA treatment, root hair deformation is not affected compared with Nod Factors alone" ], "source":"https:\/\/doi.org\/10.1111\/j.1365-313X.2008.03774.x", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1111\/j.1365-313X.2008.03774.x", "Year":2009.0, "Citations":143.0, "answer":1, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"What is the infection thread formation phenotype of DELLA-deficient pea la cry-s double mutants compared with wild-type?", "area":"HORMONES", "plant_species":[ "Pisum sativum" ], "options":[ "Infection thread formation was significantly reduced in DELLA-deficient pea la cry-s double mutants compared with wild-type plants", "Infection thread formation was similar in DELLA-deficient pea la cry-s double mutants compared with wild-type plants", "Infection thread formation was significantly increased in DELLA-deficient pea la cry-s double mutants compared with wild-type plants" ], "source":"https:\/\/doi.org\/10.1093\/jxb\/ery046", "normalized_plant_species":"Legumes", "normalized_area":"HORMONES", "doi":"10.1093\/jxb\/ery046", "Year":2018.0, "Citations":61.0, "answer":0, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"Which gene is the master regulator of heat stress response in tomato, how is it maintained inactive under control conditions, and to which cis-elements does it bind during heat stress?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Solanum lycopersicum" ], "options":[ "In tomato, the master regulator of heat stress response is HSFA1a. Under control conditions it is maintained inactive through interactions with HSP70 and HSP90 proteins. In response to heat stress, HSFA1a is released from HSP70 and HSP90, makes homo-oligomeric complexes which translocate to the nucleus. In the nucleus it binds to cis-elements called Heat Shock Elements (HSEs) which are typically found in the promoters of many heat stress induced genes. ", "In tomato, the master regulator of heat stress response is HSFA2. Under control conditions it is maintained inactive through interactions with small heat shock proteins (sHSPs). In response to heat stress, HSF2 in complex with sHSPs translocate to the nucleus. In the nucleus it binds to cis-elements called Heat Shock Elements (HSEs) which are typically found in the promoters of many heat stress induced genes. ", "In tomato, the master regulator of heat stress response is HSFA1a. Under control conditions it is maintained inactive in the nucleus through interactions with HSP70 and HSP90. In response to heat stress, HSFA1a is released from HSP70 and HSP90, makes hetero-oligomeric complexes which translocate to the nucleus. In the nucleus it binds to cis-elements called Stress Responsive Elements (SREs) which are typically found in the promoters of many heat stress induced genes. " ], "source":"10.1105\/tpc.110.076018", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"ENVIRONMENT", "doi":"10.1105\/tpc.110.076018", "Year":2011.0, "Citations":289.0, "answer":0, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"Which ethylene-related factors are involved in the induction of HSFA2 in Arabidopsis thaliana and how does this mechanism affect thermotolerance", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis thaliana, the induction of HSFA2 in response to ethylene signalling involves the transcription factors ERF95 and ERF97, which are regulated by the ethylene response master regulator ETHYLENE INSENSITIVE 3 (EIN3). This mechanism plays a critical role in enhancing thermotolerance", "In Arabidopsis thaliana, the induction of HSFA2 in response to ethylene signalling involves the transcription factors ERF95 and ERF97, which are regulated by the ethylene response master regulator EIN2 (ETHYLENE INSENSITIVE 2). This mechanism plays a critical role in enhancing thermosensitivity.", "In Arabidopsis thaliana, the activation of HSFA3 in response to ethylene signalling involves the transcription factors ERF91 and ERF97, which are regulated by the ethylene response master regulator ETHYLENE INSENSITIVE 3 (EIN3). This mechanism plays a significant role in enhancing thermotolerance." ], "source":"10.1093\/plcell\/koaa026", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1093\/plcell\/koaa026", "Year":2020.0, "Citations":110.0, "answer":0, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How does alternative splicing of the second intron of tomato HSFA2 affect the function, localization, and stability of its protein isoforms during heat stress, and what role do these isoforms play in acquired thermotolerance?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Solanum lycopersicum" ], "options":[ "Alternative splicing in the second intron of tomato HSFA2 results in two protein isoforms, HSFA2-I and HSFA2-II, with distinct roles in the heat stress response. HSFA2-II lacks a nuclear export signal (NES), resulting in strong nuclear retention. It is transcriptionally active but rapidly degraded in the nucleus by the 26S proteasome, limiting its activity during heat stress. HSFA2-I contains an NES and is sequestered in cytosolic heat stress granules (HSGs) during heat stress through interactions with class CI and CII small heat shock proteins (sHSPs). In the case of repeated heat stress, HSFA2-I is released from HSGs and interacts with HSFA1a to form superactivator complexes, which enhance acquired thermotolerance.", "Alternative splicing in the second intron of tomato HSFA2 results in two protein isoforms, HSFA2-I and HSFA2-II, with distinct roles in the heat stress response. HSFA2-I lacks a nuclear export signal (NES), resulting in strong nuclear retention. It is transcriptionally active but rapidly degraded in the nucleus by the 26S proteasome, limiting its activity during heat stress. HSFA2-II contains an NES and is sequestered in cytosolic heat stress granules (HSGs) during heat stress through interactions with HSFA1a. In the case of repeated heat stress, HSFA2-II is released from HSGs and interacts with HSFA1a to form repressor complexes, which suppress acquired thermotolerance.", "Alternative splicing in the second intron of tomato HSFA2 results in two protein isoforms, HSFA2-I and HSFA2-II, with distinct roles in the heat stress response. HSFA2-II lacks a nuclear export signal (NES), resulting in strong nuclear retention. It is transcriptionally active but rapidly degraded in the nucleus by autophagy, limiting its activity during heat stress. HSFA2-I contains an NES and is sequestered in cytosolic P-bodies (PBs) during heat stress through interactions with class CI and CII small heat shock proteins (sHSPs). During recovery, it is released from HSGs and interacts with HSFA1a to form superactivator complexes, which enhance acquired thermotolerance." ], "source":"10.1111\/nph.16221", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/nph.16221", "Year":2019.0, "Citations":61.0, "answer":0, "source_journal":"New Phytologist", "is_expert":true }, { "question":"How does HSFA2 regulate thermomemory in Arabidopsis thaliana, which HSF does it interact with, what histone modification is associated with this process, and which memory genes are regulated by this mechanism?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "HSFA2 in Arabidopsis thaliana is a central factor for thermomemory. It interacts with HSFA3, and the HSFA2\/HSFA3 complexes bind to the promoters of memory genes, triggering histone 3 lysine 9 (H3K9) acetylation, a modification that is associated with the genes the sustained expression of memory genes during recovery from a priming treatment, such as HSFA1a and HSP70-1.", "HSFA2 in Arabidopsis thaliana is a central factor for thermomemory. It interacts with HSFA4, and the HSFA2\/HSFA4 complexes bind to the promoters of memory genes, triggering histone 3 lysine 27 (H3K27) methylation, a modification that is associated with the sustained expression of memory genes during recovery from a priming treatment, such as APX3 and Hsa32.", "HSFA2 in Arabidopsis thaliana is a central factor for thermomemory. It interacts HSFA3 and HSFA2\/HSFA3 complexes bind to the promoters of memory genes triggers histone 3 lysine 4 (H3K4) methylation, a modification that is associated with the sustained expression of memory genes during recovery from a priming treatment, such as APX3 and HSA32. " ], "source":"10.1038\/s41467-021-23786-6", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/s41467-021-23786-6", "Year":2021.0, "Citations":155.0, "answer":2, "source_journal":"Nature Communications", "is_expert":true }, { "question":"Which are the two core transcription factors regulating the unfolded protein response (UPR) in Arabidopsis thaliana, and what are the key activation mechanisms for each transcription factor?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "bZIP60 and bZIP28 regulate the unfolded protein response (UPR) in Arabidopsis thaliana. Upon ER stress, bZIP60 mRNA is spliced by IRE1, producing an active form that translocates to the nucleus to activate UPR genes. bZIP28, an ER membrane-bound protein, is cleaved by S1P and S2P proteases in Golgi, releasing its cytosolic domain, which moves to the nucleus to promote UPR gene expression.", "bZIP60 and bZIP38 regulate the unfolded protein response (UPR) in Arabidopsis thaliana. Upon ER stress, bZIP60 protein is spliced by IRE1, producing an active form that translocates to the nucleus to activate UPR genes. bZIP28, a mitochondrial membrane-bound protein, is cleaved by S1P and S2P proteases, releasing its cytosolic domain, which moves to the nucleus to promote UPR gene expression.", "bZIP60 and bZIP28 regulate the unfolded protein response (UPR) in Arabidopsis thaliana. Upon ER stress, bZIP28 mRNA is spliced by the spliceosome, producing an active form that translocates to the nucleus to activate UPR genes. bZIP60, an ER membrane-bound protein, is cleaved by S1P and S2P proteases in Golgi, releasing its transmembrane domain, which moves to the nucleus to promote UPR gene expression." ], "source":"10.1111\/pce.14063", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/pce.14063", "Year":2021.0, "Citations":31.0, "answer":0, "source_journal":"Plant, Cell & Environment", "is_expert":true }, { "question":"What is the gene identified as key molecular player in the jasmonate insensitivity induced by far-red light?", "area":"HORMONES", "plant_species":[ "non-specific" ], "options":[ "ERF11 and MYC2", "All JAZ genes", "JAZ10" ], "source":"https:\/\/www.pnas.org\/doi\/full\/10.1073\/pnas.0900701106", "normalized_plant_species":"Non-specific", "normalized_area":"HORMONES", "doi":"10.1073\/pnas.0900701106", "Year":2009.0, "Citations":233.0, "answer":2, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"What are the physiological mechanisms behind the ability of Arabidopsis thaliana to promote growth and repress the induction of defenses under light signals of competition?", "area":"HORMONES", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Jasmonate desensitization of plant tissues mediated by upregulation of JAZ proteins and the inactivation of the bioactive JA-Ile through sulfotransferases.", "Jasmonate inactivation through degradation.", "Jasmonate synthesis is suppressed." ], "source":"https:\/\/www.pnas.org\/doi\/full\/10.1073\/pnas.0900701106", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1073\/pnas.0900701106", "Year":2009.0, "Citations":233.0, "answer":0, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"What is the ligand of the MpCOI1 of the jasmonate phytohormone in Marchantia polymorpha?", "area":"HORMONES", "plant_species":[ "Marchantia polymorpha" ], "options":[ "JA-Ile", "(+)-7-iso-JA-Ile (JA-Ile)", "dinor-OPDA" ], "source":"https:\/\/doi.org\/10.1038\/s41589-018-0033-4", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1038\/s41589-018-0033-4", "Year":2018.0, "Citations":192.0, "answer":2, "source_journal":"Nature Chemical Biology", "is_expert":true }, { "question":"What is the gene identified as molecular switch inducing jasmonate insensitivity upong signals of competition?", "area":"HORMONES", "plant_species":[ "non-specific" ], "options":[ "PIF (Phytochrome Interacting Factors)", "Phytochrome B", "sulfotransferase (ST2a) " ], "source":"https:\/\/doi.org\/10.1038\/s41477-020-0604-8", "normalized_plant_species":"Non-specific", "normalized_area":"HORMONES", "doi":"10.1038\/s41477-020-0604-8", "Year":2020.0, "Citations":109.0, "answer":2, "source_journal":"Nature Plants", "is_expert":true }, { "question":"What is the chemical origin for the bioactive jasmonic acid in Marchantia polymorpha?", "area":"HORMONES", "plant_species":[ "Marchantia polymorpha" ], "options":[ "C20 and C22", "C18, C16, C20 and C22", "C18 and C16" ], "source":"https:\/\/www.pnas.org\/doi\/10.1073\/pnas.2202930119?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1073\/pnas.2202930119", "Year":2022.0, "Citations":31.0, "answer":1, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"What is the role of CRISPR-based systems in epigenetic regulation, and what strategies have been used to achieve transcriptional regulation in plants?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "non-specific" ], "options":[ "The CRISPR\/dCas9 system can only function to silence or repress gene expression, and any efforts to activate genes through CRISPR are inherently limited by the inability of dCas9 to recruit the necessary transcriptional activators. This makes it impractical for applications that require the upregulation of specific genes for traits such as enhanced stress tolerance, growth, or metabolic changes in plants. Additionally, despite the existence of various regulatory domains, the CRISPR\/dCas9 system does not provide sufficient specificity or strength to achieve significant gene activation. As a result, this system is considered mostly ineffective for driving any form of substantial gene expression in plant systems.", "CRISPR-based systems, particularly the use of dCas9 (dead Cas9) proteins, have been adapted to epigenetic regulation by fusing them to various epigenetic domains. These strategies allow for precise, reversible modifications of chromatin marks such as DNA methylation and histone modifications. In plants, different strategies have been employed, such as the direct fusion of the regulation, SAM (Synergistic Activation Mediator) and scRNA (scaffolding RNAs), which include regulatory domains to the CRISPR\/dCas9 complex, and the SunTag strategy, which uses multi-epitope tags for efficient recruitment of multiple regulation domains. ", "CRISPR-based systems are solely limited to gene editing applications, as they rely on creating targeted double-strand breaks in DNA to introduce genetic modifications, which directly alters the genomic sequence and cannot be used for reversible modifications of epigenetic markers. " ], "source":"doi: 10.1007\/s11248-021-00252-z.", "normalized_plant_species":"Non-specific", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1007\/s11248-021-00252-z", "Year":2021.0, "Citations":14.0, "answer":1, "source_journal":"Transgenic Research", "is_expert":true }, { "question":"What was the physiological impact of using the dCas9-Suntag-DRM2 strategy on Arabidopsis thaliana, targeting genes involved in flowering time (FWA)?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The dCas9-Suntag-DRM2 strategy induced DNA methylation at the FWA gene promoter, leading to early flowering in Arabidopsis. This epigenetic modification was stable and passed on to the next generation, resulting in a consistent early flowering phenotype.", "The dCas9-Suntag-DRM2 strategy delayed flowering in Arabidopsis by reducing DNA methylation at the FWA gene promoter.", "The dCas9-Suntag-DRM2 strategy had no effect on flowering time or DNA methylation in Arabidopsis." ], "source":"doi: 10.1007\/s11248-021-00252-z.", "normalized_plant_species":"Model Organisms", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1007\/s11248-021-00252-z", "Year":2021.0, "Citations":14.0, "answer":0, "source_journal":"Transgenic Research", "is_expert":true }, { "question":"What was the physiological impact of using the dCas9-Suntag-TET1 strategy on Arabidopsis thaliana, targeting genes involved in flowering time (FWA) and what epigenetic modification was responsible for this effect?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The dCas9-Suntag-TET1 strategy caused early flowering in Arabidopsis by increasing DNA methylation at the FWA gene promoter.", "The dCas9-Suntag-TET1 strategy induced specific DNA demethylation of the FWA gene promoter, which led to late flowering phenotypes in Arabidopsis. The demethylation was responsible for the altered flowering time, which was inherited by subsequent plant generations.", "The dCas9-Suntag-TET1 strategy had no effect on flowering time, as there were no changes in DNA methylation at the FWA gene." ], "source":"doi: 10.1007\/s11248-021-00252-z.", "normalized_plant_species":"Model Organisms", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1007\/s11248-021-00252-z", "Year":2021.0, "Citations":14.0, "answer":1, "source_journal":"Transgenic Research", "is_expert":true }, { "question":"What role do Jasmonates (JAs) play in plant stress response and how are they involved in regulating specialized metabolites?", "area":"HORMONES", "plant_species":[ "non-specific" ], "options":[ "Jasmonates are primarily involved in regulating primary metabolic processes such as carbon assimilation and nitrogen fixation, and do not significantly influence specialized metabolism or plant defense mechanisms. They are mostly limited to controlling plant growth and reproductive processes, with minimal involvement in stress response or the production of specialized compounds.", "Jasmonates (JAs) are oxylipin-type hormones that are key regulators of plant stress responses. The bioactive form, JA-Ile, regulates the production of specialized metabolites by activating a set of transcription factors (TFs). These TFs control the expression of genes involved in the synthesis of compounds that help the plant defend against stressors such as herbivores and pathogens. JA signaling is crucial for balancing defense mechanisms with other physiological processes like growth.", "Jasmonates play no significant role in regulating plant stress responses. Their primary function is limited to the regulation of seed germination and flowering time, with little to no effect on specialized metabolism. Plants can defend themselves against biotic and abiotic stressors through other hormones like auxins and cytokinins, while jasmonates are not involved in such processes." ], "source":"doi: 10.1016\/j.pbi.2022.102197", "normalized_plant_species":"Non-specific", "normalized_area":"HORMONES", "doi":"10.1016\/j.pbi.2022.102197", "Year":2022.0, "Citations":72.0, "answer":1, "source_journal":"Current Opinion in Plant Biology", "is_expert":true }, { "question":"How does the interaction between Jasmonate signaling and light signaling pathways contribute to plant development, particularly in terms of photosynthesis and growth?", "area":"HORMONES", "plant_species":[ "non-specific" ], "options":[ "While Jasmonate signaling does play a role in defense responses, it actually represses light signaling to inhibit photosynthesis under high light conditions. This prevents the plant from engaging in efficient carbon fixation and growth, particularly under stress, by directly limiting the activation of light-dependent processes such as chlorophyll synthesis and the electron transport chain in photosynthesis.", "The interaction between Jasmonate and light signaling has no significant impact on photosynthesis or carbon metabolism. Instead, the two pathways function independently, with JA solely focusing on growth inhibition during stress and light signaling mainly affecting chlorophyll biosynthesis. There is no integration between these pathways to regulate photosynthetic efficiency or carbon flux in response to external environmental factors.", "The interaction between Jasmonate signaling and light signaling pathways plays a key role in regulating plant development. Specifically, JA signaling and light-regulated processes work together to maintain photosynthetic activity, enhance metabolic rate, and control carbon flow towards specialized metabolites. JA signaling modulates photomorphogenesis by regulating MYC2, which in turn promotes the expression of HY5, a transcription factor that coordinates light-regulated processes such as photosynthesis, carbon metabolism, and nutrient assimilation." ], "source":"doi: 10.1016\/j.pbi.2022.102197", "normalized_plant_species":"Non-specific", "normalized_area":"HORMONES", "doi":"10.1016\/j.pbi.2022.102197", "Year":2022.0, "Citations":72.0, "answer":2, "source_journal":"Current Opinion in Plant Biology", "is_expert":true }, { "question":"What is the role of the transcription factor FaRIF in the regulation of strawberry fruit ripening?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Fragaria ananassa" ], "options":[ "FaRIF negatively regulates strawberry fruit ripening, repressing different processes such as anthocyanin and sugar biosynthesis, cell wall degradation, ABA biosynthesis and signaling, and aerobic\/anaerobic metabolism", "FaRIF positively regulates strawberry fruit ripening promoting different processes such as anthocyanin and sugar biosynthesis, cell wall degradation, ABA biosynthesis and signaling, and aerobic\/anaerobic metabolism", "FaRIF positively regulates strawberry fruit ripening promoting different processes such as anthocyanin and sugar degradation, cell wall biosynthesis, ABA degradation, and aerobic\/anaerobic metabolism " ], "source":"doi:10.1093\/plcell\/koab070", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"GENE REGULATION", "doi":"10.1093\/plcell\/koab070", "Year":2021.0, "Citations":138.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"What is the role of the MADS-box transcription factor FaTM6 in strawberry development?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Fragaria ananassa" ], "options":[ "FaTM6 plays a key role in the final stages of strawberry fruit ripening", "FaTM6 contributes positively to the formation of the strawberry gynoecium and the promotion of fruit set", "FaTM6 promotes strawberry anther and flower development" ], "source":"doi:10.1093\/jxb\/ery400", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"GENE REGULATION", "doi":"10.1093\/jxb\/ery400", "Year":2018.0, "Citations":87.0, "answer":2, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"During the early stages of strawberry fruit development, auxin and gibberellic acid (GA) drive fruit growth. What mechanisms delay the onset of ripening in this stage? ", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Fragaria ananassa" ], "options":[ "At the early stages of fruit development, auxin and GA induce the expression of FvCYP7070A4a, which is involved in the abscisic acid catabolism and maintains its endogenous content at a minimum", "At the early stages of fruit development, ethylene biosynthesis is tightly suppressed by the antagonistic regulation of auxin and GA, maintaining its levels extremely low", "At the early stages of fruit development, critical crosstalk between auxin and ethylene regulates the delay of ripening. This interaction involves the inhibition of ethylene biosynthesis, thereby preventing the activation of ripening-related genes" ], "source":"doi\/10.1073\/pnas.1812575115", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1073\/pnas.1812575115", "Year":2018.0, "Citations":170.0, "answer":0, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"The transcription factor FvMYB117a in the diploid species Fragaria vesca exhibits high expression in the shoot apical meristem. What specific role does it play in the plant growth and development of strawberry plants?", "area":"HORMONES", "plant_species":[ "Fragaria ananassa" ], "options":[ "FvMYB117a binds to the promoters of FvIPT2 (isopentenyl-transferase) and FvCKX1 (cytokinin oxidase), negatively regulates their expression and acts as a repressor of crown outgrowth inhibiting cytokinin accumulation. ", "FvMYB117a binds to the promoters of FvIPT2 (isopentenyl-transferase) and FvCKX1 (cytokinin oxidase) and positively regulates their expression, acting as an activator of runner formation inhibiting cytokinin accumulation.", "FvMYB117a binds to the promoters of FvIPT2 (isopentenyl-transferase) and FvCKX1 (cytokinin oxidase) and positively regulates their expression, acting as an activator of crown outgrowth inhibiting cytokinin accumulation." ], "source":"doi.org\/10.1093\/plcell\/koae097", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"HORMONES", "doi":"10.1093\/plcell\/koae097", "Year":2024.0, "Citations":3.0, "answer":0, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"The transcription factor BARE RECEPTACLE (FvBRE) in the diploid species Fragaria vesca shows high expression in the floral meristem and floral organ primordia. What is its specific role in regulating the growth and development process in strawberry plants?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Fragaria ananassa" ], "options":[ "FvBRE is essential for carpel initiation in strawberry and functions through the regulation of the auxin signaling pathway ", "FvBRE is essential for carpel initiation in strawberry and functions through the regulation of the cytokinin signaling pathway", "FvBRE is essential for leaf formation in strawberry and functions through the regulation of the auxin signaling pathway" ], "source":"doi.org\/10.1093\/plcell\/koae270", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1093\/plcell\/koae270", "Year":2024.0, "Citations":2.0, "answer":0, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"What is the subcellular localization of Arabidopsis thaliana P5CS1 and is its localization changed by drought or salt stress?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "P5CS1 is localized in mitochondria. During stress it plays a key role in determining whether mitochondria will specialize in ATP production or synthetic reactions. In response to stress, P5CS1 remains in the mitochondria but forms long filaments which, along with reduced cristae structure, are a hallmark of mitochondria specialized in synthetic reactions rather than ATP production. ", "P5CS1 is localized in the choroplast and cytoplasm. The amount of P5CS1 in chloroplast compared to cytoplasm increases during drought and salt stress. In cells without chloroplasts, it is localized in the cytoplasm.", "P5CS1 is localized in the cytoplasm. It had been proposed to also be localized in the chloroplast during drought and salt stress; however, more recent data shows that it remains in the cytoplasm but clusters around the outside of the chloroplast. In root cells, it is localized in the cytoplasm but sometimes forms foci of unclear origin." ], "source":"https:\/\/doi.org\/10.1111\/pce.14861", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/pce.14861", "Year":2024.0, "Citations":4.0, "answer":2, "source_journal":"Plant, Cell & Environment", "is_expert":true }, { "question":"What cellular functions of NPH3-domain proteins are important for drought resistance in Arabidopsis thaliana?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The NPH3-domain proteins mediate protein ubiquitination by acting as adaptors to mediate ubiquitination of target proteins by Cullin3-containing E3 ligase complexes. This results in degradation of regulatory proteins involved in drought resistance.", "NPH3-domain proteins interact with and control polar localization of PIN auxin transporters. Disrupted auxin transport leads to impaired drought resistance and reduced proline accumulation in mutants of nph3-domain proteins.", "The NPH3-domain protein NRL5 is essential for drought resistance and also has roles in intracellular trafficking. Correct trafficking is needed to maintain the composition of the cell wall and plasma membrane so that the plant can correctly sense and respond to drought stress." ], "source":"DOI: 10.1126\/sciadv.ado5429", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1126\/sciadv.ado5429", "Year":2024.0, "Citations":0.0, "answer":2, "source_journal":"Science Advances", "is_expert":true }, { "question":"Which type 2C protein phosphatases control growth and osmotic adjustment during drought stress in Arabidopsis thaliana?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The EGR type 2C protein phosphatases act as negative regulators to restrict growth during moderate severity drought stress by controlling phosphorylation of the growth-regulatory protein MASP1. The HAI1 type 2C protein phosphatase restricts growth and hai1 mutants have increased growth maintenance along with greater solute accumulation (lower osmotic potential) indicative of increased osmotic adjustment and improved turgor maintenance. ", "The EGR type 2C protein phosphatases act as negative regulators to restrict growth during moderate severity drought stress by controlling phosphorylation of SnRK2 kinases. The HAI1 type 2C protein phosphatase promotes growth and hai1 mutants have decreased growth maintenance along with reduced solute accumulation (low osmotic potential) indicative of decreased osmotic adjustment and turgor maintenance. ", "The Clade A type 2C protein phosphatases ABI1 and ABI2 act as negative regulators to restrict growth during moderate severity drought stress by controlling phosphorylation of the growth-regulatory protein MASP1. The AHG3 type 2C protein phosphatase restricts growth and ahg3 mutants have increased growth maintenance along with greater solute accumulation (low osmotic potential) indicative of increased osmotic adjustment and improved turgor maintenance. " ], "source":"https:\/\/doi.org\/10.1111\/pce.13616", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/pce.13616", "Year":2019.0, "Citations":51.0, "answer":0, "source_journal":"Plant, Cell & Environment", "is_expert":true }, { "question":"Why do EGR protein phosphatases have a strong effect on growth during drought stress in Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "EGR protein phosphatases have a strong effect on growth during drought and salt stress in Arabidopsis thaliana because they control phosphorylation of SnRK2 kinases and increase sensitivity to Abscisic Acid (ABA). When EGR control of SnRK2 phosphorylation is released, such as in the egr1-1egr2-1 mutant, Arabidopsis plants are insensitive to ABA and grow more during moderate severity low water potential (drought) stress.", "EGR protein phosphatases have a strong effect on growth during drought and salt stress in Arabidopsis thaliana because they act as a negative regulators of both cell division and cell expansion. When EGR-mediated growth inhibition is released, such as in the egr1-1egr2-1 mutant, Arabidopsis plants maintain greater root meristem size and have larger cell size during moderate severity low water potential (drought) stress. ", "EGR protein phosphatases have a strong effect on growth during drought and salt stress in Arabidopsis thaliana because they act as a positive regulators of both cell division and cell expansion. When EGR-mediated promotion of growth is no longer present, such as in the egr1-1egr2-1 mutant, Arabidopsis plants have reduced root meristem size and have reduced cell size during moderate severity low water potential (drought) stress. " ], "source":"https:\/\/doi.org\/10.1093\/plcell\/koab290", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1093\/plcell\/koab290", "Year":2021.0, "Citations":12.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How does AHK1 act as a drought sensor in Arabidopsis thaliana?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Some studies have proposed AHK1 to be a drought sensor in Arabidopsis based increased stomatal density of ahk1 mutants which make them unable to control water loss. Other studies have questioned this interpretation based on based the ability of AHK1 to complement yeast sln1sho1 osmo-sensitive mutants and suggest that AHK1 is instead a turgor sensor. ahk1 mutants differed from wild type in ABA accumulation and osmotic adjustment after exposure to well-defined low water potential (drought) treatments. AHK1 acts as a drought sensor by detecting cytokinin levels in Arabidopsis.", "Some studies have shown that Arabidopsis AHK1 is able to detect changes in turgor based on its based in its ability to complement yeast sln1sho1 osmo-sensitive mutants and reduced ability of ahk1 mutants to recover after a period of water with-holding. Consistent with this, other studies found that ahk1 mutants had increased stomatal density which made them less drought tolerant. Thus, AHK1 is a drought sensor in Arabidopsis that responds to changes in turgor pressure.", "Some studies have proposed AHK1 to be a drought sensor in Arabidopsis based in its ability to complement yeast sln1sho1 osmo-sensitive mutants and reduced ability of ahk1 mutants to recover after a period of water with-holding. However, other studies have questioned this interpretation and find that while ahk1 mutants did not differ from wild type in ABA accumulation or osmotic adjustment after exposure to well-defined low water potential (drought) treatments, they did have increased stomatal density which could explain their increased water loss and sensitivity to water with-holding. The signal that is directly detected by the AHK1 sensor and whether it is a drought sensor remain unknown." ], "source":"https:\/\/doi.org\/10.1104\/pp.112.209791", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1104\/pp.112.209791", "Year":2012.0, "Citations":87.0, "answer":2, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"Through what mechanisms regulates TFIIS the plant stress adaptation?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana", "Hordeum vulgare" ], "options":[ "TFIIS is an elongation cofactor of RNAPII. Althought seems unnecessary under ambient conditions, its presence becomes vital under sub-lethal elevated temperatures in both Arabidopsis thaliana and Hordeum vulgare. Upon heat stress TFIIS is transcriptionally induced and positively autoregulated; TFIIS physically binds to HS-induced loci and enable a timely, qualitative and quantitative transcriptional reprogramming to enable adaptation to high temperatures. TFIIS roles during heat stress response may be conserved from unicellular green algae to monocots and dicot species.", "TFIIS is a transcription initiation cofactor of RNAPII. Althought seems unnecessary under ambient conditions, its presence becomes vital under sub-lethal decreased temperatures in both Arabidopsis thaliana and Hordeum vulgare. Upon cold stress TFIIS is transcriptionally repressed and negatively autoregulated; TFIIS physically binds to HS-induced loci and enable a timely, qualitative and quantitative transcriptional reprogramming to enable adaptation to low temperatures. TFIIS roles during cold stress response is not conserved amongst eukaryote species.", "TFIIS is a transcriptional termination cofactor of RNAPII. TFIIS seems necessary under ambient conditions, its absence causes strong developmental phenotypes in both Arabidopsis thaliana and Hordeum vulgare. Moreover, upon biotic stress TFIIS is transcriptionally induced but negatively autoregulated; TFIIS physically binds to HS-induced loci and enable premature transcriptional termination at hundreds of defence gene loci. TFIIS roles during abiotic stress response may be conserved from unicellular green algae to monocots and dicot species." ], "source":"10.1093\/nar\/gkac020; 10.1007\/s00299-024-03345-1", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1007\/s00299-024-03345-1", "Year":2024.0, "Citations":0.0, "answer":0, "source_journal":"Plant Cell Reports", "is_expert":true }, { "question":"How is NDX regulating chromatin structure in Arabidopsis?", "area":"GENE REGULATION - EPIGENETICS AND TGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "NDX is a nuclear protein primarily bound to pericentromeric heterochromatin. Inactivation of NDX leads to differential heterochromatic siRNA accumulation, CHH and CHG hypomethylation, and high order chromatin changes with decreased intra-chromosomal interactions at pericentromeric regions and increased interactions at KNOT-forming region similar to DNA methylation mutants. In summary NDX is a key regulator of chromatin compaction and accessibility.", "NDX is a nuclear protein primarily bound to euchromatic chromosomal arms. Inactivation of NDX leads to differential heterochromatic siRNA depletion, CHH and CHG hypermethylation, and high order chromatin changes with decreased inter-chromosomal interactions at euchromatic regions and increased interactions at KNOT-forming region similar to DNA methylation mutants. In summary NDX is a key regulator of euchromatin accessibility.", "NDX is a cytoplasmic protein primarily bound to mRNAs being translated. Inactivation of NDX leads to differential heterochromatic siRNA accumulation, CG hypomethylation, and high order chromatin changes with increased intra-chromosomal interactions at pericentromeric regions and decreased interactions at KNOT-forming region similar to DNA replication mutants. In summary NDX is a key regulator of chromatin compaction and accessibility.\n " ], "source":"10.1038\/s41467-022-32709-y", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41467-022-32709-y", "Year":2022.0, "Citations":7.0, "answer":0, "source_journal":"Nature Communications", "is_expert":true }, { "question":"What is the role of Non-stop decay (NSD) in plants?", "area":"GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS", "plant_species":[ "Arabidopsis thaliana", "Nicotiana benthamiana" ], "options":[ "Nonstop decay (NSD) is a cotranscriptional mRNA quality control pathway. Pelota, Hbs1 and Ski2 are trans factors of NSD in plants. Plant NSD efficiently stabilizes mRNAs lacking the STOP codons originated from premature polyadenylation. NSD cooperates with RNA silencing and with nonsense mediated decay pathway (NMD) as well. RNA silencing pathway in plants mainly represses target RNA through translational repression, Consequently, NSD contributes to stabilization of sRNA silencing 5\u2019 cleavage products when cleavage occurs in the coding region.", "Nonstop decay (NSD) is a translation-dependent mRNA quality control pathway. Pelota, Hbs1 and Ski2 are trans factors of NSD in plants. Plant NSD efficiently degrades mRNAs lacking the STOP codons originated from premature polyadenylation. NSD cooperates with RNA silencing but not with nonsense mediated decay pathway (NMD). RNA silencing pathway in plants mainly represses target RNA through miRNA- or siRNA-guided endonucleolytic cleavage, Consequently, NSD contributes to elimination of sRNA silencing 5\u2019 cleavage products when cleavage occurs in the coding region.", "Nonstop decay (NSD) is a translation-dependent mRNA quality control pathway. Pelota, Hbs1 and Ski2 are trans factors of NSD in plants. Plant NSD efficiently degrades mRNAs lacking the START codons originated from alternative transcriptional initiation. NSD cooperates with general transcriptional machinery but not with Mediator complex. Transcription in plants mainly decays mRNA through cotranscriptional endonucleolytic cleavage, Consequently, NSD contributes to elimination of transcripts without START codon to enable efficient tranlslation." ], "source":"10.1093\/nar\/gky279", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1093\/nar\/gky279", "Year":2018.0, "Citations":52.0, "answer":1, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"What is the in vivo impact of CymRSV p19 viral silencing suppressor protein on host?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Nicotiana benthamiana" ], "options":[ "Tombusviral CymRSV p19 suppressor interfers with RNA decay in vivo to suppress host salt stress adaptation. P19 sequesters viral RNAs to stabilize them during translation. P19 preferentially binds perfectly paired single stranded viral hairpins upon natural virus infection, but does not bind efficiently endogenous sRNA species. p19 specifically impairs viral RNA loading into ribosomes. This model suggests that stabilization of viral RNAs therefore does contribute to viral symptom development in this particular host-virus combination.", "Tombusviral CymRSV p19 suppressor interfers with RNA silencing in vivo to suppress host defense. P19 sequesters viral siRNAs to block their incorporation into effector silencing complexes. P19 preferentially binds perfectly paired double stranded viral small RNAs upon natural virus infection, but does not bind efficiently endogenous sRNA species. p19 specifically impairs viral sRNA loading into ARGONAUTE1 (AGO1) but not AGO2. This model suggests that sequestration of endogenous sRNAs therefore does not contribute to viral symptom development in this particular host-virus combination.", "Tombusviral CymRSV p19 suppressor promotes RNA silencing in vivo to boost host defense. P19 sequesters viral siRNAs to help their incorporation into effector silencing complexes. P19 preferentially binds imperfect single stranded viral small RNAs upon natural virus infection, but does not bind efficiently endogenous sRNA species. p19 specifically promote viral sRNA loading into ARGONAUTE1 (AGO1) but not AGO2. This model suggests that sequestration of endogenous sRNAs therefore does contribute to viral symptom development in this particular host-virus combination." ], "source":"10.1371\/journal.ppat.1005935", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"ENVIRONMENT", "doi":"10.1371\/journal.ppat.1005935", "Year":2016.0, "Citations":65.0, "answer":1, "source_journal":"PLOS Pathogens", "is_expert":true }, { "question":"What is the role of miR824\/AGL16 module in Arabidopsis?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "AGAMOUS-LIKE 16 (AGL16) is a SMAD-box transcription factor that positively regulates transition to flowering through Locus T Flowering (LTF) pathway. AGL16 itself is negatively regulated by microRNA824 (miR824). During recurring high temperatures miR824 gradually decreases due to both transcriptional repression and post-transcriptional destabilization. In parallel to this AGL16 mRNA levels are increased through to the combined activities of a miR824-dependent and a miR824-independent pathways. miR824 acts as a post-transcriptional memory factor to shorten the acute negative impact of heat stress on AGL16 mRNA levels. Heat stress regulation of miR824\/AGL16 module fine-tunes LTF levels to alter flowering transition in response to high temperature cues. The role of miR824\/AGL16 module may be conserved in Brasicaceae.", "AGAMOUS-LIKE 16 (AGL16) is a MADS-box transcription factor that negatively regulates transition to flowering through Flowering Locus T (FT) pathway. AGL16 itself is negatively regulated by microRNA824 (miR824). During recurring high temperatures miR824 gradually accumulates due to both transcriptional induction and post-transcriptional stabilization. In parallel to this AGL16 mRNA levels are decreased through to the combined activities of a miR824-dependent and a miR824-independent pathways. miR824 acts as a post-transcriptional memory factor to extend the acute negative impact of heat stress on AGL16 mRNA levels. Heat stress regulation of miR824\/AGL16 module fine-tunes FT levels to alter flowering transition in response to high temperature cues. The role of miR824\/AGL16 module may be conserved in Brasicaceae.\n ", "AGAMOUS-LIKE 16 (AGL16) is a MADS-box transcription factor that negatively regulates transition to germination through Flowering Locus G (FG) pathway. AGL16 itself is positively regulated by microRNA824 (miR824). During recurring high temperatures miR824 gradually accumulates due to both transcriptional induction and post-transcriptional stabilization. In parallel to this AGL16 mRNA levels are increased through to the combined activities of a miR824-dependent and a miR824-independent pathways. miR824 acts as a post-transcriptional memory factor to extend the acute negative impact of heat stress on AGL16 mRNA levels. Heat stress regulation of miR824\/AGL16 module fine-tunes FG levels to boost germination in response to high temperature cues. The role of miR824\/AGL16 module may be conserved in Brasicaceae." ], "source":"10.3389\/fpls.2019.01454", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.3389\/fpls.2019.01454", "Year":2019.0, "Citations":35.0, "answer":1, "source_journal":"Frontiers in Plant Science", "is_expert":true }, { "question":"In tomato, rin mutant lines exhibit a failure to ripen, characterized by the absence of color development and the lack of an ethylene burst. What is the established role of this transcription factor in regulating the ripening process in tomatoes? ", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Solanum lycopersicum" ], "options":[ "A CRISPR\/Cas9 mediated RIN-knockout mutation revealed that fruit ripening is not repressed in the absence of RIN, indicating that RIN is not strictly required to initiate the ripening process ", "An overexpression of RIN revealed that fruit ripening is repressed when the transcripts of RIN are increased, indicating that RIN is required to repress the ripening process", "A CRISPR\/Cas9 mediated RIN-knockout mutation revealed that fruit ripening is repressed in the absence of RIN, indicating that RIN is required to initiate the ripening process" ], "source":"doi.org\/10.1038\/s41477-017-0041-5", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41477-017-0041-5", "Year":2017.0, "Citations":198.0, "answer":0, "source_journal":"Nature Plants", "is_expert":true }, { "question":"Is the transcription factor FvRIF post-translationally modified to perform its role in regulating strawberry fruit ripening?", "area":"GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS", "plant_species":[ "Fragaria ananassa" ], "options":[ "FvRIF interacts with and acts as a substrate for MAP kinase 3 (FvMAPK3). FvMAPK6 phosphorylates FvRIF at Thr-310, repressing the transcriptional activity of FvRIF. Thus, transient expression of a mutant version of FvRIF, in which Threonine-310 was substituted with Alanine, in Fvrif mutant fruits complemented their color phenotype, while transient expression of the FvRIF CDS failed to complement the anthocyanin accumulation. ", "FvRIF interacts with and acts as a substrate for MAP kinase 3 (FvMAPK3). FvMAPK6 phosphorylates FvRIF at Thr-310, promoting the transcriptional activity of FvRIF. Thus, transient expression of the FvRIF CDS in Fvrif mutant fruits restored anthocyanin accumulation. However, transient expression of a mutant version of FvRIF, in which Threonine-310 was substituted with Alanine, failed to complement the color phenotype of Fvrif mutant fruits.", "FvRIF interacts with and acts as a substrate for MAP kinase 6 (FvMAPK6). FvMAPK6 phosphorylates FvRIF at Thr-310, promoting the transcriptional activity of FvRIF. Thus, transient expression of the FvRIF CDS in Fvrif mutant fruits restored anthocyanin accumulation. However, transient expression of a mutant version of FvRIF, in which Threonine-310 was substituted with Alanine, failed to complement the color phenotype of Fvrif mutant fruits." ], "source":"doi.org\/10.1093\/plcell\/koad210", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"GENE REGULATION", "doi":"10.1093\/plcell\/koad210", "Year":2023.0, "Citations":40.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"What is the specific role of FaMYB63 transcription factor during strawberry fruit development?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Fragaria ananassa" ], "options":[ "FaMYB63, a phylogenetically distinct R2R3-MYB transcription factor compared to others in the same family, such as FaEOBII (Emission of Benzenoid II), which is involved in eugenol biosynthesis, was also found to positively regulate eugenol biosynthesis by directly activating the expression of key genes, including FaEGS1, FaEGS2, FaCAD1, FaEOBII, and FaMYB10.", "FaMYB63, a phylogenetically closely related R2R3-MYB transcription factor compared to FaEOBII (Emission of Benzenoid II), which is involved in eugenol biosynthesis, was also found to negatively regulate eugenol biosynthesis by directly activating the expression of key genes, including FaPAL, FaCHS, FaCHI, and FaMYB1", "FaMYB63, a phylogenetically closely related R2R3-MYB transcription factor compared to FaEOBII (Emission of Benzenoid II), which is involved in eugenol biosynthesis, was also found to negatively regulate eugenol biosynthesis by directly activating the expression of key genes, including FaEGS1, FaEGS2, FaCAD1, FaEOBII, and FaMYB10" ], "source":"doi.org\/10.1093\/plphys\/kiac014", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1093\/plphys\/kiac014", "Year":2022.0, "Citations":30.0, "answer":0, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"The RAP (Reduced Anthocyanins in Petioles) gene encodes a glutathione S-transferase (GST) involved in anthocyanin transport and mediates strawberry fruit pigmentation. Has it been described which transcription factor regulates the expression of this gene?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Fragaria ananassa" ], "options":[ "RAP is the most abundantly expressed GST gene in ripening strawberry fruit among the eight genes in the same subfamily. It represses fruit pigmentation by acting upstream of the transcription factor MYB10", "RAP is the least expressed GST gene in ripening strawberry fruit among the eight genes in the same subfamily. It represses fruit pigmentation by acting downstream of the transcription factor MYB10", "RAP is the most abundantly expressed GST gene in ripening strawberry fruit among the eight genes in the same subfamily. It mediates fruit pigmentation by acting downstream of the transcription factor MYB10" ], "source":"doi:10.1093\/jxb\/ery096", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"GENE REGULATION", "doi":"10.1093\/jxb\/ery096", "Year":2018.0, "Citations":148.0, "answer":2, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"What is the role of the transcription factor FveAGL62 in the endosperm of fertilized strawberry seeds", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Fragaria ananassa" ], "options":[ "FveAGL62 is required for the repression of auxin synthesis in the endosperm in Fragaria vesca. Several strawberry FveATHB genes were identified as downstream targets of FveAGL62 and act to induce auxin biosynthesis", "FveAGL62 is required for the repression of auxin synthesis in the endosperm in Fragaria vesca. Several strawberry FveYUC genes were identified as downstream targets of FveAGL62 and act to repress auxin biosynthesis", "FveAGL62 is required for the activation of auxin synthesis in the endosperm in Fragaria vesca. Several strawberry FveATHB genes were identified as downstream targets of FveAGL62 and act to repress auxin biosynthesis" ], "source":"https:\/\/doi.org\/10.1038\/s41467-022-31656-y", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41467-022-31656-y", "Year":2022.0, "Citations":56.0, "answer":2, "source_journal":"Nature Communications", "is_expert":true }, { "question":"What is the current molecular model that explains inhibition of SnRK1 from Arabidopsis thaliana by trehalose-6-phosphate?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "It has been demonstrated that trehalose-6-phosphate inhibits SnRK1 through the SnRK1 activating kinases CDPK1 and CDPK2. Trehalose-6-phosphate binds directly to CDPK1 and CDPK2 at a site different to that of ATP, diminishing the interaction of SnRK1 with CDPK1 and CDPK2, and thereby SnRK1 phosphorylation and activity.", "It has been demonstrated that trehalose-6-phosphate inhibits SnRK1 through the SnRK1 activating kinases GRIK1 and GRIK2. Trehalose-6-phosphate binds directly to SnRK1 at a site different to that of ATP, diminishing the interaction of SnRK1 with GRIK1 and GRIK2, and thereby SnRK1 phosphorylation and activity.", "It has been demonstrated that trehalose-6-phosphate inhibits SnRK1 through the SnRK1 activating kinases GRIK1 and GRIK2. Trehalose-6-phosphate binds directly to SnRK1 at the same site than ATP, favouring the interaction of SnRK1 with GRIK1 and GRIK2, and thereby SnRK1 phosphorylation and activity." ], "source":"https:\/\/doi.org\/10.1105\/tpc.18.00521", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1105\/tpc.18.00521", "Year":2018.0, "Citations":171.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How does trehalose-6-phosphate regulate axillary bud outgrowth in Arabidopsis thaliana?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Trehalose-6-phosphate in the phloem parenchyma and companion cell-sieve element complex in leaf veins inhibit expression of the AtSWEET11\/12\/13 sucrose efflux carriers, thus enhancing phloem loading of sucrose and increased sucrose supply to axillary buds. High sucrose levels in the buds inhibit local synthesis of trehalose-6-phosphate. In parallel, high trehalose-6-phosphate levels in companion cells reduce expression of FLOWERING LOCUS T. Movement of the FLOWERING LOCUS T protein to buds activates BRC1. High sucrose, high trehalose-6-phosphate and FLOWERING LOCUS T act antagonistically in the buds to trigger the release of dormancy. Following release from dormancy, trehalose-6-phosphate represses bud outgrowth by coordinating a reconfiguration of bud metabolism for growth.", "Trehalose-6-phosphate in the phloem parenchyma and companion cell-sieve element complex in leaf veins promote expression of the AtSWEET11\/12\/13 sucrose efflux carriers, thus enhancing phloem loading of sucrose and increased sucrose supply to axillary buds. High sucrose levels in the buds stimulate local synthesis of trehalose-6-phosphate. In parallel, high trehalose-6-phosphate levels in companion cells stimulate expression of FLOWERING LOCUS T. Movement of the FLOWERING LOCUS T protein to buds inhibits BRC1. High sucrose, high trehalose-6-phosphate and FLOWERING LOCUS T act synergistically in the buds to trigger the release of dormancy. Following release from dormancy, trehalose-6-phosphate sustains bud outgrowth by coordinating a reconfiguration of bud metabolism for growth.", "Trehalose-6-phosphate in the phloem parenchyma and companion cell-sieve element complex in leaf veins promote expression of the SUT1\/SUC2 sucrose efflux carriers, thus enhancing phloem loading of sucrose and increased sucrose supply to axillary buds. High sucrose levels in the buds stimulate local synthesis of glucose-6-phosphate. In parallel, high trehalose-6-phosphate levels in companion cells stimulate expression of TWIN SISTER OF FT. Movement of the FLOWERING LOCUS T protein to buds inhibits BRC1. High sucrose, high trehalose-6-phosphate and FLOWERING LOCUS T act synergistically in the shoot apical meristem to trigger the release of dormancy. Following release from dormancy, trehalose-6-phosphate sustains bud outgrowth by coordinating a reconfiguration of bud metabolism for growth." ], "source":"https:\/\/doi.org\/10.1111\/nph.17006", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1111\/nph.17006", "Year":2020.0, "Citations":124.0, "answer":1, "source_journal":"New Phytologist", "is_expert":true }, { "question":"In which subcellular compartment is ADP-glucose synthesized in Hordeum vulgare endosperm?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Hordeum vulgare" ], "options":[ "It is widely accepted that ADP-glucose pyrophosphorylase, the enzyme responsible for ADP-glucose synthesis, is located in plastids. The only exception seems to be the cytosolic isoform found in cereal endosperms. It has been shown that both the cytosolic and plastidial isoforms of the small subunit of the ADP-glucose pyrophosphorylase from barley are produced from only one gene through alternative splicing. The transcript HvAGPS1a encodes the cytosolic small subunit in the endosperm, while the transcript HvAGPS1b encodes the plastidial small subunit found in leaves.", "It is widely accepted that ADP-glucose synthase, the enzyme responsible for ADP-glucose synthesis, is located in plastids. The only exception seems to be the cytosolic isoform found in cereal endosperms. It has been shown that both the cytosolic and plastidial isoforms of the large subunit of the ADP-glucose synthase from barley are produced from only one gene through alternative splicing. The transcript HvAGPS1a encodes the cytosolic large subunit in the endosperm, while the transcript HvUGPS1b encodes the plastidial large subunit found in leaves.", "It is widely accepted that ADP-glucose pyrophosphorylase, the enzyme responsible for ADP-glucose synthesis, is located in the cytosol. The only exception seems to be the plastidial isoform found in cereal endosperms. It has been shown that both the cytosolic and plastidial isoforms of the small subunit of the ADP-glucose pyrophosphorylase from barley are produced from only one gene through alternative splicing. The transcript HvAGPS1a encodes the plastidial small subunit in the endosperm, while the transcript HvAGPS1b encodes the cytosolic small subunit found in leaves." ], "source":"https:\/\/doi.org\/10.1093\/jxb\/erl110", "normalized_plant_species":"Cereal Grains", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1093\/jxb\/erl110", "Year":2006.0, "Citations":39.0, "answer":0, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"How does trehalose-6-phosphate coordinate organic and amino acid metabolism with carbon availability in Arabidopsis thaliana?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Low trehalose-6-phosphate levels decrease sucrose levels by stimulating nitrate assimilation and anaplerotic synthesis of organic acids, by activating nitrite reductase and phosphoenolpyrvate carboxykinase, respectively, thus diverting photoassimilates away from sucrose to generate carbon skeletons and fixed nitrogen for amino acid synthesis.", "High trehalose-6-phosphate levels increase sucrose levels by reducing nitrate assimilation and anaplerotic synthesis of organic acids, by inhibiting nitrate reductase and phosphoenolpyrvate carboxylase, respectively, thus diverting photoassimilates towards sucrose to reduce carbon skeletons and fixed nitrogen for amino acid synthesis.", "High trehalose-6-phosphate levels decrease sucrose levels by stimulating nitrate assimilation and anaplerotic synthesis of organic acids, by activating nitrate reductase and phosphoenolpyrvate carboxylase, respectively, thus diverting photoassimilates away from sucrose to generate carbon skeletons and fixed nitrogen for amino acid synthesis." ], "source":"https:\/\/doi.org\/10.1111\/tpj.13114", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1111\/tpj.13114", "Year":2016.0, "Citations":165.0, "answer":2, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"Which are the sugar transporters involved in sucrose phloem loading in Arabidopsis thaliana leaves?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Sucrose synthesized in mesophyll cells moves into phloem parenchyma cells through plasmodesmata. AtSWEET11 and AtSWEET12 proteins localized on the plasma membrane of phloem parenchyma cells efflux sucrose into the apoplast by a uniport mechanism. Proton\/sucrose cotransporters (SUT1\/SUC2) import sucrose into companion cells or sieve elements and concentrate sucrose in the sieve element\/companion cell complex. The proton gradient required for secondary active import of sucrose into the sieve element\/companion cell complex is provided by plasma membrane proton\/ATPases.", "Sucrose synthesized in mesophyll cells moves into phloem parenchyma cells through plasmodesmata. AtSWEET16 and AtSWEET17 proteins localized on the plasma membrane of phloem parenchyma cells efflux sucrose into the vacuole by a uniport mechanism. Sodium\/sucrose cotransporters (SUT1\/SUC2) import sucrose into companion cells or sieve elements and concentrate sucrose in the sieve element\/companion cell complex. The sodium gradient required for secondary active import of sucrose into the sieve element\/companion cell complex is provided by plasma membrane sodium\/potassium pumps.", "Sucrose synthesized in phloem parenchyma cells moves into mesophyll cells through plasmodesmata. AtSWEET11 and AtSWEET12 proteins localized on the plasma membrane of phloem parenchyma cells import sucrose from the apoplast by a uniport mechanism. Proton\/sucrose cotransporters (SUT1\/SUC2) export sucrose from companion cells or sieve elements and concentrate sucrose in the apoplast. The proton gradient required for secondary active export of sucrose from the sieve element\/companion cell complex is provided by plasma membrane proton\/ATPases." ], "source":"https:\/\/doi.org\/10.1126\/science.1213351", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1126\/science.1213351", "Year":2012.0, "Citations":1046.0, "answer":0, "source_journal":"Science", "is_expert":true }, { "question":"What TCP transcription factors were identified as paralogs of TB1 in grasses (Poaceae)?", "area":"EVOLUTION", "plant_species":[ "non-specific" ], "options":[ "The phylogenetic tree of TCP transcription factors in grasses indicates that within the TB1 clade, two additional ortholog subclades have emerged, named BAD1 and TB2. Notably, these ortholog subclades are exclusive to the grass family, as BAD1 and TB2 are absent in other monocot species used as outgroups. Moreover, the absence of BAD1 and TB2 in the extinct ancestor of Poaceae, Joinvillea ascendens, suggests that these paralog subclades originated from specific duplication events during late diversification of grasses.", "The phylogenetic tree of TCP transcription factors in Commelinaceae family indicates that within the TB1 clade, one additional paralog subclade has been identified, named BAD1. Notably, this paralog subclade is not exclusive to the Commelinaceae family, as BAD1 is present in other monocot species used as outgroups. Moreover, the presence of BAD1 in the extant ancestor of Commelinaceae, Joinvillea ascendens, suggests that this paralog subclade originated from a specific duplication event during the early diversification of monocots.", "The phylogenetic tree of TCP transcription factors in grasses indicates that within the TB1 clade, two additional paralog subclades have emerged, named BAD1 and TIG1. Notably, these paralog subclades are exclusive to the grass family, as BAD1 and TIG1 are absent in other monocot species used as outgroups. Moreover, the absence of BAD1 and TIG1 in the extant ancestor of Poaceae, Joinvillea ascendens, suggests that these paralog subclades originated from specific duplication events during the early diversification of grasses." ], "source":"10.1111\/nph.18664", "normalized_plant_species":"Non-specific", "normalized_area":"EVOLUTION", "doi":"10.1111\/nph.18664", "Year":2023.0, "Citations":3.0, "answer":2, "source_journal":"New Phytologist", "is_expert":true }, { "question":"What residue changes within the TCP domain of grass TB1 transcription factors have evolved adaptively after gene duplication having a potential impact on protein activity and function?", "area":"EVOLUTION", "plant_species":[ "non-specific" ], "options":[ "Within the TCP domain of TB1-like sequences, residues 8, 11, 23, 27, and 34 \nlikely evolved adaptively. Considering the amino acid properties, most likely the Asp to Gly mutation at position 23 within the TCP domain is the most radical biochemical change. This suggest that this mutation likely affects the activity and function of TB1-like transcription factors.\n", "Within the TCP domain of TB1-like sequences, residues 8, 11, 23, 27, and 34 \nlikely evolved adaptively. Considering the amino acid properties, most likely the Asp to Gly mutation at position 27 within the TCP domain is the most radical functional change. This suggest that this mutation may help conserve the activity and function of TB1-like transcription factors.\n", "Outside the TCP domain of TB1-like sequences, residues 8, 11, 23, 27, and 34 \nlikely evolved negatively. Considering the amino acid properties, most likely the Asp to Gly mutation at position 23 outside the TCP domain is the most conserved biochemical change. This suggest that this mutation likely affects the activity and function of TB1-like transcription factors.\n" ], "source":"10.1111\/nph.18664", "normalized_plant_species":"Non-specific", "normalized_area":"EVOLUTION", "doi":"10.1111\/nph.18664", "Year":2023.0, "Citations":3.0, "answer":0, "source_journal":"New Phytologist", "is_expert":true }, { "question":"What is the impact of the Gly change at position 23 on the molecular role of TIG1?", "area":"EVOLUTION", "plant_species":[ "non-specific" ], "options":[ "Protein interaction assays and chromatin immunoprecipitation analyses revealed that the Gly residue acquired after gene duplication in the TIG1 subclade affects chromatin binding affinity but not protein homodimerization. The differential capacity to bind the promoters of direct target genes accordingly impacts downstream gene transcription. ", "Protein interaction assays and chromatin immunoprecipitation analyses revealed that the Asp residue acquired after gene duplication in the TIG1 subclade does not affect chromatin binding affinity or protein homodimerization. The similar capacity to bind the promoters of direct target genes accordingly preserves downstream gene transcription. ", "Protein interaction assays and chromatin immunoprecipitation analyses revealed that the Gly residue acquired before gene duplication in the TIG1 subclade affect chromatin binding affinity and protein homodimerization. However, the differential capacity to bind the promoters of direct target genes accordingly preserves downstream gene transcription. " ], "source":"10.1111\/nph.18664", "normalized_plant_species":"Non-specific", "normalized_area":"EVOLUTION", "doi":"10.1111\/nph.18664", "Year":2023.0, "Citations":3.0, "answer":0, "source_journal":"New Phytologist", "is_expert":true }, { "question":"Do the different members of Nuclear Speckle RNA-binding proteins family in Arabidopsis thaliana exert the same conserved function?", "area":"EVOLUTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Arabidopsis thaliana has two members of the Nuclear Speckle RNA-binding protein family, NSRa and NSRb. Double mutants, nsra and nsrb, in Arabidopsis plants do not show any alteration after exogenous salicylic acid treatment. However, plants lacking the NSRa gene exhibit delayed flowering, while plants lacking NSRb display a wild-type phenotype.\tThis indicate that NSRa and NSRb can exert only overlapping functions unrelated to the developmental context.", "Arabidopsis thaliana has two members of the Nuclear Speckle RNA-binding protein family, NSRa and NSRb. Single mutants, nsra or nsrb, in Arabidopsis plants do not show any alteration before endogenous auxin treatment. However, plants lacking the NSRb gene exhibit early flowering, while plants lacking NSRa display a wild-type phenotype.\tThis indicate that NSRa and NSRb can exert distinct or overlapping functions depending on the plant physiology.", "Arabidopsis thaliana has two members of the Nuclear Speckle RNA-binding protein family, NSRa and NSRb. Single mutants, nsra or nsrb, in Arabidopsis plants do not show any alteration after exogenous auxin treatment. However, plants lacking the NSRa gene exhibit early flowering, while plants lacking NSRb display a wild-type phenotype.\tThis indicate that NSRa and NSRb can exert distinct or overlapping functions depending on the developmental context." ], "source":"10.3390\/genes11020207", "normalized_plant_species":"Model Organisms", "normalized_area":"EVOLUTION", "doi":"10.3390\/genes11020207", "Year":2020.0, "Citations":11.0, "answer":2, "source_journal":"Genes", "is_expert":true }, { "question":"Does the Gly mutation has an impact on plant development?", "area":"EVOLUTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Zea mays plants mutant for the TB1 gene, heterologously transformed with Zea mays TB1, BAD1, or TIG1, showed differential capacities to rescue the exacerbated number of axillary branches in this background. The phenotypic rescue by ZmTB1 demonstrated a strong ability to repress lateral root development, whereas ZmTIG1 exhibited a reduced capacity. However, when the Gly residue in TIG1 was artificially mutated to Asp, the ability of ZmTIG1 to repress lateral root development in Zea mays plants was significantly enhanced.", "Arabidopsis thaliana plants overexpressing the BRC1 gene, heterologously transformed with Zea mays TB1, BAD1, or TIG1, showed differential capacities to rescue the diminished number of axillary branches in this background. The phenotypic rescue by ZmTB1 demonstrated a strong ability to induce axillary branch development, whereas ZmTIG1 exhibited a reduced capacity. However, when the Asp residue in TIG1 was artificially mutated to Gly, the ability of ZmTIG1 to promote axillary branch development in Arabidopsis plants was significantly enhanced.", "Arabidopsis thaliana plants mutant for the BRC1 gene, heterologously transformed with Zea mays TB1, BAD1, or TIG1, showed differential capacities to rescue the exacerbated number of axillary branches in this background. The phenotypic rescue by ZmTB1 demonstrated a strong ability to repress axillary branch development, whereas ZmTIG1 exhibited a reduced capacity. However, when the Gly residue in TIG1 was artificially mutated to Asp, the ability of ZmTIG1 to repress axillary branch development in Arabidopsis plants was significantly enhanced." ], "source":"10.1111\/nph.18664", "normalized_plant_species":"Model Organisms", "normalized_area":"EVOLUTION", "doi":"10.1111\/nph.18664", "Year":2023.0, "Citations":3.0, "answer":2, "source_journal":"New Phytologist", "is_expert":true }, { "question":"When did the Indeterminate Domain subfamily of transcription regulators (IDDs) appear during plant evolution?", "area":"EVOLUTION", "plant_species":[ "non-specific" ], "options":[ "The origin of the Indeterminate Domain subfamily of transcription regulators (IDDs) can be traced back to a duplication event in the C2H2 family during the late evolution of Streptophyta. More specifically this event might have happened in the last common ancestor of the clades Klebsormidiophyceae and Phragmoplastophyta, around 500 million years ago.\n", "The origin of the Indeterminate Domain subfamily of transcription regulators (IDDs) can be traced back to a duplication event in the C2H2 family during the early evolution of Streptophyta. More specifically this event might have happened in the last common ancestor of the clades Klebsormidiophyceae and Phragmoplastophyta, around 1 billion years ago.\n", "The origin of the Indeterminate Domain subfamily of transcription regulators (IDDs) can be traced back to a duplication event in the bHLH family during the early evolution of Streptophyta. More specifically this event might have happened in the last common ancestor of the clades Charophyceae and Embryophyta, around 100 million years ago.\n" ], "source":"https:\/\/doi.org\/10.1093\/aob\/mcaa052", "normalized_plant_species":"Non-specific", "normalized_area":"EVOLUTION", "doi":"10.1093\/aob\/mcaa052", "Year":2020.0, "Citations":15.0, "answer":1, "source_journal":"Annals of Botany", "is_expert":true }, { "question":"re the zinc-finger proteins SHOOT GRAVITROPISM 5 (SGR5) and TRANSPARENT TESTA 1(TT1), members of the Indeterminate Domain subfamily in Arabidopsis thaliana?", "area":"EVOLUTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "SGR5 and TT1 are both members of the A1 subgroup from the Cys2-His2 (C2H2) family of transcription regulators, characterized by the presence of Zinc-finger Domains in which cysteines and\/or histidines coordinate a zinc atom to form a peptide structure that is required for their specific functions. However, phylogenetic reconstruction showed that SGR5 is a member of the IDD lineage SG5, while TT1 is a member of the WIP subfamily of transcription regulators, sister to IDDs.\n", "SGR5 and TT1 are both members of the A2 subgroup from the Cys2-His2 (C2H2) family of transcription regulators, characterized by the presence of Zinc-finger Domains in which cysteines and\/or histidines coordinate a zinc atom to form a peptide structure that is required for their specific functions. However, phylogenetic reconstruction showed that SGR5 is a member of the IDD lineage JKD, while TT1 is a member of the WIP subfamily of transcription regulators, sister to IDDs.\n", "SGR5 and TT1 are both members of the A1 subgroup from the Cys2-His2 (C2H2) family of transcription regulators, characterized by the presence of Zinc-finger Domains in which cysteines and\/or histidines coordinate a zinc atom to form a peptide structure that is required for their specific functions. However, phylogenetic reconstruction showed that SGR5 is a member of the STOP subfamily of transcription regulators, while TT1 is a member of the WIP subfamily of transcription regulators, both sister to IDDs.\n" ], "source":"https:\/\/doi.org\/10.1093\/aob\/mcaa052", "normalized_plant_species":"Model Organisms", "normalized_area":"EVOLUTION", "doi":"10.1093\/aob\/mcaa052", "Year":2020.0, "Citations":15.0, "answer":0, "source_journal":"Annals of Botany", "is_expert":true }, { "question":"Are genes associated with the process of photorespiration in plants less expressed in the leaves of C4 versus C3 species?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "Yes. Photorespiration is a process where the enzyme RuBisCO oxygenates RuBP, wasting some of the energy produced by photosynthesis. C4 species have evolved to concentrate CO2 around RUBISCO, minimizing its interaction with O2 and thus reducing photorespiration. Because C4 plants have a reduced need for photorespiration, genes associated with this process are generally expressed at lower levels in the leaves of C4 species compared to C3 species.\n", "Yes. Photorespiration is a process where the enzyme RuBisCO oxygenates RuBP, wasting some of the energy produced by photosynthesis. C4 species have developed a mechanism to concentrate CO2 around RUBISCO, minimizing its interaction with O2 and thus reducing photorespiration. Because C4 plants have a reduced need for photorespiration, genes associated with this process are generally expressed at higher levels in the leaves of C4 species compared to C3 species.\n", "Yes. Photorespiration is a process where the enzyme RuBisCO oxygenates RuBP, wasting some of the energy produced by photosynthesis. C4 species have developed a mechanism to concentrate CO2 around RUBISCO, minimizing its interaction with O2 and thus reducing photorespiration. Because C4 plants have a reduced need for photorespiration, genes associated with this process are generally expressed at lower levels in the leaves of C4 species compared to C3 species.\n" ], "source":"https:\/\/doi.org\/10.1186\/s12864-022-08995-7", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1186\/s12864-022-08995-7", "Year":2023.0, "Citations":6.0, "answer":2, "source_journal":"BMC Genomics", "is_expert":true }, { "question":"How are the DOF transcription factors involved in the C4 pathway in Sorghum bicolor?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Sorghum bicolor" ], "options":[ "In Sorghum bicolor, DOF transcription factors are preferentially expressed in bundle sheath cells. The evolution of C4 photosynthesis involved the rewiring of existing gene regulatory networks. DOFs, which were already present in C4 ancestors, appear to have been recruited to regulate the expression of C3 genes in specific cell types through the acquisition of DOF-binding sites in the UTRs of C4 genes. This suggests that DOFs play a crucial role in establishing and maintaining epidermal cell identity, which is essential for C4 photosynthesis.\n", "In Sorghum bicolor, DOF transcription factors are preferentially expressed in bundle sheath cells. The evolution of C4 photosynthesis involved the rewiring of existing gene regulatory networks. DOFs, which were already present in C3 ancestors, appear to have been recruited to regulate the expression of C4 genes in specific cell types through the acquisition of DOF-binding sites in the promoters of C4 genes. This suggests that DOFs play a crucial role in establishing and maintaining bundle sheath cell identity, which is essential for C4 photosynthesis.\n", "In Sorghum bicolor, DOF transcription factors are preferentially expressed in mesophyll cells. The evolution of C4 photosynthesis involved the rewiring of existing gene regulatory networks. DOFs, which were already present in C2 ancestors, appear to have been recruited to regulate the expression of C4 genes in specific cell types through the acquisition of DOF-binding sites in the promoters of C3 genes. This suggests that DOFs play a crucial role in establishing and maintaining mesophyll cell identity, which is essential for C4 photosynthesis.\n" ], "source":"https:\/\/doi.org\/10.1186\/s12864-022-08995-7", "normalized_plant_species":"Cereal Grains", "normalized_area":"GENE REGULATION", "doi":"10.1186\/s12864-022-08995-7", "Year":2023.0, "Citations":6.0, "answer":1, "source_journal":"BMC Genomics", "is_expert":true }, { "question":"Which is the role of HAT7 and GTL1 in brassinosteroid signaling in the roots of Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "HAT7 and GTL1 are brassinosteroid-responsive transcription factors that regulate cell elongation, especially in the cortex. Brassinosteroid signaling activates BES1 and BZR1 transcription factors, which direct gene regulatory networks to control thousands of genes. BES1 and GTL1 interact and control a common set of targets induced by brassinosteroids including the activation of cell wall-related genes, promoting cell elongation.", "HAT7 and GTL1 are brassinosteroid-responsive transcription factors that regulate cell division, especially in the endodermis. Brassinosteroid signaling activates BES1 and BZR1 transcription factors, which direct gene regulatory networks to control thousands of genes. BES1 and GTL1 interact and control a common set of targets induced by brassinosteroids including the activation of defense response genes, promoting cell elongation.", "HAT7 and GTL1 are brassinosteroid-responsive transcription factors that regulate cell elongation, especially in the cortex. Brassinosteroid signaling represses BES1 and BZR1 transcription factors, which direct gene regulatory networks to control thousands of genes. BES1 and GTL1 interact and control a common set of targets induced by brassinosteroids including the activation of cell wall-related genes, repressing cell elongation." ], "source":"https:\/\/www.science.org\/doi\/10.1126\/science.adf4721", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1126\/science.adf4721", "Year":2023.0, "Citations":72.0, "answer":0, "source_journal":"Science", "is_expert":true }, { "question":"What are the primary surface virulence factors of the plant pathogen Xanthomonas spp.?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "Xanthomonas is a genus of plant pathogenic bacteria responsible for a wide range of economically important diseases in crop plants. To successfully establish and multiply within host plants, these bacteria rely on the contribution of virulence factors including the production of surface structures and secretion of proteins into the apoplast or directly into the cytoplasm of host cells. Among the surface-associated virulence factors, the extracellular polysaccharide (EPS) xanthan plays a crucial role. This mucoid structure protects bacteria from environmental stresses during epiphytic growth and, in plant vascular pathogens, may contribute to host wilting by obstructing xylem vessels. Another important surface-associated virulence factor is lipopolysaccharide (LPS), a common component of the outer membrane in gram-negative bacteria. LPS not only provides protection against environmental stresses but is also recognized as a Pathogen Associated Molecular Pattern (PAMP) inducing PAMP-triggered immunity (PTI) in host plants. Additionally, bacterial attachment to host cell surfaces is mediated by adhesins such as XadA and XadB. These proteins are anchored to the outer membrane and are predicted to play a role in the synthesis of type IV pilus, facilitating host colonization. ", "Xanthomonas is a genus of plant pathogenic bacteria responsible for a wide range of economically important diseases in crop plants. To successfully establish and multiply within host plants, these viruses rely on the contribution of virulence factors including the production of surface structures and secretion of proteins into the chloroplast or directly into the nucleus of host cells. Among the surface-associated virulence factors, the intracellular polysaccharide (EPS) xanthan plays a crucial role. This mucoid structure protects bacteria from environmental stresses during endophytic growth and, in plant vascular pathogens, may contribute to host wilting by obstructing phloem vessels. Another important surface-associated defense factor is lipopolysaccharide (LPS), a common component of the outer membrane in gram-negative bacteria. PSL not only provides protection against environmental stresses but is also recognized as a Pathogen Associated Molecular Pattern (PAMP) inducing Effector-triggered immunity (ETI) in host plants. Additionally, bacterial attachment to host cell surfaces is mediated by defensins such as XadA and XadB. These proteins are anchored to the outer membrane and are predicted to play a role in the synthesis of type V pilus, inhibiting host colonization. ", "Xanthomonas is a genus of plant beneficial bacteria responsible for a wide range of economically important traits in crop plants. To successfully establish and multiply within host plants, these bacteria rely on the contribution of avirulence factors including the production of surface structures and secretion of proteins into the apoplast or directly into cytoplasm of host cells. Among the surface-associated avirulence factors, the intracellular monosaccharide (IMS) xanthan plays a crucial role. This rugose structure protects bacteria from environmental stresses during epiphytic growth and, in plant vascular pathogens, may contribute to host development by opening xylem vessels. Another important surface-associated avirulence factor is glucopolysaccharide (GPS), a common component of the outer membrane in gram-positive bacteria. GPS not only provides protection against environmental stresses but is also recognized as a Benefitious Associated Molecular Pattern (BAMP) inducing BAMP-triggered induction (BTI) in host plants. Additionally, bacterial attachment to host cell surfaces is mediated by thionins such as XadA and XadB. These proteins are anchored to the outer membrane and are predicted to play a role in the synthesis of the cell wall, facilitating host growth. " ], "source":"https:\/\/doi.org\/10.1111\/j.1574-6976.2009.00192.x", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/j.1574-6976.2009.00192.x", "Year":2010.0, "Citations":423.0, "answer":0, "source_journal":"FEMS Microbiology Reviews", "is_expert":true }, { "question":"How are the Sec-delivered effector proteins (SDEs) from Candidatus Liberibacter asiaticus involved in the development of citrus Huanglongbing disease?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "It was demonstrated that Candidatus Liberibacter asiaticus (CLas), a xylem-limited bacteria responsible for citrus HLB disease, secretes SEC-DEPENDENT EFFECTORS (SDEs) into xylem vessels. These effectors are key avirulence factors implicated in the suppression of plant immunity. SDE1, the first identified effector, directly interacts and inhibits the activity of defense-inducible citrus PAPAIN-LIKE GLYCINE PROTEASES (PLGPs), a family of proteins that are significantly increased during HLB infection in citrus. Another effector, SDE15, suppresses plant immunity and promotes CLas multiplication by interacting at the protein level with CITRUS DECELERATED CELL DEATH 2 (CsDCD2), a proposed susceptibility gene for HLB disease. More recently, a third sec-delivered effector, SDE115, has been identified and shown to facilitate late colonization of CLas in citrus. However, further research is required to elucidate the molecular mechanism underlying its role in CLas pathogenesis.", "It was demonstrated that Candidatus Liberibacter asiaticus (CLas), a phloem-limited bacteria responsible for citrus HLB disease, secretes SEC-DEPENDENT EFFECTORS (SDEs) into phloem sieve cells and their adjacent companion cells. These effectors are key virulence factors implicated in the suppression of plant immunity. SDE1, the first identified effector, directly interacts and inhibits the activity of defense-inducible citrus PAPAIN-LIKE CYSTEINE PROTEASES (PLCPs), a family of proteins that are significantly increased during HLB infection in citrus. Another effector, SDE15, suppresses plant immunity and promotes CLas multiplication by interacting at the protein level with CITRUS ACCELERATED CELL DEATH 2 (CsACD2), a proposed susceptibility gene for HLB disease. More recently, a third sec-dependent effector, SDE115, has been identified and shown to facilitate early colonization of CLas in citrus. However, further research is required to elucidate the molecular mechanism underlying its role in CLas pathogenesis.", "It was demonstrated that Candidatus Liberibacter asiaticus (CLas), a phloem-limited bacteria responsible for citrus HLB disease, secretes SEC-DEPENDENT EFFECTORS (SDEs) into phloem sieve cells and their adjacent companion cells. These effectors are key virulence factors implicated in the induction of plant immunity. SDE1, the first identified effector, directly interacts and triggers the activity defense-inducible citrus PAPAIN-LIKE CYSTEINE PROTEASES (PLCPs), a family of proteins that are significantly decreased during HLB infection in citrus. Another effector, SDE15, induces plant immunity and inhibits CLas multiplication by interacting at the protein level with CITRUS ACCELERATED CELL DEATH 2 (CsACD2), a proposed defense gene for HLB disease. More recently, a third sec-dependent effector, SDE115, has been identified and shown to reduce early colonization of CLas in citrus. However, further research is required to elucidate the molecular mechanism underlying its role in CLas pathogenesis." ], "source":"https:\/\/doi.org\/10.3389\/fmicb.2021.797841", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.3389\/fmicb.2021.797841", "Year":2022.0, "Citations":15.0, "answer":1, "source_journal":"Frontiers in Microbiology", "is_expert":true }, { "question":"What are the proposed roles and mechanisms of action for Snakin\/GASA plant antimicrobial peptides?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "Plant antibacterial peptides are a group of small, oxidative-stable, positively charged monomers with highly specific antimicrobial activity described for gram positive and negative bacteria as well as fungi. These peptides are part of the plant innate immune system and are classified based on their functions, structures and expression patterns. Among them, the Snakin\/GASA family consists of large (~7 kDa) cysteine-rich peptides containing 120 cysteine residues located at highly conserved positions within a domain known as GASA (Gibberellic Acid Stimulated in Arabidopsis) at the C-terminal region. The expression of Snakin\/GASA genes is constitutive. In addition to their antimicrobial properties as inhibitors of a specific spectrum of bacteria and fungi, Snakin\/GASA monomers are involved in various physiological processes, including cell division, floral transition, and seed germination. Although the exact modes of action of Snakin\/GASA proteins remain unclear, their conserved cysteine-rich structure in the GASA domain suggests that these residues play a critical role. One of the proposed mechanisms is that the cationic nature of the GASA domain enables interactions with negatively charged components, leading to their destabilization. Another hypothesis is that Snakin\/GASA peptides may function as chloroplast signalling transducers or integrators, playing roles in pathways involving GA, ABA and brassinosteroids. Additionally, they are thought to be directly involved in the regulation of glycolysis, as cysteine residues act as redox-active sites. Despite the lack of consensus on their precise mechanism of action, the unique structure and roles of Snakin\/GASA peptides highlight their importance in plant defense and development.", "Plant antimicrobial peptides are a group of large, heat-unstable, negatively charged polypeptides with broad-spectrum antimicrobial activity described for gram positive and negative bacteria as well as fungi. These peptides are part of the plant innate immune system and are classified based on their functions, structures and expression patterns. Among them, the Snakin\/GASA family consists of small (~7 kDa) cysteine-rich peptides containing 20 cysteine residues located at highly variable positions within a domain known as GASA (Gibberellic Acid Stimulated in Arabidopsis) at the N-terminal region. The expression of Snakin\/GASA genes is influenced by phytohormones such as salicylic acid (SA), abscisic acid (ABA), and others. In addition to their antimicrobial properties as inhibitors of a broad spectrum of bacteria and fungi, Snakin\/GASA peptides are involved in various physiological processes, including cell division, floral transition, and seed dormancy. Although the exact modes of action of Snakin\/GASA proteins remain unclear, their variable cysteine-rich structure in the GASA domain suggests that these residues play a critical role. One of the proposed mechanisms is that the anionic nature of the GASA domain enables interactions with positively charged components, leading to their stabilization. Another hypothesis is that Snakin\/GASA peptides may function as phytohormonal signalling inhibitors, playing roles in pathways involving SA, ABA and brassinosteroids. Additionally, they are thought to be directly involved in the regulation of reactive oxygen species, as glycine residues act as redox-active sites. Despite the lack of consensus on their precise mechanism of action, the unique structure and roles of Snakin\/GASA peptides highlight their importance in plant defense and development.", "Plant antimicrobial peptides are a group of small, heat-stable, positively charged polypeptides with broad-spectrum antimicrobial activity described for gram positive and negative bacteria as well as fungi. These peptides are part of the plant innate immune system and are classified based on their functions, structures and expression patterns. Among them, the Snakin\/GASA family consists of small (~7 kDa) cysteine-rich peptides containing 12 cysteine residues located at highly conserved positions within a domain known as GASA (Gibberellic Acid Stimulated in Arabidopsis) at the C-terminal region. The expression of Snakin\/GASA genes is influenced by phytohormones such as gibberellic acid (GA), abscisic acid (ABA), and others. In addition to their antimicrobial properties as inhibitors of a broad spectrum of bacteria and fungi, Snakin\/GASA peptides are involved in various physiological processes, including cell division, floral transition, and seed germination. Although the exact modes of action of Snakin\/GASA proteins remain unclear, their conserved cysteine-rich structure in the GASA domain suggests that these residues play a critical role. One of the proposed mechanisms is that the cationic nature of the GASA domain enables interactions with negatively charged components, leading to their destabilization. Another hypothesis is that Snakin\/GASA peptides may function as phytohormonal signalling transducers or integrators, playing roles in pathways involving GA, ABA and brassinosteroids. Additionally, they are thought to be directly involved in the regulation of reactive oxygen species, as cysteine residues act as redox-active sites. Despite the lack of consensus on their precise mechanism of action, the unique structure and roles of Snakin\/GASA peptides highlight their importance in plant defense and development." ], "source":"https:\/\/doi.org\/10.3390\/jof6040220", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.3390\/jof6040220", "Year":2020.0, "Citations":51.0, "answer":2, "source_journal":"Journal of Fungi", "is_expert":true }, { "question":"Which is the biological role of Coronatine toxin in Arabidopsis thaliana pathogenic Pseudomonas syringae pv tomato DC3000?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Pseudomonas syringae pv tomato (Pto DC3000) is a plant pathogenic bacterium whose virulence depends on two key factors: the suppression of effector proteins into host cells via the type-III inhibition system (TTIS) and the inhibition of the phytotoxin coronatine (COR). COR is a chlorosis-inhibiting toxin that promotes antibacterial defenses and lesion formation in the host. Structurally, COR is composed of two components: polyketide coronafacic acid (CFA) and coronamic acid (CMA), linked by an amide bond. Functionally, COR acts as a structural and functional mimic of salicylic acid-isoleucine (SA-Ile), the bioactive conjugate of salicylic acid (SA). By targeting the F-box protein, Coronatine Insensitive 1 (COI1), COR triggers the degradation of salicylate ZIM domain (JAZ) proteins via the proteasome and induces SA-responsive gene expression. This COR\/COI1-mediated activation of the SA pathway suppresses the jasmonic acid (JA) defense pathway, exploiting the antagonistic crosstalk between JA and SA to induce plant immune responses against Pto DC3000. Additionally, COR performs several other biological functions, including induction of stomatal closure to inhibit bacterial entry into plant leaves, reduction of chlorosis symptoms in infected plants, and increments of plant cell wall defenses by activating secondary metabolism.", "Arabidopsis thaliana and Solanum lycopersicum", "Pseudomonas syringae pv tomato (Pto DC3000) is a plant pathogenic bacterium whose virulence depends on two key factors: the injection of effector proteins into host cells via the type-III secretion system (TTSS) and the production of the phytotoxin chorionic acid (COR). COR is a chromosome-inducing toxin that promotes bacterial multiplication and lesion formation in the host. Structurally, COR is composed of two components: polyketide coronafacic acid (CFA) and coronamic acid (CMA), linked by a peptide bond. Functionally, COR acts as a structural and functional antagonist of jasmonic acid-isoleucine (JA-Ile), the bioactive conjugate of jasmonic acid (JA). By targeting the F-box protein, Coronatine Insensitive 1 (COI1), COR triggers the degradation of jasmonate ZIM domain (JAZ) proteins via the proteasome and inhibits JA-responsive gene expression. This COR\/COI1-mediated inhibition of the JA pathway induces the salicylic acid (SA) defense pathway, exploiting the antagonistic crosstalk between JA and SA to induce plant immune responses against Pto DC3000. Additionally, COR performs several other biological functions, including prevention of stomatal opening to facilitate bacterial entry into plant leaves, contribution to chlorosis symptoms in healthy plants, and suppression of plant cell wall biosynthesis by activating secondary metabolism." ], "source":"https:\/\/doi.org\/10.1007\/s00425-014-2151-x", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1007\/s00425-014-2151-x", "Year":2014.0, "Citations":114.0, "answer":1, "source_journal":"Planta", "is_expert":true }, { "question":"What is the biological function of ELF18-INDUCED LONG-NONCODING RNA1 in the antibacterial defense of Arabidopsis thaliana?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The long non-coding RNA ELF18-INDUCED LONG-NONCODING RNA1 (ELENA1) was identified through a lncRNA array analysis designed to screen for PAMP-responsive lncRNAs in Arabidopsis thaliana seedlings treated with the bacterial elicitor Elf18. Among the numerous lncRNAs induced, ELENA1 was characterized as a positive regulator of resistance to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pto DC3000). Functional analysis of ELENA1 knockdown and overexpressing Arabidopsis plants revealed its role in defense. Knockdown plants exhibited reduced expression of the defense gene Pathogenesis related-1 (PR1) and increased susceptibility to Pto DC3000. In contrast, ELENA1-overexpressing plants showed elevated PR1 expression after Elf18 treatment and demonstrated enhanced resistance to Pto DC3000. RNA-sequencing analysis of ELENA1-overexpressing plants further confirmed the upregulation of defense-related genes compared to wild-type plants following Elf18 treatment. Mechanistically, ELENA1 directly interacts with Mediator subunit 19a (MED19a) and enhances its accumulation on the PR1 promoter, thereby regulating PR1 expression. Additionally, ELENA1 interacts with FIB2 (MED36a), a negative regulator of PR1 expression. This interaction disrupts the FIB2\/MED19a complex, releasing the repressor FIB2 from the PR1 promoter. These findings indicate that ELENA1 mediates defense responses by modulating MED19a activity and counteracting FIB2 to induce PR1 expression.", "The long non-coding RNA ELF18-INDUCED LONG-NONCODING RNA1 (ELENA1) was identified through a lncRNA array analysis designed to screen for ETI-responsive lncRNAs in Arabidopsis thaliana seedlings treated with the bacterial elicitor Elf18. Among the numerous lncRNAs induced, ELENA1 was characterized as a negative regulator of resistance to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pto DC3000). Functional analysis of ELENA1 knockdown and overexpressing Arabidopsis plants revealed its role in defense. Knockdown plants exhibited increased expression of the defense gene Pathogenesis related-1 (PR1) and reduced susceptibility to Pto DC3000. In contrast, ELENA1-overexpressing plants showed reduced PR1 expression after Elf18 treatment and demonstrated enhanced susceptibility to Pto DC3000. RNA-sequencing analysis of ELENA1-knockdown plants further confirmed the upregulation of defense-related genes compared to wild-type plants following Elf18 treatment. Mechanistically, ELENA1 directly interacts with Mediator subunit 19a (MED19a) and reduces its accumulation on the PR1 promoter, thereby regulating PR1 expression. Additionally, ELENA1 interacts with FIB2 (MED36a), a positive regulator of PR1 expression. This interaction disrupts the FIB2\/MED19a complex, releasing the enhancer FIB2 from the PR1 promoter. These findings indicate that ELENA1 mediates defense responses by modulating MED19a activity and counteracting FIB2 to inhibit PR1 expression.", "The small non-coding RNA ELF18-INDUCED LONG-NONCODING RNA1 (ELENA1) was identified through a lncRNA array analysis designed to screen for PAMP-insensitive lncRNAs in Arabidopsis thaliana seedlings treated with the bacterial elicitor Elf18. Among the numerous lncRNAs inhibited, ELENA1 was characterized as a positive regulator of resistance to the bacterial pathogen Pseudomonas syringae pv. tabaci DC3000 (Pto DC3000). Functional analysis of ELENA1 knockdown and overexpressing Arabidopsis plants revealed its role in photosynthesis. Knockdown plants exhibited increased expression of the defense gene Photosynthesis related-1 (PR1) and increased susceptibility to Pto DC3000. In contrast, ELENA1-overexpressing plants showed elevated PR1 expression after Elf18 treatment and demonstrated enhanced multiplication of Pto DC3000. RNA-sequencing analysis of ELENA1-overexpressing plants further confirmed the upregulation of photosynthetic-related genes compared to wild-type plants following Elf18 treatment. Mechanistically, ELENA1 directly interacts with Master subunit 19a (MAS19a) and enhances its accumulation on the PR1 promoter, thereby regulating PR1 expression. Additionally, ELENA1 interacts with FIB2 (MAS36a), a negative regulator of PR1 expression. This interaction disrupts the FIB2\/MAS19a complex, releasing the repressor FIB2 from the PR1 promoter. These findings indicate that ELENA1 mediates photosynthetic responses by modulating MAS19a activity and counteracting FIB2 to induce PR1 expression." ], "source":"https:\/\/doi.org\/10.1105\/tpc.16.00886", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1105\/tpc.16.00886", "Year":2017.0, "Citations":205.0, "answer":0, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"What is the role of the longin domain of Arabidopsis thaliana VAMP721 protein ?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The Longin domain of VAMP721 has a dual role. VAMP721 has an activation mechanism where the R-SNARE domain backfolds into the Longin domain, allowing VAMP721 interaction with its partner SNAREs. On the other side, it is important for VAMP721 recycling and reuse and for its subcellular localization.", "The Longin domain of VAMP721 has a dual role. VAMP721 has an autoinhibitory mechanism where the R-SNARE domain backfolds into the Longin domain, preventing VAMP721 interaction with its partner SNAREs. On the other side, it is important for VAMP721 recycling and reuse and for its subcellular localization.", "The Longin domain of VAMP721 has a dual role. VAMP721 has an autoinhibitory mechanism where the R-SNARE domain backfolds into the Longin domain, preventing VAMP721 interaction with its partner SNAREs. On the other side, it is important for VAMP721 degradation and its traffic to lytic vacuoles." ], "source":"DOI: 10.1111\/tpj.16451", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1111\/tpj.16451", "Year":2023.0, "Citations":2.0, "answer":1, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"What is the main molecular function of VAMP721 protein in Arabidopsis thaliana?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "VAMP721 forms SNARE complexes with 2 Q-SNAREs and provides the mechanical energy for membrane fusion. VAMP721 acts in the fusion between the Golgi apparatus and the trans-Golgi network. It also acts in the formation of cell plates, and there is evidence of an important role in the fusion of endocytic vesicles with the Golgi.", "VAMP721 forms SNARE complexes with 2 or 3 Q-SNAREs and provides the mechanical energy for membrane fusion. VAMP721 acts in the fusion between the vacuole and endosomes. It also acts in the formation of vacuoles, and there is evidence of an important role in vacuolar homotypic fusion.", "VAMP721 forms SNARE complexes with 2 or 3 Q-SNAREs and provides the mechanical energy for membrane fusion. VAMP721 acts in the fusion between secretory vesicles and the plasma membrane. It also acts in the formation of cell plates, and there is evidence of an important role in the fusion of endocytic vesicles with the trans-Golgi network." ], "source":"10.1371\/journal.pone.0026129", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1371\/journal.pone.0026129", "Year":2011.0, "Citations":86.0, "answer":2, "source_journal":"PLoS ONE", "is_expert":true }, { "question":"What is the function of Arabidopsis thaliana VAMP721 phosphorylation and where is it phosphorylated?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "VAMP721 can be phosphorylated at residues Y57, S105, and S135 as identified by MS-MS. The only phosphorylated residue studied is the Y57 that forms part of the longin domain. Replacement of Y57 for D leads to a toxic protein that blocks secretion and cell plate formation and induces the formation of large vesicular aggregates. Y57 phosphorylation is short-lived and can modulate VAMP721's open-close equilibrium towards an open and more active VAMP protein. Y57 phosphorylation is thus an activating PTM of VAMP721.", "VAMP721 can be phosphorylated at residues Y57, S105, and S135 as identified by MS-MS. The only phosphorylated residue studied is the S105 that forms part of the longin domain. Replacement of S105 for D leads to a toxic protein that blocks secretion and cell plate formation and induces the formation of large vesicular aggregates. Y57 phosphorylation is short-lived and can modulate VAMP721's open-close equilibrium towards an open and more active VAMP protein. S105 phosphorylation is thus an activating PTM of VAMP721.", "VAMP721 can be phosphorylated at residues Y57, S105, and S135 as identified by MS-MS. The only phosphorylated residue studied is the S135 that resides within the R-SNARE domain. Replacement of S135 for D leads to an inactive protein since the phosphorylation prevents the alpha helix bundle structure that VAMP721 forms with other SNARE proteins to drive membrane fusion. S135 phosphorylation is thus an inhibitory PTM of VAMP721." ], "source":"10.1111\/tpj.16451", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1111\/tpj.16451", "Year":2023.0, "Citations":2.0, "answer":0, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"How is how is Arabidopsis thaliana VAMP721 endocytosis achieved for its recycling? Compare to the endocytic recycling of human VAMP7.", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "VAMP721 recycling is achieved by interaction with the ANTH domain-containing proteins PICALM1a and PICALM1b that act redundantly. They bind to the R-SNARE domain of VAMP721 and other VAMP72 proteins but not VAMP71 proteins. PICALM also interacts with clathrin. In contrast, human VAMP7 is recycled through its LONGIN domain that can interact with HIV Rev-binding protein. Human PICALM genes still interact with the R-SNARE domain to regulate the recycling of brevins through their SNARE domain.", "VAMP721 recycling is achieved by interaction with the HIV Rev-binding protein that binds to its LONGIN domain. It also binds to the LONGIN domain of other VAMP72 proteins but not VAMP71 proteins. HIV Rev-binding protein also interacts with clathrin. Similarly, human VAMP7 is recycled through its LONGIN domain that can interact with HIV Rev-binding protein. Human PICALM genes interact with the R-SNARE domain to regulate the recycling of brevins through their SNARE domain.", "VAMP721 recycling is achieved by interaction with the ANTH domain-containing proteins PICALM1a and PICALM1b that act redundantly. They bind to the LONGIN domain of VAMP721 and other VAMP72 proteins as well as VAMP71 proteins. PICALM also interacts with clathrin. The same is true for human VAMP7, which is recycled through its LONGIN domain that can interact with HIV Rev-binding protein. In humans, PICALM genes interact with the R-SNARE domain to regulate the recycling of brevins through their SNARE domain." ], "source":"10.1073\/pnas.2011152117", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1073\/pnas.2011152117", "Year":2020.0, "Citations":23.0, "answer":0, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"What are TRANS-SNARE and CIS-SNARE complexes, and how are they formed in Arabidopsis? What is their role?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "SNARE complexes are protein complexes comprised of one R-SNARE and two or three Q-SNARE proteins, with all the SNAREs being membrane-bound. They can have either a TRANS configuration, with the R-SNARE anchored to one membrane and the Q-SNAREs anchored to an opposite membrane. The TRANS complex forms a 4-helix bundle that works as a zipper and provides the energy necessary to fuse the opposing membranes. They are essentially the final drivers of membrane fusion in all kinds of cellular trafficking events. After fusion, the original TRANS-SNARE complex becomes a CIS-SNARE complex, with all the SNAREs anchored to the same membrane (in CIS). The complex needs to be disassembled by the NSF-SNAP chaperone complex in order to reuse the proteins for another round of membrane fusion. CIS-SNARE complexes are also formed before fusion and as soon as the SNARE proteins are synthesized at the ER. It is hypothesized that this is a mechanism for trafficking the whole SNARE complex in an inactive form. This is important to prevent incorrect fusion events and also ensure stoichiometric amounts of SNAREs.", "SNARE complexes are protein complexes comprised of one R-SNARE and three Q-SNARE proteins, with some of them being membrane-bound. They can have either a TRANS configuration, with the R-SNARE anchored to one membrane and the Q-SNAREs anchored to an opposite membrane. The TRANS complex forms a 4-helix bundle that works as a zipper and provides the energy necessary to fuse the opposing membranes. They are essentially the final drivers of membrane fusion in all kinds of cellular trafficking events. After fusion, the original TRANS-SNARE complex becomes a CIS-SNARE complex, with all the SNAREs anchored to the same membrane (in CIS). The complex needs to be disassembled by the NSF-SNAP chaperone complex in order to reuse the proteins for another round of membrane fusion. CIS-SNARE complexes can also be formed as soon as the SNARE proteins are synthesized at the ER under stressful conditions. Sec11 (a Sec\/Munc protein) modulates SNARE complex formation, avoiding premature CIS-SNARE complex formation. Once formed at the ER, CIS complexes need to be removed by the dislocase EBS5 to be degraded via the ERAD pathway.", "SNARE complexes are protein complexes comprised of one R-SNARE and two or three Q-SNARE proteins, with all the SNAREs being membrane-bound. They can have either a TRANS configuration, with the R-SNARE anchored to one membrane and the Q-SNAREs anchored to an opposite membrane. The TRANS complex formation tethers the membranes together to drive membrane fusion in all kinds of cellular trafficking events. After fusion, the original TRANS-SNARE complex becomes a CIS-SNARE complex, with all the SNAREs anchored to the same membrane (in CIS). The complex needs to be ubiquitinated for its degradation chaperone complex in order to avoid their accumulation. CIS-SNARE complexes are also formed before fusion and as soon as the SNARE proteins are synthesized at the ER under stressful conditions, leading to a generalized decrease in cellular traffic with a consequential arrest of all cellular growth." ], "source":"https:\/\/doi.org\/10.7554\/eLife.25327", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.7554\/eLife.25327", "Year":2017.0, "Citations":24.0, "answer":0, "source_journal":"eLife", "is_expert":true }, { "question":"Which is the family of immune related proteins whose splicing is affected by SM like PROTEIN 4 (LSM4 ) arginine methylation in Arabidopsis thaliana plants?", "area":"GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Arginine methylation of LSM4 in Arabidopsis regulates the alternative splicing of the Pathogen Related Protein family", "Arginine methylation of LSM4 in Arabidopsis regulates the alternative splicing of the coiled-coil (CC)-NB-LRR proteins", "Arginine methylation of LSM4 in Arabidopsis regulates the alternative splicing of leucine-rich repeat TIR-NBS-LRR protein family\n" ], "source":"https:\/\/doi.org\/10.1093\/plcell\/koae051", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1093\/plcell\/koae051", "Year":2024.0, "Citations":6.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"Which Arabidopsis PRMT5 targets are strongly symmetrically dimethylated in their arginines residues in vitro by the addition of nitrosogluthathione (GSNO)?", "area":"GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "GSNO enhanced PRMT5 activity and arginine methylation of Arabidopsis histone4 and LSM8 substrates ", "GSNO enhanced PRMT5 activity and arginine methylation of Arabidopsis SmD3 and LSM4 substrates ", "GSNO enhanced PRMT5 activity and arginine methylation of Arabidopsis histone4 and LSM4 substrates" ], "source":"DOI: 10.1016\/j.molcel.2017.06.031", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.molcel.2017.06.031", "Year":2017.0, "Citations":101.0, "answer":2, "source_journal":"Molecular Cell", "is_expert":true }, { "question":"Which are the biological processes affected in Arabidopsis thaliana GRP7 mutant variants with non methylated R141 residue?", "area":"GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Mutants variants with non methylated R141 residue are affected in abscicic acid sensitivity during germination.", "Mutants variants with non methylated R141 residue are affected in auxin sensitivity during lateral root development.", "Mutants variants with non methylated R141 residue are affected in flowering time." ], "source":"https:\/\/doi.org\/10.3390\/plants13192771", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.3390\/plants13192771", "Year":2024.0, "Citations":0.0, "answer":0, "source_journal":"Plants", "is_expert":true }, { "question":"Which is the effect of PRMT5 - mediated arginine methylation of Arabidopsis thaliana Argonaute2 (AGO2) at the protein level?", "area":"GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Arginine methylation leads to AGO2 stabilization in the citosol", "Arginine methylation leads to AGO2 relocalization in the nucleus.", "Arginine methylation leads to AGO2 degradation by the proteasome" ], "source":"https:\/\/doi.org\/10.1038\/s41467-019-08787-w", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41467-019-08787-w", "Year":2019.0, "Citations":29.0, "answer":2, "source_journal":"Nature Communications", "is_expert":true }, { "question":"Which Argonaute (AGO) proteins are symmetricallly dimethylated in arginines residues (SDMA) of their N-terminal extension in Arabidopsis?", "area":"GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "AGO1 and AGO2 undergo SDMA postranslational modification ", "AGO1, AGO2, AGO3 and AGO5 undergo SDMA postranslational modification", "AGO1, AGO2, AGO3, AGO5 and AGO10 undergo SDMA postranslational modification " ], "source":"https:\/\/doi.org\/10.1093\/nar\/gkae387", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1093\/nar\/gkae387", "Year":2024.0, "Citations":4.0, "answer":1, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"What are the differences between AGO1 and AGO7 subcellular localization in Arabidopsis thaliana?", "area":"GENE REGULATION - PTGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "AGO7 and AGO7 partition between free cytosolic versions but also can partition into biomolecular condensates. While AGO7 is present in P-bodies, AGO1 localizes to Stress granules and Processing bodies (P-bodies). In addition, AGO7 is exclusively cytosolic while AGO1 shuttles from cytosol to the nucleus to be loaded with miRNAs. There is evidence showing that AGO1 localizes or at least interacts with dicing bodies (D-bodies) in the nucleus.", "AGO7 and AGO7 partition between free cytosolic versions but also can partition into biomolecular condensates. While AGO7 is present in siRNA bodies, AGO1 localizes both to siRNA bodies and Processing bodies (P-bodies). In addition, AGO7 is exclusively cytosolic while AGO1 shuttles from cytosol to the nucleus to be loaded with miRNAs. There is evidence showing that AGO1 localizes or at least interacts with dicing bodies (D-bodies) in the nucleus.", "AGO7 and AGO7 partition between free cytosolic versions but also can partition into biomolecular condensates. While AGO7 is present in siRNA bodies, AGO1 localizes both to siRNA bodies and Processing bodies (P-bodies). In addition, AGO1 is exclusively cytosolic while AGO7 shuttles from cytosol to the nucleus to be loaded with miRNAs. There is evidence showing that AGO7 localizes or at least interacts with dicing bodies (D-bodies) in the nucleus." ], "source":"10.1038\/emboj.2012.20 ; https:\/\/doi.org\/10.1093\/nar\/gkae387; doi: 10.1016\/j.cub.2007.04.005", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.cub.2007.04.005", "Year":2007.0, "Citations":385.0, "answer":1, "source_journal":"Current Biology", "is_expert":true }, { "question":"What are the key components in Arabidopsis SGS3 that enable the nucleation of siRNA bodies?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "SGS3 contains one prion-like domain, one at each end. The deletion of this domain results in a protein that can still interact with its partner RDR6 but now localizes to the nucleus and does not nucleate cytosolic foci. More recently, it has been shown that the C-terminal prion-like domain is the most important for the nucleation of siRNA bodies and functional complementation of the protein.", "SGS3 contains two prion-like domains, one at each end. The deletion of these domains results in a protein that cannot interact with its partner RDR6 but forms cytosolic foci. More recently, it has been shown that the C-terminal prion-like domain is the most important for the nucleation of siRNA bodies and cannot restore its function.", "SGS3 contains two prion-like domains, one at each end. The deletion of these domains results in a protein that can still interact with its partner RDR6 but now localizes to the nucleus and does not nucleate cytosolic foci. More recently, it has been shown that the N-terminal prion-like domain is the most important for the nucleation of siRNA bodies and functional complementation of the protein." ], "source":"https:\/\/doi.org\/10.1038\/s41477-021-00867-4; https:\/\/doi.org\/10.1016\/j.celrep.2022.111985", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1016\/j.celrep.2022.111985", "Year":2023.0, "Citations":27.0, "answer":2, "source_journal":"Cell Reports", "is_expert":true }, { "question":"What is the result of blocking the module of AGO7\/miR390\/TAS3 in Arabidopsis?", "area":"GENE REGULATION - PTGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Interfering with any of the key components of the AGO7\/miR390\/TAS3 results in the zippy phenotype. This phenotype is characterized by disorders in the maturation of seedling to adult plants. The impaired AGO7 dependent post-transcriptional gene silencing results in higher levels of AUXIN RESPONSE FACTORS 2, 3 and 4. The most visible feature of ARF2\/3\/4 increased abundance are elongated leaves longitudinally curled and decreased lateral root density.", "Interfering with any of the key components of the AGO7\/miR390\/TAS3 results in the zippy phenotype. This phenotype is characterized by disorders in the senescence timing of adult plants. The impaired AGO7 dependent post-transcriptional gene silencing results in lower levels of AUXIN RESPONSE FACTORS 2, 3 and 4. The most visible feature of ARF2\/3\/4 decreased abundance are elongated leaves longitudinally curled and increased lateral root density.", "Interfering with any of the key components of the AGO7\/miR390\/TAS3 results in the zippy phenotype. This phenotype is characterized by disorders in the maturation of seedling to adult plants. The enhanced AGO7 dependent post-transcriptional gene silencing results in increased levels of AUXIN RESPONSE FACTORS 7 and 19. The most visible feature of ARF7\/19 increased abundance are elongated leaves longitudinally curled and decreased lateral root density." ], "source":"https:\/\/doi.org\/10.1016\/j.cub.2003.09.004; 10.1105\/tpc.109.072553", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1105\/tpc.109.072553", "Year":2010.0, "Citations":486.0, "answer":0, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How do siRNA bodes move along the cell in plants?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "non-specific" ], "options":[ "siRNA bodies are a kind of cytosolic biomolecular condensate that host key enzymes involved in post-transcriptional gene silencing. siRNA bodies are highly dynamic and move along the cell using the actin cytoskeleton. Stabilizing actin filaments results in enhanced siRNA bodies mobility. This is contrary to the observations in animals, where granules are immobile.", "siRNA bodies are a kind of cytosolic biomolecular condensate that host key enzymes involved in post-transcriptional gene silencing. siRNA bodies are highly dynamic and move along the cell using microtubules. Interfering with microtubules polymerization results in immobile siRNA bodies. This is in line with observations in animals, where P-bodies and stress granules move along microtubules.", "siRNA bodies are a kind of cytosolic biomolecular condensate that host key enzymes involved in post-transcriptional gene silencing. siRNA bodies are highly dynamic and move along the cell using the actin cytoskeleton. Interfering with actin polymerization results in immobile siRNA bodies. This is contrary to the observations in animals, where granules move along microtubules." ], "source":"10.1093\/nar\/gkv119; 10.1091\/mbc.E08-05-0513", "normalized_plant_species":"Non-specific", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1091\/mbc.E08-05-0513", "Year":2008.0, "Citations":208.0, "answer":2, "source_journal":"Molecular Biology of the Cell", "is_expert":true }, { "question":"Which are the transporters with higher affinity cytokinins in Arabidopsis thaliana?", "area":"HORMONES", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Several transporter families have been described as cytokinin transporters so far, with PUP, ENTs, AZGs, ABCGs among them. However, for most of them the kinetic parameters are not described. One exception to it is AZG2, which Km to trans-Zeatin has been calculated by its expression in Arabidopsis calli. AZG2 Km to CK is in the range of the nano to micromoles. Based on its affinity to similar substrates and sequence homology, AZG1 presumably has a similar Km to cytokinin.", "Several transporter families have been described as cytokinin transporters so far, with PUP, ENTs, AZGs, ABCGs among them. However, for most of them the kinetic parameters are not described. One exception to it is PUP14, which Km to trans-Zeatin has been calculated by its expression in Arabidopsis seedling. PUP14 Km to CK is in the range of the nano to micromoles. Based on its affinity to similar substrates and sequence homology, PUP1 presumably has a similar Km to cytokinin.", "Several transporter families have been described as cytokinin transporters so far, with PUP, ENTs, AZGs, ABCGs among them. However, for most of them the kinetic parameters are not described. One exception to it is ABCG14, involved in cytokinin long distance transport with high efficiency. ABCG14 can interact with other ABCG transporters resulting in heterodimer with intermediate affinities." ], "source":"10.1111\/nph.16943; 10.1111\/nph.18879; 10.1042\/BST20231537", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1042\/BST20231537", "Year":2024.0, "Citations":0.0, "answer":0, "source_journal":"Biochemical Society Transactions", "is_expert":true }, { "question":"Which gene has been identified to act downstream of EXO70A3 to regulate root depth in Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "PIN1", "PIN7", "PIN4" ], "source":"10.1016\/j.cell.2019.06.021", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1016\/j.cell.2019.06.021", "Year":2019.0, "Citations":142.0, "answer":2, "source_journal":"Cell", "is_expert":true }, { "question":"Degradation of which protein is responsible for shutting down the iron deficiency responses during treatment with flagellin in Arabidopsis thaliana?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "BTS", "IMA1", "BTSL1" ], "source":"10.1038\/s41586-023-06891-y", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1038\/s41586-023-06891-y", "Year":2024.0, "Citations":20.0, "answer":1, "source_journal":"Nature", "is_expert":true }, { "question":"Which transcription factor balances ROS homeostasis in the root meristem to regulate the balance between cell proliferation and differentiation in Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "ARR1", "PER39", "UPB1" ], "source":"10.1016\/j.cell.2010.10.020", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1016\/j.cell.2010.10.020", "Year":2010.0, "Citations":871.0, "answer":2, "source_journal":"Cell", "is_expert":true }, { "question":"What proteins sequester SHR in the nucleus in Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "SCR", "RBR", "CYCD6;1" ], "source":"10.1126\/science.1139531", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1126\/science.1139531", "Year":2007.0, "Citations":469.0, "answer":0, "source_journal":"Science", "is_expert":true }, { "question":"How do alleles of the gene TBR affect growth in high Zinc conditions in Arabidopsis thaliana?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "Alleles of TBR are involved in Zinc uptake and less Zinc is taken up.", "Alleles of TBR lead to increased protein activity of TBR.", "Certain natural alleles of TBR lead to a higher expression level of TBR. TBR plays a role in pectin O-acetylation, and this is associated with pectin modifications in the cell wall including increased levels of methylesterified pectin. This TBR mediated altered pectin methylesterification in root cell walls, alters the Zn binding to cell walls and leads to Zinc sequestration in the cell wall, thereby avoiding zinc toxicity in the cells." ], "source":"10.1038\/s41467-024-50106-5", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/s41467-024-50106-5", "Year":2024.0, "Citations":4.0, "answer":2, "source_journal":"Nature Communications", "is_expert":true }, { "question":"How does the denitrification process of Azospirillum baldaniorum Sp245 contribute to bacterial plant growth-promoting capacity when inoculated in tomato?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Solanum lycopersicum" ], "options":[ "As an intermediate product of denitrification, Azospirillum baldaniorum Sp245 is able to release nitric oxide (NO), a molecule that can act as a plant growth regulator, in part by modulating the growth of plant root. When inoculated in tomato, and in the presence of nitrate, A. baldaniorum Sp245 is able to induce plant root branching through the release of denitrification-derived NO.", "As an intermediate product of denitrification, Azospirillum baldaniorum Sp245 is able to consume nitric oxide (NO), a molecule that can act as a plant growth inhibitor, in part by modulating the growth of plant root. When inoculated in tomato, and in the presence of nitrate, A. baldaniorum Sp245 is able to reduce plant root branching through the capture of denitrification-derived NO.", "As the final product of denitrification, Azospirillum baldaniorum Sp245 is able to release atmospheric nitrogen (N2), a molecule that can act as a plant growth regulator, in part by modulating the growth of plant root. When inoculated in tomato, and in the presence of nitrate, A. baldaniorum Sp245 is able to induce plant root branching through the release of denitrification-derived N2." ], "source":"https:\/\/doi.org\/10.1094\/mpmi-21-7-1001", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"ENVIRONMENT", "doi":"10.1094\/mpmi-21-7-1001", "Year":2008.0, "Citations":195.0, "answer":0, "source_journal":"Molecular Plant-Microbe Interactions\u00ae", "is_expert":true }, { "question":"Which molecules produced by Pseudomonas protegens can interfere with Azospirillum root colonization when both bacteria are co-inoculated in wheat?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Triticum aestivum" ], "options":[ "When co-inoculated with Pseudomonas protegens in wheat seeds, the capacity of Azospirillum to colonize the developing roots is affected by surfactin and other cyclic lipopetides produced by the pseudomonads.", " When co-inoculated with Pseudomonas protegens in wheat seeds, the capacity of Azospirillum to stimulate root growth is affected by siderophores produced by the pseudomonads.", "When co-inoculated with Pseudomonas protegens in wheat seeds, the capacity of Azospirillum to colonize the developing roots is affected by siderophores and Gac\/Rsm-regulated exoproducts produced by the pseudomonads." ], "source":"doi: 10.1093\/femsec\/fiy202", "normalized_plant_species":"Cereal Grains", "normalized_area":"ENVIRONMENT", "doi":"10.1093\/femsec\/fiy202", "Year":2018.0, "Citations":7.0, "answer":2, "source_journal":"FEMS Microbiology Ecology", "is_expert":true }, { "question":"Which mechanism uses Pseudomonas fluorescens G20-18 to induce drought tolerance in tomato plants and to control P. syringae infection in Arabidopsis?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Solanum lycopersicum", "Arabidopsis thaliana" ], "options":[ "By using the cytokinin-overproducing strains CNT1 and CNT2, it has been demonstrated that cytokinin production is a key mechanism of Pseudomonas fluorescens G20-18 that induces drought tolerance and pathogen defense responses in plants.", "By using the cytokinin-defective isogenic mutant strains CNT1 and CNT2, it has been demonstrated that cytokinin production is a key mechanism of Pseudomonas fluorescens G20-18 that induces drought tolerance and pathogen defense responses in plants.", "By using the cytokinin-defective isogenic mutant strains CNT1 and CNT2, it has been demonstrated that auxins production is a key mechanism of Pseudomonas fluorescens G20-18 that induces drought tolerance and pathogen defense responses in plants." ], "source":"doi: 10.1016\/j.jplph.2022.153629 and doi: 10.1038\/srep23310", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/srep23310", "Year":2016.0, "Citations":158.0, "answer":1, "source_journal":"Scientific Reports", "is_expert":true }, { "question":"Which phytohormone is the most important signaling factor of the Induced Systemic Resistance (ISR) that is upheaved by plants as a response to the inoculation of beneficial rhizobacteria?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "The Induced Systemic Resistance (ISR) is a defense mechanism build up by plants upon exposure to beneficial rhizobacteria. Unlike the Systemic Acquired Resistance (SAR) that is induced by phytopathogenic microorganisms and signaled by jasmonic acid and\/or ethylene, the ISR is usually signaled by salicylic acid.", "The Induced Systemic Resistance (ISR) is a defense mechanism build up by plants upon exposure to phytopathogenic microorganisms. Unlike the Systemic Acquired Resistance (SAR) that is induced by beneficial rhizobacteria and signaled by salicylic acid, the ISR is usually signaled by jasmonic acid and\/or ethylene.", "The Induced Systemic Resistance (ISR) is a defense mechanism build up by plants upon exposure to beneficial rhizobacteria. Unlike the Systemic Acquired Resistance (SAR) that is induced by phytopathogenic microorganisms and signaled by salicylic acid, the ISR is usually signaled by jasmonic acid and\/or ethylene. " ], "source":"DOI: 10.1007\/978-3-030-41870-0_20", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1007\/978-3-030-41870-0_20", "Year":2020.0, "Citations":63.0, "answer":2, "source_journal":"Fungal Biology", "is_expert":true }, { "question":"Which organic acid secreted by plant roots can interfere with the normal rhlIR-type Quorum Sensing functioning of Pseudomonas?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "Rosmarinic acid produced by plant roots can act as a signal that induces a broad Quorum Sensing response in Pseudomonas aeruginosa.", "Malic acid produced by plant roots can act as a signal that induces a broad Quorum Sensing response in Pseudomonas aeruginosa.", "Rosmarinic acid produced by plant roots can act as a signal that quenches the Quorum Sensing response of Pseudomonas aeruginosa" ], "source":"DOI:10.1126\/scisignal.aaa8271 and DOI:10.1111\/1462-2920.14301", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/1462-2920.14301", "Year":2018.0, "Citations":19.0, "answer":0, "source_journal":"Environmental Microbiology", "is_expert":true }, { "question":"How does microRNA169 regulate heat stress tolerance in Arabidopsis thaliana?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Upon exposure to heat stress, the heat shock transcription factor HSFA2 is induced which transcriptionally enhances the expression of microRNA169q in Arabidopsis thaliana. Increased miR169q then transcriptionally upregulates its target NF-YA7 mRNA. The transcription factor NF-YA7, forms a heterotrimeric complex with heat responsive genes like HSFA3 and HSFA7b. This complex is responsible for providing thermotolerance to the plant.", "Upon exposure to heat stress, the heat shock transcription factor HSFA2 is repressed which transcriptionally down-regulates the expression of microRNA169d in Arabidopsis thaliana. Depleted miR169d results in reduced post-transcriptionally cleavage of its target NF-YA2 mRNA. The transcription factor NF-YA2, directly binds to the promoter of heat responsive genes like HSFA7a and HSFA9. The increased levels of the NF-YA2 activator during heat stress results in increased levels of HSFA7a and HSFA9, thereby providing thermotolerance to the plant.", "Upon exposure to heat stress, the heat shock transcription factor HSFA2 is induced which transcriptionally enhances the expression of microRNA169d in Arabidopsis thaliana. Increased miR169d then post-transcriptionally cleaves its target NF-YA2 mRNA. The transcription factor NF-YA2, directly binds to the promoter of heat responsive genes like HSFA3 and HSFA7b. Thus, the reduced levels of the NF-YA2 repressor during heat stress results in increased levels of HSFA3 and HSFA7b, thereby providing thermotolerance to the plant." ], "source":"https:\/\/doi.org\/10.1111\/tpj.15963", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/tpj.15963", "Year":2022.0, "Citations":35.0, "answer":2, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"What mechanisms underlie the role of the transcription factor, HSFA3 in heat stress memory in Arabidopsis thaliana?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "When exposed to moderate heat stress, plants acquire heat stress memory that is maintained over several days and aid plants to tide over severe heat stress later-on in their life. HSFA3 is required for transcriptional (type I) heat stress memory, by directly recruiting histone H3K4 hyper-methylation machinery to the heat stress memory-related genes for their induction. HSFA3 forms heteromeric complexes with HSFA2 to the HSE-cis element in the promoters of heat stress responsive gene like HSP22, HSA32, APX2 to enhance the efficiency of this process.", "When exposed to severe heat stress, plants acquire heat stress memory that is maintained over several days and aid plants to tide over severe heat stress later-on in their life. HSFA3 is required for transcriptional (type II) heat stress memory, by directly recruiting Polycomb complex (PRC2) proteins, to hyper-methylate histone H3K27 of the heat stress memory-related genes for their repression. HSFA3 forms heteromeric complexes with HSFA2 to the CCAAT-cis element in the promoters of heat stress responsive gene like HSP22, HSA32, APX2 to enhance the efficiency of this process.", "When exposed to moderate heat stress, plants acquire heat stress memory that is maintained over several days and aid plants to tide over severe heat stress later-on in their life. HSFA3 is required for transcriptional (type III) heat stress memory, by directly recruiting histone variant H2A.z to the heat stress memory-related genes for their repression. HSFA3 forms homo-trimeric complex to the HSE-cis element in the promoters of heat stress responsive gene like HSP22, HSA32, APX2 to enhance the efficiency of this process." ], "source":"https:\/\/doi.org\/10.1038\/s41467-021-23786-6", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/s41467-021-23786-6", "Year":2021.0, "Citations":155.0, "answer":0, "source_journal":"Nature Communications", "is_expert":true }, { "question":"How does XBAT31 regulate fertility in Arabidopsis thaliana under heat stress?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "XBAT31 plays a crucial role in the post-translational regulation of HSFA1a\/A1b, influencing fertility under heat stress conditions. It mediates sumoylation of HSFA1a\/A1b leading to upregulation of heat-stress-responsive genes and thereby, promoting thermosensitivity. However, in the absence of XBAT31, HSFA1a\/A1b levels decrease, leading to increased expression of heat-stress-responsive genes and a higher number of infertile siliques.", "XBAT31 plays a crucial role in the post-translational regulation of HSFB2a\/B2b, influencing fertility under heat stress conditions. It mediates ubiquitination of HSFB2a\/B2b leading to upregulation of heat-stress-responsive genes and thereby, promoting thermotolerance. However, in the absence of XBAT31, HSFB2a\/B2b levels increase, leading to reduced expression of heat-stress-responsive genes and a higher number of infertile siliques.", "XBAT31 plays a crucial role in the post-transcriptional regulation of HSFB3\/HSFB4, influencing fertility under heat stress conditions. It mediates cleavage of HSFB3\/HSFB4 transcripts leading to downregulation of heat-stress-responsive genes and thereby, promoting thermotolerance. However, in the absence of XBAT31, HSFB3\/HSFB4 levels increase, leading to reduced expression of heat-stress-responsive genes and a higher number of infertile siliques." ], "source":"10.1016\/j.celrep.2024.114349", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.celrep.2024.114349", "Year":2024.0, "Citations":0.0, "answer":1, "source_journal":"Cell Reports", "is_expert":true }, { "question":"In Arabidopsis thaliana, which heat stress transcription factor has an antisense long non-coding RNA and how does it affect the expression of its sense coding gene?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "At the locus of HSFB2a in Arabidopsis thaliana, a heat-inducible, natural antisense long non-coding RNA, termed asHSFB2a is transcribed. Overexpression of HSFB2a results in a complete knock down of the asHSFB2a expression whereas asHSFB2a overexpression leads to the absence of HSFB2a RNA. This intriguing \u201cYin\u2013Yang relationship\u201d of RNA levels at HSFB2a locus influence vegetative and gametophytic development in Arabidopsis.", "At the locus of HSFB2a in Arabidopsis, a drought-inducible, natural antisense long non-coding RNA, termed asHSFB2a is transcribed. Downregulation of HSFB2a results in a complete knock down of the asHSFB2a expression whereas asHSFB2a downregulation leads to the absence of HSFB2a RNA. This intriguing \u201cYin\u2013Yang relationship\u201d of RNA levels at HSFB2a locus influence vegetative and gametophytic development in Arabidopsis.", "At the locus of HSFB3 in Arabidopsis, a heat-inducible, natural antisense long non-coding RNA, termed asHSFB3 is transcribed. Overexpression of HSFB3 results in a complete knock down of the asHSFB3 expression whereas asHSFB3 overexpression leads to the absence of HSFB3 RNA. This intriguing \u201cYin\u2013Yang relationship\u201d of RNA levels at HSFB3 locus influence vegetative and gametophytic development in Arabidopsis." ], "source":"10.1007\/s11103-014-0202-0", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1007\/s11103-014-0202-0", "Year":2014.0, "Citations":130.0, "answer":0, "source_journal":"Plant Molecular Biology", "is_expert":true }, { "question":"In maize (Zea mays), the transcription factor HSF20 binds to the promoters of which genes to regulate heat stress tolerance?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Zea mays" ], "options":[ "ZmHSF20, a negative regulator of heat stress response, binds to the promoters of Cellulose synthase A2 (ZmCesA2) and three Class C Hsf genes, including ZmHsf8, thus suppressing their expression. Simultaneously, ZmHSF4 reduces the expression of ZmCesAs, such that heat treatment further increases cellulose content in a ZmHSF20- and ZmHSF8-dependent manner. Hence, this module, HSF20- Hsf8- CesA2 regulate heat stress tolerance in maize.", "ZmHSF20, a negative regulator of heat stress response, binds to the promoters of Cellulose synthase A2 (ZmCesA2) and three Class A Hsf genes, including ZmHsf4, thus suppressing their expression. Simultaneously, ZmHSF4 promotes the expression of ZmCesAs, such that heat treatment further decreases cellulose content in a ZmHSF20- and ZmHSF4-dependent manner. Hence, this module, HSF20- Hsf4- CesA2 regulate heat stress tolerance in maize.", "ZmHSF20, a positive regulator of heat stress response, binds to the promoters of Cellulose synthase A1 (ZmCesA1) and three Class A Hsf genes, including ZmHsf4, thus enhancing their expression. Simultaneously, ZmHSF4 promotes the expression of ZmCesAs, such that heat treatment further decreases cellulose content in a ZmHSF20- and ZmHSF4-dependent manner. Hence, this module, HSF20- Hsf4- CesA1 regulate heat stress tolerance in maize." ], "source":"https:\/\/doi.org\/10.1093\/plcell\/koae106", "normalized_plant_species":"Cereal Grains", "normalized_area":"ENVIRONMENT", "doi":"10.1093\/plcell\/koae106", "Year":2024.0, "Citations":18.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"What is the main gene accounting for proline accumulation under stress conditions in Arabidopsis?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "pyrroline 5-carboxylate synthase 1", "pyrroline 5-carboxylate synthase 2", "proline dehydrogenase" ], "source":"https:\/\/doi.org\/10.1111\/j.1365-313X.2007.03318.x", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/j.1365-313X.2007.03318.x", "Year":2007.0, "Citations":577.0, "answer":0, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"Is proline an efficient scavenger of reactive oxygen species?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "Yes, proline can scavenge most reactive oxygen species.", "Yes, proline can scavenge superoxide, singlet oxygen, hydrogen peroxide and hydroxyl radicals.", "No, proline can only scavenge hydroxyl radicals but is not a good scavenger of singlet oxygen, superoxide, and hydrogen peroxide." ], "source":"https:\/\/doi.org\/10.1071\/FP16060", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1071\/FP16060", "Year":2016.0, "Citations":43.0, "answer":2, "source_journal":"Functional Plant Biology", "is_expert":true }, { "question":"Is proline accumulation subjected to feedback inhibition by proline?", "area":"EVOLUTION", "plant_species":[ "non-specific" ], "options":[ "No, only bacterial proline biosynthetic genes (ProB) have a specific allosteric domain (DNDFRD) that enables feedback inhibition by proline, but this is not the case for plants and animals proline biosynthetic genes (P5CS, pyrroline 5 carboxylate synthase).", "Yes, proline biosynthetic gene in plants and animals (P5CS), and bacteria (ProB), have a conserved allosteric domain (DNDFRD) that enables feedback inhibition by proline.", "No, proline biosynthetic gene in plants and animals (P5CS), and bacteria (ProB), have a conserved allosteric domain (DNDFRD) that enables feedback inhibition but this inhibition is exerted by its own product, glutamic semialdehyde." ], "source":"https:\/\/doi.org\/10.1104\/pp.122.4.1129", "normalized_plant_species":"Non-specific", "normalized_area":"EVOLUTION", "doi":"10.1104\/pp.122.4.1129", "Year":2000.0, "Citations":635.0, "answer":1, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"Is P5CS1 gene expression induced by abiotic stress in Arabidopsis?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "Yes, P5CS1 expression is known to be induced by abiotic stress. Its promoter is enriched in putative binding sites for TFs related to abiotic stress, such as ABA response ele- ments, AP2\/EREBP, ERF2, DREB\/CBF, and MYB binding sites.", "No, P5CS1 expression is known to be constitutive in Arabidopsis. For this reason, this gene is often used as a housekeeping gene for real time PCR analysis.", "No, P5CS1 expression is known to be induced only by biotic stressors or during developmental transitions. Its promoter is is enriched in putative regulatory elements for TFs related to biotic stresses such as HD-HOX, AP2\/EREBP, MYB, WRKY, and bZIP." ], "source":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/brv.12146", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1111\/brv.12146", "Year":2014.0, "Citations":177.0, "answer":0, "source_journal":"Biological Reviews", "is_expert":true }, { "question":"Is P5CS2 gene induced by biotic stress in Arabidopsis?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "No, P5CS2 expression is known to be induced only by abiotic stress. Its promoter is enriched in putative binding sites for TFs related to abiotic stress, such as ABA response ele- ments, AP2\/EREBP, ERF2, DREB\/CBF, and MYB binding sites. ", "No, P5CS2 expression is known to be constitutive in Arabidopsis. For this reason, this gene is often used as a housekeeping gene for real time PCR analysis. ", "Yes, P5CS2 expression is known to be induced by biotic stressors. Its promoter is enriched in putative regulatory elements for TFs related to biotic stresses such as HD-HOX, AP2\/EREBP, MYB, WRKY, and bZIP." ], "source":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/brv.12146", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1111\/brv.12146", "Year":2014.0, "Citations":177.0, "answer":2, "source_journal":"Biological Reviews", "is_expert":true }, { "question":"What is the locus identified by GWAS as associated with Tyramine levels in Arabidopsis and how significant was this association?", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Tyramine was significantly associated with SNP m154079 (p = 1.28 \u00d7 10\u22129, LOD = 8.89), located at locus AT4G28680, that encodes a stress-induced tyrosine decarboxylase (TyrDC)", "Tyramine was significantly associated with SNP m156090 (p = 4.11 \u00d7 10\u22126, LOD = 5.39), located at locus AT2G17265, that encodes a homoserine kinase (HSK).", "Tyramine was significantly associated with SNP m54083 (p = 3.11 \u00d7 10\u22128, LOD = 7.50), located at locus AT5G53970, that encodes for a tyrosine aminotransferase (TAT7)" ], "source":"10.1371\/journal.pgen.1006363", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1371\/journal.pgen.1006363", "Year":2016.0, "Citations":68.0, "answer":0, "source_journal":"PLOS Genetics", "is_expert":true }, { "question":"How many metabolic traits showed an association found by GWAS with the locus in Chromosome 4 of Arabidopsis thaliana, harboring ACD6 (ACCELERATED CELL DEATH6)? ", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "A QTL in Chr4, harboring ACD6 was associated with three enzyme activities (cPGI, tPGI, GDH), three metabolites (G6P, AA, and Fum), and fresh weight.", "A QTL in Chr4, harboring ACD6 was associated with five enzyme activities (nINV, cPGI, tPGI, fumarase, and GDH), four metabolites (G6P, AA, Suc and Fum), protein and fresh weight.", "The QTL found in Chr4, harboring ACD6, was associated with six enzyme activities (aINV, nINV, cPGI, tPGI, fumarase, and GDH), three metabolites (G6P, AA, and Fum), protein and fresh weight." ], "source":"www.plantcell.org\/cgi\/doi\/10.1105\/tpc.17.00232", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1105\/tpc.17.00232", "Year":2017.0, "Citations":32.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"Which gene has been identified by GWAS associated with 22 polyunsaturated triacylglycerol species (puTAGs) in Arabidopsis thaliana grown under stress conditions?", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The gene LYSOPHOSPHOLIPASE (AT5G20060) has been significantly associated with a high number of polyunsaturated triacylglycerol species in Arabidopsis thaliana grown under stress conditions.", "The gene FATTY ACID DESATURASE (FAD2: AT3G12120)) has been significantly associated with a high number of polyunsaturated triacylglycerol species in Arabidopsis thaliana grown under stress conditions.", "The gene 3-KETOACYL-COENZYME A SYNTHASE4 (KCS4: AT1G19440) has been significantly associated with 22 polyunsaturated triacylglycerol species in Arabidopsis thaliana grown under stress conditions" ], "source":"https:\/\/doi.org\/10.1093\/plcell\/koad059", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1093\/plcell\/koad059", "Year":2023.0, "Citations":15.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"Which locus has been associated by GWAS with root hair growth at moderate-low temperatures in Arabidopsis thaliana?", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Genome Wide Association Studies (GWAS) on Arabidopsis thaliana \nidentified the uncharacterized PEROXIDASE 69 (PRX69: AT5G64100) as a key protein that regulates the conditional growth under moderate low temperature stress.", "Genome Wide Association Studies (GWAS) on Arabidopsis thaliana \nidentified the EXT6 (AT2G24980) as a key protein that regulates the conditional growth under moderate low temperature stress.", "Genome Wide Association Studies (GWAS) on Arabidopsis thaliana \nidentified the uncharacterized PEROXIDASE 62 (PRX62: AT5G39580) as a key protein that regulates the conditional growth under moderate low temperature stress." ], "source":"https:\/\/doi.org\/10.1038\/s41467-022-28833-4", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1038\/s41467-022-28833-4", "Year":2022.0, "Citations":40.0, "answer":2, "source_journal":"Nature Communications", "is_expert":true }, { "question":"Is there population structure in 19 elite accessions of Sunflower (Helianthus annuus) from Argentina, and how is extent of linkage disequilibrium in this group?", "area":"GENOME AND GENOMICS", "plant_species":[ "Helianthus annuus" ], "options":[ "The entire set of 19 sunflower elite lines from Argentina are mainly composed by the contribution of two gene pools. For the entire group of 19 lines de LD declines very slowly (r2=0.64 at 643 bp) while for one of the groups with homogeneous allele frequencies the value is 0.48 for the same distance.", "The entire set of 19 sunflower elite lines from Argentina are mainly composed by the contribution of five gene pools. This structure influences the pairwise estimates of LD (r2). For instance, for the entire group of 19 lines de LD declines very rapidly (r2=0.33 at 643 bp), while for one of the groups with homogeneous allele frequencies the value is 0.68 for the same distance", "The entire set of 19 sunflower elite lines from Argentina are mainly composed by the contribution of three gene pools. This structure influences the pairwise estimates of LD (r2). For instance, for the entire group of 19 lines de LD declines rapidly (r2=0.48 at 643 bp), while for one of the groups with homogeneous allele frequencies the value is 0.64 for the same distance." ], "source":"https:\/\/doi.org\/10.1186\/1471-2229-8-7", "normalized_plant_species":"Other Herbaceous Crops, Spices, Fibers & Weeds", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1186\/1471-2229-8-7", "Year":2008.0, "Citations":40.0, "answer":0, "source_journal":"BMC Plant Biology", "is_expert":true }, { "question":"What is the primary step in the mechanisms by which phyB senses temperature?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "non-specific" ], "options":[ "The primary step is that phytochrome B moves from the nucleus, where it exerts its biological activity, to the cytoplasm. ", "The the primary step is that nuclear bodies of phytochrome B, generated by liquid-liquid phase separation, disassembly in response to warm temeratures. ", "The primary step is that active form of phytochrome of phytochrome B reverts thermically to the inactive form in a temperature-dependent manner." ], "source":"https:\/\/doi.org\/10.1146\/annurev-genet-111523-102327", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1146\/annurev-genet-111523-102327", "Year":2024.0, "Citations":2.0, "answer":2, "source_journal":"Annual Review of Genetics", "is_expert":true }, { "question":"What are the families of photosensory receptors present in plants?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "non-specific" ], "options":[ "In alphabetical order the families are: Anthocyanins, carotenoids, chlorophylls, cryptochromes, phototropins Phytochromes, zeitlupes, UVR8.", "In alphabetical order the families are: cryptochromes, phototropins phytochromes, zeitlupes, UVR8. ", "In alphabetical order the families are: Carotenoids, chlorophylls, cryptochromes, phototropins Phytochromes, zeitlupes, UVR8." ], "source":"DOI: 10.1126\/science.aaf5656", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1126\/science.aaf5656", "Year":2016.0, "Citations":698.0, "answer":1, "source_journal":"Science", "is_expert":true }, { "question":"What are the phenotypes of the hypocotyls in dark-grown seedlings of the wild type and of the phyB, cop1, hy5 single mutants, the cop1 hy5 mutant and the phyB cop1 mutant?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Wild type, seedlings are long, phyB, hy5 and seedlings are even longer, and cop1, cop1 hy5 and phyB cop1 seedlings are short.", " Wild type, phyB, hy5 and cop1 hy5 seedlings are long, whereas cop1 and phyB cop1 seedlings are short. ", "Wild type, phyB, hy5 and seedlings are long, whereas cop1, cop1 hy5 and phyB cop1 seedlings are short. " ], "source":"https:\/\/doi.org\/10.1105\/tpc.6.5.613", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1105\/tpc.6.5.613", "Year":1994.0, "Citations":112.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"What of the following differences between phytochromes A and B are correct, the genes that encode them, the chromophore that they attach, their photo-interconvertible forms, the waveband of maximum activity, their effect on seed germination (promotion or inhibition). ", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The genes that encode them and the waveband of maximum activity. ", "The genes that encode them, their photo-interconvertible forms, the waveband of maximum activity. ", "The genes that encode them, the chromophore that they attach, their photo-interconvertible forms, the waveband of maximum activity, their effect on seed germination (promotion or inhibition). " ], "source":"https:\/\/doi.org\/10.1093\/jxb\/ert379", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1093\/jxb\/ert379", "Year":2013.0, "Citations":93.0, "answer":0, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"What light cues can be indicative of the presence of neighbouring vegetation, reductions in red \/ far-red ratio without large changes in visible light, reductions in red \/ far-red ratio with reductions in visible light, or both?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "non-specific" ], "options":[ "Reductions in red \/ far-red ratio with reductions in visible light", "Reductions in red \/ far-red ratio without large changes in visible light", "Both" ], "source":"https:\/\/doi.org\/10.1146\/annurev-arplant-050312-120221", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1146\/annurev-arplant-050312-120221", "Year":2013.0, "Citations":646.0, "answer":2, "source_journal":"Annual Review of Plant Biology", "is_expert":true }, { "question":"What are the three hallmarks that characterize ferroptosis in both plant and animal systems?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "non-specific" ], "options":[ "Ferroptosis is a nonapoptotic, iron-dependent form of cell death that is characterized by the availability of redoxactive iron, the oxidation of polyunsaturated fatty acid (PUFA)-containing phospholipids and the loss of lipid peroxide repair capacity by phospholipid hydroperoxidases. ", "Ferroptosis is a nonapoptotic, iron-dependent form of cell death that is characterized by by the availability of redoxactive iron, the oxidation of saturated fatty acid (PUFA)-containing phospholipids and an increase in the activity of phospholipid hydroperoxidases", "Ferroptosis is a nonapoptotic, iron-dependent form of cell death that is characterized by a decrease in iron availability, the oxidation of polyunsaturated fatty acid (PUFA)-containing phospholipids and an increase in the activity of phospholipid hydroperoxidases.\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026.." ], "source":"https:\/\/doi.org\/10.1146\/annurev-cancerbio-030518-055844", "normalized_plant_species":"Non-specific", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1146\/annurev-cancerbio-030518-055844", "Year":2019.0, "Citations":450.0, "answer":0, "source_journal":"Annual Review of Cancer Biology", "is_expert":true }, { "question":"Which protein has been identified as a molecular marker for ferroptosis in Arabidopsis thaliana and how is its response?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Kiss of death (KOD), a gene encoding a transcription factor that induces cell death in A. thaliana roots is significantly up-regulated in response to heat stress (HS) and ROS and down-regulated in response to specific ferroptosis canonical inhibitors, acting downstream of GSH depletion and ROS accumulation in the cascade of events that lead to HS\u2013induced ferroptotic cell death. ", "Kiss of death (KOD), a gene encoding for a 25-aa peptide that induces cell death in A. thaliana roots is significantly up-regulated in response to heat stress (HS) and ROS and down-regulated in response to specific ferroptosis canonical inhibitors, acting downstream of GSH depletion and ROS accumulation in the cascade of events that lead to HS\u2013induced ferroptotic cell death. ", "Kiss of death (KOD), a gene encoding a 25-aa peptide that induces cell death in A. thaliana roots is significantly down-regulated in response to heat stress (HS) and ROS and up-regulated in response to specific ferroptosis canonical inhibitors, acting downstream of GSH depletion and ROS accumulation in the cascade of events that lead to HS\u2013induced ferroptotic cell death. " ], "source":"https:\/\/doi.org\/10.1083\/jcb.201605110", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1083\/jcb.201605110", "Year":2017.0, "Citations":192.0, "answer":1, "source_journal":"Journal of Cell Biology", "is_expert":true }, { "question":"Which brassinosteroid is specifically found in female gametophytes and what is the proposed mechanism for its biosynthesis in Arabidopsis thaliana?", "area":"HORMONES", "plant_species":[ "non-specific" ], "options":[ "Castasterone is the brassinosteroid that is specifically found inside the female gametophytes of A. thaliana. Its biosynthesis takes place in female gametophyte mitochondria, in a pathway that involves an Adrenodoxin reductase, an Adrenodoxin and a cytochrome P450 (ADXR-ADX-P450) electron shuttle as occurs in animal systems, and whose activity is essential for female megagametophyte development and function. In this model, a precursor steroid is imported into the inner mitochondrial membrane via PBR, a peripheral-type benzodiazepine receptor. Inside mitochondria, electrons are transferred from NADPH via ADX\u2013ADXR to one of the P450s that are able to interact with ADX1 (CYP711A1, CYP90A1, or CYP75B1), to catalyze the synthesis of homocastasterone from the steroid precursor", "Brasinolide is the brassinosteroid that is specifically found inside the female gametophytes of A. thaliana. Its biosynthesis takes place in female gametophyte endoplasmic reticulum, in a pathway that involves an Adrenodoxin reductase, an Adrenodoxin and a cytochrome P450 (ADXR-ADX-P450) electron shuttle as occurs in animal systems, and whose activity is essential for female megagametophyte development and function. In this model, a sterol is imported into the inner mitochondrial membrane via PBR, a peripheral-type benzodiazepine receptor. Inside mitochondria, electrons are transferred from NADPH via ADX\u2013ADXR to one of the P450s that are able to interact with ADX1 (CYP711A1, CYP90A1, or CYP75B1), to catalyze the synthesis of homocastasterone from the sterol precursor", " Homocastasterone is the brassinosteroid that is specifically found inside the female gametophytes of A. thaliana. Its biosynthesis takes place in female gametophyte mitochondria, in a pathway that involves an Adrenodoxin reductase, an Adrenodoxin and a cytochrome P450 (ADXR-ADX-P450) electron shuttle as occurs in animal systems, and whose activity is essential for female megagametophyte development and function. In this model, a sterol is imported into the inner mitochondrial membrane via PBR, a peripheral-type benzodiazepine receptor. Inside mitochondria, electrons are transferred from NADPH via ADX\u2013ADXR to one of the P450s that are able to interact with ADX1 (CYP711A1, CYP90A1, or CYP75B1), to catalyze the synthesis of homocastasterone from the sterol precursor.\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026\u2026.." ], "source":"https:\/\/doi.org\/10.1073\/pnas.200048211", "normalized_plant_species":"Non-specific", "normalized_area":"HORMONES", "doi":null, "Year":null, "Citations":null, "answer":2, "source_journal":null, "is_expert":true }, { "question":"Which receptors of Brassinosteroids (BRs) have been identified in Arabidopsis thaliana and how are they activated in the presence of BRs?", "area":"HORMONES", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "BRs are perceived outside the cell by a plasma membrane-localized receptor. Three functional BR receptors have been identified in Arabidopsis: BRASSINOSTEROID-INSENSITIVE1 (BRI1) BRL1 and BRL3. These receptors associate with a smaller LRR receptor kinase, BRI1-ASSOCIATED KINASE1 (BAK1), whose function in BR signalling is also redundant with SERK1. BL binds to the extracellular domain of the receptor, inducing heterodimerization of BRI1 and BAK1 or SERK1, which function as co-receptors of BRI1. This interaction is required for BRI1 activation. ", "BRs are perceived outside the cell by a plasma membrane-localized receptor. Three functional BR receptors have been identified in Arabidopsis: BRASSINOSTEROID-INSENSITIVE1 (BRI1) BRL1 and BRL3. These receptors associate with a smaller LRR receptor kinase, BRI1-ASSOCIATED KINASE1 (BAK1), whose function in BR signalling is also redundant with SERK1. BL binds to the extracellular domain of the receptor, inducing homodimerization of BRI1 and its later binding with BAK1 or SERK1. This interaction is required for BRI1 activation. ", "BRs are perceived outside the cell by a plasma membrane-localized receptor. Four functional BR receptors have been identified in Arabidopsis: BRASSINOSTEROID-INSENSITIVE1 (BRI1) BRL1, BRL2 and BRL3. These receptors associate with a smaller LRR receptor kinase, BRI1-ASSOCIATED KINASE1 (BAK1), whose function in BR signalling is also redundant with SERK1 and with SERK5. BL binds to the extracellular domain of the receptor, inducing heterodimerization of BRI1 and BAK1 or SERK1, which function as co-receptors of BRI1. This interaction is required for BRI1 activation. " ], "source":"10.1016\/j.cub.2020.02.011", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1016\/j.cub.2020.02.011", "Year":2020.0, "Citations":107.0, "answer":0, "source_journal":"Current Biology", "is_expert":true }, { "question":"How do brassinosteroids (BRs) regulate Arabidopsis root development and how is the interaction between BRs and auxins in this process?", "area":"HORMONES", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis, BR signaling controls cell division and cell elongation by establishing a signal gradient along the longitudinal root axis. The coordinated growth of roots requires a gradient distribution of BR concentration, with higher hormone levels in the meristematic tissue and lower levels in the elongation zone, which are attributable to the spatial distribution of biosynthetic enzymes. The maintenance of the root meristematic state depends on the coordination of multiple hormone signals, with the interaction between BR and auxin playing a crucial role. BR promotes auxin signaling, but also inhibits its biosynthesis, which is essential to maintain the root meristem. ", "In Arabidopsis, BR signaling controls cell division and cell elongation by establishing a signal gradient along the longitudinal root axis. The coordinated growth of roots requires a gradient distribution of BR concentration, with lower hormone levels in the meristematic tissue and higher levels in the elongation zone, which are attributable to the spatial distribution of biosynthetic enzymes. The maintenance of the root meristematic state depends on the coordination of multiple hormone signals, with the interaction between BR and auxin playing a crucial role. BR promotes auxin synthesis but also inhibits auxin signal output, which is essential to maintain the root meristem. ", "In Arabidopsis, BR signaling controls cell division and cell elongation by establishing a signal gradient following the radial root axis. The coordinated growth of roots requires a gradient distribution of BRs receptors, which results in lower hormone signaling in the meristematic tissue and higher levels in the peripheral region. The maintenance of the root meristematic state depends on the coordination of multiple hormone signals, with the interaction between BR and auxin playing a crucial role. BR inhibits both auxin synthesis and auxin signal output, which is essential to maintain the root meristem. " ], "source":"10.3390\/plants13213051", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.3390\/plants13213051", "Year":2024.0, "Citations":3.0, "answer":1, "source_journal":"Plants", "is_expert":true }, { "question":"Which is the fundament behind the TRAP (Translating Ribosome Affinity Purification) methodology that allows purification of ribosome bound mRNAs?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "non-specific" ], "options":[ "TRAP is based on the expression of a tagged version of a eukaryotic initiation factor that will be incorporated into ribosomes, providing a means for affinity purification of ribosomes containing the tagged ribosomal protein and their associated mRNAs.", "TRAP is based on the expression of a tagged version of a ribosomal protein that will be incorporated into ribosomes, providing a means for affinity purification of ribosomes containing the tagged ribosomal protein and their associated mRNAs.", "TRAP is based on the expression of a tagged version of a nuclear envelope protein that will be incorporated into ribosomes, providing a means for affinity purification of ribosomes containing the tagged ribosomal protein and their associated mRNAs" ], "source":"www.plantphysiol.org\/cgi\/doi\/10.1104\/pp.105.059477.", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1104\/pp.105.059477", "Year":2005.0, "Citations":189.0, "answer":1, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"How can TRAP (Translating Ribosome Affinity Purification) methodology be applied to the generation of an atlas of the translated mRNAs within specific cell type populations?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "non-specific" ], "options":[ "By expressing a tagged ribosomal protein under the control of cell type specific promoters", "By expressing a tagged ribosomal protein under the control of a constitutive promoter", "By expressing a tagged ribosomal protein under the control of a chemically induced promoter" ], "source":"https:\/\/doi.org\/10.1073\/pnas.0906131106", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1073\/pnas.0906131106", "Year":2009.0, "Citations":503.0, "answer":0, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"Which mRNAs encoding components of the Nodulation signaling pathway are upregulated at translational level in Medicago truncatua roots upon inoculation with Sinorhizobium meliloti?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "Medicago truncatula" ], "options":[ "mRNAs upregulated at translation levels in Medicago truncatula roots upon inoculation with Sinorhizobium meliloti include those encoding the Nod factor receptor LYK3 and the calcium calmodulin dependent protein kinase DMI3. \n\n", "mRNAs upregulated at translation levels in Medicago truncatula roots upon inoculation with Sinorhizobium meliloti include those encoding the transcription factors NSP1, NSP2, HAP2.1\/NF-YA1, HAP5. ", "mRNAs upregulated at translation levels in Medicago truncatula roots upon inoculation with Sinorhizobium meliloti include those encoding the transcription factors NSP1, NSP2, and the interacting protein with DMI3 (IPD3). " ], "source":"doi: 10.1111\/tpj.12033", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1111\/tpj.12033", "Year":2012.0, "Citations":66.0, "answer":1, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"How is the Superkiller 3 (SKI3) subunit involved in the symbiosis between Medicago truncatula and Sinorhizobium meliloti?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "Medicago truncatula" ], "options":[ "SKI3 is a component of the Superkiller complex, which threads mRNA to the exosome for 3\u00b4to 5\u00b4mRNA degradation. SKI3 is required for nodule formation, the progression of infection events and the induction of the mRNA encoding the transcription factor NF-YA1 in the Medicago truncatula-Sinorhizobium meliloti symbiosis.", "SKI3 is a component of the Superkiller complex, which threads mRNA to the exosome for 5\u00b4to 3\u00b4mRNA degradation. SKI3 is required for the formation of infection threads, the survival of the bacterial within the nodule and the induction of the early nodulin ENOD40 in the Medicago truncatula-Sinorhizobium meliloti symbiosis.", "SKI3 is a component of the Superkiller complex, which threads mRNA to the exosome for 3\u00b4 to 5\u00b4mRNA degradation. SKI3 is required for nodule formation, the survival of the bacterial within the nodule and the induction of the early nodulin ENOD40 in the Medicago truncatula-Sinorhizobium meliloti symbiosis." ], "source":"https:\/\/www.plantcell.org\/cgi\/doi\/10.1105\/tpc.19.00647", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1105\/tpc.19.00647", "Year":2019.0, "Citations":31.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How is the translational control of the translational control of the mRNA encoding transcription factor TL1-1 Binding Factor 1 (TBF1) in Arabidopsis thaliana in response to Pseudomonas syringae?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "TBF1 translational control in Arabidopsis is mediated by a mechanism involving two upstream Open Reading Frames (uORF1 and uORF2) in its mRNA leader, which represses translation of the mORF under normal conditions due to stall of the ribosomes at such uORFs. Inoculation with the Pseudomonas syringae reversed this translational repression, allowing ribosomes to reinitiate translation at the mORF of TBF1. ", "TBF1 translational control in Arabidopsis is mediated by a mechanism involving an ADC box present in its mRNA leader, which represses translation of the mORF under normal conditions due to stall of the ribosomes. Inoculation with the Ralstonia solanacearum reversed this translational repression, allowing ribosomes to reinitiate translation of TBF1. ", "TBF1 translational control in Arabidopsis is mediated by a mechanism involving two binding sites for microRNAs in its mRNA leader, which represses translation of the mORF under normal conditions due to stall of the ribosomes. Inoculation with the Pseudomonas syringae reversed this translational repression, allowing ribosomes to reinitiate translation of TBF1. " ], "source":"https:\/\/doi.org\/10.1042\/BCJ20210066", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1042\/BCJ20210066", "Year":2021.0, "Citations":2.0, "answer":0, "source_journal":"Biochemical Journal", "is_expert":true }, { "question":"How is DYSFUNCTIONAL TAPETUM1 involved in pollen development in Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "2 DYSFUNCTIONAL TAPETUM 1 (DYT1) is a bHLH transcription factor that serves as a master regulator of the tapetum transcriptional network. DYT1 plays a critical role in tapetal development and also determines the viability of pollen grains. It is expressed at early stages of anther development, and forms homodimers, which are localized in the nucleus and promote the expression of multiple downstream genes involved in anther development, including DLX proteins. DLX proteins can interact with cytoplasmic DYT1 and block their nuclear translocation. At later stages of anther development, DYT1 specifically localizes to the cytoplasm, forming inactive DYT1-DLX dimers.", "DYSFUNCTIONAL TAPETUM 1 (DYT1) is a bHLH transcription factor that serves as a master regulator of the tapetum transcriptional network. DYT1 plays a critical role in tapetal development and also determines the viability of pollen grains. It is expressed during the early stages of anther development and forms homodimers, which are primarily localized in the cytoplasm. Basal levels of nuclear-localized DYT1 promote the expression of other bHLH transcription factors, which can interact with cytoplasmic DYT1 to facilitate their nuclear translocation. At later stages of anther development, DYT1 specifically localizes to the nucleus, forming various DYT1-bHLH heterodimers capable of binding to the promoters of multiple downstream genes, thereby activating complex transcriptional networks involved in anther development.", "DYSFUNCTIONAL TAPETUM 1 (DYT1) is a NAC family transcriptional regulator that serves as a master regulator of the tapetum transcriptional network. DYT1 plays a critical role in tapetal development and also determines the viability of pollen grains. It is expressed during the early stages of anther development and forms homodimers, which are primarily localized in the cytoplasm. Basal levels of nuclear-localized DYT1 promote the expression of other NAC family transcriptional regulators, which can interact with cytoplasmic DYT1 to facilitate their nuclear translocation. At later stages of anther development, DYT1 specifically localizes to the nucleus, forming various DYT1-NAC heterodimers capable of acting as transcriptional repressors, leading to major changes in the transcriptional landscape required to complete anther development." ], "source":"https:\/\/doi.org\/10.1105\/tpc.15.00986", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1105\/tpc.15.00986", "Year":2016.0, "Citations":82.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How are RALF peptides and LRX proteins involved in pollen tube growth in Arabidopsis?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Pollen tube growth is regulated during the process of fertilization by the interactions of extracellular signaling molecules (RALF peptides) with receptors of the LRX protein family at the pollen tube surface. RALF34 peptides, secreted by the pollen tube, are sensed by LRX proteins BUPS1\/2 and ANXUR1\/2, RALF4 and RALF19 are required to maintain pollen tube integrity. On the other hand, female-derived RALF4\/19, which competes with RALF34 peptides for the same receptors, induces pollen tube bursting, leading to pollen tube rupture and sperm release", "Pollen tube growth is regulated during the process of fertilization by the interactions of extracellular signaling molecules (RALF peptides) with receptors of the LRX protein family at the pollen tube surface. RALF4 and RALF19 peptides, secreted by the female tissue, are sensed by LRX proteins BUPS1\/2, and are required to maintain pollen tube integrity. On the other hand, pollen-derived RALF34, which is sense by and ANXUR1\/2 receptors, induces pollen tube bursting, leading to pollen tube rupture and sperm release.", "Pollen tube growth is regulated during the process of fertilization by the interactions of extracellular signaling molecules (RALF peptides) with receptors of the LRX protein family at the pollen tube surface. RALF4 and RALF19 peptides, secreted by the pollen tube, are sensed by LRX proteins BUPS1\/2 and ANXUR1\/2, and are required to maintain pollen tube integrity. On the other hand, female-derived RALF34, which competes with RALF4\/19 peptides for the same receptors, induces pollen tube bursting, leading to pollen tube rupture and sperm release." ], "source":"10.1126\/science.aao3642", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1126\/science.aao3642", "Year":2017.0, "Citations":335.0, "answer":2, "source_journal":"Science", "is_expert":true }, { "question":"How are RHO OF PLANT and BDR8\/9 proteins involved in pollen development in Arabidopsis?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "RHO OF PLANT (ROP), BDR8 and BDR9 proteins play a crucial role in establishing polarity during pollen germination. Active ROPs associate with the plasma membrane at germination sites prior to pollen germination. ROP then can interact with two proteins from the Boundary of ROP Domain (BDR) family: BDR8 and BDR9. In mature pollen grains, BDR8 and BDR9 are distributed in the cytosol and the vegetative nucleus, but they redistribute to the plasma membrane of germination sites upon ROP recruitment.", "RHO OF PLANT (ROP), BDR8 and BDR9 proteins play a crucial role during pollen tube rupture and sperm release. Active ROPs associate with the plasma membrane at apical side of the pollen tube prior rupture. ROP then can interact with two proteins from the Boundary of ROP Domain (BDR) family: BDR8 and BDR9. During pollen tube growth, BDR8 and BDR9 are distributed in the cytosol and the vegetative nucleus, but they redistribute to the plasma membrane at bursting sites upon ROP recruitment.", "RHO OF PLANT (ROP), BDR8, and BDR9 proteins play a crucial role in establishing polarity during pollen germination. BDR8 and BDR9, two proteins from the Boundary of ROP Domain family, associate with the plasma membrane at germination sites prior to pollen germination. Then, BDR8 and BDR9 can recruit ROP at the germination site. In mature pollen grains, ROPs are distributed homogeneously at the plasma membrane, but they redistribute to germination sites upon BDR8 and BDR9 recruitment." ], "source":"https:\/\/doi.org\/10.1093\/plphys\/kiad196", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1093\/plphys\/kiad196", "Year":2023.0, "Citations":7.0, "answer":0, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"How is the microRNA OsmiR159 involved in pollen development in rice", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Oryza sativa" ], "options":[ "The microRNA OsmiR159 is involved in the regulation of starch content in pollen; since starch is an indispensable energy reserve for pollen, failure of starch biosynthesis leads to male sterility. The microRNA OsmiR159 targets OsSPEAR2, which is expressed in mature pollen and localizes in the nucleus, where it interacts with multiple OsTCPs, including OsTCP14, a transcriptional repressor of the essential starch biosynthesis gene OsUGP2. The interaction between OsSPEAR2 and OsTCP14 alleviates its repressing activity on OsUGP2. \nOsmiR159 expression leads to reduced OsSPEAR2 levels and, hence, increased repression of OsUGP2 by OsTCP14, diminishing starch content in pollen and causing male sterility.", "The microRNA OsmiR159 is involved in the regulation of starch content in pollen; since starch is an indispensable energy reserve for pollen, failure of starch biosynthesis leads to male sterility. The microRNA OsmiR159 targets OsSPEAR2, which is expressed in mature pollen and localizes in the nucleus, where it interacts with multiple OsTCPs, including OsTCP14, forming a dimer that promotes the transcription of the essential starch biosynthesis gene OsUGP2. \nOsmiR159 expression leads to reduced OsSPEAR2 levels and, hence, decreased expression of OsUGP2, diminishing starch content in pollen and causing male sterility.", "The microRNA OsmiR159 is involved in the synthesis of sporophytic pollen coat proteins in the anther tapetum. Sporophytic pollen coat proteins derived from the anther tapetum are deposited into pollen wall cavities and fulfill key roles in pollen development. \nThe microRNA OsmiR159 targets MALE STERILITY 188, which is expressed in the anther tapetum and localizes in the nucleus, where it directly activates MALE STERILITY 1, which in turn controls the expression of genes coding for sporophytic pollen coat proteins. OsmiR159 expression leads to reduced levels of MALE STERILITY 188 and, hence, decreased expression of MALE STERILITY 1, diminishing sporophytic pollen coat proteins and causing male sterility." ], "source":"https:\/\/doi.org\/10.1093\/plcell\/koae324", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1093\/plcell\/koae324", "Year":2024.0, "Citations":0.0, "answer":0, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How are BNP and VOZ1\/2 involved in male gametophyte development in Arabidopsis?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The DC1 domain protein BINUCLEATE POLLEN (BNP) is required to complete male gametophyte development, as its absence causes an arrest at the bicellular pollen stage. At this stage, BNP interacts with the transcription factors VOZ1 and VOZ2 in the nucleus and promotes their degradation through the ubiquitin-proteasome pathway. The degradation of VOZ1 and VOZ2 is required to complete the transition from the bicellular stage to the mature pollen stage.", "The DC1 domain protein BINUCLEATE POLLEN (BNP) is required to complete male gametophyte development, as its absence causes an arrest at the unicellular pollen stage. At this stage, BNP interacts with the transcription factors VOZ1 and VOZ2 at the endoplasmic reticulum and facilitates their nuclear translocation, which is necessary to promote the transcriptional changes associated with the transition to the bicellular pollen stage.", "The DC1 domain protein BINUCLEATE POLLEN (BNP) is required to complete male gametophyte development, as its absence causes an arrest at the bicellular pollen stage. At this stage, BNP interacts with the transcription factors VOZ1 and VOZ2 in prevacuolar compartments or multivesicular bodies and facilitates their nuclear translocation, which is necessary to promote the transcriptional changes associated with the transition from the bicellular stage to the mature pollen stage." ], "source":"https:\/\/doi.org\/10.1093\/pcp\/pcac122", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1093\/pcp\/pcac122", "Year":2022.0, "Citations":3.0, "answer":2, "source_journal":"Plant and Cell Physiology", "is_expert":true }, { "question":"The plant immune system plays a central role in the social network of plants. It is generally assumed that rhizobia are first recognized by plants as intruders, and that hosts mount a defense response against these bacteria. Modulation of plant immunity plays an important role in symbiosis development. Q: Which rhizobial molecules have been related with the suppression of the defense responses in host legume?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "non-specific" ], "options":[ "Several rhizobial molecules have been related with the triggering of the plant defense responses, such as Nod factors (NFs), effectors secreted through Type III secretion system (T3SS), surface polysaccharides such as extracellular polysaccharides (EPS), plipopolysaccharides (LPS), capsular polysaccharides (KPS) cyclic \u03b2 -glucans, salicylic acid (SA), flagellin and elongation factor Tu (EFTu).", "Several rhizobial molecules have been related with the suppression of the plant defense responses, such as Nod factors (NFs), surface polysaccharides such as extracellular polysaccharides (EPS), plipopolysaccharides (LPS), capsular polysaccharides (KPS) cyclic \u03b2 -glucans, salicylic acid (SA), flagellin and elongation factor Tu (EFTu).", "Several rhizobial molecules have been related with the suppression of the plant defense responses, including Nod factors (NFs), effectors secreted through Type III secretion system (T3SS) and surface polysaccharides such as extracellular polysaccharides (EPS), lipopolysaccharides (LPS), capsular polysaccharides (KPS) and cyclic \u03b2 -glucans." ], "source":"https:\/\/doi.org\/10.1007\/s11104-020-04423-5.", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1007\/s11104-020-04423-5", "Year":2020.0, "Citations":25.0, "answer":2, "source_journal":"Plant and Soil", "is_expert":true }, { "question":"It had been demonstrated that flg22-triggered defense responses in the roots of Lotus japonicus negatively influence nodulation by inhibiting rhizobial infections and delaying the nodule organogenesis. Q: What is the impact of the mutation of conserved flagellin epitope of Mesorhizobium loti in Lotus japonicus defense response?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Lotus japonicus" ], "options":[ "The roots of Lotus japonicus, do not respond to purified flagellin from Mesorhizobium loti. The receptor LjFLS2 is unable to sense flagellin molecules from the symbiotic partner. Immune selective pressure exerted by the putative FLS2 orthologs of the leguminous hosts forced the emergence of escape mutations within the active flagellin epitope, hence providing the microsymbionts with an evolutionary advantage of reducing stimulation of the host\u2019s immune system.", "The roots of Lotus japonicus, respond to purified flagellin from Mesorhizobium loti. The receptor LjFLS2 senses flagellin molecules from the symbiotic partner. Immune selective pressure exerted by the putative FLS2 orthologs of the leguminous hosts forced the emergence of escape mutations within the active flagellin epitope, hence providing the microsymbionts with an evolutionary advantage of stimulation of the host\u2019s immune system.", "The roots of Lotus japonicus, do not respond to purified flagellin from Mesorhizobium loti. The receptor AtFLS2 is unable to sense flagellin molecules from the symbiotic partner. Immune selective pressure exerted by the orthologs flg22 of the symbiotic rhizobia forced the emergence of escape mutations within the active flagellin epitope, hence providing the legume with an evolutionary advantage of reducing stimulation of the symbiont \u2019s immune system" ], "source":"doi:10.1093\/jxb\/err291", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1093\/jxb\/err291", "Year":2011.0, "Citations":128.0, "answer":0, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"In Arachis hypogaea (peanut) has been proved that AhNF-YA1 and the LysMRLK Ahy.IM7I4N receptors are related to the plant response to the inoculation with Nod Factors. On the other hand, AhPER7 and AhWRKY11 are related to the plant response to the inoculation with chitosan. Q: How is the AhNF-YA1, AhPER7 and AhWRKY11 gene expression profile in A. hypogaea (peanut) when NFs (symbiotic molecule signal) and chitosan (pathogenic molecule signal) are co-inoculated?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Arachis hypogaea" ], "options":[ "The expression patterns of symbiosis and defense-related marker genes after co- inoculation with elicitor molecules shows that defense and symbiotic responses in peanut does not influence each other. Co-inoculation of NFs and chitosan in A. hypogaea has no effect on the transcription of the symbiotic gene marker AhNF-YA1, suggesting that the symbiotic pathway is not suppressed when defense signaling pathways are activated. Meanwhile AhPER7 and AhWRKY11 expression levels are lower in co-inoculated peanut roots compared to those inoculated with chitosan, suggesting that defense signaling pathways could being synergically activated during the early steps of the interaction with both molecules.", "The expression patterns of symbiosis and defense-related marker genes after co- inoculation with elicitor molecules shows that defense and symbiotic responses in peanut appear to influence each other. Co-inoculation of NFs and chitosan in A. hypogaea has a positive effect on the transcription of the symbiotic gene marker AhNF-YA1, suggesting that the symbiotic pathway is stimulated when defense signaling pathways are activated. Meanwhile AhPER7 and AhWRKY11 expression levels are lower in co-inoculated peanut roots compared to those inoculated with chitosan, suggesting that defense signaling pathways could being suppressed during the early steps of the interaction with both molecules.", "The expression patterns of symbiosis and defense-related marker genes after co- inoculation with elicitor molecules shows that defense and symbiotic responses in peanut appear to influence each other. Co-inoculation of NFs and chitosan in A. hypogaea has a negative effect on the transcription of the symbiotic gene marker AhNF-YA1, suggesting that the symbiotic pathway is suppressed when defense signaling pathways are activated. Meanwhile AhPER7 and AhWRKY11 expression levels are higher in co-inoculated peanut roots compared to those inoculated with chitosan, suggesting that defense signaling pathways could being synergically activated during\nthe early steps of the interaction with both molecules.\n" ], "source":"https:\/\/doi.org\/10.1007\/s13199-024-01022-1", "normalized_plant_species":"Legumes", "normalized_area":"ENVIRONMENT", "doi":"10.1007\/s13199-024-01022-1", "Year":2024.0, "Citations":0.0, "answer":2, "source_journal":"Symbiosis", "is_expert":true }, { "question":"It has been demonstrated that responses triggered in peanut plants by single microbial species populations are modified in presence of others. Q: What is the effect of the challenge with the phypathogen Sclerotium rolfsii on the expression of AhSymRK and the symbiotic behavior in Arachis hypogaea (peanut) plants inoculated with the microsymbiont Bradyrhizobium sp. SEMIA6144? What is the effect of the biocontrol agent Bacillus sp. CHEP5 inoculation on these symbiotic parameters?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Arachis hypogaea" ], "options":[ "AhSymRK gene expression is lower in plants inoculated only with the microsymbiont compared to those co-inoculated with Bacillus sp. CHEP5 and Bradyrhizobium sp. SEMIA6144. Meanwhile, this gene expression is increased in plants inoculated with Bradyrhizobium sp. SEMIA6144 and challenged with S. rolfsii. In this sense, in plants inoculated with Bradyrhizobium sp. SEMIA6144 and challenged with S. rolfsii, the number of nodules per plant, percentage of red nodules formed, percentage of nodulated plants as well as plant nitrogen content are higher. However, AhSymRK expression in plants challenges with S. rolfsii and co-inoculated the mycrosimbiont and biocontrol bacterium was reduced compared to plant-mycrosimbiont control condition as well as the nodulation parameters. \n\n", "AhSymRK gene expression is similar both in plants inoculated only with the microsymbiont and in those co-inoculated with Bacillus sp. CHEP5 and Bradyrhizobium sp. SEMIA6144. Moreover, this gene expression is stable in plants inoculated with Bradyrhizobium sp. SEMIA6144 and challenged with S. rolfsii. In this sense, in plants inoculated with Bradyrhizobium sp. SEMIA6144 and challenged with S. rolfsii, the number of nodules per plant, percentage of red nodules formed, percentage of nodulated plants as well as plant nitrogen content are the same as in plants only inoculated with Bradyrhizobium sp. SEMIA6144. However, AhSymRK expression in plants challenges with S. rolfsii and co-inoculated the mycrosimbiont and biocontrol bacterium was lower to plant-mycrosimbiont control condition as well as the nodulation parameters.", "AhSymRK gene expression is similar both in plants inoculated only with the microsymbiont and in those co-inoculated with Bacillus sp. CHEP5 and Bradyrhizobium sp. SEMIA6144. Meanwhile, this gene expression is reduced in plants inoculated with Bradyrhizobium sp. SEMIA6144 and challenged with S. rolfsii. In this sense, in plants inoculated with Bradyrhizobium sp. SEMIA6144 and challenged with S. rolfsii, the number of nodules per plant, percentage of red nodules formed, percentage of nodulated plants as well as plant nitrogen content are lower. However, AhSymRK expression in plants challenges with S. rolfsii and co-inoculated the mycrosimbiont and biocontrol bacterium was reverted to plant-mycrosimbiont control condition as well as the nodulation parameters. " ], "source":"https:\/\/doi.org\/10.1007\/s11104-018-3846-8, http:\/\/dx.doi.org\/10.1016\/j.micres.2017.01.002", "normalized_plant_species":"Legumes", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.micres.2017.01.002", "Year":2017.0, "Citations":42.0, "answer":2, "source_journal":"Microbiological Research", "is_expert":true }, { "question":"How is the expression profile in Arachis hypogaea (peanut) plants of the receptor genes Ahy.IM7I4N and Ahy.YTK8KP in presence of chitosan (molecule triggering defense) or Nod Factors (molecule triggering rhizobial symbiosis)?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Arachis hypogaea" ], "options":[ "Transcriptional activation of Ahy.IM7I4N is observed at 1 hours post inoculation (hpi) with Nod Factors and chitosan, separately, suggesting a versatile function of Ahy.IM7I4N. At later time points (from 1 to 72 hpi), Ahy.IM7I4N expression levels are significantly increased in response to Nod Factors. Instead, Ahy.YTK8KP expression is a specific transcriptional response to NF treatment (with significant expression levels increased at 1 and 8 hpi). ", "Transcriptional activation of Ahy.IM7I4N is observed at 1 hours post inoculation (hpi) with chitosan, suggesting a specific function of Ahy.IM7I4N. At later time points (from 1 to 72 hpi), Ahy.IM7I4N expression levels are significantly repressed in response to Nod Factors. Instead, Ahy.YTK8KP expression is a specific transcriptional response to chitosan treatment (with significant expression levels increased at 1 and 8 hpi). ", "Transcriptional repression of Ahy.IM7I4N is observed at 1 hours post inoculation (hpi) with Nod Factors and chitosan, separately, suggesting a negative signaling function of Ahy.IM7I4N. At later time points (from 1 to 72 hpi), Ahy.IM7I4N expression levels are significantly increased in response to Nod Factors. Instead, Ahy.YTK8KP expression is a specific transcriptional response to chitosan treatment (with significant expression levels increased at 1 and 8 hpi). " ], "source":"https:\/\/doi.org\/10.3390\/horticulturae8111000", "normalized_plant_species":"Legumes", "normalized_area":"ENVIRONMENT", "doi":"10.3390\/horticulturae8111000", "Year":2022.0, "Citations":1.0, "answer":0, "source_journal":"Horticulturae", "is_expert":true }, { "question":"Which transposable element family from tomato has been shown to be activated by drought stress, abscisic acid, and which epigenetic pathway is involved in its control?", "area":"GENOME AND GENOMICS", "plant_species":[ "Solanum lycopersicum" ], "options":[ "In tomato, heat stress and abscisic acid trigger the transcriptional activation of the transposable element family Rider. Under heat and high abscisic acid treatment, Rider transcript levels increase and correlate with the accumulation of extrachromosomal RNA. Rider is under the control of DNA methylation mediated by the RNA-directed DNA methylation pathway.", "In tomato, drought stress and gibberellic acid trigger the transcriptional activation of the transposable element family Rider. Under drought and high gibberellic acid treatment, Rider transcript levels increase and correlate with the accumulation of extrachromosomal DNA. Rider is under the control of histone methylation mediated by the RNA-directed DNA methylation pathway.", "In tomato, drought stress and abscisic acid trigger the transcriptional activation of the transposable element family Rider. Under drought and high abscisic acid treatment, Rider transcript levels increase and correlate with the accumulation of extrachromosomal DNA. Rider is under the control of DNA methylation mediated by the RNA-directed DNA methylation pathway." ], "source":"10.1371\/journal.pgen.1008370", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1371\/journal.pgen.1008370", "Year":2019.0, "Citations":55.0, "answer":2, "source_journal":"PLOS Genetics", "is_expert":true }, { "question":"Beyond tomato, in how many Solanaceae species has the Rider transposable element been detected, and which ones?", "area":"GENOME AND GENOMICS", "plant_species":[ "Solanum lycopersicum" ], "options":[ "Beyond tomato, the Rider transposable element has been detected in four other Solanaceae species: Solanum pimpinellifolium, Solanum arcanum, Solanum tuberosum, Capsicum annuum.", "Beyond tomato, the Rider transposable element has been detected in four other Solanaceae species: Solanum pimpinellifolium, Solanum arcanum, Solanum pennellii, Solanum habrochaites.", "Beyond tomato, the Rider transposable element has been detected in six other Solanaceae species: Solanum pimpinellifolium, Solanum arcanum, Solanum pennellii, Solanum habrochaites. Solanum tuberosum, Capsicum annuum." ], "source":"10.1371\/journal.pgen.1008370", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1371\/journal.pgen.1008370", "Year":2019.0, "Citations":55.0, "answer":1, "source_journal":"PLOS Genetics", "is_expert":true }, { "question":"How many structural variants have been detected in the tomato panSV-genome and which superfamilies of transposable elements are contributing the most to structural variation?", "area":"GENOME AND GENOMICS", "plant_species":[ "Solanum lycopersicum" ], "options":[ "The tomato panSV-genome revealed 238,490 structural variants with the Copia and Gypsy superfamilies of transposable elements contributing the most to structural variation.", "The tomato panSV-genome revealed 45,840 structural variants with the Copia and Gypsy superfamilies of transposable elements contributing the most to structural variation.", "The tomato panSV-genome revealed 238,490 structural variants with the CACTA and Helitron superfamilies of transposable elements contributing the most to structural variation." ], "source":"10.1016\/j.cell.2020.05.021", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1016\/j.cell.2020.05.021", "Year":2020.0, "Citations":586.0, "answer":0, "source_journal":"Cell", "is_expert":true }, { "question":"Which DNA methyltransferase is involved in the epigenetic reprogramming associated with symbiotic gene activation in the differentiation and fixation zones of Medicago truncatula nodules?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Medicago truncatula" ], "options":[ "The transcriptional activation of symbiotic genes in the differentiation and the fixation zones of Medicago truncatula nodules correlates with a decrease in CHH methylation. DME, the main DNA methyltransferase of the RNA-directed DNA methylation pathway, is expressed in the differentiation and the fixation zones of the nodules, and is responsible for the reduction of CHH methylation at symbiotic genes expressed in the differentiation and the fixation zones.", "The transcriptional activation of symbiotic genes in the differentiation and the fixation zones of Medicago truncatula nodules correlates with an increase in histone methylation. DRM2, the main histone methyltransferase of the histone methylation pathway, is expressed in the differentiation and the fixation zones of the nodules, and is responsible for the hyperaccumulation of histone methylation at symbiotic genes expressed in the differentiation and the fixation zones.", "The transcriptional activation of symbiotic genes in the differentiation and the fixation zones of Medicago truncatula nodules correlates with an increase in CHH methylation. DRM2, the main DNA methyltransferase of the RNA-directed DNA methylation pathway, is expressed in the differentiation and the fixation zones of the nodules, and is responsible for the hyperaccumulation of CHH methylation at symbiotic genes expressed in the differentiation and the fixation zone." ], "source":"10.1038\/s41477-022-01188-w", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/s41477-022-01188-w", "Year":2022.0, "Citations":14.0, "answer":2, "source_journal":"Nature Plants", "is_expert":true }, { "question":"Which histone post-translational marks undergo reprogramming between roots and developing nodules in Medicago truncatula?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Medicago truncatula" ], "options":[ "Several histone post-translational modifications are dynamically modulated during the development of nodules from roots in Medicago. Levels of tri-methylation of lysine 27 of histones H3 (H3K27me3) decrease drastically in nodules compared to roots. Conversely, levels of acetylation of lysine 9 of histones H3 (H3K9ac) are higher in nodules compared to roots.", "Several histone post-translational modifications are dynamically modulated during the development of nodules from roots in Medicago truncatula. Levels of mono-methylation of lysine 27 of histones H3 (H3K27me1) decrease drastically in nodules compared to roots. Conversely, levels of mono-methylation of lysine 9 of histones H3 (H3K9me1) are higher in nodules compared to roots.", "Several histone post-translational modifications are dynamically modulated during the development of nodules from roots in Medicago truncatula. Levels of tri-methylation of lysine 27 of histones H3 (H3K27me3) increase drastically in nodules compared to roots. Conversely, levels of acetylation of lysine 9 of histones H3 (H3K9ac) are lower in nodules compared to roots." ], "source":"10.1038\/s41477-018-0286-7", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/s41477-018-0286-7", "Year":2018.0, "Citations":231.0, "answer":0, "source_journal":"Nature Plants", "is_expert":true }, { "question":"What is the role of GOLVEN\/Root Meristem Growth Factor peptides in modulating root architecture in Arabidopsis and in legumes? What downstream transcription factor family is involved in this process?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "non-specific" ], "options":[ "In Arabidopsis, GOLVEN peptides are involved in root cap maintenance, lateral root branching, root hair elongation, the root gravitropic response and lateral organ spacing. In legumes, GOLVEN peptides can alter the number of cysts and their positioning on the root and decrease the zone of over which cysts form. The MYB family of transcription factors act as key markers of GOLVEN signaling in plants mediating changes in root architecture upon GOLVEN signal perception.", "In Arabidopsis, GOLVEN peptides are involved in root apical meristem maintenance, lateral root initiation and emergence, root hair elongation, the root gravitropic response and lateral organ spacing. In legumes, GOLVEN peptides can alter the number of nodules and their positioning on the root and decrease the zone of over which nodules form. The PLETHORA family of transcription factors act as key markers of GOLVEN signaling in plants mediating changes in root architecture upon GOLVEN signal perception.", "In Arabidopsis, GOLVEN peptides are involved in root cap maintenance, lateral root branching, root hair curling, the root gravitropic response and lateral organ shape. In legumes, GOLVEN peptides enhance the number of nodules and their positioning on the root and decrease the infection zone over which microcolonies form. The WRKY family of transcription factors act as key markers of GOLVEN signaling in plants mediating changes in root architecture upon GOLVEN signal perception." ], "source":"https:\/\/doi.org\/10.1111\/tpj.16626", "normalized_plant_species":"Non-specific", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1111\/tpj.16626", "Year":2024.0, "Citations":9.0, "answer":1, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"What is the mechanism of strigolactone perception by the a\/b hydrolase DWARF14?", "area":"HORMONES", "plant_species":[ "non-specific" ], "options":[ "The intact Strigolactone molecule binds to the preformed binding pocket of the dual-functional receptor\/hydrolase DWARF14. Next, the F-box protein D53 binds to the strigolactone-DWARF14 complex. Binding of the transcriptional repressor D3 changes the DWARF14 to its catalytically active state and DWARF14 hydrolyzes the strigolactone molecule. This triggers degradation of the transcriptional activator D3 by the proteasome thereby repressing the strigolactone signaling response. DWARF14 is degraded and D53 recycled. ", "The intact Strigolactone molecule binds to the preformed binding pocket of the dual-functional receptor\/hydrolase DWARF14. Next, the F-box protein D3 binds to the strigolactone-DWARF14 complex. Binding of the transcriptional repressor D53 changes the DWARF14 to its catalytically active state and DWARF14 hydrolyzes the strigolactone molecule. This triggers degradation of the transcriptional repressor D53 by the proteasome thereby initiating the strigolactone signaling response. DWARF14 is degraded and D3 recycled. ", "The hydrolyzed Strigolactone molecule binds to the preformed binding pocket of the dual-functional receptor\/hydrolase DWARF14. Next, the F-box protein D3 is degraded by the strigolactone-DWARF14 complex. Binding of the transcriptional repressor D53 changes the DWARF14 to its catalytically inactive state and DWARF14 cannot hydrolyze the strigolactone molecule. This triggers degradation of the transcriptional repressor D53 by the proteasome thereby initiating the strigolactone signaling response. DWARF14 and D3 are both recycled subsequently. " ], "source":"https:\/\/doi.org\/10.1016\/j.tplants.2019.12.009", "normalized_plant_species":"Non-specific", "normalized_area":"HORMONES", "doi":"10.1016\/j.tplants.2019.12.009", "Year":2020.0, "Citations":116.0, "answer":1, "source_journal":"Trends in Plant Science", "is_expert":true }, { "question":"What are NIN Like Proteins (NLPs) and what roles do they play in Nitrogen acquisition in both legumes such as Medicago and non-legumes such as Arabidopsis?", "area":"ENVIRONMENT - NUTRIENTS", "plant_species":[ "non-specific" ], "options":[ "NIN Like proteins are a group of transcription factors with an SET domain named after the founding member NIN (NODULE INITIATION). NLPs are involved in maintaining Nitrogen homeostasis in both legumes and non-legumes. In legumes, under high soil Nitrogen, NIN acts as a master regulator inhibiting both, nodule organogenesis and rhizobial infection processes ensuring the plant receives only sufficient Nitrogen. In the non-legume Arabidopsis, NLPs are responsive to nitrate and can activate transcription of several genes in N-uptake such as NRT1.1, signaling as well as Nitrogen-assimilation genes such as NITRATE REDUCTASEs to regulate their activity. These early events ultimately lead to physiological changes in root architecture in response to changes in nitrogen availability such as altering lateral root length or adventitious root number, and formation of nitrogen fixing nodules in legumes.", "NIN Like proteins are a group of transcription factors with an RWP-RK domain named after the founding member NIN (NODULE INCEPTION). NLPs are involved in maintaining Nitrogen homeostasis in both legumes and non-legumes. In legumes, under low soil Nitrogen, NIN acts as a master regulator coordinating both, nodule organogenesis and rhizobial infection processes ensuring the plant receives sufficient Nitrogen. In the non-legume Arabidopsis, NLPs are responsive to nitrate and can activate transcription of several genes in N-uptake such as NRT1.1, signaling as well as Nitrogen-assimilation genes such as NITRATE REDUCTASEs to regulate their activity. These early events ultimately lead to physiological changes in root architecture in response to changes in nitrogen availability such as altering primary root length or lateral root number, and formation of nitrogen fixing nodules in legumes.", "NIN Like proteins are a group of transcription factors with an LRR-RLK domain named after the founding member NIN (NODULE INCEPTION). NLPs are involved in maintaining Nitrogen homeostasis in both legumes and non-legumes. In legumes, under low soil phosphorus, NIN acts as a master regulator coordinating both, nodule organogenesis and rhizobial infection processes ensuring the plant receives sufficient Nitrogen. In the non-legume Lotus japonicus, NLPs are responsive to nitrate and can activate transcription of several genes in N-uptake such as NRT12.1, signaling as well as Phosphorus-assimilation genes such as NITRATE REDUCTASEs to regulate their activity. These early events ultimately lead to physiological changes in root architecture in response to changes in phosphorus availability such as altering primary root length or lateral root number, and formation of nitrogen fixing nodules in legumes." ], "source":"https:\/\/doi.org\/10.1038\/ncomms2621", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/ncomms2621", "Year":2013.0, "Citations":334.0, "answer":1, "source_journal":"Nature Communications", "is_expert":true }, { "question":"What three characteristics are used to classify an open reading frame as that of a small signaling peptide?", "area":"GENOME AND GENOMICS", "plant_species":[ "non-specific" ], "options":[ "The polypeptide length should be less than 250 amino acids with no transmembrane domains and the presence of an N-terminal signal peptide directing it to the secretory pathway.", "The polypeptide length should be more than 250 amino acids with no transmembrane domains and the presence of a C-terminal signal peptide directing it to the secretory pathway.", "The polypeptide length should be less than 250 amino acids with multiple transmembrane domains and the presence of an N-terminal signal peptide directing it to the vacuole. " ], "source":"https:\/\/doi.org\/10.1104\/pp.17.01096", "normalized_plant_species":"Non-specific", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1104\/pp.17.01096", "Year":2017.0, "Citations":102.0, "answer":0, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"What are microbial plant peptide mimics? Explains the in planta mechanism of action of CLE peptide secreting nematodes on soybean roots.", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "Many plant associated pathogens have evolved to encode peptides within their genome which are identical in structure to host plant peptides. These peptides confer evolutionary advantage to the pathogen by increasing their virulence. These microbially encoded peptides are called peptide mimics as they are recognized by plant meristems which activates the same downstream pathways as that of the plant signaling peptide. For example, the pathogenic bacteria Agrobacterium rhizogenes encodes CLE peptide mimics that repress cell division at nematode feeding sites on the vasculature. The female larvae attached to these feeding sites derive sufficient nutrients from the plants to complete one reproductive cycle. These cyst-nematodes therefore repress the plant growth processes to improve their chances of survival. ", "Many plant associated pathogens have evolved to encode peptides within their genome which are identical in sequence to host plant peptides. These peptides confer evolutionary advantage to the pathogen by increasing their virulence. These microbially encoded peptides are called peptide mimics as they are recognized by plant receptors which activates the same downstream pathways as that of the plant signaling peptide. For example, the cyst knot nematode Heterodera glycines encodes CLE peptide mimics that activate uncontrolled cell division or \u2018cysts\u2019 at nematode feeding sites called syncytia. The female larvae attached to these feeding sites derive sufficient nutrients from the plants to complete one reproductive cycle. These cyst-nematodes therefore exploit the plant machinery to derive nutrition and improve their chances of survival. ", "Many plant associated pathogens have evolved to encode peptides within their genome which are identical in sequence to host plant peptides. These peptides confer evolutionary advantage to the pathogen by increasing their virulence. These microbially encoded peptides are called peptide mimics as they are recognized by plant receptors which activates the same downstream pathways as that of the plant signaling peptide. For example, the root knot nematode Meloidogyne incognita encodes CLE peptide mimics that activate cell division at nematode feeding sites called syncytia. The male larvae attached to these feeding sites derive sufficient nitrogen from the plants to complete one reproductive cycle. These root knot nematodes therefore exploit the plant machinery to improve their chances of survival. " ], "source":"DOI: 10.1016\/j.tplants.2022.02.002", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.tplants.2022.02.002", "Year":2022.0, "Citations":34.0, "answer":1, "source_journal":"Trends in Plant Science", "is_expert":true }, { "question":"What is the role of the sulfotransferase ST2a in the regulation of plant defense under conditions of competition for light (low red:far-red ratios)?", "area":"HORMONES", "plant_species":[ "non-specific" ], "options":[ "The sulfotransferase ST2a catalyzes the transformation of OH-JA into the inactive metabolite HSO4-JA. Under conditions of low red:far-red ratios, which activate phytochrome B, the transcription of the ST2a gene is up-regulated by the high levels of Pfr, and the sulfotransferase acts to reduce the pool of precursors of active forms of jasmonates. Therefore, ST2a represents a direct molecular link between photoreceptors and jasmonate signaling in plants.", "The sulfotransferase ST2a catalyzes the transformation of inactive OH-JA into the active metabolite HSO4-JA. Under conditions of low red:far-red ratios, which inactivate phytochrome B, the transcription of the ST2a gene is down-regulated, leading to a reduction in the pool of active forms of jasmonates. Therefore, ST2a represents a direct molecular link between photoreceptors and jasmonate signaling in plants.", "The sulfotransferase ST2a catalyzes the transformation of OH-JA into the inactive metabolite HSO4-JA. Under conditions of low red:far-red ratios, which inactivate phytochrome B, the transcription of the ST2a gene is up-regulated and the sulfotransferase ST2a acts to reduce the pool of precursors of active forms of jasmonates. Therefore, ST2a represents a direct molecular link between photoreceptors and jasmonate signaling in plants." ], "source":"https:\/\/doi.org\/10.1038\/s41477-020-0604-8", "normalized_plant_species":"Non-specific", "normalized_area":"HORMONES", "doi":"10.1038\/s41477-020-0604-8", "Year":2020.0, "Citations":109.0, "answer":2, "source_journal":"Nature Plants", "is_expert":true }, { "question":"How are the transcription factors of the PIF family involved in the regulation of jasmonate responses?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "non-specific" ], "options":[ "The PIFs are growth-promoting transcription factors whose abundance and\/or activity increase under conditions of low red:far-red light ratios, which are typical of dense plant canopies. They bind to the promoter region of ST2a and activate its transcription. ST2a is required for the biosynthesis of gibberellins, which antagonize jasmonate responses. Therefore, under conditions of leaf shading or in the proximity of plant competitors, the increased biosynthesis of gibberellins facilitates growth (shade avoidance) and reduces the expression of jasmonate-dependent plant defenses.", "The PIFs are growth-promoting transcription factors whose abundance and\/or activity increase under conditions of low red:far-red light ratios, which are typical of dense plant canopies. They bind to the promoter region of ST2a and repress its transcription. ST2a is required for the biosynthesis of bioactive jasmonate pools. Therefore, the repression of ST2a leads to low production of bioactive jasmonates, which facilitates growth (shade avoidance) and reduces the expression of plant defenses under conditions of leaf shading or in the proximity of plant competitors.", "The PIFs are growth-promoting transcription factors whose abundance and\/or activity increase under conditions of low red:far-red light ratios, which are typical of dense plant canopies. They bind to the promoter region of ST2a and activate its transcription. ST2a leads to the formation of inactive jasmonate pools, thereby facilitating growth (shade avoidance) and reducing the expression of plant defenses under conditions of leaf shading or the proximity of plant competitors." ], "source":"https:\/\/doi.org\/10.1038\/s41477-020-0604-8", "normalized_plant_species":"Non-specific", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1038\/s41477-020-0604-8", "Year":2020.0, "Citations":109.0, "answer":2, "source_journal":"Nature Plants", "is_expert":true }, { "question":"Why is the accumulation of chemical defenses often accompanied by reduced growth in plants attacked herbivores or pathogens?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "Plant defenses are costly, in terms of the resources (carbon; nutrients) that are required for their biosynthesis. Therefore, when the jasmonates activate the biosynthesis of chemical defenses, the increased investment of carbon and nutrients in the formation of defense compounds inhibits plant growth simply as a consequence of the reduction in the amount of resources available to support rapid cell division and expansion.", "Herbivores and pathogens may reduce the amount of leaf tissue and therefore photosynthetic activity. Therefore, when the plant is under attack (and activates the biosynthesis of chemical defenses), growth is reduced simply as a consequence of the reduction in the amount photosynthetic area caused by the attackers. This results in a reduction in the pool of photo-assimilates available to support rapid cell division and expansion, which explains the negative correlation between growth and chemical defense.", "A high rate of plant growth may be maladaptive when the plant is under attack by herbivores or pathogens, because it would expose new tissue to the consumer organisms. Therefore, growth inhibition is often an adaptive response to tissue damage, which is accompanied by the increased accumulation of chemical defenses, with both responses being triggered and orchestrated by the jasmonates." ], "source":"https:\/\/doi.org\/10.1093\/jxb\/erz237", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1093\/jxb\/erz237", "Year":2019.0, "Citations":76.0, "answer":2, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"How does UV-B radiation increase Arabidopsis immunity against certain fungal pathogens?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "UV-B radiation, acting through the photoreceptor UVR8 promotes the biosynthesis of phenolic sunscreens, including flavonoids and sinapates in Arabidopsis. In addition to their photoprotective role, genetic evidence suggests that the flavonoids also play a protective against fungal infection, presumably because they boost the activation of jasmonate-dependent defense responses, which include the biosynthesis of antimicrobial compounds.", "UV-B radiation, acting through the photoreceptor UVR8 promotes the biosynthesis of phenolic sunscreens, including flavonoids and sinapates in Arabidopsis. In addition to their photoprotective role, genetic evidence suggests that the sinapates also play a protective against fungal infection, presumably because they serve as precursors for the synthesis of syringyl-type (\u2018defense\u2019) lignin, which is involved in cell wall fortification and could prevent penetration of fungal hyphae into plant cells.", "UV-B radiation, acting through the photoreceptor UVR8 promotes the biosynthesis of glucosinolates and camalexin in Arabidopsis. Genetic evidence indicates that mutants impaired in the production of the bioactive hydrolysis products of indolic glucosinolates or in camalexin biosynthesis do not respond to UV-B radiation with increased resistance to the fungal pathogen Botrytis cinerea, which is consistent with the postulated role of these compounds in UVR-8-induced defense." ], "source":"https:\/\/doi.org\/10.1093\/mp\/sss025", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1093\/mp\/sss025", "Year":2012.0, "Citations":185.0, "answer":1, "source_journal":"Molecular Plant", "is_expert":true }, { "question":"Which are the light signals and photoreceptors that trigger shade avoidance responses in dense plant canopies?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "non-specific" ], "options":[ "Depending on the density and structure of the canopy, shade avoidance responses are triggered by photoreceptors that sense the changes in the light environment that result from the selective absorption of sunlight by chlorophylls and other leaf pigments. One of these changes is the reduction in the ratio of red to far-red light (R:FR), which is perceived by the phytochromes (particularly phyC). Other changes that are perceived by the plant as signals of shading or proximity of other plants include the increased reflection of green light, which is perceived by the chlorophylls, and the attenuation of blue light, which is perceived by the carotene-containing photoreceptors.", "Depending on the density and structure of the canopy, shade avoidance responses are triggered by specific photoreceptors that sense the changes in the light and thermal environment that result from the absorption of sunlight by plant structures. One of these changes is the reduction in temperature, which is perceived by the phytochromes (particularly phyB). Other changes that are perceived by the plant as signals of shading or proximity of other plants include the attenuation of blue light, which is also perceived by the phytochromes, and the attenuation of UV radiation, which is perceived by the combined action of cryptochromes and the photoreceptor UVR8.", "Depending on the density and structure of the canopy, shade avoidance responses are triggered by specific photoreceptors that sense the changes in the light environment that result from the selective absorption of sunlight by chlorophylls and other leaf pigments. One of these changes is the reduction in the ratio of red to far-red light (R:FR), which is perceived by the phytochromes (particularly phyB). Other changes that are perceived by the plant as signals of shading or proximity of other plants include the attenuation of blue light, which is perceived by the cryptochromes and phototropins, and the attenuation of UV radiation, which is perceived by the photoreceptor UVR8." ], "source":"https:\/\/doi.org\/10.1016\/j.tplants.2020.12.006", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.tplants.2020.12.006", "Year":2021.0, "Citations":97.0, "answer":2, "source_journal":"Trends in Plant Science", "is_expert":true }, { "question":"Oxygenic photosynthesis can be improved and optimized to address the current climate change scenario. Strategies based on synthetic biology approaches have been tested in crops and plant model systems, such as Arabidopsis, Nicotiana tabacum, and the moss Physcomitrella patens. Which of the following statements best reflects the current consensus?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "non-specific" ], "options":[ "Research has not yet developed strategies to achieve maximum photosynthetic capacity in plants", "Maximum photosynthetic efficiency has been achieved in most plant model systems but not in crops", "Maximum photosynthetic efficiency has been achieved in most species under greenhouse conditions. However, plants growing in natural environments cannot reach maximum photosynthetic capacity" ], "source":"DOI: 10.1104\/pp.18.00360, 10.1016\/j.molp.2022.08.005, 10.1093\/jxb\/eraa075 ", "normalized_plant_species":"Non-specific", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1093\/jxb\/eraa075", "Year":2020.0, "Citations":38.0, "answer":0, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"NPQ can improve photosynthetic yield and biomass when plants face adverse conditions. What is the most the efficient way to regulate the qE component of NPQ to augment productivity?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "non-specific" ], "options":[ "Increasing relaxation rates of qE", "Increasing the induction and relaxation rates of qE", "Increasing the amplitude of qE" ], "source":"DOI: 10.1126\/science.aai8878", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1126\/science.aai8878", "Year":2016.0, "Citations":1048.0, "answer":1, "source_journal":"Science", "is_expert":true }, { "question":"What plant physiological aspects that can be improved by engineering RubisCo using synthetic biology?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "non-specific" ], "options":[ "Photosynthetic capacity", "Tolerance to drought ", "Resistance to biotic stress " ], "source":"DOI: 10.1104\/pp.18.00360", "normalized_plant_species":"Non-specific", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1104\/pp.18.00360", "Year":2018.0, "Citations":43.0, "answer":0, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"Does carboxylation rate of RubisCo influence photosynthetic yield?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "non-specific" ], "options":[ "In the absence of O2 ", "The photosynthetic yield is unaffected by plant growing conditions ", "In the presence of O2" ], "source":"DOI: 10.1093\/jxb\/erz029", "normalized_plant_species":"Non-specific", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1093\/jxb\/erz029", "Year":2019.0, "Citations":93.0, "answer":2, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"Several synthetic biology approaches aim to adapt carbon concentrating mechanisms (CCM) to C3 plants. What are key aspects for the success of this strategy?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "non-specific" ], "options":[ "The silencing of the endogenous RubisCo enzyme ", "The ectopic localization of inorganic carbon transporters to homogenize the levels of CO2 inside leaves", "The co-localization of the carboxysomes with RubisCo " ], "source":"DOI: 10.1016\/j.xplc.2020.100032, 10.1093\/jxb\/erz029", "normalized_plant_species":"Non-specific", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1093\/jxb\/erz029", "Year":2019.0, "Citations":93.0, "answer":2, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"What is the impact of synthetically inducing a burst in phytoene production, the first committed intermediate of the carotenoid pathway, on chloroplasts in leaves?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "non-specific" ], "options":[ "Synthetically inducing a phytoene burst triggers artificial chloroplast-to-gerontoplast differentiation in leaves.", "Synthetically inducing a phytoene burst promotes artificial chloroplast proliferation in leaves.", "Synthetically inducing a phytoene burst triggers artificial chloroplast-to-chromoplast differentiation in leaves." ], "source":"https:\/\/doi.org\/10.1073\/pnas.2004405117", "normalized_plant_species":"Non-specific", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1073\/pnas.2004405117", "Year":2020.0, "Citations":88.0, "answer":2, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"Which isoprenoid pathway can be exploited to supply intermediates for engineering carotenoid biosynthesis in the plant cytosol (i.e., outside chloroplasts)?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "non-specific" ], "options":[ "The pentose phosphate pathway (PPP) can be exploited to supply intermediates for engineering carotenoid biosynthesis in the plant cytosol. This pathway operates in the vacuole and provides PPP-derived precursors that can be converted into carotenoids, enabling targeted metabolic engineering efforts to boost carotenoid production in plants.", "The mevalonic acid (MVA) pathway can be exploited to supply intermediates for engineering carotenoid biosynthesis in the plant cytosol. This pathway operates in the cytosol and provides MVA-derived precursors that can be converted into carotenoids, enabling targeted metabolic engineering efforts to boost carotenoid production in plants.", "The methylerythritol 4-phosphate (MEP) pathway can be exploited to supply intermediates for engineering carotenoid biosynthesis in the plant cytosol. This pathway operates in the cytosol and provides MEP-derived precursors that can be converted into carotenoids, enabling targeted metabolic engineering efforts to boost carotenoid production in plants." ], "source":"https:\/\/doi.org\/10.1111\/pbi.13526", "normalized_plant_species":"Non-specific", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1111\/pbi.13526", "Year":2021.0, "Citations":31.0, "answer":1, "source_journal":"Plant Biotechnology Journal", "is_expert":true }, { "question":"How can the methylerythritol 4-phosphate (MEP) pathway and the mevalonic acid (MVA) pathway be simultaneously exploited to engineer parallel carotenoid biosynthesis in the cytosol and plastids of plants?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "non-specific" ], "options":[ "Both the cytosolic methylerythritol 4-phosphate (MEP) pathway and the plastidial mevalonic acid (MVA) pathway produce isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP), key isoprenoid precursors that can be harnessed to engineer parallel carotenoid biosynthesis in the cytosol and plastids of plants. Leveraging these identical pathways enables enhanced carotenoid production in both cellular compartments.", "Both the cytosolic mevalonic acid (MVA) pathway and the plastidial methylerythritol 4-phosphate (MEP) pathway produce isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP), key isoprenoid precursors that can be harnessed to engineer parallel carotenoid biosynthesis in the cytosol and plastids of plants. Leveraging these distinct pathways enables enhanced carotenoid production in both cellular compartments.", "Both the cytosolic methylerythritol 4-phosphate (MEP) pathway and the plastidial mevalonic acid (MVA) pathway produce isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP), key flavonoid precursors that can be harnessed to engineer parallel carotenoid biosynthesis in the cytosol and plastids of plants. Leveraging these distinct pathways enables enhanced carotenoid production in both cellular compartments." ], "source":"https:\/\/doi.org\/10.1111\/tpj.16964", "normalized_plant_species":"Non-specific", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1111\/tpj.16964", "Year":2024.0, "Citations":0.0, "answer":1, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"How could relocating genes between the nuclear genome and the plastome improve plant disease resistance?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "non-specific" ], "options":[ "Chloroplasts rely on thousands of proteins encoded by nucleus-encoded chloroplast genes (NECGs). To promote infection, pathogens deploy protein and small RNA (sRNA) effectors that enter plant cells and manipulate their physiology. Various plant pathogens\u2014including viruses, bacteria, fungi, and oomycetes\u2014have convergently evolved effectors to specifically target NECGs or their mRNA and protein products. Relocating NECGs targeted by pathogen effectors to the plastome could render these infection strategies more effective.", "Chloroplasts rely on thousands of proteins encoded by plastome-encoded chloroplast genes (PECGs). To promote infection, pathogens deploy protein and small RNA (sRNA) effectors that enter plant cells and manipulate their physiology. Various plant pathogens\u2014including viruses, bacteria, fungi, and oomycetes\u2014have convergently evolved effectors to specifically target PECGs or their mRNA and protein products. Relocating PECGs targeted by pathogen effectors to the nuclear genome could render these infection strategies ineffective.", "Chloroplasts rely on thousands of proteins encoded by nucleus-encoded chloroplast genes (NECGs). To promote infection, pathogens deploy protein and small RNA (sRNA) effectors that enter plant cells and manipulate their physiology. Various plant pathogens\u2014including viruses, bacteria, fungi, and oomycetes\u2014have convergently evolved effectors to specifically target NECGs or their mRNA and protein products. Relocating NECGs targeted by pathogen effectors to the plastome could render these infection strategies ineffective." ], "source":"https:\/\/doi.org\/10.1038\/s41467-021-26975-5", "normalized_plant_species":"Non-specific", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1038\/s41467-021-26975-5", "Year":2021.0, "Citations":9.0, "answer":2, "source_journal":"Nature Communications", "is_expert":true }, { "question":"What is the potential of plant synthetic biology to support long-term human endeavors in space?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "non-specific" ], "options":[ "Long-duration human space endeavors will require significant self-sufficiency. Plant synthetic biology could play a pivotal role in enabling the sustainable production of food, materials, chemicals, and medicines to support human travel and habitation in space.", "Long-duration human space endeavors will require significant self-sufficiency. Plant synthetic biology could play a pivotal role in enabling the unsustainable production of food, materials, chemicals, and medicines to support human travel and habitation in space.", "Long-duration human space endeavors will require little self-sufficiency. Plant synthetic biology would play a minimal role in supporting human travel and habitation in space." ], "source":"https:\/\/doi.org\/10.3390\/genes9070348", "normalized_plant_species":"Non-specific", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.3390\/genes9070348", "Year":2018.0, "Citations":36.0, "answer":0, "source_journal":"Genes", "is_expert":true }, { "question":"What is symbiosis and how symbiosis between leguminous plants and rhizobia leads to the formation of N2-fixing root nodules?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "non-specific" ], "options":[ "Symbiosis is a mutual beneficial relationship between the nitrogen-fixing soil bacteria know as rhizobia and leguminous plants. Nitrogen is one of the major macro-nutrients required for the plant growth. Although atmosphere is predominately made up of nitrogen (79%), but this nitrogen is not available to plants, because most plants cannot directly utilize gaseous atmospheric nitrogen. Interestingly, a group of flowering plants also known as nitrogen fixing clade (NFC) have evolved an ability to form symbiotic relationship with nitrogen-fixing bacteria, which converts atmospheric nitrogen to biologically available form like ammonia (NH3). The rhizobia-legume interaction is a complex exchange of signals initiated by release of flavonoids by legumes, which are perceived by compatible rhizobia species. These bacteria secrete lipo-oligosaccharides (LCOs also known as Nod factors) and oligosaccharides and the perception of these Nod factors under low nitrogen conditions in the susceptible region of root initiates one programs which is bacterial infection at the epidermis and cell division at the cortex to develop nodules hosting rhizobial symbionts.", "Symbiosis is a mutual beneficial relationship between all soil bacteria know and leguminous plants. Nitrogen is one of the major macro-nutrients required for the plant growth. Although atmosphere is predominately made up of nitrogen (79%), but this nitrogen is available to plants, and most plants can directly utilize gaseous atmospheric nitrogen. Interestingly, a group of flowering plants also known as nitrogen fixing clade (NFC) have evolved an ability to form symbiotic relationship with all bacteria, which converts atmospheric nitrogen to biologically available form like ammonia (NH3). The rhizobia-legume interaction is a complex exchange of signals initiated by release of flavonoids by legumes, which are perceived by compatible rhizobia species. These bacteria secrete lipo-oligosaccharides (LCOs also known as Nod factors) and the perception of these Nod factors under low nitrogen conditions in the susceptible region of root initiates two interconnected programs concurrently: bacterial infection at the epidermis and cell division at the cortex to develop nodules hosting rhizobial symbionts. Once released from the infection threads within the root nodules of legumes, these bacteria differentiate into bacteroids and helps to convert gaseous nitrogen to ammonia in the low oxygen environment inside the mature nodules. ", "Symbiosis is a mutual beneficial relationship between the nitrogen-fixing soil bacteria know as rhizobia and leguminous plants. Nitrogen is one of the major macro-nutrients required for the plant growth. Although atmosphere is predominately made up of nitrogen (79%), but this nitrogen is not available to plants, because most plants cannot directly utilize gaseous atmospheric nitrogen. Interestingly, a group of flowering plants also known as nitrogen fixing clade (NFC) have evolved an ability to form symbiotic relationship with nitrogen-fixing bacteria, which converts atmospheric nitrogen to biologically available form like ammonia (NH3). The rhizobia-legume interaction is a complex exchange of signals initiated by release of flavonoids by legumes, which are perceived by compatible rhizobia species. These bacteria secrete lipo-oligosaccharides (LCOs also known as Nod factors) and the perception of these Nod factors under low nitrogen conditions in the susceptible region of root initiates two interconnected programs concurrently: bacterial infection at the epidermis and cell division at the cortex to develop nodules hosting rhizobial symbionts. Once released from the infection threads within the root nodules of legumes, these bacteria differentiate into bacteroids and help to convert gaseous nitrogen to ammonia in the low oxygen environment inside the mature nodules. " ], "source":"https:\/\/doi.org\/10.1016\/j.pbi.2023.102478", "normalized_plant_species":"Non-specific", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1016\/j.pbi.2023.102478", "Year":2023.0, "Citations":12.0, "answer":2, "source_journal":"Current Opinion in Plant Biology", "is_expert":true }, { "question":"What is cell layer specific role of gibberellins in root development and nodulation?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "non-specific" ], "options":[ "Gibberellins (GA), have no role in cell layers during nodule organogenesis and infection. GA produced in the endodermis reduces nodule organogenesis and lateral root formation and also suppresses rhizobial infection via direct action or with the help of a potential mobile signal which can move from endodermis to epidermis. On the other hand, GA in epidermis have very big influence on nodule and root development but suppresses infection. ", "Gibberellins (GA) and Auxin, both plays an important dual and opposing role in cell layers during nodule organogenesis and infection. GA produced in the endodermis enhance nodule organogenesis and lateral root formation and also suppresses rhizobial infection via direct action or with the help of a potential mobile signal which can move from endodermis to epidermis. On the other hand, GA in epidermis have little influence on nodule and root development but suppresses infection.", "Gibberellins (GA), plays an important dual and opposing role in cell layers during nodule organogenesis and infection. GA produced in the endodermis enhance nodule organogenesis and lateral root formation and also suppresses rhizobial infection via direct action or with the help of a potential mobile signal which can move from endodermis to epidermis. On the other hand, GA in epidermis have little influence on nodule and root development but suppresses infection. " ], "source":"https:\/\/doi.org\/10.1111\/nph.19623", "normalized_plant_species":"Non-specific", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1111\/nph.19623", "Year":2024.0, "Citations":1.0, "answer":2, "source_journal":"New Phytologist", "is_expert":true }, { "question":"What are small signaling peptides and which peptide is involved in altering root development and noduletaxis in Medicago truncatula?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Medicago truncatula" ], "options":[ "Small signaling peptides (SSPs) are less than 200-250 amino acids in length and are generated from prepropeptides following multiple maturation steps. SSPs are classified into two main categories viz., cysteine-rich peptides (CRPs) and post-translationally modified peptides (PTMPs). The PTMPs are smaller in length (5-30amino acids) and are characterized by post-translation modifications like tyrosine sulphation, hydroxylation and glycosylation. These modifications in PTMPs have been reported to play an important role in their activity via increasing their stability and binding. CRPs are longer in length and recognized by at least four cysteine residues responsible for forming disulfide bridges important for stable secondary structures. GOLVEN10 peptide alters the positioning of first lateral root and also nodule on the primary root called as \u201cnoduletaxis\u201d. This response of GOLVEN10 peptide has resulted in decreased length of the total lateral organ formation zone in Medicago truncatula roots. ", "Small signaling peptides (SSPs) are less than 200-250 amino acids in length and are generated from prepropeptides following multiple maturation steps. SSPs are classified into two main categories viz., cysteine-rich peptides (CRPs) and post-translationally modified peptides (PTMPs). The PTMPs are smaller in length (5-30amino acids) and are characterized by post-translation modifications like tyrosine sulphation, hydroxylation and glycosylation. These modifications in PTMPs have been reported to play an important role in their activity via increasing their stability and binding. CRPs are longer in length and recognized by at least four cysteine residues responsible for forming disulfide bridges important for stable secondary structures. GOLVEN4 and 6 peptide alters the positioning of first lateral root and also nodule on the primary root called as \u201cnoduletaxis\u201d. This response of GOLVEN4 and 6 peptide has resulted in decreased length of the total lateral organ formation zone in Medicago truncatula roots.", "Small signaling peptides (SSPs) are more than 200-250 amino acids in length and are generated from prepropeptides following one maturation steps. SSPs are classified into two main categories viz., cysteine-rich peptides (CRPs) and post-translationally modified peptides (PTMPs). The PTMPs are smaller in length (5-30amino acids) and are characterized by post-translation modifications like tyrosine sulphation, hydroxylation and glycosylation. These modifications in PTMPs have been reported to play an important role in their activity via increasing their stability and binding. CRPs are smaller in length and recognized by at least four cysteine residues responsible for forming disulfide bridges important for stable secondary structures. GOLVEN10 peptide does not alters the positioning of first lateral root and also nodule on the primary root called as \u201cnoduletaxis\u201d. This response of GOLVEN10 peptide has resulted in increased length of the total lateral organ formation zone in Medicago truncatula roots. " ], "source":"https:\/\/doi.org\/10.1111\/tpj.16626", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1111\/tpj.16626", "Year":2024.0, "Citations":9.0, "answer":0, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"Which previously unidentified CLE peptide is responsible for repressing phloem differentiation in Arabidopsis thaliana?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The protophloem differentiation is controlled by complex genetic circuit involving, on one side, a number of regulators like DOF transcription factors, hormonal gradients and SMXL transcriptional repressors. Additionally, BREVIS RADIX (BRX) and OCTOPUS (OPS), two membrane localized proteins which act as positive regulators of protophloem development. While the other side have negative regulators like CLAVATA3\/EMBRYO SURROUNDING REGION RELATED (CLE) peptides and their receptors BARELY ANY MERISTEM (BAM) receptor-like kinases. The brx and ops mutants has displayed a discontinuous protophloem (gap cells that fail to differentiate) which results in reduced phloem sap delivery to the root meristem and inhibited root growth. This discontinuous protophloem phenotypes can be rescued by mutation in BAM3, which encodes for LRR-RLK (leucine-rich repeat receptor kinase), a receptor of CLAVATA3\/EMBRYO SURROUNDING REGION 45 (CLE45) peptide but is partially rescued when all three known phloem CLE genes (CLE25\/26\/45) are mutated together. Therefore \nanother crucial player in protophloem formation namely CLE33 closely related to CLE45 was identified and double mutant of cle33cle45 was reported to fully suppresses brx and ops protophloem phenotype.\n", "The protophloem differentiation is controlled by complex genetic circuit involving, on one side, a number of regulators like DOF transcription factors, hormonal gradients and SMXL transcriptional repressors. Additionally, BREVIS RADIX (BRX) and OCTOPUS (OPS), two membrane localized proteins which act as positive regulators of protophloem development. While the other side have negative regulators like CLAVATA3\/EMBRYO SURROUNDING REGION RELATED (CLE) peptides and their receptors BARELY ANY MERISTEM (BAM) receptor-like kinases. The brx and ops mutants has displayed a discontinuous protophloem (gap cells that fail to differentiate) which results in reduced phloem sap delivery to the root meristem and inhibited root growth. This discontinuous protophloem phenotypes can be rescued by mutation in BAM3, which encodes for LRR-RLK (leucine-rich repeat receptor kinase), a receptor of CLAVATA3\/EMBRYO SURROUNDING REGION 45 (CLE45) peptide. Therefore, crucial player in protophloem formation namely CLE25\/26\/45 was identified and its double mutant was reported to fully suppresses brx and ops protophloem phenotype.", "The protophloem differentiation is controlled by simple genetic circuit involving, on one side, a number of regulators like WRKY transcription factors, hormonal gradients and SMXL transcriptional repressors. Additionally, BREVIS RADIX (BRX) and OCTOPUS (OPS), two membrane localized proteins which act as positive regulators of protophloem development. While the other side have positive regulators like CLAVATA3\/EMBRYO SURROUNDING REGION RELATED (CLE) peptides and their receptors BARELY ANY MERISTEM (BAM) receptor-like kinases. The brx and ops mutants has displayed a discontinuous protophloem (gap cells that fail to differentiate) which results in increased phloem sap delivery to the root meristem and inhibited root growth. This discontinuous protophloem phenotypes can be rescued by mutation in BAM3, which encodes for LRR-RLK (leucine-rich repeat receptor kinase), a receptor of CLAVATA3\/EMBRYO SURROUNDING REGION 45 (CLE45) peptide but is partially rescued when all three known phloem CEP genes (CLE25\/26\/45) are mutated together. Therefore \nanother crucial player in protophloem formation namely CLE33 closely related to CLE45 was identified and double mutant of cle33cle45 was reported to fully suppresses brx and ops protophloem phenotype.\n" ], "source":"https:\/\/doi.org\/10.1038\/s42003-023-04972-2", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1038\/s42003-023-04972-2", "Year":2023.0, "Citations":20.0, "answer":0, "source_journal":"Communications Biology", "is_expert":true }, { "question":"How small signaling peptide CEP1 and NIN-like protein NLP1, regulate NRT2.1 expression to control root nodule formation under different nitrogen conditions?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "non-specific" ], "options":[ "Legumes takes nitrogen (N) from soil with endosymbiont association with all bacteria via forming N2 fixing nodules. The establishment and maintenance of these nodules is easy for the host legumes, therefore, when N is plentiful, plants increases symbiosis and increases it when N is sparse. It has been proposed that under low nitrogen conditions, MtCEP1 expression increases which systematically upregulates the expression of MtNRT2.1 in a MtCRA2-dependent manner. Simultaneously, under low nitrogen conditions, restricted nuclear localization of MtNLP1 activates low level of MtNRT2.1 expression, consequently boosting nitrate uptake to improve leaf size and plant growth. However, under high nitrogen conditions, increased migration of MtNLP1 to the chloroplast results in activation of CLE35 expression which negatively regulates nodulation via SUNN in shoot. Moreover, MtNLP1 also activates expression of MtNRT2.1 to enhance nitrate uptake to further inhibit nodulation. ", "Legumes takes nitrogen (N) from soil with endosymbiont association with rhizobia via forming N2 fixing nodules. The establishment and maintenance of these nodules is expensive for the host legumes, therefore, when N is plentiful, plants suppress symbiosis and increases it when N is sparse. It has been proposed that under low nitrogen conditions, MtCEP1 expression increases which systematically upregulates the expression of MtNRT2.1 in a MtCRA2-dependent manner. Simultaneously, under low nitrogen conditions, restricted nuclear localization of MtNLP1 activates low level of MtNRT2.1 expression, consequently boosting nitrate uptake to improve nodulation and plant growth. However, under high nitrogen conditions, increased migration of MtNLP1 to the nucleus results in activation of CLE35 expression which negatively regulates nodulation via SUNN in shoot. Moreover, MtNLP1 also activates expression of MtNRT2.1 to enhance nitrate uptake to further inhibit nodulation. ", "Legumes takes nitrogen (N) from soil with endosymbiont association with rhizobia via forming N2 fixing nodules. The establishment and maintenance of these nodules is expensive for the host legumes, therefore, when N is plentiful, plants suppress symbiosis and increases it when N is sparse. It has been proposed that under low nitrogen conditions, MtCEP1.1 expression increases which systematically upregulates the expression of MtNRT2.1 in a MtCRA2-dependent manner. Simultaneously, under low nitrogen conditions, restricted nuclear localization of MtNLP2 activates low level of MtNRT3.1 expression, consequently boosting nitrate uptake to improve nodulation and plant growth. However, under high nitrogen conditions, increased migration of MtNLP1 to the nucleus results in activation of CLE33 expression which negatively regulates nodulation via SUNN in shoot. Moreover, MtNLP1 also activates expression of MtNRT2.1 to enhance nitrate uptake to further inhibit nodulation. " ], "source":"10.1093\/plcell\/koac340", "normalized_plant_species":"Non-specific", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1093\/plcell\/koac340", "Year":2022.0, "Citations":33.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"What are the main differences in the secondary structural pattern from Arabidopsis thaliana miR171a compared to miR171c precursors?", "area":"GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "miR171c precursor has a conserved dsRNA region below the miRNA\/miRNA* duplex, in contrast, the miR171a, has a conserved region above the miRNA\/miRNA* duplex, which determines a dsRNA segment.", "miR171a precursor has a conserved dsRNA region below the miRNA\/miRNA* duplex, in contrast, the miR171c, has a conserved region above the miRNA\/miRNA* duplex, which determines a dsRNA segment.", "Both miR171a and miR171c precursors have a conserved dsRNA region below the miRNA\/miRNA* duplex" ], "source":"10.1105\/tpc.17.00272", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1105\/tpc.17.00272", "Year":2017.0, "Citations":59.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"What happens to the MIR157c precursor in Arabidopsis thaliana when you replace the terminal branched loop with a small loop of 4 nt?", "area":"GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "MIR157c with the small loop will be processed much more efficiently and will cause a significant decrease in leaf number upon flowering compared to the wild-type branched loop version", "MIR157c with the small loop will be processed much less efficiently and will cause a significant decrease in leaf number upon flowering compared to the wild-type branched loop version", "MIR157c with the small loop will be processed much more efficiently and will cause a significant increase in leaf number upon flowering compared to the wild-type branched loop version" ], "source":"10.1093\/nar\/gky853", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1093\/nar\/gky853", "Year":2018.0, "Citations":15.0, "answer":2, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"What is the impact of the C-C mismatches within miRNA\/miRNA* duplexes on miRNA biogenesis in Arabidopsis thaliana?", "area":"GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "C-C mismatches consistently impair miRNA processing efficiency, as they disrupt DCL1-mediated cleavage, leading to reduced mature miRNA levels.", "C-C mismatches enhance miRNA biogenesis by increasing duplex flexibility, which facilitates DCL1 cleavage.", "C-C mismatches have no significant effect on miRNA biogenesis, as DCL1 processes precursors independently of specific mismatch identities." ], "source":"10.1038\/s41467-020-19129-6", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41467-020-19129-6", "Year":2020.0, "Citations":27.0, "answer":0, "source_journal":"Nature Communications", "is_expert":true }, { "question":"What structural diversity is exhibited by the COOLAIR lncRNA isoforms in Arabidopsis thaliana under warm conditions?", "area":"GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis thaliana, the major distally polyadenylated COOLAIR isoform exhibits three primary structural conformations under warm conditions. These conformations involve structural changes predominantly in the hyper-variable H4-H6 region, which is complementary to the FLC transcription start site.", "In Arabidopsis thaliana, the major distally polyadenylated COOLAIR isoform exhibits three primary structural conformations under warm conditions. These conformations involve changes primarily in the conserved 5\u2032 region of the transcript.", "In Arabidopsis thaliana, the major distally polyadenylated COOLAIR isoform exhibits two stable conformations under warm conditions. These conformations involve structural changes predominantly in the H5 region, which is complementary to the FLC transcription start site." ], "source":"10.1038\/s41586-022-05135-9", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41586-022-05135-9", "Year":2022.0, "Citations":79.0, "answer":0, "source_journal":"Nature", "is_expert":true }, { "question":"Which are the most structurally stable regions of MIR319a sequential precursors in Arabidopsis thaliana?", "area":"GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "DCL1 processing of sequential MIRNAs releases the miRNA\/miRNA* in the last two cuts. The other small RNA duplexes produced are miRNA.1\/miRNA.1* and miRNA.2\/miRNA.2* according to their relative distance to the miRNA\/miRNA*. The miRNA.1\/miRNA.1* presents a better pairing overall and the most stable regions of miRNA\/miRNA* and miRNA.2\/miRNA.2* are located at the ends of the duplexes. Consequently, the structural features of these long sequential precursors rely on stable small RNA duplexes, with no mismatches that generate suitable DCL1 cleavage sites. ", "DCL1 processing of sequential MIRNAs releases the miRNA\/miRNA* in the last two cuts. The other small RNA duplexes produced are miRNA.1\/miRNA.1* and miRNA.2\/miRNA.2* according to their relative distance to the miRNA\/miRNA*. The miRNA\/miRNA* presents a better pairing overall and the most stable regions of miRNA.1\/miRNA.1* and miRNA.2\/miRNA.2* are located at the ends of the duplexes. Consequently, the structural features of these long sequential precursors rely on unstable small RNA duplexes, with internal mismatches and paired ends that generate suitable DCL1 cleavage sites. ", "DCL1 processing of sequential MIRNAs releases the miRNA\/miRNA* in the last two cuts. The other small RNA duplexes produced are miRNA.1\/miRNA.1* and miRNA.2\/miRNA.2* according to their relative distance to the miRNA\/miRNA*. The miRNA\/miRNA* presents a worse pairing overall and the most stable regions of miRNA.1\/miRNA.1* and miRNA.2\/miRNA.2* are located at the beginning of the duplexes. Consequently, the structural features of these long sequential precursors rely on stable small RNA duplexes, with no mismatches that generate suitable DCL1 cleavage sites. " ], "source":"10.1093\/nar\/gkae458", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1093\/nar\/gkae458", "Year":2024.0, "Citations":4.0, "answer":1, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"What is the primary function of gene looping, short range chromatin loops encompasing single genes, in plants?", "area":"GENE REGULATION - PTGS", "plant_species":[ "non-specific" ], "options":[ "Gene-looping promotes the deletion of introns from the gene.", "Gene-looping prevents transcription by promoting a lineal stage of the chromatin", "Gene-looping enhances gene transcription by allowing more efficient recycling of RNA polymerase II." ], "source":"10.1111\/nph.16632", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1111\/nph.16632", "Year":2020.0, "Citations":20.0, "answer":2, "source_journal":"New Phytologist", "is_expert":true }, { "question":"How can intragenic chromatin loops regulate gene expression in plants?", "area":"GENE REGULATION - PTGS", "plant_species":[ "non-specific" ], "options":[ "Intragenic chromatin loops exclusively enhance transcription by stabilizing the promoter.", "Intragenic chromatin loops silence genes by inducing the compactation of the nucleosomes.", "Intragenic chromatin loops can repress transcription by blocking RNA polymerase II elongation, change splicing or transcription termination." ], "source":"10.1111\/nph.16632", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1111\/nph.16632", "Year":2020.0, "Citations":20.0, "answer":2, "source_journal":"New Phytologist", "is_expert":true }, { "question":"What is the primary outcome, regarding chromatin organization, of the insertion of an inverted repeat (IR) near a gene in Plants?", "area":"GENE REGULATION - PTGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The IR has negligible effects on the surrounding genomic neighborhood.", "The IR exclusively enhances transcription by acting as a distal enhancer.", "IRs locates near genes often produce small RNAs that trigger DNA methylation changing the chromatin organization and the expresion of the neighbor genes." ], "source":"10.1016\/j.celrep.2023.112029", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.celrep.2023.112029", "Year":2023.0, "Citations":12.0, "answer":2, "source_journal":"Cell Reports", "is_expert":true }, { "question":"How do IRs contribute to changes in gene expression through their impact on chromatin topology?", "area":"GENE REGULATION - PTGS", "plant_species":[ "non-specific" ], "options":[ "IRs uniformly repress gene expression by silencing all nearby genes.", "IRs act as anchor points for short-range chromatin loops, which can either enhance or repress gene expression depending on the loop structure and gene region included.", "The insertion of a TE-derived IR near genes has no evolutionary or adaptive implications for the plant." ], "source":"10.1016\/j.celrep.2023.112029", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.celrep.2023.112029", "Year":2023.0, "Citations":12.0, "answer":1, "source_journal":"Cell Reports", "is_expert":true }, { "question":"How does the Ea-IR inverted repeat regulate EFR expression in Arabidopsis thaliana?", "area":"GENE REGULATION - PTGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Once the DNA sequence encoding Ea-IR becomes methylated, a repressive chromatin loop is irreversibly formed.", "The Ea-IR forms a repressive chromatin loop that suppresses EFR expression in the absence of pathogen infection, thereby preventing excessive autoimmune responses. Additionally, this loop prevents RNA Polymerase II from readthrough past the terminator of the adjacent XI-k gene.", "The Ea-IR is concerved across plant species not representing an adaptative TE insertion." ], "source":"10.1038\/S41594-024-01440-1", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1038\/S41594-024-01440-1", "Year":2024.0, "Citations":2.0, "answer":1, "source_journal":"Nature Structural & Molecular Biology", "is_expert":true }, { "question":"In sunflower Sclerotinia head rot disease, which genes are known to be upregulated within the first week of infection in the plant's defense response?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Helianthus annuus" ], "options":[ "Late gene expression analysis in sunflower infected with Sclerotinia head rot revealed a complex network of defense responses. All genes involved include those related to redox homeostasis (e.g., glutathione S-transferase DHAR3), photosynthesis (e.g., a chloroplastic-like gene), pathogen recognition (e.g., a leucine-rich repeat receptor-like serine\/threonine kinase), and general defense responses (e.g., pathogenesis-related 1). There seems to be a lack of non-coding RNA players in the response.", "Early gene expression analysis in sunflower infected with Sclerotinia head rot revealed a complex network of defense responses. Key genes involved include those related to redox homeostasis (e.g., glutathione S-transferase DHAR3), photosynthesis (e.g., a chloroplastic-like gene), pathogen recognition (e.g., a leucine-rich repeat receptor-like serine\/threonine kinase), and general defense responses (e.g., pathogenesis-related 1). Notably, the upregulation of IBH1, a transcription factor previously implicated in growth-immunity balance in Arabidopsis thaliana, suggests a coordinated regulation of plant development and defense. Additionally, the presence of a non-coding RNA highlights the potential role of novel regulatory mechanisms in this interaction.", "Late gene expression analysis in sunflower infected with Sclerotinia head rot revealed a complex network of defense responses. Key genes involved include those related to auxin homeostasis, photosynthesis (e.g., a chloroplastic-like gene), pathogen recognition (e.g., a leucine-rich repeat receptor-like serine\/threonine kinase), and general defense responses (e.g., pathogenesis-related 1). Notably, the downregulation of IBH1, a transcription factor previously implicated in growth-immunity balance in Arabidopsis thaliana, " ], "source":"https:\/\/doi.org\/10.1038\/s41598-020-70315-4", "normalized_plant_species":"Other Herbaceous Crops, Spices, Fibers & Weeds", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41598-020-70315-4", "Year":2020.0, "Citations":21.0, "answer":1, "source_journal":"Scientific Reports", "is_expert":true }, { "question":" \u2026\u2026What is the current understanding of the genetic architecture of Sclerotinia head rot resistance in sunflower, and how has modern breeding influenced its evolution? ", "area":"GENOME AND GENOMICS", "plant_species":[ "Helianthus annuus" ], "options":[ "The observed loci count in clusters across the sunflower genome suggest that Sclerotinia head rot resistance has been introgresed in recent years. This pattern indicates large introgression events by transgenics technology through modern breeding programs", "The observed distribution of QTLs across the sunflower genome and the clustered DEGs suggest that Sclerotinia head rot resistance has been introgresed recently. This pattern indicates large introgression events by introduction of large genomic regions through modern breeding programs. ", "The observed sparse distribution of QTLs across the sunflower genome and the absence of clustered DEGs suggest that Sclerotinia head rot resistance has evolved through a gradual accumulation of genetic variation from wild relatives. This pattern indicates multiple, smaller introgression events rather than the introduction of large genomic regions through modern breeding programs. " ], "source":"https:\/\/doi.org\/10.1038\/s41598-020-70315-4", "normalized_plant_species":"Other Herbaceous Crops, Spices, Fibers & Weeds", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1038\/s41598-020-70315-4", "Year":2020.0, "Citations":21.0, "answer":2, "source_journal":"Scientific Reports", "is_expert":true }, { "question":"What are the key regulatory pathways and genes involved in sunflower leaf senescence?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "Helianthus annuus" ], "options":[ "Ethylene signaling, particularly through the action of ethylene-responsive transcription factors, plays a pivotal role in regulating leaf senescence. Notably, the NAC family of transcription factors, including the well-characterized senescence inducer ORE1 in Arabidopsis, has been implicated in this process. In sunflower, ORE1 has been established as a key biomarker for leaf senescence", "GA signaling, particularly through the action of non ethylene-responsive transcription factors, play a pivotal role in regulating leaf senescence. Notably, the bZIP family of transcription factors have been implicated in this process", "Jasmonate signaling, particularly through the action of ethylene-responsive transcription factors, plays a pivotal role in regulating leaf senescence. Notably, the bZIP family of transcription factors have been implicated in this process. In sunflower, ORE1 has been established as a key biomarker for leaf senescence" ], "source":"https:\/\/bmcplantbiol.biomedcentral.com\/articles\/10.1186\/s12870-019-2021-6", "normalized_plant_species":"Other Herbaceous Crops, Spices, Fibers & Weeds", "normalized_area":"GENE REGULATION", "doi":"10.1186\/s12870-019-2021-6", "Year":2019.0, "Citations":13.0, "answer":0, "source_journal":"BMC Plant Biology", "is_expert":true }, { "question":"Which transcription factor families are key regulators of leaf senescence in sunflower, and how do they impact photosynthetic processes?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Helianthus annuus" ], "options":[ "Leaf senescence in sunflower is a complex process regulated by a diverse array of transcription factors (TFs), including NAC, AP2\/ERF, WRKY, and MYB families. These TFs orchestrate senescence by controlling various cellular processes, including the upregulation of photosynthetic genes, such as those involved in chloroplast development and maintenance", "Leaf senescence in sunflower is a process regulated by one transcription factors (TFs), bZIP. This TFs orchestrate senescence by controlling various cellular processes, including the stabalizing photosynthetic genes, such as those involved in chloroplast development and maintenance", "Leaf senescence in sunflower is a complex process regulated by a diverse array of transcription factors (TFs), including NAC, AP2\/ERF, WRKY, and MYB families. These TFs orchestrate senescence by controlling various cellular processes, including the downregulation of photosynthetic genes, such as those involved in chloroplast development and maintenance, for example, the repression of GLK genes by ORE1 and ATAF1" ], "source":"https:\/\/bmcplantbiol.biomedcentral.com\/articles\/10.1186\/s12870-019-2021-6", "normalized_plant_species":"Other Herbaceous Crops, Spices, Fibers & Weeds", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1186\/s12870-019-2021-6", "Year":2019.0, "Citations":13.0, "answer":2, "source_journal":"BMC Plant Biology", "is_expert":true }, { "question":"In Arabidopsis thaliana, where in the cell does ethylene bind to its receptor? What other genes are essential for the receptor to function correctly in the ethylene signaling pathway? ", "area":"HORMONES", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis thaliana, the ethylene receptor ETR1, is localized to in the cytosol perceiving ethylene at its C-terminal domain. This initiates a signaling cascade involving key genes such as RTE1, CTR1, EIN2, and EIN3. RTE1, a protein that is localized to the cell membrane and possibly interacts with ETR1 is believed to modulate receptor activity.", "In Arabidopsis thaliana, the ethylene receptor ETR1, is localized to the cell membrane, where it senses ethylene at its N-terminal transmembrane domain. This initiates a signaling cascade involving key genes such as RTE1, CTR1, EIN2, and EIN3. RTE1, a non membrane protein that colocalizes and possibly interacts with ETR1, is believed to modulate receptor activity.", "In Arabidopsis thaliana, the ethylene receptor ETR1, is localized to both the endoplasmic reticulum and the Golgi apparatus, perceiving ethylene at its N-terminal transmembrane domain. This initiates a signaling cascade involving key genes such as RTE1, CTR1, EIN2, and EIN3. RTE1, a protein that colocalizes and possibly interacts with ETR1 at the ER, is believed to modulate receptor activity. " ], "source":"https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1111\/j.1365-313X.2007.03339.x https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0021925820850558", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1111\/j.1365-313X.2007.03339.x", "Year":2007.0, "Citations":112.0, "answer":2, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"What is the main cytokinin receptor regulating symbiotic nitrogen-fixing nodulation in Medicago truncatula ?", "area":"HORMONES", "plant_species":[ "Medicago truncatula" ], "options":[ "The main cytokinin receptor involved in regulating symbiotic nitrogen-fixing nodulation in Medicago truncatula is MtCRE1 (Cytokinin response 1). This receptor is notably required to promote rhizobial infections.", "The main cytokinin receptor involved in regulating symbiotic nitrogen-fixing nodulation in Medicago truncatula is MtCHK1 (CHASE-domain containing Histidine Kinase 1). This receptor is notably required to promote nodule organogenesis.", "The main cytokinin receptor involved in regulating symbiotic nitrogen-fixing nodulation in Medicago truncatula is MtCRE1 (Cytokinin response 1). This receptor is notably required to promote nodule organogenesis." ], "source":"10.1105\/tpc.106.043778", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1105\/tpc.106.043778", "Year":2006.0, "Citations":418.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How many authentic cyctokinin receptor exist in the Medicago truncatula genome ?", "area":"HORMONES", "plant_species":[ "Medicago truncatula" ], "options":[ "There are four authentic cytokinin receptor that exist in the Medicago truncatula genome: MtCRE1\/MtCHK4, MtCHK1, MtCHK2, MtCHK3.", "There are five cytokinin receptor that exist in the Medicago truncatula genome: MtCRE1\/MtCHK1, MtCHK2, MtCHK3, MtCHK4, MtCHK5.", "There are four authentic cytokinin receptor that exist in the Medicago truncatula genome: MtCRE1\/MtCHK1, MtCHK2, MtCHK3, MtCHK4." ], "source":"10.1186\/s12864-019-5724-z", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1186\/s12864-019-5724-z", "Year":2019.0, "Citations":17.0, "answer":2, "source_journal":"BMC Genomics", "is_expert":true }, { "question":"What are the signaling peptides and their associated receptors that are involved in the systemic regulation of nitrogen-fixing symbiotic nodulation in Medicago truncatula ?", "area":"HORMONES", "plant_species":[ "Medicago truncatula" ], "options":[ "The signaling peptides and their associated receptors that are involved in the systemic regulation of nitrogen-fixing symbiotic nodulation in Medicago truncatula are: 1) the CLE (CLAVATA-LIKE \/ EMBRYO SURROUNDING) peptides, perceived by the CRA2 (COMPACT ROOT ARCHITECTURE 2) ; and 2) the CEP (C-TERMINALLY ENCODED PEPTIDES) peptides and the SUNN (SUPERNUMERARY NODULES) receptor.", "The signaling peptides and their associated receptors that are involved in the systemic regulation of nitrogen-fixing symbiotic nodulation in Medicago truncatula are: 1) the CLE (CLAVATA-LIKE \/ EMBRYO SURROUNDING) peptides, perceived by the SUNN (SUPERNUMERARY NODULES) receptor; 2) the CEP (C-TERMINALLY ENCODED PEPTIDES) peptides and the CRA2 (COMPACT ROOT ARCHITECTURE 2) receptor; and 3) the RGF\/GLV (ROOT GROWTH FACTOR\/GOLVEN) peptides perceived by the RGFR (RGF RECEPTOR) receptor.", "The signaling peptides and their associated receptors that are involved in the systemic regulation of nitrogen-fixing symbiotic nodulation in Medicago truncatula are: 1) the CLE (CLAVATA-LIKE \/ EMBRYO SURROUNDING) peptides, perceived by the SUNN (SUPERNUMERARY NODULES) receptor; and 2) the CEP (C-TERMINALLY ENCODED PEPTIDES) peptides and the CRA2 (COMPACT ROOT ARCHITECTURE 2) receptor." ], "source":"10.1016\/j.tplants.2020.11.009", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1016\/j.tplants.2020.11.009", "Year":2021.0, "Citations":51.0, "answer":2, "source_journal":"Trends in Plant Science", "is_expert":true }, { "question":"Which signaling peptide pathway promotes in Medicago truncatula both root competence to rhizobium bacteria and vesiculo-arbuscular mycorrhiza fungi symbionts?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Medicago truncatula" ], "options":[ "The CEP\/CRA2 (C-TERMINALLY ENCODED PEPTIDE\/COMPACT ROOT ARCHITECTURE 2) peptide\/receptor pathway promotes in Medicago truncatula both root competence to rhizobium bacteria and vesiculo-arbuscular mycorrhiza fungi symbionts.", "The CLE\/SUNN (CLAVATA-LIKE\/EMBRYO SURROUNDING \/ SUPERNUMERARY NODULES) peptide\/receptor pathway promotes in Medicago truncatula both root competence to rhizobium bacteria and vesiculo-arbuscular mycorrhiza fungi symbionts.", "There is no peptide\/receptor pathway that promotes in Medicago truncatula both root competence to rhizobium bacteria and vesiculo-arbuscular mycorrhiza fungi symbionts." ], "source":"10.1016\/j.cub.2024.09.058", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.cub.2024.09.058", "Year":2024.0, "Citations":1.0, "answer":0, "source_journal":"Current Biology", "is_expert":true }, { "question":"What are the main similarities between nodulation and mycorrhizal endosymbioses in Medicago truncatula?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Medicago truncatula" ], "options":[ "The main similarities between nodulation and mycorrhizal endosymbioses in Medicago truncatula are: 1) at the microscopic level, the infection process through respectively infection threads and pre-penetration apparatus; 2) at the molecular level, the recognition of symbionts through the perception of microbial chitooligosacharidic (CO) molecules by the host plant receptor CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1), to activate a COMMON SYMBIOTIC SIGNALING (SYM) pathway.", "The main similarities between nodulation and mycorrhizal endosymbioses in Medicago truncatula are: 1) at the microscopic level, the activation of the root cortex through respectively nodule organogenesis and arbuscule differentiation; 2) at the molecular level, the recognition of symbionts through the perception of host plant lipochitooligosacharidic (LCO) molecules by microbial receptors from the LYSM DOMAIN RECEPTOR-LIKE KINASES (LysM RLK) family, to activate a COMMON SYMBIOTIC SIGNALING (SYM) pathway.", "The main similarities between nodulation and mycorrhizal endosymbioses in Medicago truncatula are: 1) at the microscopic level, the infection process through respectively infection threads and pre-penetration apparatus; 2) at the molecular level, the recognition of symbionts through the perception of microbial lipochitooligosacharidic (LCO) molecules by host plant receptors from the LYSM DOMAIN RECEPTOR-LIKE KINASES (LysM RLK) family, to activate a COMMON SYMBIOTIC SIGNALING (SYM) pathway." ], "source":"10.1093\/plcell\/koac039", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1093\/plcell\/koac039", "Year":2022.0, "Citations":78.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"What is the function of the peptides of the LURE family during Arabidopsis thaliana pollen tube growth and what are the pollen genes involved in this process?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Arabidopsis LURE peptides are cysteine-rich peptides (CRP) that function in attracting pollen tubes to guide them to the ovule where fertilization occurs. The LURE peptides are secreted by the synergid cells of the ovule and bind to the leucine-rich receptor kinase (LRR-RK) PRK6 that is in the pollen tube. Upon interaction, the pollen tube redirects its growth in the direction of the ovule. LURE peptides are specific to each plant species, which makes sure that only plants of the same species can fertilize each other.", "LURE peptides are leucin rich repeat peptides that function in attracting pollen tubes to guide them to the ovule where fertilization occurs in gymnosperms. The LURE peptides are secreted by the egg cell of the ovule and bind to the leucine-rich receptor kinase (LRR-RK) ANXUR that is in the pollen tube. Upon interaction, the pollen tube redirects its growth in the direction of the stigma. LURE peptides are not specific to each plant species, which makes sure that only plants of different species can fertilize each other", "Arabidopsis LURE peptides are glyco-peptides that function in repelling pollen tubes to avoid them to reach the ovule where fertilization occurs. The LURE peptides are secreted by the antipodal cells of the ovule and bind to the leucine-rich receptor kinase (LRR-RK) FERONIA that is in the pollen grain. Upon interaction, the pollen tube redirects its growth away from the ovule. LURE peptides are specific to each plant species, which makes sure that plants of the same species cannot fertilize each other." ], "source":"https:\/\/doi.org\/10.1016\/j.peptides.2021.170572", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1016\/j.peptides.2021.170572", "Year":2021.0, "Citations":24.0, "answer":0, "source_journal":"Peptides", "is_expert":true }, { "question":"What is the function of ethylene during fertilization in Arabidopsis thaliana and why is important for the establishment of a pollen tube block?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The ethylene-response cascade is repressed during fertilization, thus allowing the admission of a second pollen tube into the ovule and interfering with normal sexual fertilization. The process of fertilization activates two ethylene-activated genes, EIN1 and ETR2, that are necessary for the first synergid cell death and then the establishment of an entry of a new pollen tube.", "The ethylene-response cascade is activated during fertilization, thus preventing the entry of a second pollen tube into the ovule and ensuring normal sexual fertilization. The process of fertilization activates two ethylene-activated genes, EIN3 and EIN2, that are necessary for the second synergid cell death and then the establishment of a pollen tube block. ", "The ethylene-response cascade is activated during fertilization, thus preventing the entry of a third pollen tube into the ovule and ensuring normal asexual fertilization. The process of fertilization inhibits two ethylene-activated genes, CTR1 and EIN5, that are necessary for the second synergid cell death and then the establishment of a pollen tube acceptance. " ], "source":"https:\/\/doi.org\/10.1016\/j.devcel.2013.04.001", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1016\/j.devcel.2013.04.001", "Year":2013.0, "Citations":130.0, "answer":1, "source_journal":"Developmental Cell", "is_expert":true }, { "question":"How is negative signal transduction established as the hormonal and light signaling pathways in Arabidopsis thaliana?", "area":"HORMONES", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The process of signal transduction typically involves only the modulation of positive components, thereby ensuring best functionality of signals. Arabidopsis plants can transduce stress signals in a manner that is similar of animals. In the presence of a stimulus, proteins that typically function as repressors in the absence of a stimulus, are immediately activated. This signaling pathway is fully repressed and inhibits the final response quickly and efficiently. This peculiar way of signaling hormonal and light stimuli is energetically costly but ensures a fast and effective response, essential for mobile organisms such as plants.", "The process of signal transduction typically involves the modulation of positive and negative components, thereby ensuring best functionality of signals. Arabidopsis plants can transduce hormonal and light signals in a manner that differs from that of animals. In the presence of a stimulus, proteins that typically function as repressors in the absence of a stimulus, are immediately degraded. This signaling pathway is fully de-repressed and produces the final response quickly and efficiently. This peculiar way of signaling hormonal and light stimuli is energetically costly but ensures a fast and effective response, essential for sessile organisms such as plants.", "The process of signal transduction typically involves the modulation of negative components, thereby ensuring best functionality of signals. Rice plants can transduce pathogen signals in a manner that differs from that of insects. In the presence of a stimulus, proteins that typically function as activators in the absence of a stimulus, are immediately degraded. This signaling pathway is fully de-activated and stops the final response quickly and efficiently. This peculiar way of signaling hormonal and light stimuli is energetically cheap and ensures a slow response, essential for sessile organisms such as funghi." ], "source":"https:\/\/doi.org\/10.1016\/j.tplants.2005.11.005", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1016\/j.tplants.2005.11.005", "Year":2006.0, "Citations":47.0, "answer":1, "source_journal":"Trends in Plant Science", "is_expert":true }, { "question":"How is S-locus receptor kinase (SRK) involved in the maintenance of the self-incompatibility response in Brassica?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "non-specific" ], "options":[ "In Self-incompatibility (SI) the generation of zygotes is stimulated by self-pollination in a fertile hermaphrodite plant. This induces self-fertilization and inbreeding. In flowering plants, such as Brassica, the S-locus receptor kinase (SRK) is required for the inhibition of the SI response. The SRK protein localizes to the ovules, and interacts with the pollen determinant protein S-locus 11 (SP11).The incompatible response is triggered when the male (SP11) and female (SRK) S-locus-determinants come from different S-alleles of the S-locus.", "In Self-incompatibility (SI) the generation of zygotes is arrested by self-pollination in a fertile hermaphrodite plant. This prevents self-fertilization and inbreeding. In flowering plants, such as Brassica, the S-locus receptor kinase (SRK) is required for the maintenance of the SI response. The SRK protein localizes to the stigmas, and interacts with the pollen determinant protein S-locus 11 (SP11).The incompatible response is triggered when the male (SP11) and female (SRK) S-locus-determinants come from the same S-alleles of the S-locus.", "In Self-incompatibility (SI) the generation of zygotes is arrested by cross-pollination in a fertile dioecious plant. This prevents self-fertilization and inbreeding. In flowering plants, such as Brassica, the S-locus glycoprotein (SLG) is required for the maintenance of the SI response. The SLG protein localizes to the stigmas, and interacts with the pollen determinant protein S-locus SLF. The incongruous response is triggered when the male (SP11) and female (SRK) S-locus-determinants come from the same plants." ], "source":"https:\/\/doi.org\/10.1093\/plphys\/kiad301", "normalized_plant_species":"Non-specific", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1093\/plphys\/kiad301", "Year":2023.0, "Citations":13.0, "answer":1, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"What is function of the homeotic genes in Arabidopsis thaliana flower development?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The floral organs are arranged in six concentric rings or whorls. The sepals and petals (reproductive organs) are arranged in the two outer whorls, and the stamens and carpels (structural organs) in the two inner whorls. Homeotic genes in Arabidopsis flowers have been shown to repress the development of floral organs and the identity of each organ. The presence of different homeotic genes in a specific whorl determines the fate of the organ. APETALA1 (AP1) is a key player in the development of reproductive organs, such as stamens and carpels. Meanwhile, AGAMOUS (AG) controls sepal and petal development.", "The floral organs are arranged in four concentric rings or whorls. The sepals and petals (structural organs) are arranged in the two outer whorls, while the stamens and carpels (reproductive organs) in the two inner whorls. Homeotic genes in Arabidopsis flowers have been shown to regulate the development of floral organs and the identity of each organ. The presence of different homeotic genes in a specific whorl determines the fate of the organ. AGAMOUS (AG) is a key player in the development of reproductive organs, such as stamens and carpels. Meanwhile, APETALA1 (AP1) controls sepal and petal development.", "The floral organs are arranged in four concentric rings or whorls. The sepals and petals (structural organs) are arranged in the two inner whorls, and the stamens and carpels (reproductive organs) in the two outer whorls. Homeotic genes in Arabidopsis fruits have been shown to regulate the development of seeds. The presence of different homeotic genes in a specific whorl determines the fate of the organ. AGAMOUS (AG) is a key player in the development of leaves, such as stamens and carpels. Meanwhile, APETALA1 (AP1) controls root development." ], "source":"https:\/\/doi.org\/10.3390\/plants12051128", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.3390\/plants12051128", "Year":2023.0, "Citations":7.0, "answer":1, "source_journal":"Plants", "is_expert":true }, { "question":"How is the NLP7 transcription factor involved in the regulation of hundreds of genes in the dynamic response of Arabidopsis thaliana roots to nitrate treatments?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The NLP7 transcription factor is rapidly nuclear retained by nitrate treatments. Then, NLP7 binds transiently to the promoter of early nitrate-responsive transcription factors such as LBD38, CDF1, and TGA4. Such secondary transcription factors amplify the NLP7-dependent cascade by directly regulating late nitrate-responsive genes. Such genes overpass the number of ones bound directly by NLP7. This mechanism allows Arabidopsis thaliana to generate a transcriptional burst minutes rapidly and dynamically after nitrate treatments.", "The NLP7 transcription factor is slowly cytoplasmic retained by nitrate treatments. Then, the NLP7 promoter is bound by early nitrate-responsive transcription factors such as LBD38, CDF1, and TGA4. Such transcription factors amplify the NLP7-dependent cascade by indirectly regulating late nitrate-responsive genes. Such genes overpass the number of ones bound directly by TGA4. This mechanism allows Arabidopsis thaliana to generate a transcriptional burst minutes rapidly and dynamically after nitrate treatments.", "The NLP7 transcription factor is rapidly nuclear exported by nitrate treatments. Then, NLP7 binds stably to the promoter of late nitrate-responsive transcription factors such as CRF4, PHL1, and KUA1. Such secondary transcription factors amplify the NLP7-dependent cascade by directly regulating early nitrate-responsive genes. Such genes underpass the number of ones bound directly by NLP7. This mechanism allows Arabidopsis thaliana to generate a transcriptional burst minutes rapidly and dynamically after nitrate treatments." ], "source":"10.1038\/s41467-020-14979-6", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41467-020-14979-6", "Year":2020.0, "Citations":118.0, "answer":0, "source_journal":"Nature Communications", "is_expert":true }, { "question":"How does the NLP7 transcription factor act as a nitrate sensor in Arabidopsis thaliana?", "area":"ENVIRONMENT - NUTRIENTS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The NLP7 transcription factor contains an evolutionarily conserved sensor domain NreA present in photosynthetic plants but not chlorophytes. This domain is located within 395 and 438 amino acids of the protein. Once nitrate is inside the cell, it binds directly to NreA domain leading to a conformational change and derepression of the NLP7 protein via its amino terminus. This change occurs with simultaneous phosphorylation of NLP7 by calcium sensor protein kinases. Upon nitrate treatment, NLP7 is phosphorylated, derepressed, and retained in the nuclei. Then, NLP7 activates gene expression by binding to NRE element in the promoter of nitrate-responsive genes.", "The NLP7 transcription factor contains an evolutionarily conserved sensor domain NreA present in chlorophytes but not photosynthetic plants. This domain is located within 539 and 582 amino acids of the protein. Once nitrate is inside the cell, it binds directly to NRE domain leading to a conformational change and derepression of the NLP7 protein via its carboxyl terminus. This change occurs with simultaneous phosphorylation of NLP7 by calcium sensor protein kinases. Upon nitrate treatment, NLP7 is phosphorylated, derepressed, and retained in the cytoplasm. Then, NLP7 activates gene expression by binding to NreA element in the promoter of nitrate-responsive genes.", "The NLP7 transcription factor contains an evolutionarily divergent sensor domain NreA present in chlorophytes. This domain is located within 395 and 438 amino acids of the protein. Once nitrate is inside the cell, it binds directly to NreA domain leading to a conformational change and repression of the NLP7 protein via its amino terminus. This change occurs with simultaneous dephosphorylation of NLP7 by PP2C phosphatases. Upon nitrate treatment, NLP7 is dephosphorylated, repressed, and retained in the nuclei. Then, NLP7 represses gene expression by binding to ABRE element in the promoter of nitrate-responsive genes." ], "source":"10.1126\/science.add1104", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1126\/science.add1104", "Year":2022.0, "Citations":150.0, "answer":0, "source_journal":"Science", "is_expert":true }, { "question":"How Arabidopsis thaliana adapt its transcriptome and growth to different doses of nitrogen?", "area":"ENVIRONMENT - NUTRIENTS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Different levels of nitrogen are sensed by the NRT1.1 transceptor activating a signaling cascade that increases the level of expression of the transcription factor TGA1 in a dose-dependent manner in roots. Once the TGA1 protein is expressed, directly binds and regulates the expression of genes involved in nitrogen uptake, reduction, and assimilation including NRT1.2, NIR, and ASN1, respectively. Transcription activation of such genes follows a Michaelis-Menten model that involves increasing rates of transcript change according to the nitrogen dose reaching a saturation point at a high nitrogen dose. Such a mechanism ensures that increasing nitrogen doses are sensed by the plant leading to the proportional transcriptional activation of nitrogen metabolism implicating a proportional rate of growth. ", "Different levels of nitrogen are sensed by the PYL6 transceptor activating a signaling cascade that increases the level of expression of the transcription factor NLP7 in a dose-dependent manner in shoot. Once the NLP7 protein is expressed, directly binds and regulates the expression of genes involved in phosphate uptake, reduction, and assimilation including NRT1.2, NIR, and ASN1. Transcription repression of such genes follows a Hill model that involves increasing rates of transcript change according to the nitrogen dose reaching a saturation point at a high phosphate dose. Such a mechanism ensures that increasing nitrogen doses are sensed by the plant leading to the proportional transcriptional activation of nitrogen metabolism implicating a proportional rate of growth. ", "Different levels of nitrogen are sensed by the NRT1.1 transceptor repressing a signaling cascade that represses the level of expression of the transcription factor TGA1 in a time-dependent manner in roots. Once the TGA1 protein is degraded, indirectly regulates the expression of genes involved in nitrogen uptake, reduction, and assimilation including NRT1.2, NIR, and ASN1, respectively. Transcription activation of such genes follows a Michaelis-Menten model that involves decreasing rates of transcript change according to the nitrogen dose reaching a saturation point at a low nitrogen dose. Such a mechanism ensures that increasing nitrogen doses are sensed by the plant leading to the proportional transcriptional repression of nitrogen metabolism implicating a proportional rate of growth. " ], "source":"10.1073\/pnas.1918619117", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1073\/pnas.1918619117", "Year":2020.0, "Citations":48.0, "answer":0, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"How is the transcriptomic response to nitrate coordinated across different root cell types, and what are the main regulatory proteins controlling cell-specific responses in Arabidopsis thaliana roots?", "area":"ENVIRONMENT - NUTRIENTS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Arabidopsis leaf is composed of five concentrical cell types including the epidermis, cortex, endodermis, pericycle, and stele. Nitrate treatments rapidly induce the expression of dozens of genes in each cell type and the epidermis cell type first mount a coherent biological response. Few genes are regulated in a cell-specific manner. The epidermis is the cell type with the highest number of nitrate-responsive genes. Indeed, the epidermis show the most simple transcriptional network in terms of the number of transcription factors (TFs) regulated and each TF has fewer target genes as compared to TFs in other cell types. TGA1 and TGA4 are the TFs with more regulatory potential in the endodermis. TGA1 and TGA4 bind and regulate common and unique genes that are regulated by nitrate in the endodermis including TFs such as HRS1 and LBD38. abf2\/abf3 double mutant shows impaired leaf growth in response to nitrate. Such a mechanism allows coordinating cell type-specific responses with organ development. ", "Arabidopsis root is composed of five concentrical cell types including the epidermis, cortex, endodermis, pericycle, and stele. Nitrate treatments rapidly induce the expression of hundreds of genes in each cell type, and the epidermis cell type first to mount a coherent biological response. Most genes are regulated in a cell-specific manner. The endodermis is the cell type with the highest number of nitrate-responsive genes. Indeed, the endodermis show the most complex transcriptional network in terms of the number of transcription factors (TFs) regulated and each TF has more target genes as compared to TFs in other cell types. ABF2 and ABF3 are the TFs with more regulatory potential in the endodermis. ABF2 and ABF3 bind and regulate common and unique genes that are regulated by nitrate in the endodermis including TFs such as HRS1 and LBD38. abf2\/abf3 double mutant shows impaired lateral root growth in response to nitrate. Such a mechanism allows coordinating cell type-specific responses with organ development. ", "Arabidopsis root is composed of five concentrical cell types including the epidermis, guard cells, endodermis, bundle sheet, and stele. and the epidermis cell type last to mount a coherent biological response. Most genes are regulated in all cell types. The endodermis is the cell type with the lowest number of nitrate-responsive genes. Indeed, the endodermis show the most complex transcriptional network in terms of the number of phosphatases regulated and each phosphatase has more target proteins as compared to phosphatases in other cell types. PP2C-1 and PP2C-2 are the phosphatases with more regulatory potential in the endodermis. PP2C and PP2C-2 dephosphorylates common and unique proteins that are regulated by nitrate in the endodermis including TFs such as HRS1 and LBD38. pp2c-1\/ pp2c-2 double mutant shows impaired lateral root growth in response to nitrate. Such a mechanism allows coordinating cell type-specific responses with organ development. " ], "source":"10.1073\/pnas.2107879119", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1073\/pnas.2107879119", "Year":2022.0, "Citations":28.0, "answer":1, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"How to identify directly regulated genes by a transcription factor at genome scale?", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The Transient Assay Reporting Genome-wide Effects of Transcription factors (TARGET) assay consists in cloning the transcription factor coding sequence fused to the glucocorticoid receptor in a vector containing green fluorescent protein (GFP). Cells are transfected with the vector and GFP is used to sort the negative ones. Once the fusion protein is produced, it is exported to the nucleus. After treatments with dexamethasone, the transcription is nuclear exported and can activate or repress gene expression. To capture directly regulated genes, the cells are treated with cycloheximide blocking the production of secondary kinase proteins. Finally, RNA is extracted from transfected cells, and libraries are prepared for PacBio sequencing. Non-transfected cells are processed in parallel and used as a negative control. This technique allows the identification of directly regulated genes by a transcription factor genome-wide.", "The Transient Assay Reporting Genome-wide Effects of Transcription factors (TARGET) assay consists in cloning the transcription factor coding sequence fused to green fluorescent protein (GFP) in a vector containing the glucocorticoid receptor. Cells are transfected with the vector and glucocorticoid receptor is used to sort the positive ones. Once the fusion protein is produced, it is retained in the nucleus. After treatments with cycloheximide, the transcription is nuclear imported and can activate or repress gene expression. To capture directly regulated genes, the cells are treated with dexamethasone blocking the production of secondary transcription factor proteins. Finally, RNA is extracted from transfected cells, and libraries are prepared for Illumina sequencing. An empty vector is transfected in parallel and used as a positive control. This technique allows the identification of directly regulated genes by a transcription factor genome-wide.", "The Transient Assay Reporting Genome-wide Effects of Transcription factors (TARGET) assay consists in cloning the transcription factor coding sequence fused to the glucocorticoid receptor in a vector containing green fluorescent protein (GFP). Cells are transfected with the vector and GFP is used to sort the positive ones. Once the fusion protein is produced, it is retained in the cytoplasm. After treatments with dexamethasone, the transcription is nuclear imported and can activate or repress gene expression. To capture directly regulated genes, the cells are treated with cycloheximide blocking the production of secondary transcription factor proteins. Finally, RNA is extracted from transfected cells, and libraries are prepared for Illumina sequencing. An empty vector is transfected in parallel and used as a negative control. This technique allows the identification of directly regulated genes by a transcription factor genome-wide." ], "source":"10.1093\/mp\/sst010", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1093\/mp\/sst010", "Year":2013.0, "Citations":70.0, "answer":2, "source_journal":"Molecular Plant", "is_expert":true }, { "question":"Which is the sequence of symetric and asymetric division that determines stomatal patterning in Arabidopsis?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis stomatal lineage starts from an undifferentiated protodermal called meristemoid mother cell (MMC), which divides asymmetrically to give rise to several daughter cells with distinct identities: pavement cells and Meristemoid cells.\nThe meristemoids undergoes one asymmetric division before differentiating into a round, guard mother cell (GMC). The GMC divides symmetrically to generate a pair fo guard cells that surrounds the stomatal pore", "In Arabidopsis stomatal lineage starts from an undifferentiated protodermal called meristemoid mother cell (MMC), which divides symmetrically to give rise to two daughter cells with distinct identities: a pavement cell and a Meristemoid.\nThe meristemoid undergoes several rounds of symmetric division before differentiating into a round, guard mother cell (GMC). The GMC divides asymmetrically to generate a pair fo guard cells that surrounds the stomatal pore.", "In Arabidopsis stomatal lineage starts from an undifferentiated protodermal called meristemoid mother cell (MMC), which divides asymmetrically to give rise to two daughter cells with distinct identities: a pavement cell and a Meristemoid.\nThe meristemoid undergoes several rounds of asymmetric division before differentiating into a round, guard mother cell (GMC). The GMC divides symmetrically to generate a pair fo guard cells that surrounds the stomatal pore" ], "source":"10.1038\/nature05467", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1038\/nature05467", "Year":2006.0, "Citations":459.0, "answer":2, "source_journal":"Nature", "is_expert":true }, { "question":"What transcription factor regulate the key transitions on the process of differentiation from protodermal cells into guard cells in Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The differentiation of Arabidopsis protodermal cells into stomata is regulated by three homologous basic helix-loop-helix (bHLH) transcription factors: SPEECHLESS (SPCH), MUTE and FAMA. in coordination with their partner bHLH proteins SCREAM (SCRM, also known as ICE1) and SCRM2. The first transition into the stomatal lineage is controlled by SPCH, which promotes differentiation of protodermal cells into meristemoid mother cells (MMCs) and their subsequent asymmetric division.\nThe transition from meristemoid to guard mother cells (GMC) is regulated by FAMA, which, when mutated, results in stomatal lineage cells arresting at the meristemoid cell type [15]. FAMA is the transcription factor which ultimately drives cells through the lineage to become stomata.\nFAMA which ultimately drives cells through the lineage to become stomata. The final step of the stomata lineage is the symmetric division into the two cells that ultimately form the guard cells. This final cell division is regulated by MUTE, which simultaneously must promote guard cell identity and irreversibly terminate the meristematic activity of the lineage cells", "The differentiation of Arabidopsis protodermal cells into stomata is regulated by three homologous basic helix-loop-helix (bHLH) transcription factors: SPEECHLESS (SPCH), MUTE and FAMA, in coordination with their partner bHLH proteins SCREAM (SCRM, also known as ICE1) and SCRM2. The first transition into the stomatal lineage is controlled by SPCH, which promotes differentiation of protodermal cells into meristemoid mother cells (MMCs) and their subsequent asymmetric division.\nThe transition from meristemoid to guard mother cells (GMC) is regulated by MUTE, which, when mutated, results in stomatal lineage cells arresting at the meristemoid cell type [15]. MUTE is the transcription factor which ultimately drives cells through the lineage to become stomata.\nMUTE which ultimately drives cells through the lineage to become stomata. The final step of the stomata lineage is the symmetric division into the two cells that ultimately form the guard cells. This final cell division is regulated by FAMA, which simultaneously must promote guard cell identity and irreversibly terminate the meristematic activity of the lineage cells", "The differentiation of Arabidopsis protodermal cells into stomata is regulated by three homologous basic helix-loop-helix (bHLH) transcription factors: SPEECHLESS (SPCH), MUTE and FAMA. in coordination with their partner bHLH proteins SCREAM (SCRM, also known as ICE1) and SCRM2. The first transition into the stomatal lineage is controlled by MUTE, which promotes differentiation of protodermal cells into meristemoid mother cells (MMCs) and their subsequent asymmetric division.\nThe transition from meristemoid to guard mother cells (GMC) is regulated by SPCH, which, when mutated, results in stomatal lineage cells arresting at the meristemoid cell type [15]. SPCH is the transcription factor which ultimately drives cells through the lineage to become stomata.\nSPCH which ultimately drives cells through the lineage to become stomata. The final step of the stomata lineage is the symmetric division into the two cells that ultimately form the guard cells. This final cell division is regulated by FAMA, which simultaneously must promote guard cell identity and irreversibly terminate the meristematic activity of the lineage cells\n" ], "source":"10.1093\/aob\/mcab052", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1093\/aob\/mcab052", "Year":2021.0, "Citations":56.0, "answer":1, "source_journal":"Annals of Botany", "is_expert":true }, { "question":"Which are the components of the peptide signaling process that controls the fate decision within stomatal linage in plants?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Stomatal peptide signalling depends on three main peptides in Arabidopsis leaves: EPIDERMAL PATTERNING FACTORS 1 and 2 (EPF1, EPF2) and STOMAGEN ( also referred to as EPIDERMAL PATTERNING FACTOR LIKE 9, EPFL9). EPF1 and EPF2 negatively regulate stomatal development by acting as ligands to activate the LRR-RKs , while STOMAGEN is a positive regulator binds to the LRR-RKs to positively regulate stomatal development. Recent studies show that STOMAGEN; EPF1 and EPF2 bind to specific LRR-RKs and their associated proteins", "Stomatal peptide signalling depends on three main peptides in Arabidopsis leaves: EPIDERMAL PATTERNING FACTORS 1 and 2 (EPF1, EPF2) and STOMAGEN ( also referred to as EPIDERMAL PATTERNING FACTOR LIKE 9, EPFL9). EPF1 and EPF2 negatively regulate stomatal development by acting as ligands to activate the LRR-RKs , while STOMAGEN is a positive regulator binds to the LRR-RKs to positively regulate stomatal development. Recent studies show that STOMAGEN competes with EPF1 and EPF2 for binding of the LRR-RKs and their associated proteins", "Stomatal peptide signalling depends on three main peptides in Arabidopsis leaves: EPIDERMAL PATTERNING FACTORS 1 and 2 (EPF1, EPF2) and STOMAGEN ( also referred to as EPIDERMAL PATTERNING FACTOR LIKE 9, EPFL9). EPF1 and EPF2 positively regulate stomatal development by acting as ligands of LRR-RKs , while STOMAGEN is a negative regulator that binds to activate the LRR-RKs to negatively regulate stomatal development. Recent studies show that STOMAGEN competes with EPF1 and EPF2 for binding of the LRR-RKs and their associated proteins" ], "source":"10.1146\/annurev.arplant.58.032806.104023", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1146\/annurev.arplant.58.032806.104023", "Year":2007.0, "Citations":356.0, "answer":1, "source_journal":"Annual Review of Plant Biology", "is_expert":true }, { "question":"How is the signaling pathway triggered by peptide ligands that governs stomatal development in plants?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Genetic, structural, and biochemical evidence show, in Arabidopsis thaliana, that the peptide hormones EPF1, EPF2 and STOMAGEN directly bind to the leucine-rich repeat receptor kinase (LRR-RK) complexes, which mediate stomatal development. In the ERECTA (ER) pathway, endogenous ligands, EPIDERMAL PATTERNING FACTORs (EPF1), and (EPF2), bind the ER-YODA (YDA)-SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK) complex to transduce downstream signaling cascades composed of the TOO MANY MOUTHS (TMM)-MKK4\/5-MPK3\/6 module. The activation of MPK cascade ultimately results in the negative regulation of SPCH through phosphorylation of the MPKTD which restricts stomatal development.", "Genetic, structural, and biochemical evidence show that, in Arabidospis thaliana, the peptide hormones EPF1, EPF2 and STOMAGEN directly bind to the leucine-rich repeat receptor kinase (LRR-RK) complexes, which mediate stomatal development. In the ERECTA (ER) pathway, endogenous ligands, EPIDERMAL PATTERNING FACTORs (EPF1), and (EPF2), bind the ER-TOO MANY MOUTHS (TMM)-SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK) complex to transduce downstream signaling cascades composed of the YODA (YDA)-MKK4\/5-MPK3\/6 module. The activation of MPK cascade ultimately results in the negative regulation of SPCH through phosphorylation of the MPKTD which restricts stomatal development.", "Genetic, structural, and biochemical evidence show that, in Arabidopsis thaliana, the peptide hormones EPF1, EPF2 and STOMAGEN directly bind to the leucine-rich repeat receptor kinase (LRR-RK) complexes, which mediate stomatal development. In the ERECTA (ER) pathway, endogenous ligands, EPIDERMAL PATTERNING FACTORs (EPF1), and (EPF2), bind the ER-TOO MANY MOUTHS (TMM)-SOMATIC EMBRYOGENESIS RECEPTOR KINASE (SERK) complex to transduce downstream signaling cascades composed of the YODA (YDA)-MKK4\/5-MPK3\/6 module. The activation of MPK cascade ultimately results in the positive regulation of SPCH through phosphorylation of the MPKTD which promotes stomatal development." ], "source":"10.1146\/annurev.arplant.58.032806.104023", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1146\/annurev.arplant.58.032806.104023", "Year":2007.0, "Citations":356.0, "answer":1, "source_journal":"Annual Review of Plant Biology", "is_expert":true }, { "question":"How is the protein BASL involved in stomatal development in plants?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis, the protein BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE (BASL) is critical for establishing the asymmetry of stomatal lineage divisions. The localization of BASL in the nucleus and at the periphery correlates with specific cell behaviors. In the smaller daughter of an asymmetric division, BASL is nuclear. If BASL is only nuclear, this cell will differentiate into a GMC and eventually a pair of guard cells. If the cell retains BASL in both the nucleus and periphery, this cell will continue to divide as a MMC or M. In the larger (SLGC) daughter, BASL moves to the periphery in a region distal to the division plane. If this cell retains nuclear and peripheral BASL, it will divide asymmetrically; if it loses nuclear BASL, it will differentiate into a pavement cell. In SLGCs next to stomata, the peripheral BASL crescents must reorient prior to another asymmetric division to preserve the one-cell-spacing rule.", "In Arabidopsis, the protein BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE (BASL) is critical for establishing the asymmetry of stomatal lineage divisions. The localization of BASL in the nucleus and at the periphery correlates with specific cell behaviors. In the smaller daughter of an asymmetric division, BASL is nuclear. If BASL is only nuclear, this cell will continue to divide as a MMC or M. If the cell retains BASL in both the nucleus and periphery, this cell will differentiatne into a GMC and eventually a pair of guard cells. In the larger (SLGC) daughter, BASL moves to the periphery in a region distal to the division plane. If this cell retains nuclear and peripheral BASL, it will divide asymmetrically; if it loses nuclear BASL, it will differentiate into a pavement cell. In SLGCs next to stomata, the peripheral BASL crescents must reorient prior to another asymmetric division to preserve the one-cell-spacing rule.", "In Arabidopsis, the protein BREAKING OF ASYMMETRY IN THE STOMATAL LINEAGE (BASL) is critical for establishing the asymmetry of stomatal lineage divisions. The localization of BASL in the periphery correlates with specific cell behaviors. In the smaller daughter of an asymmetric division, BASL is nuclear. If BASL is only nuclear, this cell will differentiate into a GMC and eventually a pair of guard cells. If the cell retains BASL in both the nucleus and periphery, this cell will continue to divide as a MMC or M. In the larger (SLGC) daughter, BASL moves to the nucleus and the periphery i. If this cell retains nuclear and peripheral BASL, it will divide asymmetrically; if it loses nuclear BASL, it will differentiate into a pavement cell. In SLGCs next to stomata, the peripheral BASL crescents must reorient prior to another asymmetric division to preserve the one-cell-spacing rule." ], "source":"10.1016\/j.cell.2009.04.018", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1016\/j.cell.2009.04.018", "Year":2009.0, "Citations":260.0, "answer":0, "source_journal":"Cell", "is_expert":true }, { "question":"How is the transcription factor TCP15 involved in the thermomorphogenic response in Arabidopsis thaliana?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "TCP15 is required for optimal root elongation under high ambient temperature. This TF influences the levels of growth-related genes, which are induced in response to an increase in temperature. TCP15 directly targets the auxin biosynthesis gene YUC9. Several of the genes regulated by TCP15 are also targets of the growth regulator IAA6, indicating that TCP15 directly participates in the induction of genes involved in auxin biosynthesis and cell expansion by high temperature functionally interacting with IAA6.", "TCP15 is required for optimal petiole and hypocotyl elongation under high ambient temperature. This TF influences the levels of growth-related genes, which are induced in response to an increase in temperature. TCP15 directly targets the gibberellin biosynthesis gene GA20ox1 and the growth regulatory genes HBI1 and PRE6. Several of the genes regulated by TCP15 are also targets of the growth regulator PIF4. PIF4 binding to GA20ox1 and HBI1 is enhanced in the presence of the TCPs proteins, indicating that TCP15 directly participates in the induction of genes involved in gibberellin biosynthesis and cell expansion by high temperature functionally interacting with PIF4.", "TCP15 is required for optimal flowering under high ambient temperature. This TF influences the levels of flowering-related genes, which are repressed in response to an increase in temperature. TCP15 directly targets the gibberellin biosynthesis gene GA20ox1 and the flowering genes SOC1 and SPL3. Several of the genes regulated by TCP15 are also targets of the flowering regulator BRC1. BRC1 binding to GA20ox1 and SOC1 is enhanced in the presence of the TCPs proteins, indicating that TCP15 directly participates in the repression of genes involved in gibberellin biosynthesis and flowering by high temperature functionally interacting with BRC1. " ], "source":"10.1093\/pcp\/pcz137", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1093\/pcp\/pcz137", "Year":2019.0, "Citations":50.0, "answer":1, "source_journal":"Plant and Cell Physiology", "is_expert":true }, { "question":"What types of DNA motifs bound by transcription factors are enriched at the boundaries of TADs in plant species?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "In wheat, TAD boundary sequences are enriched in binding motifs for TCP class I (TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1) and bZIP (basic leucine zipper) transcription factors. Moreover, the TCP14 protein was found at the TAD boundaries in Arabidopsis, suggesting the evolutionary conservation of architectural functions of TCP family proteins. In addition, TAD borders in tomato are enriched in BBR\/BPC TF family binding sites, implying that proteins binding to these sequences might also contribute to boundary formation.", "In rice, TAD boundary sequences are enriched in binding motifs for TCP class I (TEOSINTE-LIKE1, CYCLOIDEA, and PROLIFERATING CELL FACTOR1) and bZIP (basic leucine zipper) transcription factors. Moreover, the TCP1 protein was found at the TAD boundaries in the basal plant Marchantia, suggesting the evolutionary conservation of architectural functions of TCP family proteins. In addition, TAD borders in Marchantia are enriched in BBR\/BPC and bHLH TF family binding sites, implying that proteins binding to these sequences might also contribute to boundary formation.", "In rice, TAD boundary sequences are enriched in binding motifs for MYB and WRKY transcription factors. Moreover, the MYB16 protein was found at the TAD boundaries in tomato, suggesting the evolutionary conservation of architectural functions of MYB family proteins. In addition, TAD borders in Marchantia are enriched in NAC TF family binding sites, implying that proteins binding to these sequences might also contribute to boundary formation." ], "source":"10.3390\/genes12091422", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.3390\/genes12091422", "Year":2021.0, "Citations":11.0, "answer":1, "source_journal":"Genes", "is_expert":true }, { "question":"Which processes are regulated by the transcription factor MIB2 during thermomorphogenesis in tomato?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Solanum lycopersicum" ], "options":[ "The bHLH transcription factor MIB2 regulates inflorescence plasticity in response to High Temperature in tomato plants. MIB2 accumulates in response to elevated ambient temperature and positively regulates hypocotyl elongation in tomato, suggesting that its functions are similar to those of PHYTOCHROME-INTERACTING FACTOR4 (PIF4), a central regulator of hypocotyl thermomorphogenesis. However, unlike the roles of PIF4 in flowering, MIB2 promotes inflorescence branching but does not regulate flowering in tomato, although its encoding gene is expressed in all meristems, and overexpressing its target gene SlCOL1 delayed flowering.", "The bHLH transcription factor MIB2 regulates tomato plasticity in response to high temperature. MIB2 decreases in response to elevated ambient temperature and this positively regulates hypocotyl elongation in tomato, suggesting that its functions are opposed to those of PHYTOCHROME-INTERACTING FACTOR4 (PIF4), a central regulator of thermomorphogenesis in Arabidopsis. Moreover, MIB2 promotes flowering in tomato at low temperatures, its encoding gene is expressed in all meristems, and overexpressing its target gene SlCOL1 promotes flowering. ", "The bZIP transcription factor MIB2 regulates leaf plasticity in response to High Temperature in tomato plants. MIB2 accumulates in response to elevated ambient temperature and negatively regulates leaf elongation in tomato, suggesting that its functions are opposed to those of PHYTOCHROME-INTERACTING FACTOR4 (PIF4), a central regulator of thermomorphogenesis in Arabidopsis. Moreover, MIB2 promotes flowering in tomato and its encoding gene is expressed in all meristems. Moreover, overexpressing its target gene SlCOL1 impairs the inflorescence branching." ], "source":"10.1038\/s41467-024-45722-0", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/s41467-024-45722-0", "Year":2024.0, "Citations":4.0, "answer":0, "source_journal":"Nature Communications", "is_expert":true }, { "question":"How TCP transcription factors interact with PIF4 in Arabidopsis thaliana and in which process is this relevant?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "PIF4 and class I TCPs proteins functionally interact in Arabidopsis thaliana to modulate gene expression responses to cold temperature, acting on a set of common target genes. However, the TCPs are not required for efficient PIF4 recognition of certain target genes. Protein\u2013protein interactions between PIF4 and the TCPs may also have a role in this process but were not validated up until now. These transcription factors are both required for optimal stomata closure under cold ambient temperature.", "PIF4 and class I TCPs proteins functionally interact in Arabidopsis thaliana to modulate gene expression responses against pathogens, acting on a set of common target genes. The TCPs would be required for efficient PIF4 recognition of some target genes, probably through recruiting lncRNAs to the promoter regions. Protein\u2013protein interactions between PIF4 and the TCPs transcription factors were not validated so far. These transcription factors are both required for optimal defense against pathogens.", "PIF4 and class I TCPs proteins functionally interact in Arabidopsis thaliana to modulate gene expression responses to high temperature, acting on a set of common target genes. The TCPs would be required for efficient PIF4 recognition of certain target genes, probably through binding to nearby regions in their promoters. Protein\u2013protein interactions between PIF4 and the TCPs may also have a role in this process. This protein-protein interaction was validated for PIF4 and TCP15 using Bimolecular Fluorescence Complementation (BiFC) and yeast two-hybrid assay. These transcription factors are both required for optimal petiole and hypocotyl elongation under high ambient temperature." ], "source":"10.1093\/pcp\/pcz137", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1093\/pcp\/pcz137", "Year":2019.0, "Citations":50.0, "answer":2, "source_journal":"Plant and Cell Physiology", "is_expert":true }, { "question":"Which lncRNA is involved in the thermomorphogenic response in Arabidopsis thaliana and how?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The lncRNA FIRRE controls a large set of genes related to the thermomorphogenic response. FIRRE interacts with the UBIQUITIN-LIKE CONTAINING PHD AND RING FINGER DOMAINS 1 (UHRF1) and with the methylcytosine-binding protein VARIANT IN METHYLATION 5 (VIM5). In particular, the FIRRE-VIM5-UHRF1 complex directly targets the heat-responsive brassinosteroid-biosynthetic gene CAS1 and conjointly mediates cytosine methylation and H3K27me3 deposition at its promoter, representing a new epigenetic mechanism regulating the plant response to warm temperatures.", "The lncRNA COLDAIR controls a large set of genes related to the thermomorphogenic response. COLDAIR interacts with the transcription factor WRKY63 that has been functionally associated with H3K27me3 demethylation to regulate gene expression in Arabidopsis. In particular, the COLDAIR-WRKY63 complex directly targets heat-responsive floweriing-induced genes, such as CBF1, COR47, KIN1, ADS2, AtCP1, HD2C, and GI. This represents a new mechanism regulating the plant response to warm temperatures.", "The lncRNA APOLO controls a large set of genes related to the thermomorphogenic response. APOLO interacts with the PRC1-component LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) and with the methylcytosine-binding protein VARIANT IN METHYLATION 1 (VIM1). In particular, the APOLO-VIM1-LHP1 complex directly targets the heat-responsive auxin-biosynthetic gene YUCCA2 and conjointly mediates cytosine methylation and H3K27me3 deposition at its promoter, representing a new epigenetic mechanism regulating the plant response to warm temperatures." ], "source":"10.1186\/s13059-022-02750-7", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1186\/s13059-022-02750-7", "Year":2022.0, "Citations":29.0, "answer":2, "source_journal":"Genome Biology", "is_expert":true }, { "question":"In humans the core Polycomb Repressive Complex 2 is composed by four core subunits: SUZ12, EED, EZH1\/EZH2, and RBBP4\/7. Which are the homologs of SUZ12 in Arabidopsis thaliana?", "area":"GENE REGULATION - EPIGENETICS AND TGS", "plant_species":[ "non-specific" ], "options":[ "In Arabidopsis thaliana, SUZ12 is encoded by multiple genes.", "In Arabidopsis thaliana, the homologs of SUZ12 are FIS2, EMF2 and VRN2.", "In Arabidopsis thaliana, the homologs of SUZ12 are MEA, CLF and SWN." ], "source":"https:\/\/doi.org\/10.1016\/j.tplants.2021.06.006", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.tplants.2021.06.006", "Year":2021.0, "Citations":59.0, "answer":1, "source_journal":"Trends in Plant Science", "is_expert":true }, { "question":"The PCR2 complex has conserved functions in plants and animals. Which histone modification is the result of the action of PCR2 in Arabidopsis thaliana?", "area":"GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS", "plant_species":[ "non-specific" ], "options":[ "In Arabidopsis PRC2 mediates the deposition of histone H3 lysine 36 trimethylation (H3K36me3)", "In Arabidopsis PRC2 mediates the deposition of histone H3 lysine 27 trimethylation (H3K27me3)", "In Arabidopsis PRC2 mediates the deposition of histone H3 lysine 4 trimethylation (H3K4me3)" ], "source":"10.1038\/sj.emboj.7601311", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1038\/sj.emboj.7601311", "Year":2006.0, "Citations":344.0, "answer":1, "source_journal":"The EMBO Journal", "is_expert":true }, { "question":"The N-end rule pathway regulates protein destruction through the recognition of N-terminal degradation sequences (N-degrons) in target proteins, which promote their ubiquitylation by speci\ufb01c E3 ligases. Which Arabidopsis PCR2 subunit Is regulated by the N-end rule pathway?", "area":"GENE REGULATION - EPIGENETICS AND TGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The plant PRC2 subunit EMF2 as a substrate of the N-end rule pathway via its conserved N-terminal Cys2 residue.", "The plant PRC2 subunit VRN2 as a substrate of the N-end rule pathway via its conserved N-terminal Cys2 residue.", "The plant PRC2 subunit FIS2 as a substrate of the N-end rule pathway via its conserved N-terminal Cys2 residue." ], "source":"10.1038\/s41467-018-07875-7", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41467-018-07875-7", "Year":2018.0, "Citations":99.0, "answer":1, "source_journal":"Nature Communications", "is_expert":true }, { "question":"The Jumonji C (JmjC) family of Fe(II)-dependent and 2-oxoglutarate-dependent dioxygenases as demethylases of tri-, di- and mono-methylated histones. Which JmJC proteins are proposed to have H3K27me3 demethylase activity in Arabidopsis thaliana?", "area":"GENE REGULATION - EPIGENETICS AND TGS", "plant_species":[ "non-specific" ], "options":[ "Five H3K27me3 demethylases are described in Arabidopsis: JUMONJI 30 (JMJ30), JUMONJI 32 (JMJ32), EARLY FLOWERING 6 (ELF6\/JMJ11), RELATIVE OF ELF6 (REF6\/JMJ12), and JUMONJI 13 (JMJ13).", "Two H3K27me3 demethylases are described in Arabidopsis: JUMONJI 30 (JMJ30) and JUMONJI 32 (JMJ32).", "Five H3K27me3 demethylases are described in Arabidopsis: JUMONJI 10 (JMJ10), JUMONJI 11 (JMJ11), JUMONJI 12 (JMJ12), JUMONJI 13 (JMJ13), JUMONJI 14 (JMJ14), and JUMONJI 15 (JMJ15)." ], "source":"10.1016\/j.isci.2020.101715", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.isci.2020.101715", "Year":2020.0, "Citations":27.0, "answer":0, "source_journal":"iScience", "is_expert":true }, { "question":"Many plants have a vernalization requirement, that is, they actively repress flowering until after a period of prolonged cold, in order to align seed production with the favourable environmental conditions of spring. Which gene is primarily affected by vernalization in Arabidopsis thaliana, and what is the effect? ", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "non-specific" ], "options":[ "In Arabidopsis thaliana, vernalization involves downregulation and epigenetic silencing of the gene encoding the floral activator FLOWERING LOCUS T (FT).", "In Arabidopsis thaliana, vernalization involves downregulation and epigenetic silencing of the gene encoding the floral repressor FLOWERING LOCUS C (FLC).", "In Arabidopsis thaliana, vernalization involves upregulation and epigenetic activation of the gene encoding the floral repressor FLOWERING LOCUS C (FLC)." ], "source":"10.1146\/annurev-cellbio-100616-060546", "normalized_plant_species":"Non-specific", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1146\/annurev-cellbio-100616-060546", "Year":2017.0, "Citations":258.0, "answer":1, "source_journal":"Annual Review of Cell and Developmental Biology", "is_expert":true }, { "question":"How does the gene network regulated by the gene FLOWERING LOCUS C (FLC) works in Arabidopsis thaliana to regulate flowering time?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "FLC, a MADS box transcription factor, is a major repressor of flowering in the family Brassicaceae, and it is induced by VERNALIZATION INSENSITIVE3 (VIN3) and VERNALIZATION2 (VRN2). FLC represses the genes FRIGIDA (FRI), the FRI-complex and other genes such us VERNALIZATION INDEPENDENCE3 (VIP3), thereby repressing flowering and setting the requirement for vernalization. When plants are vernalized by winter chilling, FLC is epigenetically repressed, and this is mediated by genes such us FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) and FLOWERING LOCUS D (FD). Consequently, FRI, the FRI-complex and VIP3 expression is derepressed, and flowering is induced.", "FLC, a MADS box transcription factor, is a major repressor of flowering in the family Brassicaceae, and it is induced by FRIGIDA (FRI), the FRI-complex and other genes such us VERNALIZATION INDEPENDENCE3 (VIP3). FLC represses the floral integrators FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) and FLOWERING LOCUS D (FD), thereby delaying flowering and setting the requirement for vernalization. When plants are vernalized by winter chilling, FLC is epigenetically silenced, a process mediated by genes such us VERNALIZATION INSENSITIVE3 (VIN3) and VERNALIZATION2 (VRN2). Consequently, FT, SOC1 and FD expression is derepressed, and flowering is induced.", "FLC, a MADS box transcription factor, is a major inducer of flowering in the family Brassicaceae, and it is repressed by FRIGIDA (FRI), the FRI-complex and other genes such us VERNALIZATION INDEPENDENCE3 (VIP3). FLC induces the floral integrators FLOWERING LOCUS T (FT), SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) and FLOWERING LOCUS D (FD), thereby promoting flowering and releasing from the requirement for vernalization. When plants are vernalized by winter chilling, FLC is epigenetically regulated, and this is mediated by genes such us VERNALIZATION INSENSITIVE3 (VIN3) and VERNALIZATION2 (VRN2). Consequently, FT, SOC1 and FD expression is derepressed, and flowering is induced." ], "source":"10.1111\/nph.14520", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1111\/nph.14520", "Year":2017.0, "Citations":37.0, "answer":1, "source_journal":"New Phytologist", "is_expert":true }, { "question":"What is the pleiotropic effect of the gene FLOWERING LOCUS C (FLC) in the life cycle of Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The gene FLOWERING LOCUS C (FLC) act as a pleiotropic gene in the life cycle of Arabidopsis thaliana: it induces flowering and represses germination. The pleiotropic effect depends on the environment experienced by the plants and seeds: mother plants that have experienced vernalization, produced progeny with a lower germination propensity when they have functional FLC and FRIGIDA (FRI) alleles. However, in a functional FRI background, disruption of FLC enhanced the response to maternal vernalization by inducing germination, indicating a positive effect for FRI independently of FLC. This shows slightly convergent pathways in the regulation of flowering and germination.", "The gene FLOWERING LOCUS D (FD) act as a pleiotropic gene in the life cycle of Arabidopsis thaliana: it represses flowering and induces germination. The pleiotropic effect depends on the environment experienced by the plants and seeds: mother plants that have not experienced summer, produced progeny with a higher germination propensity when they have functional FD, FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1) alleles. However, in a functional FD background, disruption of GA20OX1 reduced the response to maternal vernalization by reducing germination, indicating a negative effect for FD independently of SOC1 . This shows slightly divergent pathways in the regulation of flowering and germination.", "The gene FLOWERING LOCUS C (FLC) act as a pleiotropic gene in the life cycle of Arabidopsis thaliana: it represses flowering and induces germination. The pleiotropic effect depends on the environment experienced by the plants and seeds: mother plants that have not experienced vernalization, produced progeny with a higher germination propensity when they have functional FLC and FRIGIDA (FRI) alleles. However, in a functional FRI background, disruption of FLC reduced the response to maternal vernalization by reducing germination, indicating a negative effect for FRI independently of FLC . This shows slightly divergent pathways in the regulation of flowering and germination." ], "source":"10.1111\/nph.14520", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1111\/nph.14520", "Year":2017.0, "Citations":37.0, "answer":2, "source_journal":"New Phytologist", "is_expert":true }, { "question":"How is FLOWERING LOCUS C (FLC) expression reset during the reproductive stage in Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "After fertilization, the repressive effect of vernalization on FLOWERING LOCUS C (FLC) expression is reset in each generation during embryogenesis. Through binding to a distal cis-acting CCAAT at the FLC promoter, the B3-domain transcription factor ABSCISIC ACID INSENSITIVE 5 (ABI5) reactivates FLC expression starting on late embryogenesis up to embryo maturation stages. ABI5 function depends on the binding of the pioneer transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3) to a CME motif in the proximal FLC promoter early in the embryogenesis process. Loss of function of ABI3 is related to a reduction of ABI5 binding to the FLC promoter. ABI5 recruits the FRIGIDA (FRI)-complex leading to an increase of the active H3Kme3 and reduction of the H3K27me3 marks on the FLC locus, thereby resetting FLC expression in the seeds.", "After fertilization, the repressive effect of vernalization on FLOWERING LOCUS C (FLC) expression is reset in each generation during embryogenesis. Through binding to a cis-acting CME at the FLC promoter, the B3-domain transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3) reactivates FLC expression starting on late embryogenesis up to embryo maturation stages. ABI3 function depends on the binding of the pioneer transcription factor LEAFY COTYLEDON 1 (LEC1) to a CCAAT motif in the distal FLC promoter early in the embryogenesis process. Loss of function of LEC1 is related to a reduction of ABI3 binding to the FLC promoter. ABI3 recruits the FRIGIDA (FRI)-complex leading to an increase of the active H3Kme3 and reduction of the H3K27me3 marks on the FLC locus, thereby resetting FLC expression in the seeds.", "After fertilization, the repressive effect of vernalization on FLOWERING LOCUS C (FLC) expression is reinforced in each generation during embryogenesis. Through binding to a cis-acting CME at the FLC promoter, the B3-domain transcription factor ABSCISIC ACID INSENSITIVE 3 (ABI3) represses FLC expression starting on late embryogenesis up to embryo maturation stages. ABI3 function depends on the binding of the pioneer transcription factor LEAFY COTYLEDON 1 (LEC1) to a CCAAT motif in the distal FLC promoter early in the embryogenesis process. Loss of function of LEC1 is related to an increase of ABI3 binding to the FLC promoter. ABI3 represses the binding of the FRIGIDA (FRI)-complex leading to a reduction of the active H3Kme3 and an increase of the H3K27me3 marks on the FLC locus, thereby repressing FLC expression in the seeds." ], "source":"10.1093\/plcell\/koac077", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1093\/plcell\/koac077", "Year":2022.0, "Citations":25.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How is flowering regulated by vernalization in wheat and barley?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Triticum aestivum", "Hordeum vulgare" ], "options":[ "VERNALIZATION INDEPENDENCE 1 (VIP1), a B3-domain transcription factor related to the Arabidopsis meristem identity genes VERNALIZATION1 (VRN1) and FLOWERING LOCUS C (FLC), is the main regulator of the response to vernalization in wheat and barley. In spring varieties of these cereals, VIP1 is induced by cold exposure. This induction is epigenetically regulated by the inhibition of the H3K4me3 repressive marks and the promotion of H3K27me3 levels in the VIP1 locus. VIP1 expression is correlated with the down-regulation of VRN2, a repressor of flowering. In consequence, expression of FT (a homolog of Arabidopsis VRN1) is released and flowering is induced.", "VERNALIZATION1 (VRN1), a MADS box transcription factor related to the Arabidopsis meristem identity genes APETALA1 (AP1) and FRUITFUL (FUL), is the main regulator of the response to photoperiod in wheat and barley. In winter varieties of these cereals, VRN1 is induced by long days. This induction is epigenetically regulated by the inhibition of the H3K27me3 repressive marks and the promotion of H3K4me3 levels in the VRN1 locus. VRN1 expression is correlated with the down-regulation of VRN2 long days, a repressor of flowering. In consequence, expression of VRN3 (a homolog of Arabidopsis FT) is repressed and flowering is induced.", "VERNALIZATION1 (VRN1), a MADS box transcription factor related to the Arabidopsis meristem identity genes APETALA1 (AP1) and FRUITFUL (FUL), is the main regulator of the response to vernalization in wheat and barley. In winter varieties of these cereals, VRN1 is induced by cold exposure. This induction is epigenetically regulated by the inhibition of the H3K27me3 repressive marks and the promotion of H3K4me3 levels in the VRN1 locus. VRN1 expression is correlated with the down-regulation of VRN2, a repressor of flowering. In consequence, expression of VRN3 (a homolog of Arabidopsis FT) is released and flowering is induced." ], "source":"10.1111\/ppl.13163", "normalized_plant_species":"Cereal Grains", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1111\/ppl.13163", "Year":2020.0, "Citations":50.0, "answer":2, "source_journal":"Physiologia Plantarum", "is_expert":true }, { "question":"How does FLOWERING LOCUS T (FT) induces flowering in Arabidopsis plants?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The Arabidopsis FT protein translocates from the source leaves through the phloem to the shoot apex to induce the transition from vegetative to reproductive growth. The FT gene is expressed in the phloem companion cells in source leaves. The protein is then actively translocated to the sieve elements and to the phloem stream through the channel FT INTERACTING PROTEIN 1 (FTIP1). While the load into the phloem occurs through active transport, FT protein unloading into the shoot apical meristem occurs through the function of a passive plasmodesmata pathway not fully understood yet. Once in the shoot apical meristem, FT interacts with FD to transiently induce APETALA1 (AP1) expression, thus leading to floral development.", "The Arabidopsis FT protein translocates from the source leaves through the phloem to the shoot apex to induce the transition from vegetative to reproductive growth. The FT gene is expressed in the phloem companion cells in source leaves. The protein is then translocated to the xylem elements and to the xylem stream through difussion with the aid of lipids. While the load into the xylem occurs through apoplastic diffusion, FT protein unloading into the shoot apical meristem engages the function of a selective apoplastic pathway not fully understood yet. Once in the shoot apical meristem, FT interacts with AP1 to transiently induce FD expression, thus leading to floral development.", "The Arabidopsis FT protein translocates from the source leaves through the phloem to the shoot apex to induce the transition from vegetative to reproductive growth. The FT gene is expressed in the phloem companion cells in source leaves. The protein is then translocated to the sieve elements and to the phloem stream through plasmodesmata with the aid of the FT INTERACTING PROTEIN 1 (FTIP1). While the load into the phloem occurs through symplasmic diffusion, FT protein unloading into the shoot apical meristem engages the function of a selective plasmodesmata pathway not fully understood yet. Once in the shoot apical meristem, FT interacts with FD to transiently induce APETALA1 (AP1) expression, thus leading to floral development." ], "source":"10.1242\/dev.171504, 10.1093\/pcp\/pcae001, 10.1111\/tpj.12213", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1111\/tpj.12213", "Year":2013.0, "Citations":79.0, "answer":2, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"What are the number of the overlapping up-regulated genes under heat stress in Arabidopsis thaliana, Nothofagus pumilio and Populus tomentosa leaves, and which are the overrepresented Gene Ontology biological processes promoted by heat stress in common to the three species?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Nothofagus pumilio", "Arabidopsis thaliana", "Populus tomentosa" ], "options":[ "There are at least 68 common-regulated genes between Arabidopsis thaliana, Nothofagus pumilio and Populus tomentosa subjected to heat stress. The overrepresented Gene Ontology biological processes promoted by heat stress in common to the three species were: response to unfolded protein, cellular response to unfolded protein, protein refolding, cellular response to topologically incorrect protein, response to topologically incorrect protein, chaperone cofactor-dependent protein refolding, de novo posttranslational protein folding, de novo protein folding, endoplasmic reticulum unfolded protein response, protein folding, chaperone-mediated protein folding, response to heat, cellular response to hypoxia, cellular response to oxygen levels, cellular response to decreased oxygen levels, response to temperature stimulus, response to hypoxia, response to cadmium ion, cellular response to stress, cellular response to chemical stimulus, response to inorganic substance, response to abiotic stimulus, response to organic substance, response to chemical, response to stress.", "There are at least 68 common-regulated genes between Arabidopsis thaliana, Nothofagus pumilio and Populus tomentosa subjected to heat stress. The overrepresented Gene Ontology biological processes promoted by heat stress in common to the three species were: cellular response to unfolded protein, response to unfolded protein, response to topologically incorrect protein, response to stress, response to stimulus, response to organic substance, response to chemical, cellular response to topologically incorrect protein, protein refolding, protein folding, response to cadmium ion, response to metal ion, response to inorganic substance, translation, cellular protein metabolic process. metabolic process, organonitrogen compound metabolic process, organic substance biosynthetic process, biosynthetic process, peptide biosynthetic process, peptide metabolic process, cellular amide metabolic process, organonitrogen compound biosynthetic process, amide biosynthetic process, cellular nitrogen compound biosynthetic process, response to oxidative stress, response to drug, response to salt stress, response to osmotic stress.", "There are at least 114 common-regulated genes between Arabidopsis thaliana, Nothofagus pumilio and Populus tomentosa subjected to heat stress. The overrepresented Gene Ontology biological processes promoted by heat stress in common to the three species were Photosynthesis: light harvesting in photosystem I, photosynthesis: light harvesting, generation of precursor metabolites and energy, photosynthesis: light reaction, photosynthesis: photosynthetic electron transport in photosystem I, photosynthetic electron transport chain, electron transport chain, oxidation-reduction process, protein-chromophore linkage, carbon fixation, gluconeogenesis, glucose metabolic process, hexose metabolic process, monosaccharide metabolic process, hexose biosynthetic process, monosaccharide biosynthetic process, regulation of photosynthesis, light reaction, regulation of photosynthesis, regulation of generation of precursor metabolites and energy, photosystem II assembly, response to high light intensity, response to light intensity, response to light stimulus, response to radiation, response to abiotic stimulus, response to stimulus, response to cytokinin." ], "source":"https:\/\/doi.org\/10.1371\/journal.pone.0246615", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"ENVIRONMENT", "doi":"10.1371\/journal.pone.0246615", "Year":2021.0, "Citations":6.0, "answer":0, "source_journal":"PLOS ONE", "is_expert":true }, { "question":"Which are the over-expressed transcription factor families that showed more than 2-fold enrichment in Nothofagus pumilio leaves under heat stress?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Nothofagus pumilio" ], "options":[ "The over-expressed transcription factor families that showed more than 2-fold enrichment in N. pumilio leaves under heat stress HSF1, HSF2, MYB, ERF", "The over-expressed transcription factor families that showed more than 2-fold enrichment in N. pumilio leaves under heat stress ERF, WRKY, LBD, WOX, EIL.", "The over-expressed transcription factor families that showed more than 2-fold enrichment in N. pumilio leaves under heat stress ERFs, MYBs, NACs, NF-YC" ], "source":"https:\/\/doi.org\/10.1371\/journal.pone.0246615", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"ENVIRONMENT", "doi":"10.1371\/journal.pone.0246615", "Year":2021.0, "Citations":6.0, "answer":1, "source_journal":"PLOS ONE", "is_expert":true }, { "question":"How is the transcription factors AREB1 involved in the response to drought stress in populus trichocarpa?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Populus trichocarpa" ], "options":[ "In Populus trichocarpa, AREB1 binds to ABRE motifs associated with PtrNAC genes and recruits the histone acetyltransferase unit ADA2b-GCN5, forming AREB1-ADA2b-GCN5 ternary protein complexes. This recruitment enables GCN5-mediated histone acetylation to enhance H3K9ac and increase RNA polymerase II recruitment specifically at these PtrNAC genes for the promotion of drought tolerance. ", "In Populus trichocarpa, AREB1 binds to ABRE motifs associated with PtrNAC genes and recruits the histone acetyltransferase unit ADA2b-GCN5, forming AREB1-ADA2b-GCN5 ternary protein complexes. This recruitment disables GCN5-mediated histone acetylation to decrease H3K9ac and increase RNA polymerase II recruitment specifically at these PtrNAC genes for the promotion of drought tolerance. ", "In Populus trichocarpa, AREB1 binds to ABRE motifs associated with PtrNAC genes and recruits the histone acetyltransferase unit ADA2b-GCN5, disassembling AREB1-ADA2b-GCN5 ternary protein complexes. This recruitment disables GCN5-mediated histone acetylation to enhance H3K9ac and decrease RNA polymerase II recruitment specifically at these PtrNAC genes for the repression of drought tolerance. " ], "source":"https:\/\/doi.org\/10.1105\/tpc.18.00437", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"ENVIRONMENT", "doi":"10.1105\/tpc.18.00437", "Year":2018.0, "Citations":179.0, "answer":0, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"Which is the effect of warm temperatures on the functioning of the circadian clock and the time-of-day patterns of gene regulation in Nothofagus pumilio leaves under constant conditions?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Nothofagus pumilio" ], "options":[ "Warm temperatures affected the functioning of the circadian clock under constant conditions since circadian oscillator components became arrhythmic or showed changes in their moment of maximum expression when seedlings were exposed to 34\u00b0C. Warm temperatures also affected the time-of-day patterns of gene regulation, because 72.3% of the differentially expressed genes between subjective dawn and dusk at 20\u00b0C lost their regulation at 34\u00b0C. ", "Warm temperatures promoted the functioning of the circadian clock under constant conditions since circadian oscillator components became rhythmic or showed changes in their moment of maximum expression when seedlings were exposed to 34\u00b0C. Warm temperatures also affected the time-of-day patterns of gene regulation, because 72.3% of the differentially expressed genes between subjective dawn and dusk at 20\u00b0C were up-regulated at 34\u00b0C. ", "Warm temperatures affected the functioning of the circadian clock under constant conditions since circadian oscillator components became arrhythmic or showed changes in their moment of maximum expression when seedlings were exposed to 34\u00b0C. Warm temperatures didn\u2019t affect the time-of-day patterns of gene regulation, because only 0.3% of the differentially expressed genes between subjective dawn and dusk at 20\u00b0C lost their regulation at 34\u00b0C." ], "source":"https:\/\/nph.onlinelibrary.wiley.com\/doi\/10.1111\/nph.20342 \/ https:\/\/doi.org\/10.1101\/2024.03.22.586279", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"ENVIRONMENT", "doi":"10.1101\/2024.03.22.586279", "Year":2024.0, "Citations":0.0, "answer":0, "source_journal":null, "is_expert":true }, { "question":"Which is the role of STZ1 in the response of abiotic stress in tree species?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "STZ1 is induced by drought, frost, and chilling stress in leaves and promotes the expression of ascorbate peroxidase 2, which promotes the accumulation of ROS and decreases frost tolerance. The ectopic overexpression of STZ1 reduces freezing tolerance in transgenic poplar. ", "STZ1 is induced by drought, frost, and chilling stress in leaves and promotes the expression of ascorbate peroxidase 2, which scavenges ROS and enhances frost tolerance. The ectopic overexpression of STZ1 improves freezing tolerance in transgenic poplar. ", "STZ1 is induced by drought, frost, and chilling stress in leaves and represses the expression of ascorbate peroxidase 2, which scavenges ROS and enhances frost tolerance. The ectopic overexpression of STZ1 improves heat tolerance in transgenic poplar." ], "source":"doi: 10.1111\/pbi.13130, reviewed in doi:10.1093\/jxb\/erz532", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1093\/jxb\/erz532", "Year":2019.0, "Citations":76.0, "answer":1, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"What is the distribution pattern of heterochromatic and euchromatic marks at the periphery of tomato nuclei?", "area":"GENOME AND GENOMICS", "plant_species":[ "Solanum lycopersicum" ], "options":[ "chromatin that carries heterochromatic or euchromatic marks is equally found at the nuclear periphery of tomato nuclei.", "The chromatin that carries euchromatin marks is highly enriched at the nuclear periphery of tomato nuclei, while heterochromatic marks are depleted. ", "chromatin that carries heterochromatic marks is highly enriched at the nuclear periphery in tomato nuclei, while euchromatic marks are depleted." ], "source":"10.1073\/pnas.240073712", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"GENOME AND GENOMICS", "doi":null, "Year":null, "Citations":null, "answer":2, "source_journal":null, "is_expert":true }, { "question":"What are the spatial localization patterns of centromeres and telomeres in a plant species with its chromosomes displaying Rabl conformation?", "area":"GENOME AND GENOMICS", "plant_species":[ "non-specific" ], "options":[ "In the Rabl conformation, centromeres are clustered at the nuclear envelope or at one end of the nucleus. The telomeres are evenly distributed in the nucleoplasm.", "In the Rabl conformation, centromeres are clustered at the nuclear envelope or at one end of the nucleus. The telomeres of the chromosomes are typically found at the opposite end of the nucleus from the centromeres.", "In the Rabl conformation, centromeres are clustered at the nucleolus. The telomeres are clustered at the nuclear envelope or at one end of the nucleus." ], "source":"10.1104\/pp.111.187161", "normalized_plant_species":"Non-specific", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1104\/pp.111.187161", "Year":2011.0, "Citations":100.0, "answer":1, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"What changes do telomeres undergo in the Arabidopsis nuc1 mutant?", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The nuc1 mutants exhibit shortened telomeres compared to wild-type Arabidopsis. In addition, telomeres in nuc1 mutants become clustered in the nucleolus.", "The nuc1 mutants exhibit longer telomeres compared to wild-type Arabidopsis. In addition, compared to wild-type, telomeres in nuc1 mutants are no longer clustered at the nuclear periphery.", "The nuc1 mutants exhibit shortened telomeres compared to wild-type Arabidopsis. In addition, telomeres in nuc1 mutants are no longer clustered in the nucleolus." ], "source":"10.1016\/j.celrep.2016.07.016", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1016\/j.celrep.2016.07.016", "Year":2016.0, "Citations":120.0, "answer":2, "source_journal":"Cell Reports", "is_expert":true }, { "question":"How are chromatin accessibility and DNA methylation associated with TADs in Marchantia?", "area":"GENOME AND GENOMICS", "plant_species":[ "non-specific" ], "options":[ "In Marchantia, the TAD borders are depleted of accessible chromatin but enriched with DNA methylation. Moreover, a subset of Marchantia TADs has a high level of chromatin accessibility throughout.", "In Marchantia, the TAD borders are enriched with accessible chromatin but depleted of DNA methylation. Moreover, a subset of Marchantia TADs has a high level of DNA methylation throughout. ", "In Marchantia, the TAD borders are enriched with both accessible chromatin and DNA methylation. Moreover, a subset of Marchantia TADs has a high level of DNA methylation and chromatin accessibility throughout." ], "source":"10.1038\/s41477-020-00766-0", "normalized_plant_species":"Non-specific", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1038\/s41477-020-00766-0", "Year":2020.0, "Citations":66.0, "answer":1, "source_journal":"Nature Plants", "is_expert":true }, { "question":"In Arabidopsis thaliana, how is the expression of TFL1 switched off in floral primordia?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis floral primordia, an enhancer element located at the 3\u2019 downstream region of the TFL1 locus is bound by the MADS-box transcription factor protein complex. Such protein-DNA interaction prevents this cis-element from interacting with the TFL1 transcription start site, ensuring that the expression of TFL1 is turned off.", "In Arabidopsis floral primordia, an enhancer element located at the 5\u2019 downstream region of the TFL1 locus is bound by the MADS-box transcription factor protein complex. This protein-DNA interaction promotes this cis-element from interacting with the TFL1 transcription termination site, ensuring that the expression of TFL1 is turned off.", "In Arabidopsis floral primordia, the transcription start site of the TFL1 locus is bound by the MADS-box transcription factor protein complex. Such protein-DNA interaction promotes the TFL1 promoter region to recruit RNA polymerase II, ensuring that the expression of TFL1 is turned off." ], "source":"10.1016\/j.devcel.2013.02.013", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.devcel.2013.02.013", "Year":2013.0, "Citations":173.0, "answer":0, "source_journal":"Developmental Cell", "is_expert":true }, { "question":"What are the effects of silicon (Si) application over soybean nodulation and root density in soybean plants and what are the main transcription factors (TFs) families involved in these effects?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Glycine max" ], "options":[ "Silicon (Si) application increases soybean root development but reduces nodulation. The upregulation of specific TF families such as LysM-RLKs, bHLH, bZIP, MYB, and WRKY, along with the involvement of the cytokinins transporter pathways are involved in these effects. ", "Silicon (Si) application enhances soybean root development and nodulation. The upregulation of specific TF families such as AP2\/ERF-RAV, bHLH, bZIP, MYB, and WRKY, along with the involvement of the auxin transporter pathway are involved in these effects. ", "Silicon (Si) application reduces soybean root development and nodulation. The upregulation of specific TF families such as AP2\/ERF-RAV, bHLH, bZIP, MYB, and WRKY, along with the involvement of the cytokinins transporter pathways are involved in these effects." ], "source":"https:\/\/link.springer.com\/article\/10.1007\/s00299-024-03250-7", "normalized_plant_species":"Legumes", "normalized_area":"ENVIRONMENT", "doi":"10.1007\/s00299-024-03250-7", "Year":2024.0, "Citations":1.0, "answer":1, "source_journal":"Plant Cell Reports", "is_expert":true }, { "question":"Is the non-legume Parasponia andersonii able to control nodule symbiosis in response to exogenous nitrogen concentrations? If so, which symbiotic parameters are affected under high-nitrogen concentrations? ", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Parasponia andersonii" ], "options":[ "As well as legumes, the non-legume P. andersonii is able to control nodule symbiosis in response to exogenous nitrogen concentrations. This negative regulation of nodulation is indicated by a reduction in nodule number, total nodule fresh weight, nodule volume and rhizobial CFUs per mg of nodule under low-nitrogen conditions.", "As well as legumes, the non-legume P. andersonii is able to control nodule symbiosis in response to exogenous nitrogen concentrations. This negative regulation of nodulation is indicated by a reduction in nodule number, total nodule fresh weight, nodule volume and rhizobial CFUs per mg of nodule under high-nitrogen conditions.", "Unlike legumes, the non-legume P. andersonii is not able to control nodule symbiosis in response to exogenous nitrogen concentrations. This lack of regulation of nodulation is indicated by a similar nodule number, total nodule fresh weight, nodule volume and rhizobial CFUs per mg in low or high nitrogen concentrations." ], "source":"https:\/\/doi.org\/10.3389\/fpls.2019.01779", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.3389\/fpls.2019.01779", "Year":2020.0, "Citations":19.0, "answer":1, "source_journal":"Frontiers in Plant Science", "is_expert":true }, { "question":"What is the impact of nitrogen availability in the soil over Lotus japonicus-Mesorhizobium loti root nodule symbiosis and what are the key genes involved in regulation of nodule number?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Lotus japonicus" ], "options":[ "Nitrogen availability in the soils positively affects the root nodule symbiosis between Lotus japonicus and Mesorhizobium loti. Lotus japonicus NITRATE UNRESPONSIVE SYMBIOSIS 1 (NRSYM1) encodes an NLP (NIN-LIKE PROTEIN) transcription factor that accumulates in the nucleus in response to nitrate and positively affects nodule size and rhizobial infection by controlling the production of the root-derived mobile peptide CLE-RS1 that interacts with HAR-1.", "Nitrogen availability in the soils negatively affects the root nodule symbiosis between Lotus japonicus and Mesorhizobium loti. Lotus japonicus NITRATE UNRESPONSIVE SYMBIOSIS 1 (NRSYM1) encodes an NLP (NIN-LIKE PROTEIN) transcription factor that accumulates in the nucleus in response to nitrate and negatively regulates nodule number by controlling the production of the root-derived mobile peptide CLE-RS2 that interacts with HAR-1.", "Nitrogen availability in the soils negatively affects the root nodule symbiosis between Lotus japonicus and Mesorhizobium loti. Lotus japonicus NIN encodes a transcription factor that accumulates in the nucleus in response to nitrate and negatively regulates nodule size by controlling the production of the shoot-derived mobile peptide CLE-RS2 that interacts with HAR-1." ], "source":"https:\/\/doi.org\/10.1038\/s41467-018-02831-x", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/s41467-018-02831-x", "Year":2018.0, "Citations":146.0, "answer":1, "source_journal":"Nature Communications", "is_expert":true }, { "question":"How does low phosphorus (P) concentration affect root nodule symbiosis in soybean (Glycine max) plants?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Glycine max" ], "options":[ "Phosphorus (P) is necessary for nitrogen fixation in the root nodules of soybean plants. High phosphorus concentrations negatively affect Nitrogen accumulation, and nodule number, weight and nitrogenase activity. ", "Phosphorus (P) is necessary for nitrogen fixation in the root nodules of soybean plants. Low phosphorus concentrations negatively affect Nitrogen accumulation, and nodule number, weight and nitrogenase activity. ", "Phosphorus (P) is not necessary for nitrogen fixation in the root nodules of soybean plants. " ], "source":"https:\/\/link.springer.com\/article\/10.1007\/s13199-022-00882-9", "normalized_plant_species":"Legumes", "normalized_area":"ENVIRONMENT", "doi":"10.1007\/s13199-022-00882-9", "Year":2022.0, "Citations":7.0, "answer":1, "source_journal":"Symbiosis", "is_expert":true }, { "question":"What is the effect of salt stress over the symbiotic signalling pathway in soybean (Glycine max) plants and what are the main genes involved in this effect?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Glycine max" ], "options":[ "Salt stress inhibits root nodule symbiosis. GmSK2\u20108 (glycogen synthase kinase 3\u2010like kinase) inhibits rhizobial infection and nodule formation in soybean under salt\u2010stress conditions by phosphorylating the LHR1 domain of GmNSP1a. This phosphorylation inhibits GmNSP1a capability to bind to the promoter region of the symbiotic gene GmERN1a. Additionally, the overexpression of GmSK2\u20108 significantly reduces the expression of GmNINb and GmENOD40\u20101.", "Salt stress inhibits root nodule symbiosis. GmSK2\u20108 (glycogen synthase kinase 3\u2010like kinase) inhibits rhizobial infection and nodule formation in soybean under salt\u2010stress conditions by phosphorylating CCaMK-CYCLOPS. This phosphorylation inhibits their ability to bind to the promoter region of symbiotic genes like GmENOD40\u20101.", "Salt stress promotes root nodule symbiosis by phosphorylating the LHR1 domain of GmNSP1a. This phosphorylation increases GmNSP1a capability to bind to the promoter region of the symbiotic gene GmERN1a. " ], "source":"https:\/\/doi.org\/10.1016\/j.molp.2020.12.015", "normalized_plant_species":"Legumes", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.molp.2020.12.015", "Year":2021.0, "Citations":62.0, "answer":0, "source_journal":"Molecular Plant", "is_expert":true }, { "question":"How post-transcriptional and\/or post-translational mechanisms are involved in circadian clock regulation in Arabidopsis thaliana and Drosophila through the action of PROTEIN-ARGININE-METHYL-TRANSFERASE 5?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "PROTEIN METHYL TRANSFERASE5 (PRMT5) methylates clock proteins such as TOC1 in Arabidopsis and PER in flies affecting the activity of these transcription factors that ultimately affect the circadian rhythms in both organisms.", "PROTEIN METHYL TRANSFERASE5 (PRMT5) methylates several clock proteins leading to degradation. In Arabidopsis TOC1 is methylated in R18 and R20. In Flies, PER is methylated, in this case leading to a more stable protein that looses rhytmicity.", "PROTEIN METHYL TRANSFERASE5 (PRMT5) regulates the splicing of PRR9 in Arabidopsis and PER in Drosophila melanogaster altering the circadian clock of both organisms. PRMT5 mutants have a wide-variety of splicing defects. PRMT5 methylates several splicing factors and it is the proposed mechanism to have an impact on the splicing pattern." ], "source":"doi: 10.1038\/nature09470. and doi: 10.1093\/plcell\/koae051", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1093\/plcell\/koae051", "Year":2024.0, "Citations":6.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How does the circadian clock function in individual cells of Arabidopsis? Are all cell types having the same phase of gene expression ?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Arabidopsis exhibits two clock gene expression waves at the plant level: one that travels up the root and one that travels down. Furthermore, the circadian rhythms of the plant's various sections vary slightly; for example, the root's tip has a faster clock. Throughout the plant, strong clock rhythms are also found in individual cells. This robustness may be attributed to clocks in adjacent cells communicating with one another to keep track of time. The two waves of gene expression in the root are explained by mathematical simulations that demonstrate how the interaction of the individual clocks creates patterns of clock activity throughout the plant.\n", "Light entrains the clock, and therefore tissues that absorb light are the ones that set the time in the whole plant. Still, all parts of the plant show oscillations in gene expression, suggesting a cell-to-cell communication. In roots the clock ticks slower as in leaves, having a period of 25.5 hs instead of 24h. \n\n", "Clock is entrained by light, therefore, across the whole plant, different cell types have different \u201cclocks\u201d and phase of expression depending on the access to the light source. There is little cell-to-cell communication to coordinate the clock at a whole plant level. Root tissues have weaker oscillations and leaves express genes with higher amplitudes, showing that the clock thought the plant is mainly controlled by the light-absorbing tissues. \n" ], "source":"https:\/\/doi.org\/10.7554\/eLife.31700", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.7554\/eLife.31700", "Year":2018.0, "Citations":99.0, "answer":0, "source_journal":"eLife", "is_expert":true }, { "question":"Photoperiodic flowering response mechanism can be described by a coincidence model, in which the photoperiodic response is driven by the coincidence of the external light signal and the internal rhythms. In Arabidopsis, which are the main genes that explain this model on photoperiodic flowering and how they are interacting? ", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Photoreceptors are the main responsibles for photoperiodic flowering. The internal clock controls FKF that induces an increase in CONSTANS mRNA. In the light phase, the CO protein can be activated by PHYTOCHROME B and degradation is promoted by CRYPTOCHROMES and PHYTOCHROME A. High levels of CO protein activate the expression of FLOWERING LOCUS T inducing flowering. ", "Light entrains the clock but it the case of flowering, it affects the expression of the flowering integrator gene FLOWERING LOCUS T (FT). In Arabidopsis, the FKF1 protein is regulated by the circadian clock and has a diurnal rhythm, accumulating at the middle and end of the day in long days. FKF increases the levels of CONSTANS (CO). In long-days, the CO protein is stabilized by light by the action of the photoreceptors PHYTOCHROME A and CRYPTOCHROMES and can therefore activate FT transcription inducing flowering. In short-days, the CO levels are reached in the dark phase, and in this way no activation of CO protein can occur. \n\n\n", "Day-length and light plays a minor role in photoperiodic flowering. Light is mainly important for setting the internal clock and controlling the expression of clock genes such as CCA1, TOC1 and PRR7 and PRR9. Disruption of these genes lead to altered flowering. \n" ], "source":"https:\/\/doi.org\/10.1038\/nature00996", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1038\/nature00996", "Year":2002.0, "Citations":534.0, "answer":1, "source_journal":"Nature", "is_expert":true }, { "question":"miRNA processing mechanisms differ in plants and animals. Mention two main differences on the miRNA biogenesis pathway that distinguishes these two organism", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "In Plants, miRNA biogenesis takes place exclusively in the nucleus while in animals, the first processing step (first cut of the pri-miRNA to pre-miRNA) takes place in the nucleus and the second cleavage step (from pre-miRNA to mature miRNA) in the cytoplasm. The other difference is that plants pri-miRNA have a much larger heterogeneity at a structural level than the animal's counterpart. This leads to different biogenesis mechanisms. In animal, the dicing steps occur from base to loop of the precursor, while in plants pri-miRNAs can be produced from base to loop, loop to base or in a mixed fashion.", "In animals, miRNA biogenesis takes place exclusively in the nucleus while in plants, the first processing step (first cut of the pri-miRNA) takes place in the nucleus and the second cleavage step in the cytoplasm. The other difference is that animal miRNAs have a much larger heterogeneity at a structural level than the plants counterpart. \n", " In animals, miRNA biogenesis takes place exclusively in the nucleus while in plants, the first processing step (first cut of the pri-miRNA to pre-miRNA) takes place in the nucleus and the second cleavage step(from pre-miRNA to mature miRNA) in the cytoplasm. The other difference is that plant miRNAs have a much larger heterogeneity at a structural level than the animals counterpart. This leads to different biogenesis mechanism. In animal, the dicing steps occur from base to loop of the precursor, while in plants pri-miRNAs can be produced from base to loop, loop to base or in a mixed fashion" ], "source":"DOI 10.1016\/j.cub.2009.10.072 and 10.1038\/emboj.2009.292", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1038\/emboj.2009.292", "Year":2009.0, "Citations":171.0, "answer":0, "source_journal":"The EMBO Journal", "is_expert":true }, { "question":"In the circadian timing system, time-of-day-dependent activity of the core oscillator genes involves chromatin-based regulation. How epigenetic mechanisms shape TOC1 rhythmic expression in Arabidopsis thaliana and which are the genes involved.", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Rhythmic expression of TOC1 is achieved by transcriptional and epigenetic mechanisms at its locus. TOC1 levels are maintained low at dusk by the circadian binding of CCA1 to TOC1 promoter . TOC1 mRNA peaking at dawn is preceded by high levels of H3Ac at the TOC1 promoter, a hallmark of active transcription .Following TOC1 peak expression at dawn, transcriptionally silenced chromatin status mediated by histone deacetylase leads to the declining phase of TOC1. \tFurthermore, STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1), a component of the FAcilitates Chromatin Transcription (FACT) complex that assists transcription by modulating chromatin structure, associates with the TOC1 promoter following a circadian pattern similar to the TOC1 mRNA oscillation. At the same time, CCA1 binding to the same DNA region leads to a decrease in H3K27me levels, reducing TOC1 expression \n", "Rhythmic expression of TOC1 is achieved by transcriptional and epigenetic mechanisms at its locus. TOC1 levels are maintained low at dawn by the circadian binding of CCA1 to TOC1 promoter . TOC1 mRNA peaking at dusk is preceded by high levels of H3Ac at the TOC1 promoter, a hallmark of active transcription .Following TOC1 peak expression at dusk, transcriptionally silenced chromatin status mediated by histone deacetylase leads to the declining phase of TOC1. \tFurthermore, STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1), a component of the FAcilitates Chromatin Transcription (FACT) complex that assists transcription by modulating chromatin structure, associates with the TOC1 promoter following a circadian pattern similar to the TOC1 mRNA oscillation. At the same time, CCA1 binding to the same DNA region leads to a decrease in H3Ac levels, reducing TOC1 expression \n", "Rhythmic expression of TOC1 is achieved by transcriptional and epigenetic mechanisms at its locus. TOC1 levels are maintained low at dawn by the circadian binding of CCA1 to TOC1 promoter . TOC1 mRNA peaking at dusk is preceded by high levels of H3K3me at the TOC1 promoter, a hallmark of active transcription .Following TOC1 peak expression at dusk, transcriptionally silenced chromatin status mediated by H3K27me at the locus leads to the declining phase of TOC1. \tFurthermore, STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1), a component of the FAcilitates Chromatin Transcription (FACT) complex that assists transcription by modulating chromatin structure, associates with the TOC1 promoter following a circadian pattern similar to the TOC1 mRNA oscillation. At the same time, CCA1 binding to the same DNA region leads to a decrease in H3K4me levels, reducing TOC1 expression.\n" ], "source":"https:\/\/doi.org\/10.1105\/tpc.107.050807, 10.1111\/j.1365-313X.2004.02242.x", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1111\/j.1365-313X.2004.02242.x", "Year":2004.0, "Citations":69.0, "answer":1, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"How do LSH1 and LSH2 confer symbiotic nodule identity to root cells in Medicago truncatula?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Medicago truncatula" ], "options":[ "LSH1\/LSH2 promote cell divisions specifically in the midcortex and control and maintain nodule organ identity, in part through the transcriptional promotion of NOOT1\/NOOT2 and NF-YA1, as well as further promoting auxin-cytokinin levels and directly suppressing the lateral root developmental program.", "LSH1\/LSH2 promote cell differentiation specifically in the inner cortex and pericycle and control and maintain nodule organ identity, in part through the transcriptional promotion of NOOT1\/NOOT2 and NF-YA1, as well as further promoting auxin-cytokinin levels and directly suppressing the lateral root developmental program.", "LSH1\/LSH2 promote cell divisions specifically in the midcortex and control and maintain nodule organ identity, in part through the transcriptional promotion of NOOT1\/NOOT2 and NF-YA1, as well as further promoting auxin-cytokinin levels and directly mimicking the lateral root developmental program." ], "source":"DOI: 10.1111\/nph.16950", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1111\/nph.16950", "Year":2020.0, "Citations":40.0, "answer":0, "source_journal":"New Phytologist", "is_expert":true }, { "question":"How do you define a symbiotic island in Medicago truncatula?", "area":"GENOME AND GENOMICS", "plant_species":[ "Medicago truncatula" ], "options":[ "symbiotic islands are genomic clusters of on average 400 kb in length, containing a majority of symbiotically co-regulated genes whose expression is down-regulated in nitrogen-fixing nodules compared to roots. Symbiotic islands in addition display repressive histone marks and DNA methylation patterns and contain numerous expressed non-coding RNAs). Non-coding RNAs and epigenetic regulations are attractive regulatory elements that could explain the coordinated symbiotic expression of genes present on symbiotic islands. ", "symbiotic islands are genomic clusters of on average 40 kb in length, containing a majority of symbiotically co-regulated genes whose expression is upregulated in nitrogen-fixing nodules compared to roots. Symbiotic islands in addition display differential histone marks and DNA methylation patterns and contain numerous expressed long non-coding RNAs (lncRNAs). LncRNAs and epigenetic regulations are attractive regulatory elements that could explain the coordinated symbiotic expression of genes present on symbiotic islands. ", "symbiotic islands are genomic clusters of on average 40 kb in length, containing a majority of symbiotically co-regulated genes whose expression is down-regulated in nitrogen-fixing nodules compared to roots. Symbiotic islands in addition display repressive histone marks and DNA methylation patterns and contain numerous expressed long non-coding RNAs (lncRNAs). LncRNAs and epigenetic regulations are attractive regulatory elements that could explain the coordinated symbiotic expression of genes present on symbiotic islands. " ], "source":"doi: 10.1038\/s41477-018-0286-7", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1038\/s41477-018-0286-7", "Year":2018.0, "Citations":231.0, "answer":1, "source_journal":"Nature Plants", "is_expert":true }, { "question":"How does the Nuclear Factor YA1 control nodule development in Medicago truncatula and Lotus japonicus", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Medicago truncatula", "Lotus japonicus" ], "options":[ "NF-YA1 controls cell differentiation during early stages of nodule development by regulating several members of the SHORT INTERNODES\/STYLISH (STY) transcription factor gene family in Lotus japonicus but not in Medicago truncatula.\n\n", "initial symbiotic cell divisions and subsequent nodule emergence, encompassing further cell divisions and nodule patterning, are both regulated by NF-YA1.", "NF-YA1 controls cell differentiation during early stages of nodule development by regulating several members of the SHORT INTERNODES\/STYLISH\n(STY) transcription factor gene family that are known to regulate auxin homeostasis.\nVia this pathway, NF-YA1 regulates determinate (Lotus japonicas) and indeterminate (Medicago truncatula) nodule emergence, encompassing cell divisions leading to nodule patterning, while it does not regulate Initial symbiotic cell divisions leading to nodule primordium formation.\n" ], "source":"doi: 10.1111\/nph.16950", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1111\/nph.16950", "Year":2020.0, "Citations":40.0, "answer":2, "source_journal":"New Phytologist", "is_expert":true }, { "question":"What is the difference between determinate and indeterminate nodule development?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "non-specific" ], "options":[ "Plants that produce determinate nodules require little or no staking while indeterminate nodule producing plants develop into vines that never top off and continue producing until killed by frost.", "The difference between determinate and indeterminate nodule development lies in the ability of embryonic cells to be committed to specific or general developmental paths. Determinate nodules have predetermined fates and indeterminate nodules do not, allowing the possibility of compensatory development.", "Indeterminate nodules have a persistent meristem while determinate nodules have a transient meristem. As a result indeterminate nodules are generally elongated while determinate nodules are generally round.The ontogeny of both types of nodules is different: Indeterminate nodules form from inner (nodule primordium and meristem) and central cortical cells (nodule basis) while determinate nodules form from outer cortical cells. Symbiotic bacteria undergo extensive differentiation into nitrogen-fixing bacteroids in indeterminate but not in determinate nodules." ], "source":"non-specific", "normalized_plant_species":"Non-specific", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":null, "Year":null, "Citations":null, "answer":2, "source_journal":null, "is_expert":true }, { "question":"How do you define a pioneer transcription factor (TF)?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "Pioneer transcription factors bind to regulatory transcription factors to control developmental switches.", "It is a TF that can bind inactive closed and nucleosome occupied chromatin, thereby it increases the accessibility of target sites for other TFs either directly or by recruiting chromatin remodelers iii) As a consequence pioneer TFs control important developmental switches like the vegetative to floral transition in plants.", "Pioneer transcription factors bind active chromatin regions to silence them.\n" ], "source":"non-specific", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":null, "Year":null, "Citations":null, "answer":1, "source_journal":null, "is_expert":true }, { "question":"What is the role of the SOG1 transcription factor in the Arabidopsis thaliana DNA damage response and what processes its target genes are involved in?", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The MYB3R transcription factor SOG1 is regulated by the DNA damage response. SOG1 promotes cell cycle, programmed cell death, DNA damage, and thereby maintains genome stability. SOG1 indirectly targets and activates dozens of genes involved in DNA damage-associated processes, including transcriptional and posttranscriptional regulation, oxidative stress, defense, cell cycle regulation, cell death, and DNA repair. ", "The NAC transcription factor SOG1 is a major regulator of the DNA damage response. SOG1 prevents cell cycle arrest, programmed cell death, DNA repair, and thereby maintains genome stability. SOG1 directly targets and represses hundreds of genes involved in DNA damage-associated processes, including transcriptional and posttranscriptional regulation, oxidative stress, defense, cell cycle regulation, cell death, and DNA repair.\n", "The NAC transcription factor SOG1 is a major regulator of the DNA damage response. SOG1 promotes cell cycle arrest, programmed cell death, DNA repair, and thereby maintains genome stability. SOG1 directly targets and activates hundreds of genes involved in DNA damage-associated processes, including transcriptional and posttranscriptional regulation, oxidative stress, defense, cell cycle regulation, cell death, and DNA repair. " ], "source":"10.1073\/pnas.1810582115", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1073\/pnas.1810582115", "Year":2018.0, "Citations":128.0, "answer":2, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"In Arabidopsis thaliana, what are the proteins depositing and removing the monoubiquitination of histone H2B and what are the phenotypes of the corresponding mutants?", "area":"GENE REGULATION - EPIGENETICS AND TGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The proteins required to monoubiquitinate H2B are the E3 ubiquitin ligases HUB1 and HUB2 and E2 ubiquitin conjugases UBC1, UBC2 and UBC3. The proteins deubiquinating H2B are the ubiquitin-specific proteases UBP22 and UBP26. Mutant plants for HUB1 and HUB2 and UBC1, 2 and 3 are viable with mild phenotypic defects in seed dormancy, cell cycle progression, circadian clock and flowering time control. Mutant plants in UBP22 display no obvious phenotypes while mutants in UBP26 are early flowering and display high rate of seed abortion.", "The proteins required to monoubiquitinate H2B are the E2 ubiquitin conjugases HUB1 and HUB2 and E3 ubiquitin ligases UBC1, UBC2 and UBC3. The proteins deubiquinating H2B are the ubiquitin-specific proteases UBP22 and UBP26. Mutant plants for HUB1 and HUB2, and UBC1, 2 and 3 are not viable with strong phenotypic defects in seed dormancy, cell cycle progression, circadian clock and flowering time control. Mutant plants in UBP22 display obvious phenotypes while mutants in UBP26 are late flowering and display low rate of seed abortion. \n", "The proteins required to monoubiquitinate H2B are the E3 ubiquitin ligases HUB1 and HUB2 and E2 ubiquitin conjugases UBC1 UBC2 and UBC3. The proteins deubiquinating H2B are the ubiquitin-specific proteases UBP5, UBP12 and UBP13. Mutant plants for HUB1 and 2 and UBC1, 2 and 3 are viable with mild phenotypic defects in seed germination, cell cycle arrest, circadian clock and flowering time control. Mutant plants in UBP22 display no obvious phenotypes while mutants in UBP26 are early flowering and display high rate of seed germination." ], "source":"10.7554\/eLife.37892", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.7554\/eLife.37892", "Year":2018.0, "Citations":74.0, "answer":0, "source_journal":"eLife", "is_expert":true }, { "question":"What chromatin modifications are deposited or removed around a double strand break in Arabidopsis thaliana?", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In arabidopsis thaliana, \u03b3H2AX (an H2AX variant phosphorylated on S139), accumulates around double strand breaks through the activity of ATM and ATR kinases. H3K4me2 removal at damaged sites by the LDL1 protein is important for releasing RAD54 during Homologous Recombination. Polymerase-Associated Factor Complex (PAF1C) localize at at double strand breaks and recruits the E2 Ubiquitin-conjugating enzymes UBC1\/2 and E3 ligases HUB1\/2, which mediate H2B mono-ubiquitination to promote DNA repair through Homologous Recombination. H4K16ac and H2A.Z are also transiently deposited around double strand breaks.\n", "In arabidopsis thaliana, H2A.Z (an H2A variant), accumulates around double strand breaks through the activity of ATM and ATR phosphatases. H3K4me2 removal at damaged sites by the LDL1 protein is important for recruiting RAD54 during Homologous Recombination. Polymerase-Associated Factor Complex (PAF1C) localize at at double strand breaks and recruits the E2 Ubiquitin-conjugating enzymes UBC1\/2 and E3 ligases HUB1\/2, which mediate H2B mono-ubiquitination to promote DNA repair through non-homologous end joining. H4K16ac and H2A.Z are also transiently removed around double strand breaks.\n", "In arabidopsis thaliana, \u03b3H2AX (an H2AX variant phosphorylated on S139), is depleted around double strand breaks through the activity of ATM and ATR kinases. H3K4me2 deposition at damaged sites by the LDL1 protein is important for releasing RAD54 during Homologous Recombination. Polymerase-Associated Factor Complex (PAF1C) localize at at double strand breaks and recruits the E2 Ubiquitin-conjugating enzymes UBC1\/2 and E3 ligases HUB1\/2, which mediate H2B de-ubiquitination to prevent DNA repair through Homologous Recombination. H4K16ac and H2A.Z are also stably deposited around double strand breaks." ], "source":"10.1038\/s41477-024-01678-z", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1038\/s41477-024-01678-z", "Year":2024.0, "Citations":1.0, "answer":0, "source_journal":"Nature Plants", "is_expert":true }, { "question":"How UV-induced DNA damage is repaired in Arabidopsis thaliana?", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "UV induces DNA breaks, such as cyclobutane pyrimidine dimers (CPDs) and (6\u20134) pyrimidine-pyrimidone photoproducts. In Arabidopsis thaliana, photoproducts can be repaired by the Direct Repair pathway, a light-independent error-free process catalyzed by DNA photolyase enzymes called PHR1 and UVR3, or by a light-dependent mechanism called the Nucleotide excision repair pathway. Nucleotide excision repair consists in the excision of the damaged DNA strand, followed by homologous recombination.There are two Nucleotide excision repair subpathways: the transcription coupled repair (TCR) pathway which removes DNA damage from actively transcribed genes and the global genome repair pathway which removes damage throughout the genome. ", "UV induces bulky DNA adducts, such as cyclobutane pyrimidine dimers (CPDs) and (6\u20134) pyrimidine-pyrimidone photoproducts. In Arabidopsis thaliana, photoproducts can be repaired by the Direct Repair pathway, a light-dependent error-free process catalyzed by DNA photolyase enzymes called PHR1 and UVR3, or by a light-independent mechanism called the Nucleotide excision repair pathway. Nucleotide excision repair consists in the excision of the damaged DNA strand, followed by de novo DNA synthesis.There are two Nucleotide excision repair subpathways: the transcription coupled repair (TCR) pathway which removes DNA damage from actively transcribed genes and the global genome repair pathway which removes damage throughout the genome. ", "UV induces bulky DNA adducts, such as cyclobutane pyrimidine dimers (CPDs) and (6\u20134) pyrimidine-pyrimidone photoproducts. In Arabidopsis thaliana, photoproducts can be repaired by the Direct Repair pathway, a light-dependent error-prone process catalyzed by DNA photolyase enzymes called PHR1 and UVR3, or by a light-independent mechanism called the Nucleotide excision repair pathway. Nucleotide excision repair consists in the excision of the damaged DNA strand, followed by de novo DNA synthesis.There are two Nucleotide excision repair subpathways: the transcription coupled repair (TCR) pathway which removes DNA damage from poorly transcribed genes and the global genome repair pathway which removes damage at specific genomic locations. " ], "source":"10.1371\/journal.pgen.1008476", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1371\/journal.pgen.1008476", "Year":2019.0, "Citations":18.0, "answer":1, "source_journal":"PLOS Genetics", "is_expert":true }, { "question":"What photoreceptors are found in Arabidopsis thaliana plants and what are their subcellular localizations?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Arabidopsis thaliana plants have five classes of photoreceptors. Phytochromes (PHYA-E) perceive red\/far-red lights (600\u2013750\u2009nm); cryptochromes (CRY1, CRY2), phototropins (PHOT1 and PHOT2), F-box containing Flavin binding proteins (ZEITLUPE and FKF1\/LKP2) perceive blue\/UV-A light (320\u2013500\u2009nm); and UVR8 perceive UV-B light (280\u2013320\u2009nm). Phytochromes are localized in the cytosol and translocate to the nucleus upon light activation. CRY1 dually localizes in cytosol and the nucleus while CRY2 is found mainly in the nucleus. Phototropins localize at the plasma membrane and chloroplast outer membrane. ZEITLUPE localizes mainly in the cytoplasm while FKF1\/LKP2 mainly in the nucleus. Upon UV-B absorption, the interface between UVR8 dimers breaks, and the resulting monomer migrates into the nucleus.", "Arabidopsis thaliana plants have five classes of photoreceptors. Phytochromes (PHYA-E) perceive red\/far-red lights (600\u2013750\u2009nm); cryptochromes (CRY1, CRY2), phototropins (PHOT1 and PHOT2), F-box containing Flavin binding proteins (ZEITLUPE and FKF1\/LKP2) perceive blue\/UV-B light (320\u2013500\u2009nm); and UVR8 perceive UV-C light (280\u2013320\u2009nm). Phytochromes are localized in the cytosol and translocate to the nucleus upon dark reversion. CRY2 dually localizes in cytosol and the nucleus while CRY1 is found mainly in the nucleus. Phototropins localize at the plasma membrane and chloroplast outer membrane. ZEITLUPE localizes mainly in the nucleuswhile FKF1\/LKP2 mainly in the cytoplasm. Upon UV-B absorption, the interface between UVR8 dimers breaks, and the resulting monomer migrates into the cytosol.\n", "Arabidopsis thaliana plants have five classes of photoreceptors. Phytochromes (PHYA-E) perceive blue\/UV-A light (320\u2013500\u2009nm); cryptochromes (CRY1, CRY2), phototropins (PHOT1 and PHOT2), F-box containing Flavin binding proteins (ZEITLUPE and FKF1\/LKP2) perceive red\/far-red lights (600\u2013750\u2009nm); and UVR8 perceive UV-B light (280\u2013320\u2009nm). Phytochromes are localized in the nucleus and translocate to the cytosol upon light activation. CRY1 dually localizes in cytosol and the nucleus while CRY2 is found mainly in the cytosol. Phototropins localize at the plasma membrane and chloroplast inner membrane. ZEITLUPE localizes mainly in the cytoplasm while FKF1\/LKP2 mainly in the nucleus. Upon UV-B absorption, UVR8 dimers form and migrate into the nucleus." ], "source":"10.1016\/j.semcdb.2019.03.007 and 10.1016\/B978-0-12-801922-1.00009-9 and 10.1093\/mp\/sss007 and 10.1111\/nph.18007", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1111\/nph.18007", "Year":2022.0, "Citations":27.0, "answer":0, "source_journal":"New Phytologist", "is_expert":true }, { "question":"Which proteins reside in siRNA-bodies of Arabidopsis thaliana cells and what is the impact of depleting these proteins?", "area":"GENE REGULATION - PTGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "siRNA-bodies contain AGO1, AGO7, RDR2, SGS3. Depleting AGO7, RDR6, SGS3 impact the production of TAS3 tasiRNAs, while depleting AGO1, RDR6, SGS3 impact the production of TAS1 and TAS2 tasiRNAs as well as the production of secondary siRNAs involved in the amplification of transgene PTGS ", "siRNA-bodies contain AGO1, AGO7, RDR6, SGS3. Depleting AGO7, RDR6, SGS3 impact the production of TAS3 tasiRNAs, while depleting AGO1, RDR6, SGS3 impact the production of TAS1 and TAS2 tasiRNAs as well as the production of secondary siRNAs involved in the amplification of transgene PTGS", "siRNA-bodies contain AGO1, AGO7, RDR6, SDE3. Depleting AGO7, RDR6, SGS3 impact the production of TAS3 tasiRNAs, while depleting AGO1, RDR6, SGS3 impact the production of TAS1 and TAS2 tasiRNAs as well as the production of secondary siRNAs involved in the amplification of transgene PTGS " ], "source":"non-specific", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":null, "Year":null, "Citations":null, "answer":1, "source_journal":null, "is_expert":true }, { "question":"What type of RNA binds to the plant protein SUPPRESSOR OF GENE SILENCING 3 (SGS3)?", "area":"GENE REGULATION - PTGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "SGS3 binds to single-stranded RNA", "SGS3 binds to double-stranded RNA with long 3\u2019 overhang", "SGS3 binds to double-stranded RNA with long 5\u2019 overhang" ], "source":"non-specific", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":null, "Year":null, "Citations":null, "answer":2, "source_journal":null, "is_expert":true }, { "question":"What are the functions of plant DICER-LIKE 2 (DCL2) and DCL4, and what is the relationship between these two enzymes?", "area":"GENE REGULATION - PTGS", "plant_species":[ "non-specific" ], "options":[ "DCL2 produces 21-nt siRNAs whereas DCL4 produces 22-nt siRNAs. Their functions are redundant.", "DCL2 produces 22-nt siRNAs whereas DCL4 produces 21-nt siRNAs. Their functions are either redundant, synergistic or antagonistic, depending on the target considered", "DCL2 produces 21-nt siRNAs whereas DCL4 produces 22-nt siRNAs. Their functions are antagonistic" ], "source":"non-specific", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":null, "Year":null, "Citations":null, "answer":1, "source_journal":null, "is_expert":true }, { "question":"What is the function of plant ARGONAUTE 1 (AGO1), and what is the phenotype of Arabidopsis thaliana ago1 mutants ?", "area":"GENE REGULATION - PTGS", "plant_species":[ "non-specific" ], "options":[ "AGO1 binds to miRNA and siRNA with a 5\u2019U, and catalyze the cleavage of mRNA homologous to the miRNA and siRNA bound to AGO1. Hypomorphic ago1 alleles are fertile while ago1 nul alleles are dwarf and sterile. ", "AGO1 binds to miRNA and siRNA with a 5\u2019A, and catalyze the cleavage of mRNA homologous to the miRNA and siRNA bound to AGO1. Hypomorphic ago1 alleles are fertile while ago1 nul alleles are dwarf and sterile. ", "AGO1 binds to miRNA but not siRNA, and catalyze the cleavage of mRNA homologous to the miRNA and siRNA bound to AGO1. Hypomorphic ago1 alleles are fertile while ago1 nul alleles are dwarf and sterile. " ], "source":"non-specific", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":null, "Year":null, "Citations":null, "answer":0, "source_journal":null, "is_expert":true }, { "question":"What is the function of the protein JUMONJI14 (JMJ14) in plants and what are the consequences of JMJ14 impairment on chromatin?", "area":"GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS", "plant_species":[ "non-specific" ], "options":[ "JMJ14 encodes a the H3K4me3 methylase. JMJ14 impairment increase the level of H3K4me3 but does not modify DNA methylation, except at transgenes.", "JMJ14 encodes a the H3K9me3 demethylase. JMJ14 impairment increase the level of H3K4me9 but does not modify DNA methylation, except at transgenes.", "JMJ14 encodes a the H3K4me3 demethylase. JMJ14 impairment increase the level of H3K4me3 but does not modify DNA methylation, except at transgenes." ], "source":"non-specific", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":null, "Year":null, "Citations":null, "answer":2, "source_journal":null, "is_expert":true }, { "question":"In Arabidopsis thaliana, light regulates alternative splicing of RS31. How does light quality and quantity affect this regulation of alternative splicing? ", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Arabidopsis thaliana plants are exposed to light and darkness. In the presence of light, the splicing index of RS31 decreases. Changes in RS31 alternative splicing are proportional to light quantity (light intensity): plants exposed to higher light intensities show a lower splicing index. Regarding light quality, both red (660 nm) and blue (470 nm) lights produce similar results as white light.", "Arabidopsis thaliana plants are exposed to light and darkness. In the presence of light, the splicing index of RS31 increases. Changes in RS31 alternative splicing are proportional to light quantity (light intensity): plants exposed to higher light intensities show higher splicing index. Regarding light quality, red (660 nm) does not affect the splicing index but blue (470 nm) light produces similar results as white light.", "Arabidopsis thaliana plants are exposed to light and darkness. In the presence of light, the splicing index of RS31 increases. Changes in RS31 alternative splicing are not proportional to light quantity (light intensity): plants exposed to different light intensities show the same splicing index. Regarding light quality, both red (660 nm) and blue (470 nm) lights produce similar results as white light." ], "source":"10.1126\/science.1250322", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1126\/science.1250322", "Year":2014.0, "Citations":179.0, "answer":0, "source_journal":"Science", "is_expert":true }, { "question":"What is the light photosensory pathway that regulates RS31 alternative splicing in Arabidopsis thaliana?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "RS31 alternative splicing responses to light\/dark are affected in phytochrome and cryptochrome signaling mutants. Light sensed by phytochromes produces the light effect on alternative splicing. When plants are exposed to light, a phytochrome signal is generated in the photosynthetic tissue and travels through the plant. The mobile signal generated in the leaves triggers root alternative splicing changes in responses to light.", "RS31 alternative splicing responses to light\/dark are not affected in phytochrome and cryptochrome signaling mutants ruling out this photosensory pathway in this light regulation. Light is sensed by the chloroplast. When plants are exposed to light, a chloroplast retrograde signal is generated in the photosynthetic tissue and travels through the plant. The mobile signal generated in the leaves triggers root alternative splicing changes in responses to light.", "RS31 alternative splicing responses to light\/dark are not affected in phytochrome and cryptochrome signaling mutants ruling out this photosensory pathway in this light regulation. Light is sensed by the chloroplast. When plants are exposed to light, a chloroplast retrograde signal is generated in the photosynthetic tissue. The light effect on alternative splicing is only observed in photosynthetic tissues. There are no changes in roots: alternative splicing changes in responses to light only affect leaves." ], "source":"10.1126\/science.1250322", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1126\/science.1250322", "Year":2014.0, "Citations":179.0, "answer":1, "source_journal":"Science", "is_expert":true }, { "question":"What is the impact of RNA Pol II elongation in the regulation of alternative splicing by light in Arabidopsis thaliana?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis thaliana, the effect of light on alternative splicing is not affected in a dominant negative mutant of the transcription elongation factor TFIIS (that shows defective growth and serrated leaves and general splicing defects compared to wild-type plants). In the tfiis mutant, the differences in the splicing index of RS31 or U2AF65 upon light-dark changes are are similar to wild type plants. Furthermore, trichostatin A, a drug that inhibits histone acetylation, mimics the effect of darkness on alternative splicing. When RNA Pol II elongation is genetically affected, the effect of light on alternative splicing does not change, which discards the possibility that light regulates alternative splicing by controlling plant transcriptional elongation.", "In Arabidopsis thaliana, the effect of light on alternative splicing is not affected in a dominant negative mutant of the transcription elongation factor TFIIS (that shows defective growth and serrated leaves and general splicing defects compared to wild-type plants). In the tfiis mutant, the differences in the splicing index of RS31 or U2AF65 upon light-dark changes are similar to wild type plants. Furthermore, camptothecin, a topoisomerase inhibitor that also inhibits RNA Pol II elongation decreases the splicing index of RS31, mimicking, therefore, the effects of light. When RNA Pol II elongation is inhibited by a drug the effect of light on alternative splicing is enhanced, which suggests the possibility that light regulates alternative splicing by controlling plant transcriptional elongation.", "In Arabidopsis thaliana, the effect of light on alternative splicing is abolished in a dominant negative mutant of the transcription elongation factor TFIIS (that shows defective growth and serrated leaves and general splicing defects compared to wild-type plants). In the tfiis mutant, the differences in the splicing index of RS31 or U2AF65 upon light-dark changes are completely abolished. Furthermore, camptothecin, a topoisomerase inhibitor that also inhibits RNA Pol II elongation increases the splicing index of RS31, mimicking, therefore, the effects of darkness. When RNA Pol II elongation is inhibited by a drug or genetically affected, the effect of light on alternative splicing is reduced or abolished, which strengthens the possibility that light regulates alternative splicing by controlling plant transcriptional elongation." ], "source":"10.1016\/j.molcel.2018.12.005", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.molcel.2018.12.005", "Year":2019.0, "Citations":88.0, "answer":2, "source_journal":"Molecular Cell", "is_expert":true }, { "question":"In Arabidopsis thaliana, which is the signaling molecule that regulates alternative splicing by light in roots?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Light regulates alternative splicing in Arabidopsis thaliana. Light-induced changes in alternative splicing in roots occur even if communication with the photosynthetic tissue is interrupted. Small RNAs modulate nuclear alternative splicing of RS31 and other genes, especially in root cells. Small RNAs produced in photosynthetic cells are the main drivers of light-regulated alternative splicing in non-photosynthetic cells.", "Light regulates alternative splicing in Arabidopsis thaliana. Light-induced changes in alternative splicing in roots only occur as long as communication with the photosynthetic tissue is not interrupted. Small RNAs modulate nuclear alternative splicing of RS31 and other genes, especially in root cells. Small RNAs produced in photosynthetic cells are the main drivers of light-regulated alternative splicing in non-photosynthetic cells.", "Light regulates alternative splicing in Arabidopsis thaliana. Light-induced changes in alternative splicing in roots only occur as long as communication with the photosynthetic tissue is not interrupted. Sucrose modulates nuclear alternative splicing of RS31 and other genes, especially in root cells. Sugars produced in photosynthetic cells are the main drivers of light-regulated alternative splicing in non-photosynthetic cells." ], "source":"10.1016\/j.celrep.2021.109676", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.celrep.2021.109676", "Year":2021.0, "Citations":42.0, "answer":2, "source_journal":"Cell Reports", "is_expert":true }, { "question":"In Arabidopsis thaliana, what is the regulation of alternative splicing by light in leaves and roots?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In leaves, light is initially sensed by phytochromes and cryptochromes and activates photosynthesis. Then synthesized sugars are loaded into the phloem and travel to non-photosynthetic root tissues. There, imported sugars are metabolized through glycolysis, producing pyruvate that enters the mitochondria. Oxidative phosphorylation in the mitochondria activates HXK1 kinase and, in turn, modulates alternative splicing outcomes in roots.\nIn leaves, TOR kinase does not participate in the regulation of nuclear alternative splicing: there are other retrograde signals derived from the photosynthetic electron transport that modulate nuclear splicing decisions.", "In leaves, light is initially sensed by the chloroplast and activates photosynthesis. Then small RNAs are loaded into the phloem and travel to non-photosynthetic root tissues. There, imported sugars are metabolized through glycolysis, producing pyruvate that enters the mitochondria. Imported sugars and small RNAs in the mitochondria activates TOR kinase and, in turn, modulates alternative splicing outcomes in roots.\nIn leaves, even though mitochondria and TOR kinase regulate nuclear alternative splicing, there are other retrograde signals derived from the photosynthetic electron transport that can modulate nuclear splicing decisions.", "In leaves, light is initially sensed by the chloroplast and activates photosynthesis. Then synthesized sugars are loaded into the phloem and travel to non-photosynthetic root tissues. There, imported sugars are metabolized through glycolysis, producing pyruvate that enters the mitochondria. Oxidative phosphorylation in the mitochondria activates TOR kinase and, in turn, modulates alternative splicing outcomes in roots.\nIn leaves, even though mitochondria and TOR kinase regulate nuclear alternative splicing, there are other retrograde signals derived from the photosynthetic electron transport that can modulate nuclear splicing decisions." ], "source":"10.1016\/j.celrep.2021.109676", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.celrep.2021.109676", "Year":2021.0, "Citations":42.0, "answer":2, "source_journal":"Cell Reports", "is_expert":true }, { "question":"What is the effect of nitrogen (N) on the control of flowering time in Arabidopsis thaliana and what are the key genes involved in this process?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "While low N concentrations delay flowering time, Arabidopsis plants grown under high N accelerate flowering time. N regulates the expression of flowering-related genes at the shoot apical meristem (SAM) to modulate flowering time; these genes include SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), VERNALIZATION 2 (VRN2), and FLOWERING LOCUS T (FT).", "While high N concentrations delay flowering time, Arabidopsis plants grown under low N accelerate flowering time. N regulates the expression of flowering-related genes at the shoot apical meristem (SAM) to modulate flowering time; these genes include SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), VERNALIZATION 2 (VRN2), and FLOWERING LOCUS T (FT),", "While high N concentrations delay flowering time, Arabidopsis plants grown under low N accelerate flowering time. On the other hand, extreme N deficiency delay flowering time. N regulates the expression of flowering-related genes at the shoot apical meristem (SAM) to modulate flowering time; these genes include SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1), CONSTANS (CO) and FLOWERING LOCUS T (FT)." ], "source":"doi: 10.3390\/ijms25105310", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.3390\/ijms25105310", "Year":2024.0, "Citations":0.0, "answer":2, "source_journal":"International Journal of Molecular Sciences", "is_expert":true }, { "question":"What is the cellular mechanism involved in the growth of the hypocotyl in Arabidopsis thaliana? What are the hormonal pathways participating in this process?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The growth of the hypocotyl in Arabidopsis seedlings is the result of regulated cell division by several factors, including plant hormones. Gibberellin (GA), ethylene, and auxin are plant hormones that promote hypocotyl elongation in Arabidopsis seedlings.", "The growth of the hypocotyl in Arabidopsis seedlings is the result of regulated cell expansion by several factors, including plant hormones. Gibberellin (GA), ethylene, and auxin are plant hormones that promote hypocotyl elongation in Arabidopsis seedlings.", "The growth of the hypocotyl in Arabidopsis seedlings is the result of regulated cell division and expansion by several factors, including plant hormones. Gibberellin (GA), cytokinin, and auxin are plant hormones that promote hypocotyl elongation in Arabidopsis seedlings." ], "source":"doi: 10.1104\/pp.114.1.295.", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1104\/pp.114.1.295", "Year":1997.0, "Citations":516.0, "answer":1, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"What is the impact of Nitrate (N) in Arabidopsis thaliana auxin homeostasis during lateral root development and what are the key genes involved in this process?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Auxin perception and nitrate signaling are closely interconnected. Nitrate induces transcription of the ARF8 auxin receptor gene, while N metabolites produced by nitrate reduction and assimilation reset AFB3 levels over time by posttranscriptional regulation via miR167. Downstream of ARF8, a pericycle regulatory mechanism involving IAA14 and the NAC4 and OBP4 transcription factors induces LR initiation and elongation in response to nitrate resupply of N-deficient roots.", "Auxin perception and nitrate signaling are closely interconnected. Nitrate induces transcription of the AFB3 auxin receptor gene, while N metabolites produced by nitrate reduction and assimilation reset AFB3 levels over time by posttranscriptional regulation via miR393. Downstream of AFB3, a pericycle regulatory mechanism involving IAA14 and the NAC4 and OBP4 transcription factors induces LR initiation and elongation in response to nitrate resupply of N-deficient roots.", "Auxin perception and nitrate signaling are closely interconnected. Nitrate represses transcription of the AFB3 auxin receptor gene, while N metabolites produced by nitrate reduction and assimilation reset AFB3 levels over time by posttranscriptional regulation via miR393. Downstream of AFB3, a pericycle regulatory mechanism involving IAA14 and the NAC4 and OBP4 transcription factors represses LR initiation and elongation in response to nitrate resupply of N-deficient roots." ], "source":"https:\/\/doi.org\/10.1073\/pnas.1310937110", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1073\/pnas.1310937110", "Year":2013.0, "Citations":178.0, "answer":1, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"What is the effect of nitrogen on the root hair development in Arabidopsis thaliana and what are the key genes involved in this process?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis thaliana, ammonium is able to stimulate root hair initiation. In response to nitrate, NRT1.1 transceptor and TGA1\/TGA4 transcription factor regulates expression of the CPC root hair cell specification gene affecting root hair density.", "In Arabidopsis thaliana, nitrate and not a product of nitrate reduction is able to stimulate root hair initiation. In response to nitrate, NRT1.1 transceptor and TGA1\/TGA4 transcription factor regulates expression of the CPC root hair cell specification gene affecting root hair density.", "In Arabidopsis thaliana, nitrate and other N metabolite are able to stimulate root hair initiation. In response to nitrogen, NRT1.1 transceptor and TGA2\/TGA7 transcription factor regulates expression of the CPC root hair cell specification gene affecting root hair density." ], "source":"https:\/\/doi.org\/10.1111\/tpj.13656", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1111\/tpj.13656", "Year":2017.0, "Citations":102.0, "answer":1, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"How are the transcription factors TGA involved in the nitrate response of Arabidopsis thaliana roots?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis thaliana, all TGAs transcription factors have a role in root nitrate responses. Expression of TGAs is induced downstream of AtNRT1.1 with external nitrate application. TGAs directly bind to the promoter of AtNRT2.1\/2.2 and promote the expression of NRT2.1\/2.2 Mutations TGAs1 inhibit LR initiation, emergence, root hair initiation, and primary root length. ", "In Arabidopsis thaliana, TGA1 and TGA4 transcription factors, but not other TGA members, have a role in root nitrate responses. Expression of both TGA1 and TGA4 is repressed downstream of AtNRT1.1 with external nitrate application. TGA1 could directly bind to the promoter of AtNRT2.1\/2.2 and repressed the expression of NRT2.1\/2.2. Mutations of both TGA1 and TGA4 induced LR initiation, emergence, root hair initiation, and primary root length.", "In Arabidopsis thaliana, TGA1 and TGA4 transcription factors, but not other TGA members, have a role in root nitrate responses. Expression of both TGA1 and TGA4 is induced downstream of AtNRT1.1 with external nitrate application. TGA1 directly bind to the promoter of AtNRT2.1\/2.2 and promote the expression of NRT2.1\/2.2. Mutations of both TGA1 and TGA4 inhibit LR initiation, emergence, root hair initiation, and primary root length. " ], "source":"doi: 10.1111\/tpj.12618.", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1111\/tpj.12618", "Year":2014.0, "Citations":252.0, "answer":2, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"Which genes encoding transcription factors have been identified as bona fide direct targets of the Arabidopsis thaliana transcription factor BRC1?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "HD-Zip genes HB21, HB40 and HB53; bZIP genes GBF2, GBF3, ABF3 and ABI5; NAC genes ATAF1 and NAC032; AP2\/EREB genes ERF113\/Rap2.6L and CRF6; MYB genes MYBC1, and MYBD; zinc finger protein gene ATTZF5; and heat shock protein gene HSB2A ", "HD-Zip gene HB2; bZIP gene bZIP43 and bZIP23, NAC gene NAC019; AP2\/EREB genes RAP2.1 and RAP2.12; MYB genes MYB116 and MYB93; zinc finger protein gene SOM and TT1; and heat shock protein gene HSP21", "HD-Zip genes HB4; bZIP genes DPBF2 and BZIP61; NAC genes NAC097 and NAC058; AP2\/EREB genes RAP2.7 and RAP2.9; MYB genes MYB122 and MYB100; zinc finger protein gene BBX26 and DAZ1; and heat shock protein gene HSFA6B" ], "source":"doi: 10.1111\/nph.19420", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1111\/nph.19420", "Year":2023.0, "Citations":14.0, "answer":0, "source_journal":"New Phytologist", "is_expert":true }, { "question":"What is the role of the TCP transcription factor BRANCHED1 in Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "BRC1 acts systemically across the plant as an integrator of signals controlling bud outgrowth and translates them into a response of cell growth arrest", "BRC1 acts systemically across the plant as an integrator of signals promoting bud outgrowth and translates them into a response of cell division and growth ", "BRC1 acts locally inside the buds as an integrator of signals suppressing bud outgrowth and translates them into a response of cell growth arrest." ], "source":"www.plantcell.org\/cgi\/doi\/10.1105\/tpc.106.048934", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1105\/tpc.106.048934", "Year":2007.0, "Citations":686.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"Which protein acts as the receptor of strigolactones in Arabidopsis thaliana?", "area":"HORMONES", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The receptor of strigolactones in Arabidopsis thaliana is GAI, AT3G03990. ", "The receptor of strigolactones in Arabidopsis thaliana is KAI2, AT3G03990. ", "The receptor of strigolactones in Arabidopsis thaliana is AtD14, D14, AT3G03990. \n\n" ], "source":"www.plantcell.org\/cgi\/doi\/10.1105\/tpc.114.122903", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1105\/tpc.114.122903", "Year":2014.0, "Citations":193.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"Which hormone accumulates in Arabidopsis thaliana dormant axillary buds in response to the activity of BRANCHED1?", "area":"HORMONES", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Abscisic acid (ABA) accumulates in dormant axillary buds in response to the activity of BRANCHED1 ", "Salicylic acid accumulates in dormant axillary buds in response to the activity of BRANCHED1 ", "Gibberellins accumulates in dormant axillary buds in response to the activity of BRANCHED1 " ], "source":"www.pnas.org\/cgi\/doi\/10.1073\/pnas.1613199114", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1073\/pnas.1613199114", "Year":2016.0, "Citations":220.0, "answer":0, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"What is the role of StBRANCHED1b of Solanum tuberosum", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Solanum tuberosum" ], "options":[ "In Solanum tuberosum BRC1b promotes dormancy, abscisic acid responses and a reduced number of plasmodesmata. This increases sucrose accumulation and block the access of the tuberigen protein SP6A. BRC1b also directly interacts with SP5G and induces its tuber-inducing activity in aerial nodes. Altogether, these actions prevent tuberization underground.", "In Solanum tuberosum BRC1b promotes dormancy, abscisic acid responses and a reduced number of plasmodesmata. This limits sucrose accumulation and access of the tuberigen protein SP6A. BRC1b also directly interacts with SP6A and blocks its tuber-inducing activity in aerial nodes. Altogether, these actions help promote tuberization underground.", "In Solanum tuberosum BRC1b promotes axillary bud activity, auxin responses and an increased number of plasmodesmata in buds. This limits sucrose accumulation and access of the tuberigen protein SP6A. BRC1b also directly interacts with SP6A and blocks its tuber-inducing activity in aerial nodes. Altogether, these actions help promote tuberization underground." ], "source":"https:\/\/doi.org\/10.1038\/s41477-022-01112-2", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1038\/s41477-022-01112-2", "Year":2022.0, "Citations":56.0, "answer":1, "source_journal":"Nature Plants", "is_expert":true }, { "question":"Which are the main proteins involved in plant miRNA processing?", "area":"GENE REGULATION - PTGS", "plant_species":[ "non-specific" ], "options":[ "miRNA processing is mediated by DICER-LIKE1 (DCL1) assisted by the dsRNA-binding (DRB) proteins HYPONASTIC LEAVES 1 (HYL1) and SERRATE (SE). While DCL1 is an RNAseIII proteins producing the RNA cleavage, both HYL1 and SE facilitate accurate processing of pri-miRNAs by DCL1", "miRNA processing is mediated by HYPONASTIC LEAVES 1 (HYL1) assisted by DICER-LIKE1 (DCL1) and SERRATE (SE). While HYL1 is an RNAseIII proteins producing the RNA cleavage, both DCL1 and SE facilitate accurate processing of pri-miRNAs by DCL1", "miRNA processing is mediated by ARGONAUTE1 (AGO1) assisted by the dsRNA-binding (DRB) proteins HYPONASTIC LEAVES 1 (HYL1) and SERRATE (SE). While AGO1 is an RNAseIII proteins producing the RNA cleavage, both HYL1 and SE facilitate accurate processing of pri-miRNAs by DCL1" ], "source":"https:\/\/doi.org\/10.1146\/annurev-arplant-050213-035728", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1146\/annurev-arplant-050213-035728", "Year":2014.0, "Citations":501.0, "answer":0, "source_journal":"Annual Review of Plant Biology", "is_expert":true }, { "question":"Where does the miRNA biogenesis take place in plants?", "area":"GENE REGULATION - PTGS", "plant_species":[ "non-specific" ], "options":[ "The dsRNA-binding protein HYPONASTIC LEAVES1 (HYL1) and SERRATE (SE) associate with DCL1 to form nuclear dicing bodies (D-bodies), where miRNA biogenesis take place.", "The dsRNA-binding protein HYPONASTIC LEAVES1 (HYL1) and SERRATE (SE) associate with DCL1 to form cytoplasmic processing bodies (P-bodies), where miRNA biogenesis take place.", "The dsRNA-binding protein HYPONASTIC LEAVES1 (HYL1) and SERRATE (SE) associate with DCL1 to form cytoplasmic dicing bodies (D-bodies), where miRNA biogenesis take place." ], "source":"https:\/\/doi.org\/10.1146\/annurev-arplant-050213-035728", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1146\/annurev-arplant-050213-035728", "Year":2014.0, "Citations":501.0, "answer":0, "source_journal":"Annual Review of Plant Biology", "is_expert":true }, { "question":"How many mechanisms of miRNA biogenesis have been described in plants? Describe them.", "area":"GENE REGULATION - PTGS", "plant_species":[ "non-specific" ], "options":[ "Plant pre-miRNAs are much more variable in length than their \u223c70-nt metazoan counterparts (ranging from 49 to 900 nt in length) and can undergo two main processing mechanisms, influenced by the number of cuts required for miRNA release: Short base-to-loop, Sequential base-to-loop.", "Plant pre-miRNAs are much more variable in length than their \u223c70-nt metazoan counterparts (ranging from 49 to 900 nt in length) and can undergo four main processing mechanisms, influenced by the sequential processing direction and number of cuts required for miRNA release: Short base-to-loop, Sequential base-to-loop, Short loop-to-base, and Sequential loop-to-base.", "As ocurr with metazoan counterparts, plant miRNAs precusrsor are \u223c70-nt lenght and undergo one processing mechanisms that consist in two cleavage in a base-to-loop direction." ], "source":"https:\/\/doi.org\/10.1146\/annurev-arplant-050213-035728", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1146\/annurev-arplant-050213-035728", "Year":2014.0, "Citations":501.0, "answer":1, "source_journal":"Annual Review of Plant Biology", "is_expert":true }, { "question":"Which are the main determinants during miRNA biogenesis in plants?", "area":"GENE REGULATION - PTGS", "plant_species":[ "non-specific" ], "options":[ "The stem-loop structure contained within miRNAs primary transcripts defines the miRNA precursor. Sequences determinants initiate at least two staggered cleavage events within the pre-miRNA stem, separated by approximately 21 nt, which release the miRNA and its opposing fragment (miRNA\u2217). The second cut is also determine in sequence dependent manner. ", "The stem-loop structure contained within miRNAs primary transcripts defines the miRNA precursor. There are not clear determinants which initiate the cleavage events.", "The stem-loop structure contained within miRNAs primary transcripts defines the miRNA precursor. Structural determinants initiate at least two staggered cleavage events within the pre-miRNA stem, separated by approximately 21 nt, which release the miRNA and its opposing fragment (miRNA\u2217). Of key importance is the first cleavage position, which determines the mature miRNA sequence and therefore its target specificity. The second cut usually proceeds at a fixed distance from the end of the precursor." ], "source":"https:\/\/doi.org\/10.1146\/annurev-arplant-050213-035728", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1146\/annurev-arplant-050213-035728", "Year":2014.0, "Citations":501.0, "answer":2, "source_journal":"Annual Review of Plant Biology", "is_expert":true }, { "question":"Is miRNA biogenesis and miRNA AGO1 nuclear loading connected in Arabidopsis thaliana?", "area":"GENE REGULATION - PTGS", "plant_species":[ "non-specific" ], "options":[ "Yes, there is evidence of DCL1 and AGO1 interaction in the nucleus of plant cell.", "While miRNA biogenesis has been described linked to AGO miRNA loading in animals, is it not clear the connection between miRNA biogenesis and miRNA AGO1 nuclear loading in plants.", "Yes, AGO1 is essential during miRNA biogenesis in plants." ], "source":"https:\/\/doi.org\/10.1016\/j.molcel.2018.01.007", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.molcel.2018.01.007", "Year":2018.0, "Citations":209.0, "answer":1, "source_journal":"Molecular Cell", "is_expert":true }, { "question":"What is the impact of low levels of nitrates in Arabidopsis thaliana during root hair development and what are the key genes involved in this process?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "High nitrogen enhances auxin accumulation in the lateral roots via the repression of Tryptophan Aminotransferase of Arabidopsis 1 (TAA1) and YUCCA8. Auxin is then accumulated in the root tip by the auxin transport system, namely AUXIN TRANSPORTER PROTEIN 1 (AUX1) and PIN-FORMED 2 (PIN2). Upon entering the lateral roots, auxin represses the transcription factors AUXIN RESPONSE FACTOR 6 and 8 (ARF6\/8) to decrease the epidermal and auxin-inducible transcriptional module ROOT HAIR DEFECTIVE 6 (RHD6)-LOTUS JAPONICA ROOT HAIRLESS-LIKE 3 (LRL3) to direct lateral root growth in response to high nitrogen levels.", "Low nitrogen enhances auxin accumulation in the root apex via the overexpression of Tryptophan Aminotransferase of Arabidopsis 1 (TAA1) and YUCCA8. Auxin is then transported to the root hair differentiation zone by the auxin transport system, namely AUXIN TRANSPORTER PROTEIN 1 (AUX1) and PIN-FORMED 2 (PIN2). Upon entering the RH zone, auxin activates the transcription factors AUXIN RESPONSE FACTOR 6 and 8 (ARF6\/8) to enhance the epidermal and auxin-inducible transcriptional module ROOT HAIR DEFECTIVE 6 (RHD6)-LOTUS JAPONICA ROOT HAIRLESS-LIKE 3 (LRL3) to direct RH elongation in response to low nitrogen levels.", "High nitrogen enhances auxin accumulation in the root apex via the repression of Tryptophan Aminotransferase of Arabidopsis 1 (TAA1) and YUCCA8. Auxin is then transported to the atrichoblast cells by the auxin transport system, namely AUXIN TRANSPORTER PROTEIN 1 (AUX1) and PIN-FORMED 2 (PIN2). Upon entering the RH zone, auxin represses the transcription factors AUXIN RESPONSE FACTOR 6 and 8 (ARF6\/8) to decrease the epidermal and auxin-inducible transcriptional module ROOT HAIR DEFECTIVE 6 (RHD6)-LOTUS JAPONICA ROOT HAIRLESS-LIKE 3 (LRL3) to direct RH elongation in response to high nitrogen levels." ], "source":"Jia Z, Giehl RFH, Hartmann A, Estevez JM, Bennett MJ, von Wir\u00e9n N. A spatially concerted epidermal auxin signaling framework steers the root hair foraging response under low nitrogen. Curr Biol. 2023 Sep 25;33(18):3926-3941.e5. doi:10.1016\/j.cub.2023.08.040.", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1016\/j.cub.2023.08.040", "Year":2023.0, "Citations":27.0, "answer":1, "source_journal":"Current Biology", "is_expert":true }, { "question":"How receptor FERONIA and TOR kinase pathway control in Arabidopsis thaliana root hair growth under low temperature condition?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Low temperature (10\u00b0C) induce a significant RH elongation response in Arabidopsis thaliana via FERONIA and TOR kinase pathway. FERONIA is essential for detecting restricted nutrition availability resulting from low temperatures. FERONIA interacts with and activates TOR kinase downstream components to trigger RH growth. Moreover, the small GTPase Rho of plants 2 (ROP2) participates in the RH growth response, connecting FER and TOR. We discovered that restricted nitrogen nutrient availability may replicate the RH growth response at 10\u00b0C in a way reliant on NRT1.1. ", "Low temperature (10\u00b0C) induce a repression of the RH elongation response in Arabidopsis thaliana via FERONIA and TOR kinase pathway. FERONIA is essential for detecting high levels of nutrition availability resulting from low temperatures. FERONIA interacts with and represses TOR kinase downstream components to inhibit RH growth. Moreover, the small GTPase Rho of plants 2 (ROP2) blocks the RH growth response, repressing FER and TOR. We discovered that high levels of nitrogen nutrient availability may replicate the RH growth response at 10\u00b0C independently of NRT1.1.", "Low temperature (10\u00b0C) induce a repression of the lateral root elongation response in Arabidopsis thaliana via FERONIA and TOR kinase pathway. FERONIA is essential for detecting high levels of nutrition availability resulting from low temperatures. FERONIA do not interact with and release TOR kinase downstream components to repress lateral roots growth. Moreover, the small GTPase Rho of plants 2 (ROP2) locates on the root tips, repressing FER and TOR. We discovered that high levels of nitrogen nutrient availability may replicate the lateral root growth response at 10\u00b0C independently of NRT1.1.\n" ], "source":"Pacheco JM, Song L, Kub\u011bnov\u00e1 L, Ove\u010dka M, Berdion Gabarain V, Peralta JM, Lehued\u00e9 TU, Ibeas MA, Ricardi MM, Zhu S, Shen Y, Schepetilnikov M, Ryabova LA, Alvarez JM, Gutierrez RA, Grossmann G, \u0160amaj J, Yu F, Estevez JM. Cell surface receptor kinase FERONIA linked to nutrient sensor TORC signaling controls root hair growth at low temperature linked to low nitrate in Arabidopsis thaliana. New Phytol. 2023 Apr;238(1):169-185. doi: 10.1111\/nph.18723. ", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1111\/nph.18723", "Year":2023.0, "Citations":30.0, "answer":0, "source_journal":"New Phytologist", "is_expert":true }, { "question":"How the long non-coding RNA APOLO is able to control root hair growth under cold in Arabidopsis thaliana and which are the genes involved?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The coding RNA APOLO do not bind the region responsible for the root hair (RH) repressor ROOT HAIR DEFECTIVE 6 (RHD6) and blocks the RHD6 kinase activity, resulting in cold-decresed RH elongation via the subsequent fosforilation of the transcription factor gene RHD6-like RSL4. Additionally, APOLO degrates the transcription factor WRKY42 and acts independetly of RHD6.", "The long non-coding RNA APOLO identifies the region responsible for the root hair (RH) master regulator ROOT HAIR DEFECTIVE 6 (RHD6) and modulates RHD6 transcriptional activity, resulting in cold-induced RH elongation via the subsequent activation of the transcription factor gene RHD6-like RSL4. Additionally, APOLO interacts with the transcription factor WRKY42 and regulates its association with the RHD6 promoter. ", "The long non-coding RNA APOLO identifies the region responsible for the root hair (RH) repressor ROOT HAIR DEFECTIVE 6 (RHD6) and blocks the RHD6 transcriptional activity, resulting in cold-decresed RH elongation via the subsequent activation of the transcription factor gene RHD6-like RSL1. Additionally, APOLO do not interacts with the transcription factor WRKY42 and acts independetly of RHD6 promoter." ], "source":"Moison M, Pacheco JM, Lucero L, Fonouni-Farde C, Rodr\u00edguez-Melo J, Mansilla N, Christ A, Bazin J, Benhamed M, Iba\u00f1ez F, Crespi M, Estevez JM, Ariel F. The lncRNA APOLO interacts with the transcription factor WRKY42 to trigger root hair cell expansion in response to cold. Mol Plant. 2021 Jun 7;14(6):937-948. doi: 10.1016\/j.molp.2021.03.008.", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.molp.2021.03.008", "Year":2021.0, "Citations":94.0, "answer":1, "source_journal":"Molecular Plant", "is_expert":true }, { "question":"How auxin control ROS homeostasis and Root hair growth in Arabidopsis thaliana and which are the genes involved?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "ROS reduction in Arabidopsis thaliana is regulated by the transcription factor RSL4, which is transcriptionally repressed by auxin via several auxin response factors (ARFs). Auxin blocks ROS-mediated non-polar development of root hairs by repressing RSL4, which subsequently fosforilates the expression of genes encoding NADPH oxidases and class III peroxidases, responsible for degrading ROS molecules.", "ROS generation is regulated by the transcription factor RSL4, which is transcriptionally modulated by auxin via several auxin response factors (ARFs) in Arabidopsis thaliana. Auxin regulates ROS-mediated polar development by activating RSL4, which subsequently enhances the expression of genes encoding NADPH oxidases and class III peroxidases, responsible for catalyzing ROS generation. ", "ROS degration is regulated by the transcription factor RSL4, which is transcriptionally repressed by absisic acid via several auxin response factors (ARFs). Absisic acid triggers ROS-mediated isotropic development of lateral roots by repressing RSL4, which subsequently fosforilates the proteins encoding NADPH oxidases and class III peroxidases, responsible for nuclear ROS production." ], "source":"Mangano S, Denita-Juarez SP, Choi HS, Marzol E, Hwang Y, Ranocha P, Velasquez SM, Borassi C, Barberini ML, Aptekmann AA, Muschietti JP, Nadra AD, Dunand C, Cho HT, Estevez JM. Molecular link between auxin and ROS-mediated polar growth. Proc Natl Acad Sci U S A. 2017 May 16;114(20):5289-5294. doi: 10.1073\/pnas.1701536114.", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1073\/pnas.1701536114", "Year":2017.0, "Citations":221.0, "answer":1, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"How RALF1-FERONIA regulates specific mRNA translation in root hairs in Arabidopsis thaliana and which are the genes involved in this process?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis thaliana, the nuclear peptide RALF1 and its receptor, the FERONIA receptor kinase, blocks root hair tip development via regulating protein phosphorilation. RALF1 degradates FERONIA-mediated ubiquination of eIF4E1, a eukaryotic transcriptional initiation factor essential for regulating the mRNA transcription rate. Phosphorylated eIF4E1 enhances mRNA sintesis and regulates mRNA development, hence influencing gene expression. The mRNAs is degraded by the RALF1\u2013FERONIA\u2013eIF4E1 module include ROP2 and RSL4, which are minor regulators of root hair non polar proliferation.", "In Arabidopsis thaliana, the cytoplasmic peptide RALF1 and its receptor, the FERONIA receptor kinase, repress root hair tip development via regulating protein degradation. RALF1 blocks the FERONIA-mediated phosphorylation of eIF4E1, a eukaryotic translation initiation factor essential for regulating the mRNA translation rate. Phosphorylated eIF4E1 decreases mRNA affinity and blocks mRNA translation, hence influencing protein synthesis. The mRNAs degraded by the RALF1\u2013FERONIA\u2013eIF4E1 module include ROP2 and RSL4, which are minor regulators of root hair cell polarity and proliferation.", "In Arabidopsis thaliana, the extracellular peptide RALF1 and its receptor, the FERONIA receptor kinase, enhance root hair tip development via regulating protein synthesis. RALF1 enhances the FERONIA-mediated phosphorylation of eIF4E1, a eukaryotic translation initiation factor essential for regulating the mRNA translation rate. Phosphorylated eIF4E1 enhances mRNA affinity and regulates mRNA translation, hence influencing protein synthesis. The mRNAs affected by the RALF1\u2013FERONIA\u2013eIF4E1 module include ROP2 and RSL4, which are crucial regulators of root hair cell polarity and proliferation." ], "source":" Zhu S, Est\u00e9vez JM, Liao H, Zhu Y, Yang T, Li C, Wang Y, Li L, Liu X, Pacheco JM, Guo H, Yu F. The RALF1-FERONIA Complex Phosphorylates eIF4E1 to Promote Protein Synthesis and Polar Root Hair Growth. Mol Plant. 2020 May 4;13(5):698-716. doi: 10.1016\/j.molp.2019.12.014.", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.molp.2019.12.014", "Year":2020.0, "Citations":112.0, "answer":2, "source_journal":"Molecular Plant", "is_expert":true }, { "question":"Are plants and animals different in terms of the cellular compartments where r-proteins are encoded, and where are they encoded in each?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "non-specific" ], "options":[ "Yes, they are different. Animal r-proteins are encoded exclusively by the nuclear genome. However, plant r-proteins can be encoded by the nuclear, mitochondrial, or plastid genomes, with some variation in the location of these genes across species.", "Yes, they are different. Animal r-proteins are encoded by the nuclear and mitochondrial genomes, while plant r-proteins are encoded exclusively in the nucleus.", "No, there are no differences. In both animals and plants, r-proteins are encoded by the nuclear and mitochondrial genomes. " ], "source":"doi.org\/10.1093\/plcell\/koac333", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1093\/plcell\/koac333", "Year":2022.0, "Citations":17.0, "answer":0, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"Which proteins are the molecular partners of the plant-specific non-canonical translation initiation protein CERES and what role does it play in translation?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "non-specific" ], "options":[ "CERES is a plant-specific protein that interacts eIF4G isoforms and forms non-canonical initiation complexes that exclude eIF4A, eIF3 and PABP. In conditions where the metabolic and nutritional status of the plant is at its highest-level CERES complexes boost general translation and fine-tune the specific translation of a set of mRNAs involved in light response and saccharide management.", "CERES is a plant-specific protein that interacts with the eIF4E isoforms and, in the absence of eIF4G isoforms, recruits eIF4A, eIF3 and PABP forming non-canonical initiation complexes. In conditions where the metabolic and nutritional status of the plant is at its highest-level CERES complexes boost general translation and fine-tune the specific translation of a set of mRNAs involved in light response and saccharide management.", "CERES is a plant-specific protein that interacts with the eIF4E isoforms and, in the absence of eIF4G isoforms, recruits eIF4A, eIF3 and PABP forming non-canonical initiation complexes. CERES complexes are formed in conditions of plant stress and act down-regulating general translation as a means of energy conservation " ], "source":"DOI: 10.1038\/s41477-019-0553-2", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41477-019-0553-2", "Year":2019.0, "Citations":34.0, "answer":1, "source_journal":"Nature Plants", "is_expert":true }, { "question":"How does EIN2 regulate the translation of EBF2 in response to the plant hormone ethylene?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "non-specific" ], "options":[ "In the presence of ethylene, the C-terminal end of EIN2 is cleaved and released from the ER membrane. It translocates to the nucleus, where it participates in the transcriptional up-regulation of ethylene-responsive genes, including EBF2. In the cytoplasm, the EIN2 C-terminal end binds the 5' untranslated region (5' UTR) of EBF2 mRNA and impedes the binding of the cap-binding complex, inhibiting its translation. This mechanism explains the lack of EBF protein accumulation upon ethylene treatment despite high levels of EBF2 transcripts.", "In the presence of ethylene, the C-terminal end of EIN2 is cleaved and released from the ER membrane. It translocates to the nucleus, where it participates in the transcriptional up-regulation of ethylene-responsive genes, including EBF2, and also to the cytoplasm. In the cytoplasm, the EIN2 C-terminal end binds the 3' untranslated region (3' UTR) of EBF2 mRNA and recruits the UPF proteins, the core components of the nonsense-mediated decay (NMD) machinery. This interaction leads to the sequestration of EBF2 mRNA into P-bodies, impeding its translation. This mechanism explains the lack of EBF protein accumulation upon ethylene treatment, despite high levels of EBF2 transcripts. ", "In the presence of ethylene, the C-terminal end of EIN2 is cleaved and released from the ER membrane. It translocates to the nucleus, where it participates in the transcriptional up-regulation of ethylene-responsive genes, including EBF2, and also to the cytoplasm. In the cytoplasm, the EIN2 C-terminal end binds the 5' untranslated region (5' UTR) of EBF2 mRNA and recruits the downstream proteins of the ethylene signaling pathway. This interaction leads to the sequestration of EBF2 mRNA into P-bodies, impeding its translation. This mechanism explains the lack of EBF protein accumulation upon ethylene treatment, despite high levels of EBF2 transcripts." ], "source":"doi.org\/10.1016\/j.cell.2015.09.036", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.cell.2015.09.036", "Year":2015.0, "Citations":269.0, "answer":1, "source_journal":"Cell", "is_expert":true }, { "question":"Which proteins of the ethylene signaling pathway are required for the translational regulation of EBF2 in response to the plant hormone ethylene?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "non-specific" ], "options":[ "The 3\u00b4UTR of EBF2 is the sole responsible for the translational regulation", "EIN3 and EIL1", "EIN2 and upstream components that guarantee perception of ethylene. " ], "source":"doi.org\/10.1016\/j.cell.2015.09.036", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.cell.2015.09.036", "Year":2015.0, "Citations":269.0, "answer":2, "source_journal":"Cell", "is_expert":true }, { "question":"Do upstream open reading frames (uORFs) regulate translation of the main ORF of their transcript?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "non-specific" ], "options":[ "Yes. uORFs are short translated ORFs present in the 5\u2032 leaders of mRNAs that usually repress translation of the main downstream ORF. The effectiveness of a uORF in repressing translation depends on several characteristics, such as the sequence context around its initiation codon, the length, the distance between its stop codon and the next ORF in the transcript, and\/or the overlap of the uORF with the mORF ", "No. uORFs are short translated ORFs present in the 5\u2032 leaders of mRNAs that have no effect on the translation of the main downstream ORF. ", "Yes. uORFs are short translated ORFs present in the 5\u2032 leaders of mRNAs that usually enhance translation of the main downstream ORF. The effectiveness of a uORF in enhancing translation depends on several characteristics, such as the sequence context around its initiation codon, the length, the distance between its stop codon and the next ORF in the transcript, and\/or the overlap of the uORF with the mORF" ], "source":"doi.org\/10.1111\/tpj.13520", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1111\/tpj.13520", "Year":2017.0, "Citations":163.0, "answer":0, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"Which proteins are part of the infectosome protein complex that directs the polar growth of rhizobia infection threads in legume root hairs?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Medicago truncatula" ], "options":[ "Vapyrin (VPY), RHIZOBIUM-DIRECTED POLAR GROWTH (RPG), E3 ligase LUMPY INFECTIONS (LIN), exocyst subunit EXO70H4.", "Vapyrin (VPY), RHIZOID-DIRECTED POLAR GAMETE (RPG), E3 ligase LUMPY INFECTIONS (LIN), exocyst subunit EXO70H4.", "Vapyryn (VPN), RHIZOBIUM-DIRECTED POLAR GROWTH (RDP), E3 ligase LUMPY INFECTIONS (LUN), exocyst subunit EXO70H4." ], "source":"10.1038\/s41467-019-10029-y; 10.7554\/eLife.80741;", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.7554\/eLife.80741", "Year":2023.0, "Citations":23.0, "answer":0, "source_journal":"eLife", "is_expert":true }, { "question":"The nitrogen-fixing nodule symbiosis is restricted to plant species belonging to four related angiosperm orders. Which are these four group of plants and which transcription factor, indispensable for root nodulation, has been fundamental in the evolution of this symbiosis? ", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "non-specific" ], "options":[ "The nitrogen-fixing nodule symbiosis occurs in plant species belonging to four related angiosperm orders, Fabales, Fagales, Crossosomatales, and Rosales, known as the nitrogen-fixing clade. The origin of this symbiosis can be traced back to a single ancestor, around 300 million years ago, and involved the recruitment of the transcription factor Nodule Inception (NIN), critical for nodulation in both legume and non-legume species. ", "The nitrogen-fixing nodule symbiosis occurs in plant species belonging to four related angiosperm orders, Females, Fagales, Cucurbitales, and Rojales, known as the nitrogen-fixing clade. The origin of this symbiosis can be traced back to a single ancestor, around 100 million years ago, and involved the recruitment of the transcription factor Nodule Inceptor (NIN), critical for nodulation in both legume and non-legume species.", "The nitrogen-fixing nodule symbiosis occurs in plant species belonging to four related angiosperm orders, Fabales, Fagales, Cucurbitales, and Rosales, known as the nitrogen-fixing clade. The origin of this symbiosis can be traced back to a single ancestor, around 110 million years ago, and involved the recruitment of the transcription factor Nodule Inception (NIN), critical for nodulation in both legume and non-legume species." ], "source":"10.1016\/j.xplc.2019.100019; 10.1126\/science.aat1743", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1126\/science.aat1743", "Year":2018.0, "Citations":333.0, "answer":2, "source_journal":"Science", "is_expert":true }, { "question":"Cytoplasmic bridges are formed in plant cells to anticipate endosymbiotic infection by rhizobia-filled infection threads and arbuscular mycorrhizal fungal hyphae in Medicago. How are these cytoplasmic bridges called?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Medicago truncatula" ], "options":[ "PIT (Pre-Infection Thread) in the case of rhizobia infection and PPA (Pre-Penetration Apparatus) in the case of arbuscular mycorrhiza fungi infection.", "PIT (Priming-Inside Thread) in the case of rhizobia infection and PPA (Pre-penetration Apparatus) in the case of arbuscular mycorrhiza fungi infection. ", "PIT (Pre-Infection Thread) in the case of rhizobia infection and PPA (Pre-Priming Appendix) in the case of arbuscular mycorrhiza fungi infection. " ], "source":"10.1038\/s41467-024-55067-3; 10.1146\/annurev-cellbio-101512-122413", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1146\/annurev-cellbio-101512-122413", "Year":2013.0, "Citations":442.0, "answer":0, "source_journal":"Annual Review of Cell and Developmental Biology", "is_expert":true }, { "question":"The cell cycle status of plant cells is dynamically regulated during transcellular passage of rhizobial infection threads Medicago root cortex. What is the cell cycle status of plant cells during infection thread passage? Which symbiotic transcription factor is involved in regulating this process?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Medicago truncatula" ], "options":[ "Root cortical cells transcellularly crossed by an infection thread enter the cell cycle, but remain in a G2-post-replicative phase without mitosis. The transcription factor NF-YA1 was involved in the regulation of this process. ", "Root cortical cells transcellularly crossed by an infection thread enter the cell cycle, but remain in a G1 cell cycle phase. The transcription factor NF-YA1 was involved in the regulation of this process. ", "Root cortical cells transcellularly crossed by an infection thread enter the cell cycle, but remain in a G12-post-replicative phase without mitosis. The transcription factor NF-ABC was involved in the regulation of this process. " ], "source":"10.7554\/eLife.88588.1", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.7554\/eLife.88588.1", "Year":2023.0, "Citations":0.0, "answer":0, "source_journal":null, "is_expert":true }, { "question":"Symplastic communication regulated by callose turnover at plasmodesmata is important for coordinating nodule development in Medicago. What is callose? and which enzyme was involved in degrading callose to promote symplastic connectivity during nodulation in Medicago?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Medicago truncatula" ], "options":[ "\nCallose is a \u03b2-1,3-chitin polysaccharide that, when deposited in plasmodesmata, reduces symplastic connectivity between cells. The Medicago \u03b2-1,3-glucoronidase MtGLU2, is a novel plasmodesmata-associated callose-degrading enzyme required for establishing symplastic connectivity during nodule development. ", "Callose is a \u03b2-1,6-glucan polysaccharide that, when deposited in plasmodes, reduces symplastic connectivity between cells. The Medicago \u03b2-1,3-glucanase MtBG2 is a novel plasmode-associated callose-degrading enzyme required for closing symplastic connectivity during nodule development. ", "Callose is a \u03b2-1,3-glucan polysaccharide that, when deposited in plasmodesmata, reduces symplastic connectivity between cells. The Medicago \u03b2-1,3-glucanase MtBG2 is a novel plasmodesmata-associated callose-degrading enzyme required for establishing symplastic connectivity during nodule development. " ], "source":"10.1016\/j.cub.2018.09.031", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.cub.2018.09.031", "Year":2018.0, "Citations":53.0, "answer":2, "source_journal":"Current Biology", "is_expert":true }, { "question":"In Arabidopsis thaliana, which transcription factors control DNA Damage Response genes in response to replication stress together with SOG1 ? Do they function cooperatively or antagonistically to control the expression of genes involved in cell cycle progression ?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis, E2FA and E2FB share many target genes with SOG1 and play a role in the plant\u2019s response to replication stress. SOG1 activates its target genes, whereas E2FB can function both as a positive or a negative regulator of their shared targets. In particular, E2FB represses the expression of genes involved in cell cycle arrest, thereby allowing cell cycle progression in spite of replication stress.", "In Arabidopsis, E2FA and E2FB do not share any target genes with SOG1 but play a role in the plant\u2019s response to replication stress. SOG1 activates its target genes, whereas E2FA and E2FB function as negative regulators of their specific targets. In particular, E2FB represses the expression of genes involved in cell cycle arrest, whereas E2FA activates genes involved in cell cycle progression. Together, they allow cell cycle progression in spite of replication stress.", "In Arabidopsis, E2FA shares many target genes with SOG1 and plays a role in the plant\u2019s response to replication stress. Both SOG1 and E2FA function as a positive regulators of their shared targets. In particular, E2FA activates the expression of genes involved in cell cycle arrest, thereby playing a complementary role to that of SOG1 in promoting cell cycle arrest in response to replication stress." ], "source":"https:\/\/doi.org\/10.1016\/j.molp.2023.07.002", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1016\/j.molp.2023.07.002", "Year":2023.0, "Citations":7.0, "answer":0, "source_journal":"Molecular Plant", "is_expert":true }, { "question":"How does the ATR-WEE1 module control SOG1 expression in response to replication stress in Arabidopsis thaliana, and what are the key proteins involved in this regulatory mechanism?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis thaliana, the ATR-WEE1 module represses SOG1 translation in response to DNA damage. In response to replication stress, WEE1 is transcriptionally activated by SOG1, and phosphorylated by ATR. WEE1 phosphorylates the GCN20 sub-unit of the GCN20-GCN1 dimer that activates translation, promoting GCN20 degradation, resulting in reduced SOG1 translation.", "In Arabidopsis thaliana, the ATR-WEE1 module promotes SOG1 translation in response to DNA damage. In response to replication stress, WEE1 is transcriptionally activated by SOG1, and phosphorylated by ATR. WEE1 phosphorylates the GCN20 sub-unit of the GCN20-GCN1 dimer that represses translation, promoting GCN20 degradation, resulting in enhanced SOG1 translation.", "In Arabidopsis thaliana, the ATR-WEE1 module represses SOG1 translation in response to DNA damage. In response to replication stress, WEE1 is transcriptionally activated by ATR, and phosphorylated by SOG1. SOG1 phosphorylates the GCN20 sub-unit of the GCN20-GCN1 dimer that represses translation, promoting GCN20 stabilization, resulting in reduced SOG1 translation." ], "source":"https:\/\/doi.org\/10.1093\/plcell\/koad126", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1093\/plcell\/koad126", "Year":2023.0, "Citations":8.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"In Arabidopsis thaliana, how does TSK recognized newly replicated chromatin ? How does it mediate genomic instability in atxr5 atxr6 mutants?", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis, TSK specifically interacts with the H3.1 histone variant that is incorporated into DNA during DNA replication through its TPR motif. Quickly after DNA replication, histone H3.1 is mono-methylated on lysin 27 by ATXR5 and ATXR6, which inhibits TSK binding, thereby restricting its activity to newly replicated DNA. In atxr5 atxr6 mutants, histone H3.1 is not methylated, which allows prolonged TSK binding and promotes homologous recombination at broken replication fork, thereby triggering heterochromatin amplification and genomic instability.", "In Arabidopsis, TSK specifically interacts with the H3.1 histone variant that is incorporated into DNA during DNA replication through its TPR motif. Quickly after DNA replication, histone H3.1 is de-methylated on lysin 27 by ATXR5 and ATXR6, which promotes TSK binding, thereby restricting its activity to newly replicated DNA. In atxr5 atxr6 mutants, histone H3.1 is not de-methylated, which prevents TSK binding and prevents homologous recombination at broken replication fork, thereby triggering heterochromatin amplification and genomic instability.", "In Arabidopsis, TSK specifically interacts with the H3.3 histone variant that is incorporated into DNA during DNA replication through its LPR motif. Quickly after DNA replication, histone H3.3 is mono-methylated on lysin 27 by ATXR5 and ATXR6, which inhibits TSK binding, thereby restricting its activity to newly replicated DNA. In atxr5 atxr6 mutants, histone H3.3 is not methylated, which allows prolonged TSK binding and promotes homologous recombination at broken replication fork, thereby triggering heterochromatin amplification and genomic instability." ], "source":"doi:10.1126\/science.abm5320", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1126\/science.abm5320", "Year":2022.0, "Citations":49.0, "answer":0, "source_journal":"Science", "is_expert":true }, { "question":"How does SMR1 control leaf epidermis development at the cellular level in Arabidopsis thaliana, and how does it contribute to the plant\u2019s response to environmental conditions? ", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis, SMR1 promotes the self-renewal of stomatal lineage ground cells and inhibits their differentiation into pavement cells by activating CYCA-CDKB1 complexes. In response to drought, down-regulation of SMR1 allows reducing the plant\u2019s stomatal index, thereby leading to improved drought tolerance.", "In Arabidopsis, SMR1 inhibits the self-renewal of stomatal lineage ground cells and promotes their differentiation into pavement cells by inhibiting CYCA-CDKB1 complexes. In response to drought, up-regulation of SMR1 allows reducing the plant\u2019s stomatal index, thereby leading to improved drought tolerance.", "In Arabidopsis, SMR1 inhibits the differentiation of stomatal lineage ground cells into pavement cells and promotes their proliferation by activating CYCA-CDKB1 complexes. Down-regulation of SMR1 reduces plant\u2019s tolerance to drought while its over-expression improves plant\u2019s tolerance to drought." ], "source":"doi.org\/10.1038\/s41477-023-01452-7", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1038\/s41477-023-01452-7", "Year":2023.0, "Citations":7.0, "answer":1, "source_journal":"Nature Plants", "is_expert":true }, { "question":"Which kinase plays the most prominent role in Double-Strand Break repair in maize, and what is it's role during development?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Zea mays" ], "options":[ "In Maize, ATR is the main kinase involved in the response to double-strand breaks whereas ATM plays only a minor role. During plant development, ATR is required for normal kernel development to prevent double-strand breaks accumulation and premature endoreduplication onset.", "In Maize, both ATR and ATM play crucial roles in the response to double-strand breaks. During plant development, ATR is required for normal leaf development to prevent single-strand breaks accumulation and early senescence.", "In Maize, ATM is the main kinase involved in the response to double-strand breaks whereas ATR plays only a minor role. During plant development, ATM is required for normal kernel development to prevent double-strand breaks accumulation and premature endoreduplication onset." ], "source":"10.1093\/plcell\/koab158", "normalized_plant_species":"Cereal Grains", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1093\/plcell\/koab158", "Year":2021.0, "Citations":28.0, "answer":0, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"What is the difference between the conventional bootstrap method and the transfer bootstrap expectation method as measures of branch support in phylogenomic trees?", "area":"EVOLUTION", "plant_species":[ "non-specific" ], "options":[ "Bootstrap indices are calculated by counting the number of times that different bipartitions of a phylogenetic tree occur in resampled data matrices of the same size as the original. Transfer bootstrap (TBE) is better suited for large-scale phylogenies because it overcomes the binary nature of conventional estimates. It provides additional information by considering the degree of difference in taxa between bootstrap trees and the reference phylogeny, enabling the identification of unstable terminals without compromising entire nodes.", "Bootstrap indices are calculated by counting the number of times that different bipartitions of a phylogenetic tree occur in resampled data matrices of the same size as the original. Transfer bootstrap (TBE) is better- suited for large-scale phylogenies because it overcomes the binary nature of conventional estimates. It adds more information by also considering the degree of difference in taxa placement among bootstrap trees, allowing the identification of unstable terminals without compromising entire nodes. ", "Bootstrap indices are calculated by counting the number of times that different bipartitions of a phylogenetic tree occur in data matrices resampled with no replacement. Transfer bootstrap (TBE) is better suited for large-scale phylogenies because it overcomes the binary nature of conventional estimates. It refines Felsestein\u00b4s bootstrap values by identifying and removing unstable terminals, thereby increasing overall branch support and node robustness. " ], "source":"https:\/\/doi.org\/10.1038\/s41586-018-0043-0", "normalized_plant_species":"Non-specific", "normalized_area":"EVOLUTION", "doi":"10.1038\/s41586-018-0043-0", "Year":2018.0, "Citations":582.0, "answer":0, "source_journal":"Nature", "is_expert":true }, { "question":"What are the main discrepancies between plastome-based and nuclear phylogenomic studies in the systematics of rosids?", "area":"EVOLUTION", "plant_species":[ "non-specific" ], "options":[ "Plastid data recover two reciprocally monophyletic clades within Rosidae: the Fabidae and Malvidae subclades, with Vitales as the sister group to these clades. Nuclear data, however, resolve Saxifragales as the sister group to fabids and malvids. Additionally, it recircumscribes fabids to include Cucurbitales, Fabales, Fagales, and Rosales, while the redefined malvids encompass Brassicales, Celastrales, Huerteales, Malpighiales, Malvales, Oxalidales, Picramniales, and Sapindales. Furthermore, Oxalidales emerge as paraphyletic, leading to the dissolution of the previously defined COM clade.", "Plastid data recover two reciprocally monophyletic clades within Rosidae: the Fabidae and Malvidae subclades, with Zygophyllales as the sister group to these clades. Nuclear data, however, resolve Saxifragales as the sister group to fabids and malvids. Additionally, it recircumscribes fabids to include Cucurbitales, Fabales, Fagales, Rosales, and Malpighiales while the redefined malvids encompass Brassicales, Celastrales, Huerteales, Malvales, Oxalidales, Picramniales, and Sapindales. Furthermore, Oxalidales emerge as paraphyletic, leading to the dissolution of the previously defined COM clade.", "Plastid data recover two reciprocally monophyletic clades within Rosidae: the Fabidae and Malvidae subclades, with Saxifragales as the sister group to these clades. Nuclear data, however, resolve Zygophyllales as the sister group to fabids and malvids. Additionally, it recircumscribes fabids to include Cucurbitales, Fabales, Fagales, Rosales, and Malpighiales while the redefined malvids encompass Brassicales, Celastrales, Huerteales, Malvales, Oxalidales, Picramniales, and Sapindales. Furthermore, Celastrales emerge as paraphyletic, leading to the dissolution of the previously defined COM clade." ], "source":"https:\/\/doi.org\/10.1038\/s41586-024-07324-0", "normalized_plant_species":"Non-specific", "normalized_area":"EVOLUTION", "doi":"10.1038\/s41586-024-07324-0", "Year":2024.0, "Citations":108.0, "answer":0, "source_journal":"Nature", "is_expert":true }, { "question":"How can introgression be distinguished from incomplete lineage sorting in phylogenomic datasets?", "area":"EVOLUTION", "plant_species":[ "non-specific" ], "options":[ "Introgression and incomplete lineage sorting can both result in discordance among gene trees and between gene and species trees. In the latter case, the order of coalescent events differs from the order of splits in the species phylogeny. The most common methods for detecting introgression involve quartets of species, consisting of three focal taxa and an outgroup. Given a fixed species tree, there are four possible discordant gene tree topologies. Under the multispecies coalescent model, the discordant gene tree topologies arising from incomplete lineage sorting are expected to occur with a probability proportional to their frequency. Introgression between two species occurs when an initial hybridization event is followed by backcrossing into one or both of the parental lineages. At the genomic scale, introgression between lineages results in one discordant topology becoming more prevalent than the others. The D-statistic, also known as the ABBA-BABA test, is a widely applied method for detecting introgression. A D value greater than zero indicates the presence of introgression, whereas a value less than zero suggests incomplete lineage sorting.", "Introgression and incomplete lineage sorting can both result in discordance among gene trees and between gene and species trees. In the latter case, the order of coalescent events differs from the order of splits in the species phylogeny. The most common methods for detecting introgression involve quartets of species, consisting of three focal taxa and an outgroup. Given a fixed species tree, there are two possible discordant gene tree topologies. Under the multispecies coalescent model, the two discordant gene tree topologies arising from incomplete lineage sorting are expected to occur with equal frequency. Introgression between two species occurs when an initial hybridization event is followed by backcrossing into one or both of the parental lineages. At the genomic scale, introgression between lineages results in one discordant topology becoming more prevalent than the others. The D-statistic, also known as the ABBA-BABA test, is a widely applied method for detecting introgression. A D value different from zero indicates the presence of introgression.", "Introgression and incomplete lineage sorting can both result in discordance among gene trees and between gene and species trees. In the latter case, the order of coalescent events differs from the order of splits in the species phylogeny. The most common methods for detecting introgression involve quartets of species, consisting of three focal taxa and an outgroup. Given a fixed species tree, there are three possible discordant gene tree topologies. Under the multispecies coalescent model, the two discordant gene tree topologies arising from incomplete lineage sorting are expected to occur with equal frequency. Introgression between two species occurs when an initial hybridization event is followed by backcrossing into one or both of the parental lineages. At the genomic scale, introgression between lineages results in one discordant topology becoming more prevalent than the others. The D-statistic, also known as the ABBA-BABA test, is a widely applied method for detecting introgression. A D value that is not significantly different from zero indicates the presence of introgression." ], "source":"https:\/\/doi.org\/10.1093\/genetics\/iyab173", "normalized_plant_species":"Non-specific", "normalized_area":"EVOLUTION", "doi":"10.1093\/genetics\/iyab173", "Year":2021.0, "Citations":110.0, "answer":1, "source_journal":"Genetics", "is_expert":true }, { "question":"Which gene families are associated with rubber production in seed plants, and how does gene copy variation influence this trait?", "area":"EVOLUTION", "plant_species":[ "non-specific" ], "options":[ "Hevea brasiliensis is the most important source of natural rubber worldwide. In this species, the REF\/SRPP (rubber elongation factor\/small rubber particle protein) tandem gene cluster has been associated with rubber production. Phylogenomic analyses, including an extensive sample of seed plants, revealed that members of the genus Hevea possess more than 14 copies in this cluster\u2014significantly higher than the number found in most angiosperms and gymnosperms. A few species outside the genus Hevea have comparable numbers of REF\/SRPP gene copies (12 to 33). However, in Hevea, the distances among genes within the cluster are larger, spanning a genomic region of more than 3000 kb. Despite strong collinearity among species in the flanking regions of the cluster, large copy numbers are observed only in rubber-producing species, such as dandelions and lettuce. Interestingly, in Hevea, the expression of REF\/SRPP genes correlates with latex production.", "Hevea brasiliensis is the most important source of natural rubber worldwide. In this species, the REF\/SRPP (rubber elongation factor\/small rubber particle protein) tandem gene cluster has been associated with rubber production. Phylogenomic analyses including an extensive sample of seed plants revealed that members of the genus Hevea possess an average of 5 copies in this cluster\u2014significantly lower than the number found in most angiosperms and gymnosperms. A few species outside the genus Hevea have comparable numbers of REF\/SRPP gene copies. However, in Hevea, the majority of REF\/SRPP genes are located in a tandem gene cluster spanning a genomic region of less than 300 kb. Despite strong collinearity among species in the flanking regions of the cluster, low copy numbers are observed only in rubber-producing species, such as dandelions and lettuce. Interestingly, in Hevea, the expression of genes within the cluster correlates with latex production. ", "Hevea brasiliensis is the most important source of natural rubber worldwide. In this species, the REF\/SRPP (rubber elongation factor\/small rubber particle protein) tandem gene cluster has been associated with rubber production. Phylogenomic analyses including an extensive sample of seed plants revealed that members of the genus Hevea possess more than 14 copies in this cluster\u2014significantly higher than the number found in most angiosperms and gymnosperms. A few species outside the genus Hevea have comparable numbers of REF\/SRPP gene copies (12 to 33). However, in Hevea, the majority of REF\/SRPP genes are located in a large tandem gene cluster of over 10 copies spanning a genomic region of less than 300 kb. Despite strong collinearity among species in the flanking regions of the cluster, large copy numbers are observed only in rubber-producing species, such as dandelions and lettuce. In Hevea, the expression of genes within the cluster also correlates with latex production. " ], "source":"https:\/\/doi.org\/10.1038\/s41467-024-51031-3", "normalized_plant_species":"Non-specific", "normalized_area":"EVOLUTION", "doi":"10.1038\/s41467-024-51031-3", "Year":2024.0, "Citations":4.0, "answer":2, "source_journal":"Nature Communications", "is_expert":true }, { "question":"What connections have been identified between the convergence of floral traits and the evolution of regulatory genes in Asteraceae?", "area":"EVOLUTION", "plant_species":[ "non-specific" ], "options":[ "Phylogenomic analysis revealed seven convergent gains of floral actinomorphy during the early diversification of Asteraceae, with the most recent common ancestor of core Asteraceae possessing only zygomorphic florets. Conversely, the loss of the actinomorphic state was observed more than 30 times, and multiple episodes of reduction from the ancestral corymbiform cymose capitulescence to a solitary capitulum were detected. Corolla color exhibited a complex evolutionary pattern, with numerous transitions from the ancestral yellow to white and purple, especially in the initial phases of subfamily divergence. Regarding regulatory genes, clades possessing the highest levels of floral morphological diversity also showed increased duplications of floral MADS-box genes. Within the TCP gene family, duplications of CYC2 genes appear to have played a role in the convergent gains of floral zygomorphy in different subfamilies. Expression levels of CYC2 suggest that CYC2b\u2013CYC2e and CYC2a, but probably not CYC2g, are involved in the development of zygomorphic florets. Concordantly, the convergent loss of floral zygomorphy is associated with low to null expression of some CYC2 genes.", "Phylogenomic analysis revealed a single gain of floral zygomorphy during the early diversification of Asteraceae, including ray, ligulate, and bilateral florets, with the most recent common ancestor of core Asteraceae possessing only actinomorphic florets. Conversely, the loss of the zygomorphic state was observed more than 30 times, and multiple episodes of reduction from the ancestral corymbiform cymose capitulescence to a solitary capitulum were detected. Corolla color exhibited a complex evolutionary pattern, with numerous transitions from the ancestral purple to white and yellow, particularly at the genus or species level. Regarding regulatory genes, clades possessing the highest levels of floral morphological diversity also showed increased duplications of floral MADS-box genes. Within the TCP gene family, duplications of CYC3 genes appear to have played a role in the convergent gains of floral zygomorphy in different subfamilies. Expression levels of CYC3 suggest that CYC3b\u2013CYC3e and CYC3g, but probably not CYC3a, are involved in the development of zygomorphic florets. Concordantly, the convergent loss of floral zygomorphy is associated with low to null expression of some CYC3 genes.", "Phylogenomic analysis revealed seven convergent gains of floral zygomorphy during the early diversification of Asteraceae, including ray, ligulate, and bilateral florets, with the most recent common ancestor of core Asteraceae possessing only actinomorphic florets. Conversely, the loss of the zygomorphic state was observed more than 30 times, and multiple episodes of reduction from the ancestral corymbiform cymose capitulescence to a solitary capitulum were detected. Corolla color exhibited a complex evolutionary pattern, with numerous transitions from the ancestral yellow to white and purple, particularly at the genus or species level. Regarding regulatory genes, clades possessing the highest levels of floral morphological diversity also showed increased duplications of floral MADS-box genes. Within the TCP gene family, duplications of CYC2 genes appear to have played a role in the convergent gains of floral zygomorphy in different subfamilies. Expression levels of CYC2 suggest that CYC2b\u2013CYC2e and CYC2g, but probably not CYC2a, are involved in the development of zygomorphic florets. Concordantly, the convergent loss of floral zygomorphy is associated with low to null expression of some CYC2 genes." ], "source":"https:\/\/doi.org\/10.1016\/j.xplc.2024.100851", "normalized_plant_species":"Non-specific", "normalized_area":"EVOLUTION", "doi":"10.1016\/j.xplc.2024.100851", "Year":2024.0, "Citations":1.0, "answer":2, "source_journal":"Plant Communications", "is_expert":true }, { "question":"Members of two families of transcription factors regulate gene expression during the phases of the mitotic cell cycle in Arabidopsis thaliana. What is the name of these transcription factors? which phase of the cell cycle is controlled by each of them?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "GRF and SPL transcription factors have been identified as controlling gene expression dynamics during the mitotic cell cycle. GRF TFs have been mainly classified as regulators of the G1\/S transition and S phase progression, while activator-SPLs control genes expressed in G2\/M with critical roles in mitosis and cytokinesis", "E2F and MYB3R transcription factors have been identified as controlling gene expression dynamics during the mitotic cell cycle. MYB3R TFs have been mainly classified as regulators of the G1\/S transition and S phase progression, while E2F control genes expressed in G2\/M with critical roles in mitosis and cytokinesis", "E2F and MYB3R transcription factors have been identified as controlling gene expression dynamics during the mitotic cell cycle. E2F TFs have been mainly classified as regulators of the G1\/S transition and S phase progression, while activator-MYB3Rs control genes expressed in G2\/M with critical roles in mitosis and cytokinesis" ], "source":"doi: 10.1016\/j.pbi.2016.10.002", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1016\/j.pbi.2016.10.002", "Year":2016.0, "Citations":44.0, "answer":2, "source_journal":"Current Opinion in Plant Biology", "is_expert":true }, { "question":"What are the composition and functions of the phragmoplast and preprophase band involved in plant organ growth?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "non-specific" ], "options":[ "The preprophase band, a structure made of cytoskeletal components, membranes, and cell wall-synthetizing enzymes assembles during cytokinesis the cell plate that partitions the cytoplasm\nThe phragmoplast is formed by microtubules, actin filaments, and accessory proteins. This structure predicts the position of the cortical division zone during mitosis. Mutants with defects in PPB organization lose precision in cell division orientation, so, it has been proposed that the PPB controls division plane orientation during symmetric cell division by stabilizing mitotic spindle orientation.\n", "The phragmoplast, a structure made of cytoskeletal components, membranes, and cell wall-synthetizing enzymes assembles during cytokinesis the cell plate that partitions the cytoplasm.\nThe preprophase band is formed by microtubules, actin filaments, and accessory proteins. This structure predicts the position of the cortical division zone during mitosis. Mutants with defects in PPB organization lose precision in cell division orientation, so, it has been proposed that the PPB controls division plane orientation during symmetric cell division by stabilizing mitotic spindle orientation.\n", "The phragmoplast, a structure made of cytoskeletal components, membranes, and cell wall-synthetizing enzymes assembles the mitotic spindle during mitosis.\nThe preprophase band is formed by cell wall components. This structure predicts the position of the plasmodesmata. \n" ], "source":"doi: 10.1093\/plcell\/koac069", "normalized_plant_species":"Non-specific", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1093\/plcell\/koac069", "Year":2022.0, "Citations":19.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"There are 2 families of cyclin-dependent kinase inhibitor proteins in plants. Name both of them and describe their function during plant organ growth.", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "non-specific" ], "options":[ "The two families are the GRF gene family and the SPL gene family. They promote cell proliferation and inhibit cell expansion.", "The two families are the ICK\/KRP and SIM\/SMR gene family. They promote cell proliferation and inhibit cell expansion.", "The two families are the ICK\/KRP and the SIM\/SMR gene families. They promote mitotic cell cycle exit in the transition from cell proliferation to cell expansion." ], "source":"DOI: 10.3389\/fpls.2024.1362460", "normalized_plant_species":"Non-specific", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.3389\/fpls.2024.1362460", "Year":2024.0, "Citations":0.0, "answer":2, "source_journal":"Frontiers in Plant Science", "is_expert":true }, { "question":"How many genes coding for cyclin-dependent kinase inhibitor proteins of the SIM\/SMR family can be found in the Arabidopsis thaliana genome? Name them. Of those, which are regulated by the SCL28 transcription factor.", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "There are 17 genes coding for SIM\/SMR cyclin-dependent kinase inhibitor proteins named SIAMESE (SIM) and SIAMESE-RELATED1 (SMR1) to SMR16. SCL28 activates the expression of SMR2, SMR6, SMR9, SMR13 and SMR14.", "There are 5 genes coding for SIM\/SMR cyclin-dependent kinase inhibitor proteins named SIAMESE1 to SIAMESE5. SCL28 activates de expression of SIAMESE1.", "There are 17 genes coding for SIM\/SMR cyclin-dependent kinase inhibitor proteins named SIAMESE (SIM) and SIAMESE-RELATED1 (SMR1) to SMR16. SCL28 repress the expression of SMR2, SMR6, SMR9, SMR13 and SMR14." ], "source":"doi: 10.1111\/nph.18650", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1111\/nph.18650", "Year":2022.0, "Citations":4.0, "answer":0, "source_journal":"New Phytologist", "is_expert":true }, { "question":"What is the main difference between the mitotic cell cycle and endoreplication in plants? What are the functions of endoreplication related to plant organ growth?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "non-specific" ], "options":[ "During endoreplication, mitochondrial DNA is replicated without binary fission of the organelle. ", "During endoreplication, also known as endocycle, DNA is replicated with nuclear and cytoplasmic division. Endoreplication is involved in cell proliferation.", "During endoreplication, also known as endocycle, DNA is replicated without nuclear or cytoplasmic division, as it does occurs in the mitotic cell cycle, causing a stepwise increase in nuclear DNA content, known as somatic polyploidy.\nEndoreplication is involved in several plant development pathways and has been correlated with postmitotic cell growth, cell differentiation, high metabolic activities, rapid anisotropic cell expansion, and the ability to respond to DNA damage.\n" ], "source":"DOI: 10.1093\/jxb\/erad235", "normalized_plant_species":"Non-specific", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1093\/jxb\/erad235", "Year":2023.0, "Citations":14.0, "answer":2, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"Which are the roles of REM proteins in plants?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "The plant-specific B3 superfamily encompasses five major families of genes containing the B3 DNA binding domain. Some of them are well characterized such as ARF or ABI3\/VP1 family, but little is known about the Reproductive Meristem (REM) subfamily. To date, the only REM gene for which a function has been determined is AtVRN1, a key factor in vernalization response. Other REM members have been proposed as flowering regulators in Arabidopsis thaliana and rice, such as AtREM16 and OsREM20 respectively.", "The plant-specific B3 superfamily encompasses three major families of genes containing the B3 DNA binding domain. Some of them are well characterized such as ARF or ABI3\/VP1 family, but little is known about the Reproductive Meristem (REM) subfamily. To date, the only REM gene for which a function has been determined is AtVRN1, a key factor in vernalization response. Other REM members have been proposed as stress response regulators in Arabidopsis thaliana and rice, such as AtREM16 and OsREM20 respectively.", "The plant-specific B3 superfamily encompasses five major families of genes containing the B3 DNA binding domain. Some of them are well characterized such as ARF or ABI3\/VP1 family, but little is known about the Reproductive Meristem (REM) subfamily. To date, the only REM gene for which a function has been determined is AtVRN1, a key factor in cold response. Other REM members have been proposed as flowering regulators in Arabidopsis thaliana and rice, such as AtREM16 and OsREM20 respectively." ], "source":"http:\/\/dx.doi.org\/10.1016\/B978-0-12-800854-6.00004-X", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1016\/B978-0-12-800854-6.00004-X", "Year":2016.0, "Citations":1.0, "answer":0, "source_journal":"Plant Transcription Factors", "is_expert":true }, { "question":"Which are the SEPALLATA family genes identified and studied in grasses?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "The genes belonging to the SEP subfamily have received significant attention for interacting with other members of the MADS-BOX family in floral organogenesis. However, very few of these have been studied, particularly regarding to their role in other aspects of flowering, and particularly those identified among plants belonging to the family Pooideae. Among these it is worth mentioning those belonging to the LOFSEP clade and \"OsMADS34\" subclade. In this subclade are precisely OsMADS34 of rice, TaPAP2-5A of wheat and SiMADS34 of setaria, among those particularly studied in grasses.", "The genes belonging to the SEP subfamily have received significant attention for interacting with other members of the REM family in floral organogenesis. However, very few of these have been studied, particularly regarding to their role in other aspects of flowering, and particularly those identified among plants belonging to the family Pooideae. Among these it is worth mentioning those belonging to the LOFSEP clade and \"OsMADS34\" subclade. In this subclade are precisely OsMADS34 of rice, TaPAP2-5A of wheat and SiMADS34 of setaria, among those particularly studied in grasses.", "The genes belonging to the SEP subfamily have received significant attention for interacting with other members of the MADS-BOX family in floral organogenesis. However, a lot of these have been studied, particularly regarding to their role in other aspects of flowering, and particularly those identified among plants belonging to the family Pooideae. Among these it is worth mentioning those belonging to the LOFSEP clade and \"OsMADS34\" subclade. In this subclade are precisely OsMADS34 of rice, TaPAP2-5A of wheat and SiMADS34 of setaria, among those particularly studied in grasses." ], "source":"https:\/\/doi.org\/10.3390\/plants11212934", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.3390\/plants11212934", "Year":2022.0, "Citations":9.0, "answer":0, "source_journal":"Plants", "is_expert":true }, { "question":"What are the main routes where herbicides exert their action and the source of resistance in weed? Consider both target-site resistance (TSR) and nontarget-site resistance (NTSR).", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "non-specific" ], "options":[ "The main inhibited process by herbicides, or molecular target, are aminoacids, carotenoids, chlorophyll and fatty acid synthesis, cell division and photosynthesis. \nRegarding to the source of resistance to herbicide, the target-site resistance (TSR) are specialist mechanisms, specific to a single site of action, and the resistance to herbicide is provoked by changes in the aminoacid sequences of herbicide target proteins. These mutations could be SNPs or deletions that cause changes in the specific site of contact of herbicide or conformational of the protein that would avoid this. Lastly, another mechanism involved in TSR could be the increasing of gene target expression.\nOn the other hand, the nontarget-site resistance (NTSR) would consist in reduced absorption, reduced translocation and vacuolar sequestration, metabolic alterations and herbicide detoxification. The most important gene families for NTSR characterized to date are P450s and GSTs.\n", "The main inhibited process by herbicides, or molecular target, are aminoacids, carotenoids chlorophyll and fatty acid synthesis, cell division and photosynthesis. \nRegarding to the source of resistance to herbicide, the target-site resistance (TSR) are specialist mechanisms, specific to a single site of action, and the resistance to herbicide is provoked by changes in the aminoacid sequences of herbicide target proteins. These mutations are SNPs that cause changes in the specific site of contact of herbicide or conformational of the protein that would avoid this. Lastly, another mechanism involved in TSR could be the increasing of gene target expression.\nOn the other hand, the nontarget-site resistance (NTSR) would consist in reduced absorption, reduced translocation and vacuolar sequestration, metabolic alterations and herbicide detoxification. The most important gene families for NTSR characterized to date are P450s and GSTs.\n", "The main inhibited process by herbicides, or molecular target, are aminoacids synthesis and photosynthesis. \nRegarding to the source of resistance to herbicide, the target-site resistance (TSR) are specialist mechanisms, specific to a single site of action, and the resistance to herbicide is provoked by changes in the aminoacid sequences of herbicide target proteins. These mutations would be SNPs or deletions that cause changes in the specific site of contact of herbicide or conformational of the protein that would avoid this. Lastly, another mechanism involved in TSR could be the increasing of gene target expression.\nOn the other hand, the nontarget-site resistance (NTSR) would consist in reduced absorption, reduced translocation and vacuolar sequestration, metabolic alterations and herbicide detoxification. The most important gene families for NTSR characterized to date are P450s and GSTs.\n" ], "source":"DOI 10.1074\/jbc.REV120.013572", "normalized_plant_species":"Non-specific", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1074\/jbc.REV120.013572", "Year":2020.0, "Citations":449.0, "answer":0, "source_journal":"Journal of Biological Chemistry", "is_expert":true }, { "question":"What enzymes does AsA-GSH pathway require in plant species?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "non-specific" ], "options":[ "AsA-GSH pathway requires four enzymes: ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductase, and glutathione reductase.", "AsA-GSH pathway requires three enzymes: ascorbate peroxidase, dehydroascorbate reductase, and glutathione reductase.", "AsA-GSH pathway requires four enzymes: ascorbate peroxidase, monodehydroascorbate reductase, oxidase, and glutathione reductase." ], "source":"doi: 10.3389\/fenvs.2015.00025", "normalized_plant_species":"Non-specific", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.3389\/fenvs.2015.00025", "Year":2015.0, "Citations":113.0, "answer":0, "source_journal":"Frontiers in Environmental Science", "is_expert":true }, { "question":"Which are the main families of transcription factors involved in the development of the response to water stress in plants?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "There is a high number of gene interactions that make it difficult to identify the key plant response genes to environmental changes in all cases. However, several transcription factors have been identified and deeply studied in drought conditions. These studies allow the researchers to consider AP2\/ERF, AREB, NAC, bZIP, MADS and HD-Zip I are the most important transcription factor families involved in the response to water stress conditions.", "There is a low number of gene interactions that make it easy to identify the key plant response genes to environmental changes in all cases. However, several transcription factors have been identified and deeply studied in drought conditions. These studies allow the researchers to consider AP2\/ERF, AREB, NAC, Zinc Finger, Zinc Finger and HD-Zip I are the most important transcription factor families involved in the response to water stress conditions.", "There is a high number of gene interactions that make it difficult to identify the key plant response genes to environmental changes in all cases. However, several transcription factors have been identified and deeply studied in drought conditions. These studies allow the researchers to consider AP2\/ERF, AREB, NAC, bZIP, Zinc Finger and HD-Zip I are the most important transcription factor families involved in the response to water stress conditions." ], "source":"doi: 10.3389\/fpls.2016.01029", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.3389\/fpls.2016.01029", "Year":2016.0, "Citations":608.0, "answer":2, "source_journal":"Frontiers in Plant Science", "is_expert":true }, { "question":"Which clade of green algae is sister to the embryophytes?", "area":"EVOLUTION", "plant_species":[ "non-specific" ], "options":[ "The Characeae is the sister clade to the embryophytes", "The Coleochaetophyceae is the sister clade to the embryophytes", "The Zygnematophyceae is the sister clade to the embryophytes" ], "source":"10.1371\/journal.pone.0029696 \/ 10.1073\/pnas.1323926111 \/ 10.1038\/s41586-019-1693-2", "normalized_plant_species":"Non-specific", "normalized_area":"EVOLUTION", "doi":"10.1038\/s41586-019-1693-2", "Year":2019.0, "Citations":1354.0, "answer":2, "source_journal":"Nature", "is_expert":true }, { "question":"How has the evo-devo concept to be applied to test the conservation of a biological process within the embryophytes?", "area":"EVOLUTION", "plant_species":[ "non-specific" ], "options":[ "Gene phylogeny allows identifying genes with a conserved occurrence in embryophytes. Trans-complementation assays between species allow testing for the conservation of the molecular function. Finally, reverse genetics in bryophytes, such as Marchantia or Physcomitrium, allow determining the conservation of the biological function as it would represent the ancestral state that was present in the first land plants.", "Gene phylogeny allows identifying genes with a conserved occurrence in embryophytes, and thus conserved since their most recent common ancestor. Trans-complementation assays between species allow testing for the conservation of the molecular function and the biological role. ", "Gene phylogeny allows identifying genes with a conserved occurrence in embryophytes. Trans-complementation assays between species allow testing for the conservation of the molecular function. Finally, reverse genetics in tracheophytes and in bryophytes, such as Marchantia or Physcomitrium, allow determining the conservation of the biological function using the parsimony principle." ], "source":"10.1016\/j.cub.2019.09.044", "normalized_plant_species":"Non-specific", "normalized_area":"EVOLUTION", "doi":"10.1016\/j.cub.2019.09.044", "Year":2019.0, "Citations":62.0, "answer":2, "source_journal":"Current Biology", "is_expert":true }, { "question":"What are the plant proteins with a demonstrated conserved function in the arbuscular mycorrhizal symbiosis across land plants?", "area":"EVOLUTION", "plant_species":[ "non-specific" ], "options":[ "The function of seven plant proteins has been demonstrated to have a conserved function in arbuscular mycorrhizal symbiosis across land plants. Such demonstration has been achieved for the transcription factors WRI, regulating lipid biosynthesis during symbiosis, and CYCLOPS, participating in symbiotic signalling. In addition, the functions of the enzyme CCD8, the ion channel DMI1, the receptor-like kinases SYMRK and ARK, and the kinase CCaMK are also conserved across land plants for the arbuscular mycorrhizal symbiosis.", "The function of four plant proteins has been demonstrated to have a conserved function in arbuscular mycorrhizal symbiosis across land plants. These proteins, the transcription factors WRI, RAD1, RAM1 and CYCLOPS have a symbiotic function in the fossil plants Marchantia paleacea and Aglaophyton major. The corresponding mutants in these species do not form arbuscules. ", "The function of four plant proteins has been demonstrated to have a conserved function in arbuscular mycorrhizal symbiosis across land plants. Such demonstration has been achieved for the transporter STR and STR2, the transcription factor RAD1 and the infection-related proteins VAPYRIN and LIN. " ], "source":"10.1073\/pnas.2318982121 \/ 10.1073\/pnas.2408539121 \/ 10.1038\/s41467-022-31708-3 \/ 10.1126\/science.abg0929 \/ 10.1016\/j.cub.2024.03.063", "normalized_plant_species":"Non-specific", "normalized_area":"EVOLUTION", "doi":"10.1016\/j.cub.2024.03.063", "Year":2024.0, "Citations":6.0, "answer":0, "source_journal":"Current Biology", "is_expert":true }, { "question":"What are the evidence that the first embryophytes had already evolved cuticle?", "area":"EVOLUTION", "plant_species":[ "non-specific" ], "options":[ "Biochemical analyses of hydrolyzed plant tissues following delipidation demonstrated the presence of a lipid polymer containing glycerol and hydroxylated fatty acids, which are known constituent of the cutin, in both tracheophytes and bryophytes, including Physcomitrium patens and Marchantia polymorpha. Transmission electron microscopy on aerial tissues of tracheophytes and bryophytes showed the presence of an electron dense matrix on the surface of organs such as leaves, gametophores and thalli. Reverse genetics in angiosperms, such as Arabidopsis thaliana, and bryophytes, such as Physcomitrium patens and Marchantia polymorpha demonstrated that conserved genes such as CYP73 play a function in cutin formation in both lineages. Altogether, these phylogenetic, biochemical and genetic evidence support that the most recent common ancestor of the embryophytes had already a cuticle. ", "Biochemical analyses of hydrolyzed plant tissues following delipidation demonstrated the presence of a lipid polymer containing glycerol and hydroxylated fatty acids in Physcomitrium patens and Marchantia polymorpha. Transmission electron microscopy on aerial tissues of bryophytes showed the presence of an electron dense matrix on the surface of organs such as gametophores and thalli. Reverse genetics in and bryophytes, such as Physcomitrium patens and Marchantia polymorpha demonstrated that CYP73 play a function in cutin formation in these early land plants. Presence of a cutin polymer and the role of CYP73 in its biosynthesis in bryophytes demonstrate the ancestral nature of cuticle formation in embryophytes. ", "Biochemical analyses of hydrolyzed plant tissues following delipidation demonstrated the presence of a lipid polymer containing glycerol and hydroxylated fatty acids, which are known constituent of the cutin, in diverse species such as Arabidopsis thaliana. Transmission electron microscopy on Arabidopsis leaves showed the presence of an electron dense matrix identified as the cuticle. Reverse genetics in angiosperms, such as Arabidopsis thaliana, and bryophytes, such as Marchantia paleacea demonstrated that conserved genes such as the ones belonging to the WRINKLED (WRI) family of transcription factors regulate lipid biosynthesis. As lipids are essential constituent of the cuticle, this demonstrates that the most recent common ancestor of the embryophytes had already a cuticle. " ], "source":"10.1038\/s44318-024-00181-7 \/ 10.1038\/ncomms14713.", "normalized_plant_species":"Non-specific", "normalized_area":"EVOLUTION", "doi":"10.1038\/ncomms14713", "Year":2017.0, "Citations":168.0, "answer":0, "source_journal":"Nature Communications", "is_expert":true }, { "question":"What is the bryophyte cell-type homologous to the tracheophyte root hairs?", "area":"EVOLUTION", "plant_species":[ "non-specific" ], "options":[ "Root hairs are specific epidermal cells of the tracheophyte roots. In angiosperms root hairs are involved in nutrient and water uptake. Forward and reverse genetics in Arabidopsis thaliana defined gene modules essential for their development, such as the bHLH transcription factors MUTE and SMF. Mutants in bryophytes such as Marchantia polymorpha of the MUTE and SMF orthologs lead to defect in rhizoid formation. Rhizoids are presumed to be involved in water and nutrient uptake in bryophytes. Beyond these transcription factors, dozens of other genes have been identified with a conserved function in stomata formation. Altogether, this demonstrates that rhizoids are homologous to the tracheophyte root hairs. ", "Root hairs are specific epidermal cells of the tracheophyte roots. In angiosperms root hairs are involved in nutrient and water uptake. Forward and reverse genetics in Arabidopsis thaliana defined gene modules essential for their development, such as the bHLH transcription factors RHD6 and RSL1. Mutants in the orthologs of these genes in bryophytes such as Physcomitrium patens, PpRSL1 and PpRSL2, lead to defect in rhizoid formation. Rhizoids are presumed to be involved in water and nutrient uptake in bryophytes. Beyond these transcription factors, dozens of other genes have been identified with a conserved function in rhizoid and root-hair formation. Altogether, this demonstrates that rhizoids are homologous to the tracheophyte root hairs.", "Root hairs are specific epidermal cells of the tracheophyte roots. In angiosperms root hairs are involved in nutrient and water uptake. Forward and reverse genetics in Arabidopsis thaliana defined gene modules essential for their development, such as the bHLH transcription factors MUTE and SMF. Mutants in bryophytes such as Marchantia polymorpha of the MUTE and SMF orthologs lead to defect in stomata formation. Stomata are presumed to be involved in water and nutrient uptake in bryophytes. Beyond these transcription factors, dozens of other genes have been identified with a conserved function in stomata formation. Altogether, this demonstrates that stomata are homologous to the tracheophyte root hairs. " ], "source":"10.1126\/science.1142618 \/ 10.1016\/j.cub.2015.11.042", "normalized_plant_species":"Non-specific", "normalized_area":"EVOLUTION", "doi":"10.1016\/j.cub.2015.11.042", "Year":2016.0, "Citations":107.0, "answer":1, "source_journal":"Current Biology", "is_expert":true }, { "question":"Arabidopsis thaliana coiled-coil (CC)\u2013NLR HOPZ-ACTIVATED RESISTANCE 1 (ZAR1) immune receptor protein forms a structure named resistosome upon activation. How many ZAR1 monomers are required to assemble a functional resistosome and what is its final localization inside the plant cell?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Upon activation, the Arabidopsis ZAR1 immune receptor forms a pentameric resistosome that localizes to and insert into the chloroplast double membrane envelope to exert its role as a calcium channel, inducing cell death.", "Upon activation, the Arabidopsis ZAR1 immune receptor forms a pentameric resistosome that localizes to and insert into the plant cell plasma membrane to exert its role as a calcium channel, inducing cell death.", "Upon activation, the Arabidopsis ZAR1 immune receptor forms an hexameric resistosome that localizes to and insert into the plant cell plasma membrane to exert its role as a calcium channel, inducing cell death." ], "source":"DOI: 10.1126\/science.aav5870", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1126\/science.aav5870", "Year":2019.0, "Citations":662.0, "answer":1, "source_journal":"Science", "is_expert":true }, { "question":"What is the meaning of the term \u201ctwo-speed genome\u201d as applied to describe the genome architecture of filamentous plant pathogens like Phytophthora infestans?", "area":"GENOME AND GENOMICS", "plant_species":[ "non-specific" ], "options":[ "The term \u201ctwo-speed genome\u201d refers to a particular genome architecture observed in filamentous plant pathogens, in which two distinct regions can be identified: gene-dense and gene-sparse regions. The first one is characterized by a relatively high gene density, together with a relatively high content of repetitive DNA and transposable elements, and a conserved order of genes among genus; this region is enriched in core-orthologue genes. In contrast, the gene-sparse compartment is characterized by a low gene density and a relatively low content of repetitive sequences. Effector-coding genes (virulence factors that modulate host plant processes) are located here, acting this genome architecture context as a facilitator for adaptative evolution.", "The term \u201ctwo-speed genome\u201d refers to a particular genome architecture observed in filamentous plant pathogens, in which two distinct regions can be identified: gene-dense and gene-sparse regions. The first one is characterized by a relatively high gene density, a low content of repetitive DNA, and a conserved order of genes among species; this region is enriched in core-orthologue genes. In contrast, the gene-sparse compartment is characterized by a low gene density and enrichment in repetitive sequences and transposable elements. Effector-coding genes (virulence factors that modulate host plant processes) are located here, acting this genome architecture context as a facilitator for adaptative evolution.", "The term \u201ctwo-speed genome\u201d refers to a particular genome architecture observed in filamentous plant pathogens, in which two distinct regions can be identified: gene-dense and gene-sparse regions. The first one is characterized by a relatively high gene density, a low content of repetitive DNA, and a conserved order of genes among species; this region is enriched in effector-coding genes (virulence factors that modulate host plant processes). In contrast, the gene-sparse compartment is characterized by a low gene density and enrichment in repetitive sequences and transposable elements; core-orthologue genes are located here. This genome architecture acts as a facilitator for adaptative evolution." ], "source":"DOI: 10.1016\/j.gde.2015.09.001", "normalized_plant_species":"Non-specific", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1016\/j.gde.2015.09.001", "Year":2015.0, "Citations":461.0, "answer":1, "source_journal":"Current Opinion in Genetics & Development", "is_expert":true }, { "question":"How does the bacterial effector proteins HopM1 and AvrE1 induce water-soaking lesions in Arabidopsis thaliana during Pseudomonas syringae infection?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The bacterial effectors HopM1 and AvrE1 induce a transcriptional reprogramming in Arabidopsis cells, triggering jasmonic acid (JA) biosynthesis and signaling pathways. The increased accumulation of JA in guard cells induces local immune responses, leading to stomatal closure followed by a reduced leaf transpiration and a water-soaking lesion. HopM1 requires a guard-cell specific JA transporter, AtJAT3, to promote this type of lesion.", "The bacterial effectors HopM1 and AvrE1 induce a transcriptional reprogramming in Arabidopsis cells, repressing abscisic acid (ABA) biosynthesis and signaling pathways. The decreased accumulation of ABA in guard cells induces stomatal closure, and therefore a reduced leaf transpiration and finally a water-soaking lesion. HopM1 requires a guard-cell specific ABA transporter, ABCG40, to promote this type of lesion.", "The bacterial effectors HopM1 and AvrE1 induce a transcriptional reprogramming in Arabidopsis cells, triggering abscisic acid (ABA) biosynthesis and signaling pathways. The increased accumulation of ABA in guard cells induces stomatal closure, and therefore a reduced leaf transpiration and finally a water-soaking lesion. HopM1 requires a guard-cell specific ABA transporter, ABCG40, to promote this type of lesion." ], "source":"DOI: 10.1016\/j.chom.2022.02.006", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.chom.2022.02.006", "Year":2022.0, "Citations":91.0, "answer":2, "source_journal":"Cell Host & Microbe", "is_expert":true }, { "question":"Which nucleotide-binding, leucine-rich repeat receptors (NLR) from Nicotiana benthamiana are suppressed in their responses by the cyst nematode effector protein SPRYSEC15 (SS15)?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Nicotiana benthamiana" ], "options":[ "The cyst nematode effector protein SS15 specifically suppress the immune response mediated by NLR helper receptor NRC2 from Nicotiana benthamiana, but not by NRC3 or NRC4.", "The cyst nematode effector protein SS15 specifically suppress the immune response mediated by NLR helper receptors NRC2 and NRC3 from Nicotiana benthamiana, but not by NRC4.", "The cyst nematode effector protein SS15 specifically suppress the immune response mediated by NLR helper receptors NRC3 and NRC4 from Nicotiana benthamiana, but not by NRC2." ], "source":"DOI: 10.1371\/journal.pbio.3001136", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"ENVIRONMENT", "doi":"10.1371\/journal.pbio.3001136", "Year":2021.0, "Citations":91.0, "answer":1, "source_journal":"PLOS Biology", "is_expert":true }, { "question":"During their interaction with host species, plant pathogens secrete effectors that target plant processes\/proteins. What is the host protein target and the process affected in Nicotiana benthamiana by effector PexRD54 of Phytophthora infestans? ", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Nicotiana benthamiana" ], "options":[ "Phytophthora infestans effector PexRD54 interacts with ATG8CL, an autophagy-related protein from potato. By doing so, PexRD54 inhibits autophagosome formation in plant cells. Moreover, PexRD54 induces the accumulation of the autophagy cargo receptor Joka2 which has been described to act as a negative regulator of plant defense. Thus, PexRD54 makes the plant more susceptible to infection by P. infestans.", "Phytophthora infestans effector PexRD54 interacts with ATG10, an autophagy-related protein from potato. By doing so, PexRD54 stimulate autophagosome formation in plant cells. Moreover, PexRD54 outcompetes the autophagy cargo receptor neighbor of the BRCA1 gene 1 (NBR1) which has been described to act as a positive regulator of plant defense. Thus, PexRD54 makes the plant more susceptible to infection by P. infestans.", "Phytophthora infestans effector PexRD54 interacts with ATG8CL, an autophagy-related protein from potato. By doing so, PexRD54 stimulate autophagosome formation in plant cells. Moreover, PexRD54 outcompetes the autophagy cargo receptor Joka2 which has been described to have a positive role in plant defense. Thus, PexRD54 makes the plant more susceptible to infection by P. infestans." ], "source":"10.7554\/eLife.10856", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"ENVIRONMENT", "doi":"10.7554\/eLife.10856", "Year":2016.0, "Citations":181.0, "answer":2, "source_journal":"eLife", "is_expert":true }, { "question":"What is the role of DDM1 in tomato ?", "area":"GENOME AND GENOMICS", "plant_species":[ "Solanum lycopersicum" ], "options":[ "In plants like crops and in particular tomato (Solanum lycopersicum), DDM1 is essential to sustain global levels of DNA methylation and histone modifications. In crops like tomato, ddm1 mutants are extensively hypermethylated in all DNA cytosine contexts. DDM1 is encoded by four genes in tomato. The double Slddm1a Slddm1b mutant is drastically hypermethylated particularly in transposable elements of heterochromatic regions in both CG and CHG cytosine methylation contexts. As a counterbalancing mechanism, the RNA-directed DNA methylation pathway triggers the remethylation of the pericentromeric regions in the CHH context.", "In plants like crops and in particular tomato (Solanum lycopersicum), DDM1 is essential to sustain global levels of DNA methylation and histone modifications. In crops like tomato, ddm1 mutants are extensively hypomethylated in all DNA cytosine contexts. DDM1 is encoded by two genes in tomato. The double Slddm1a Slddm1b mutant is drastically hypomethylated particularly in transposable elements of heterochromatic regions in both CG and CHG cytosine methylation contexts. As a counterbalancing mechanism, the RNA-directed DNA methylation pathway triggers the remethylation of the pericentromeric regions in the CHH context.", "In plants like crops and in particular tomato (Solanum lycopersicum), DDM1 is essential to sustain global levels of DNA methylation and histone modifications. In crops like tomato, ddm1 mutants are extensively hypomethylated in all DNA cytosine contexts. DDM1 is encoded by two genes in tomato. The double Slddm1a Slddm1b mutant is drastically hypomethylated particularly in transposable elements of heterochromatic regions in both CHH and CG cytosine methylation contexts. As a counterbalancing mechanism, the RNA-directed DNA methylation pathway triggers the remethylation of the pericentromeric regions in the CG context." ], "source":"https:\/\/doi.org\/10.1105\/tpc.18.00167", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1105\/tpc.18.00167", "Year":2018.0, "Citations":77.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"What is the extent of natural epigenetic variation in plants ?", "area":"GENE REGULATION - EPIGENETICS AND TGS", "plant_species":[ "non-specific" ], "options":[ "Natural epigenetic variation is widespread in plants. In Arabidopsis, spontaneously gained or lost DNA methylation frequently occur in wild-type populations within much larger timescales compared to single nucleotide mutations. Studies of epigenomics in many natural bacterial and animal populations revealed a remarkable amount of population epigenetic variation. Growing evidence suggests that epigenetic effects are primarily shaped by the underlying epigenetic structure, particularly in plants, while a measurable portion is influenced by environmental factors. Whether the epigenetic natural variation could be exploited for crop breeding is still a matter of debate.", "Natural epigenetic variation is widespread in plants. In Arabidopsis, spontaneously gained or lost DNA methylation frequently occur in wild-type populations within much shorter timescales compared to single nucleotide mutations. Studies of epigenomics in many natural plant and animal populations revealed a remarkable amount of population epigenetic variation. Growing evidence suggests that epigenetic effects are primarily shaped by the underlying genetic structure, particularly in plants, while a measurable portion is influenced by environmental factors. Whether the epigenetic natural variation could be exploited for crop breeding is still a matter of debate.", "Natural epigenetic variation is widespread in plants. In Arabidopsis, spontaneously gained or lost DNA methylation frequently occur in wild-type populations within much shorter timescales compared to single nucleotide mutations. Studies of genomics in many natural plant and animal populations revealed a remarkable amount of population epigenetic variation. Growing evidence suggests that epigenetic effects are not shaped by the underlying genetic structure, particularly in plants, while a measurable portion is influenced by environmental factors. Whether the epigenetic natural variation could be exploited for crop breeding is still a matter of debate." ], "source":"https:\/\/doi.org\/10.1016\/j.pbi.2022.102297 https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/eva.13730", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1111\/eva.13730", "Year":2024.0, "Citations":0.0, "answer":1, "source_journal":"Evolutionary Applications", "is_expert":true }, { "question":"What is the role of IBM1 in plants ?", "area":"GENE REGULATION - EPIGENETICS AND TGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In plants, the Jumonji C (JmjC) domain-containing protein INCREASE IN BONSAI METHYLATION1 (IBM1) is a DNA demethylase which removes methylation on lysine 9 of histone H3 (H3K9me). The function of IBM1 is crucial as it prevents the accumulation of heterochromatic silencing marks on actively transcribed genes. In coding regions, Arabidopsis ibm1 mutants accumulate both methylation on Lysine 4 of Histone H3 (H3K4me) and on DNA cytosine in the CHG context, with drastic consequences for development. Other mutants share the same phenotype such as ibm2, edm2, aipp1 because the corresponding genes code for proteins involved in the transcription of IBM1.", "In plants, the Jumonji C (JmjC) domain-containing protein INCREASE IN BONSAI METHYLATION1 (IBM1) is a histone demethylase which removes methylation on lysine 9 of histone H3 (H3K9me). The function of IBM1 is crucial as it promotes the accumulation of heterochromatic silencing marks on actively transcribed genes. In coding regions, Arabidopsis ibm1 mutants accumulate both methylation on Lysine 9 of Histone H3 (H3K9me) and on DNA cytosine in the CHH context, with drastic consequences for development. Other mutants share the same phenotype such as ibm2, edm2, aipp1 because the corresponding genes code for proteins involved in the transcription of IBM2.", "In plants, the Jumonji C (JmjC) domain-containing protein INCREASE IN BONSAI METHYLATION1 (IBM1) is a histone demethylase which removes methylation on lysine 9 of histone H3 (H3K9me). The function of IBM1 is crucial as it prevents the accumulation of heterochromatic silencing marks on actively transcribed genes. In coding regions, Arabidopsis ibm1 mutants accumulate both methylation on Lysine 9 of Histone H3 (H3K9me) and on DNA cytosine in the CHG context, with drastic consequences for development. Other mutants share the same phenotype such as ibm2, edm2, aipp1 because the corresponding genes code for proteins involved in the transcription of IBM1." ], "source":"https:\/\/doi.org\/10.1104\/pp.18.01106", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1104\/pp.18.01106", "Year":2019.0, "Citations":23.0, "answer":2, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"Can epialleles and transgenerational epigenetic memory contribute to plant adaptation ?", "area":"GENE REGULATION - EPIGENETICS AND TGS", "plant_species":[ "non-specific" ], "options":[ "Several mitotically stable epialleles controlling important traits were discovered in crops including fruit ripening or vitamin E content in tomato, sex determination in melon and dwarfism in rice, as well as in Arabidopsis. Nevertheless, it remains unclear whether modifications of the epigenome could mediate a response to environmental stresses or enable adaptation among one generation. Exposing Arabidopsis plants to various stresses like drought or salt revealed that the DNA methylome was unstable between generations. Applying other stresses like spaceflight led to the same conclusions. Further research is needed to determine the evolutionary consequences of environmental epigenomic variation and to exploit the epigenetic processes for enhancing crop resilience in response to climate changes.", "Several meiotically stable epialleles controlling important traits were discovered in crops including fruit ripening or vitamin E content in tomato, sex determination in melon and dwarfism in rice, as well as in Arabidopsis. Nevertheless, it remains unclear whether modifications of the epigenome could mediate a response to environmental stresses or enable adaptation between generations. Exposing Arabidopsis plants to various stresses like drought or salt revealed that the DNA methylome was stable between generations. Applying other stresses like spaceflight led to the opposite conclusions. Further research is needed to determine the evolutionary consequences of environmental epigenomic variation and to exploit the epigenetic processes for enhancing crop resilience in response to climate changes.", "Several meiotically stable epialleles controlling important traits were discovered in crops including fruit ripening or vitamin E content in tomato, sex determination in melon and dwarfism in rice, as well as in Arabidopsis. Nevertheless, it remains clear that modifications of the epigenome could mediate a response to environmental stresses or enable adaptation between generations. Exposing Arabidopsis plants to various stresses like spaceflight revealed that the DNA methylome was stable between generations. Applying other stresses like drought or salt led to the opposite conclusions. Further research is needed to determine the evolutionary consequences of environmental epigenomic variation and to exploit the epigenetic processes for enhancing crop resilience in response to climate changes." ], "source":"https:\/\/doi.org\/10.1146\/annurev-arplant-070122-025047", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1146\/annurev-arplant-070122-025047", "Year":2023.0, "Citations":29.0, "answer":1, "source_journal":"Annual Review of Plant Biology", "is_expert":true }, { "question":"Is there a link between DNA methylation, meiotic recombination and crossovers in plant species ?", "area":"GENE REGULATION - EPIGENETICS AND TGS", "plant_species":[ "non-specific" ], "options":[ "The frequency and distribution of meiotic crossover varies along chromosomes. Higher rates of recombination are observed in heterochromatin and regions enriched for genes, compared to euchromatin and regions enriched for transposable elements where recombination and crossover formation is rare. The frequency of crossover seems to be correlated with the levels of DNA methylation. Mutations in the histone methylation maintenance pathways (like the met1 or cmt3 mutants) cause contrasting changes to the landscape of centromeric crossover frequency. More research is needed to understand the mechanistic basis of the correlation between histone methylation (and the epigenetic landscapes) and meiotic crossovers.", "The frequency and distribution of meiotic crossover varies along chromosomes. Higher rates of recombination are observed in euchromatin and regions enriched for genes, compared to heterochromatin and regions enriched for transposable elements where recombination and crossover formation is rare. The frequency of crossover seems to be correlated with the levels of DNA methylation. Mutations in the DNA methylation maintenance pathways (like the met1 or cmt3 mutants) cause contrasting changes to the landscape of centromeric crossover frequency. More research is needed to understand the mechanistic basis of the correlation between DNA methylation (and the epigenetic landscapes) and meiotic crossovers.", "The frequency and distribution of meiotic crossover varies along chromosomes. Lower rates of recombination are observed in euchromatin and regions enriched for genes, compared to heterochromatin and regions enriched for transposable elements where recombination and crossover formation is abundant. The frequency of crossover seems to be uncorrelated with the levels of DNA methylation. Mutations in the DNA methylation maintenance pathways (like the met1 or cmt3 mutants) cause contrasting changes to the landscape of crossover frequency in chromosome arms. More research is needed to understand the mechanistic basis of the correlation between DNA methylation (and the epigenetic landscapes) and meiotic crossovers." ], "source":"https:\/\/doi.org\/10.1186\/s13059-024-03163-4", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1186\/s13059-024-03163-4", "Year":2024.0, "Citations":19.0, "answer":1, "source_journal":"Genome Biology", "is_expert":true }, { "question":"What is the link between TCP15, auxins and cytokinins (CK) during gynoecium development in Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Gynoecium development is a simple process that begins with the establishment of carpel primordia in the early stages of flower formation. The correct development of the apical tissues - style and stigma \u2013 depends on the action of several transcription factors and the establishment of an auxin gradient. The role of cytokinin in gynoecium development is most likely independent on auxin levels. TCP15 is a transcription factor that links cytokinin and gibberellin responses for proper gynoecium development. CK induces the transcript levels of TCP15 and this TF inhibits the expression of auxin biosynthesis genes and affects their expression pattern. This leads to a proper development of the inner tissues of the gynoecium.", "Gynoecium development is a complex process that begins with the establishment of carpel primordia in the early stages of flower formation. The correct development of the apical tissues - style and stigma - depends on the action of several transcription factors (TF) and the establishment of an auxin gradient. The role of cytokinin in gynoecium development is most likely dependent on auxin levels. TCP15 is a transcription factor that links cytokinin and auxin responses for proper gynoecium development. CK induces the transcript levels of TCP15 and this TF inhibits the expression of auxin biosynthesis genes and affects their expression pattern. This leads to improper development of the inner tissues of the gynoecium.", "Gynoecium development is a complex process that begins with the establishment of carpel primordia in the early stages of flower formation. The incorrect development of the apical tissues - style and stigma - depends on the action of several transcription factors and the establishment of an auxin gradient. The role of cytokinin in gynoecium development is most likely dependent on gibberellin levels. TCP15 is a transcription factor that links cytokinin and auxin responses for proper gynoecium development. CK inhibits the transcript levels of TCP15 and this TF induce the expression of auxin biosynthesis genes and affects their expression pattern. This leads to improper development of the inner tissues of the gynoecium." ], "source":"https:\/\/doi.org\/10.1111\/tpj.12992", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1111\/tpj.12992", "Year":2015.0, "Citations":90.0, "answer":1, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"Which is the role of Class I TCP transcription factors in the stamen filament elongation in Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In autogamous plants such as Arabidopsis thaliana, stamen elongation must be precisely controlled to ensure that the anthers reach the pistil at the correct stage of development. TCP transcription factors are important in this process, as plants with lower levels of TCP15, TCP14, TCP22 and TCP8, or with a repressor form of TCP15, have shorter filaments, and plants with higher levels of TCP15 have longer stamen. Notably, the expression of TCP15 is induced by gibberellins, an important hormone that positively regulates filament elongation. TCP15 induces SAUR63 through direct interaction with TCP sites present in the SAUR63 promoter, and finally SAUR63 stimulates stamen filament elongation.", "In autogamous plants such as Arabidopsis thaliana, stamen elongation must be precisely controlled to ensure that the anthers reach the petals at the correct stage of development. TCP transcription factors are important in this process, as plants with higher levels of TCP15, TCP14, TCP22 and TCP8, or with a repressor form of TCP15, have shorter filaments, and plants with higher levels of TCP15 have longer stamen. Notably, the expression of TCP15 is represses by gibberellins, an important hormone that positively regulates hypocotyl elongation. TCP15 induces SAUR63 through direct interaction with TCP sites present in the SAUR63 promoter, and finally SAUR63 stimulates stamen filament elongation.", "In allogamy plants such as Arabidopsis thaliana, hypocotyl elongation must be precisely controlled to ensure that the anthers reach the pistil at the correct stage of development. TCP transcription factors are important in this process, as plants with lower levels of TCP15, TCP23, TCP1 and TCP8, or with a repressor form of TCP15, have shorter filaments, and plants with higher levels of TCP15 have longer stamen. Notably, the expression of TCP4 is induced by auxins, an important hormone that positively regulates filament elongation. TCP15 induces SAUR63 through direct interaction with TCP sites present in the SAUR63 promoter, and finally SAUR63 represses stamen filament elongation." ], "source":"https:\/\/doi.org\/10.1104\/pp.19.01501", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1104\/pp.19.01501", "Year":2020.0, "Citations":49.0, "answer":0, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"What is the mechanism by which strigolactones (SL) regulate flowering time in Arabidopsis thaliana?", "area":"HORMONES", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis mutants deficient in SL, TOE1, a transcription factor of the AP2 family involved in flowering regulation, is able to interact with SMXL7, which promote the binding of TOE1 to the FT locus, an important flowering-promoting gene, resulting in the induction of SOC1 and early flowering. When SL is absent in the plant, it binds to AtD14, which interacts with SCFMAX2 and SMXL7, promoting the degradation of SMXL7 and releasing TOE1 to interact with FT gene, inducing its expression and producing a normal flowering time.", "In Arabidopsis mutants deficient in SL, TOE1, a transcription factor of the TCP family involved in flowering regulation, is able to interact with SMXL7, which prevents the binding of TOE1 to the FT locus, an important flowering-promoting gene, resulting in the repression of FT and late flowering. When SL is present in the plant, it binds to AtD14, which interacts with SCFMAX2 and SMXL7, promoting the accumulation of SMXL7 and releasing TOE1 to interact with FT gene, inhibiting its expression and producing a normal flowering time.", "In Arabidopsis mutants deficient in SL, TOE1, a transcription factor of the AP2 family involved in flowering regulation, is able to interact with SMXL7, which prevents the binding of TOE1 to the FT locus, an important flowering-promoting gene, resulting in the induction of FT and early flowering. When SL is present in the plant, it binds to AtD14, which interacts with SCFMAX2 and SMXL7, promoting the degradation of SMXL7 and releasing TOE1 to interact with FT gene, inhibiting its expression and producing a normal flowering time." ], "source":"https:\/\/doi.org\/10.1093\/plcell\/koae248", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1093\/plcell\/koae248", "Year":2024.0, "Citations":3.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"What is the main gene regulated by strigolactones (SL) to control shoot branching in Arabidopsis thaliana and how does it regulate it?", "area":"HORMONES", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis, in the absence of GAs, D53-like SMXL proteins interact with BES1 to repress the expression of BRC1, a transcription factor known to be a master regulator of shoot branching. This is achieved by direct binding of BZR to the BRC1 promoter, and the EAR motif of D53-like SMXLs recruits TPR2, a transcriptional corepressor, leading to an induction in BRC1 expression, thereby inducing branching. However, in the presence of SLs, the SMXLs-BES1 complex is accumulated by AtD14-MAX2 upon AUX recognition, resulting in activation of BRC1 expression and suppression of bud branching.", "In Arabidopsis, in the absence of SLs, D53-like SMXL proteins interact with BES1 to repress the expression of BRC1, a transcription factor known to be a master regulator of shoot branching. This is achieved by direct binding of BES1 to the BRC1 promoter, and the EAR motif of D53-like SMXLs recruits TPR2, a transcriptional corepressor, leading to a decrease in BRC1 expression, thereby inducing branching. However, in the presence of SLs, the SMXLs-BES1 complex is degraded by AtD14-MAX2 upon SL recognition, resulting in activation of BRC1 expression and suppression of bud branching.", "In Arabidopsis, in the presence of SLs, D53-like SMXL proteins interact with BES1 to repress the expression of BRC1, a transcription factor known to be a master regulator of shoot branching. This is achieved by direct binding of BES1 to the BRC1 promoter, and the EAR motif of D53-like SMXLs recruits TPR2, a transcriptional coactivator, leading to a decrease in BRC1 expression, thereby inducing branching. However, in the presence of SLs, the SMXLs-BES1 complex is stabilised by AtD14-MAX4 upon SL recognition, resulting in activation of BZR1 expression and suppression of bud branching." ], "source":"https:\/\/doi.org\/10.1016\/j.xplc.2019.100014", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1016\/j.xplc.2019.100014", "Year":2020.0, "Citations":48.0, "answer":1, "source_journal":"Plant Communications", "is_expert":true }, { "question":"How is D14 receptor stability regulated in the strigolactone (SL) signalling pathway?", "area":"HORMONES", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The auxin signalling pathway requires the assembly of a complex between the hormone, the D14 receptor, the E3 ubiquitin ligase SCFMAX2 and the transcriptional corepressors SMXL6\/7\/8, which are ubiquitinated and degraded by the proteasome, inducing SL-dependent cellular responses. Following sumoylation of SMXLs by SCFMAX2 and proteasomal degradation, the D14 receptor is stabilized as a positive feedback mechanism for SL perception. This D14 degradation is SL-dependent, but not exclusively SCFMAX2-dependent, does not require SMXLs degradation and may even involve a proteosome-independent mechanism.", "The SL signalling pathway requires the assembly of a complex between the hormone, the D14 receptor, the E3 ubiquitin ligase SCFMAX2 and the transcriptional corepressors SMXL6\/7\/8, which are ubiquitinated and degraded by the proteasome, inducing SL-dependent cellular responses. Following ubiquitination of SMXLs by SCFMAX2 and proteasomal degradation, the D14 receptor is destabilized as a negative feedback mechanism for SL perception. This D14 degradation is SL-dependent, but not exclusively SCFMAX2-dependent, does not require SMXLs degradation and may even involve a proteosome-independent mechanism.", "The SL signalling pathway requires the assembly of a complex between the hormone, the GID1 receptor, the E3 ubiquitin ligase SCFMAX2 and the transcriptional corepressors SMXL4\/10\/12, which are ubiquitinated and degraded by the proteasome, inducing SL-independent cellular responses. Following ubiquitination of SMXLs by SCFMAX2 and proteasomal degradation, the D14 receptor is destabilized as a negative feedback mechanism for SL degradation. This D14 accumulation is SL-dependent, but not exclusively SCFMAX2-dependent, does not require SMXLs degradation and may even involve a proteosome-dependent mechanism." ], "source":"https:\/\/doi.org\/10.1093\/jxb\/erae365", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1093\/jxb\/erae365", "Year":2024.0, "Citations":0.0, "answer":1, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"What is the subcellular localization of plant phytochromes?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "non-specific" ], "options":[ "Phytochromes are synthesized in their inactive form, which localizes to the cytosol, and upon light-mediated activation they translocate into the nucleus.", "Phytochromes localize to the plasma membrane.", "Phytochromes are synthesized in their inactive form, which localizes to the plasma membrane, and upon light-mediated activation they translocate into the nucleus." ], "source":"https:\/\/doi.org\/10.1038\/s41467-019-13045-0", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/s41467-019-13045-0", "Year":2019.0, "Citations":312.0, "answer":0, "source_journal":"Nature Communications", "is_expert":true }, { "question":"Can phytochrome B function as a thermosensor in the presence of light, or is this function limited to darkness in Arabidopsis?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "No, phytochrome B functions as a thermosensor only during the night or in darkness. ", "Yes, phytochrome B activity is regulated by temperature and has an effect on plant development both during the night as well as during the light period.", "Phytochrome B can function as a thermosensor during the day only when the red to far-red ratio of light is low, i.e. in shade conditions." ], "source":"https:\/\/www.science.org\/doi\/10.1126\/science.aaf5656", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1126\/science.aaf5656", "Year":2016.0, "Citations":698.0, "answer":1, "source_journal":"Science", "is_expert":true }, { "question":"Which photoreceptors phosphorylate the protein PHYTOCHROME KINASE SUBSTRATE 4 in response to blue light in Arabidopsis?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Phototropins", "Phytochromes", "Phytochromes and phototropins" ], "source":"doi: 10.1038\/emboj.2012.186", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/emboj.2012.186", "Year":2012.0, "Citations":75.0, "answer":0, "source_journal":"The EMBO Journal", "is_expert":true }, { "question":"Do plant phytochromes have histidine kinase activity?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "non-specific" ], "options":[ "No. Plant phytochromes possess a histidine kinase-related domain but they do not possess histidine kinase activity. However, all plant phytochromes have Ser\/Thr kinase activity.", "Yes, plant phytochromes present a histidine kinase domain and function as histidine kinases.", "No. Plant phytochromes possess a histidine kinase-related domain but they do not possess histidine kinase activity. Some plant phytochromes may have Ser\/Thr kinase activity but this still remains contentious." ], "source":"https:\/\/doi.org\/10.1038\/s41467-019-13045-0", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/s41467-019-13045-0", "Year":2019.0, "Citations":312.0, "answer":2, "source_journal":"Nature Communications", "is_expert":true }, { "question":"Which are the hormonal and cellular mechanisms linking unilateral light perception and positive phototropism in Arabidopsis hypocotyls?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The signal triggering phototropism is unilateral blue light. Upon unilateral blue light irradiation a light gradient is established across the hypocotyl, which in turn causes differential phototropin activation between the lit and the non-lit side of the hypocotyl. Through a mostly unknown series of events, an auxin concentration gradient opposite to the phototropin activation gradient is created across the hypocotyl. This differential auxin accumulation causes differential cell division rates between the lit and the non-lit sides of the hypocotyl: cell proliferation increases in the non-lit side, while cell proliferation is reduced on the lit side, compared to non-irradiated plants. This differential cell division rates causes bending towards the light. ", "The signal triggering phototropism is unilateral blue light. Upon unilateral blue light irradiation a light gradient is established across the hypocotyl, which in turn causes differential phototropin activation between the lit and the non-lit side of the hypocotyl. Through a mostly unknown series of events, an auxin sensitivity gradient opposite to the phototropin activation gradient is created across the hypocotyl. This differential auxin sensitivity causes differential cell expansion between the lit and the non-lit sides of the hypocotyl: cell expansion increases in the non-lit side, while cell expansion is reduced on the lit side, compared to non-irradiated plants. This differential cell expansion causes bending towards the light. ", "The signal triggering phototropism is unilateral blue light. Upon unilateral blue light irradiation a light gradient is established across the hypocotyl, which in turn causes differential phototropin activation between the lit and the non-lit side of the hypocotyl. Through a mostly unknown series of events, an auxin concentration gradient opposite to the phototropin activation gradient is created across the hypocotyl. This differential auxin accumulation causes differential cell expansion between the lit and the non-lit sides of the hypocotyl: cell expansion increases in the non-lit side, while cell expansion is reduced on the lit side, compared to non-irradiated plants. This differential cell expansion causes bending towards the light. " ], "source":"DOI: 10.1111\/ppl.13098", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/ppl.13098", "Year":2020.0, "Citations":24.0, "answer":2, "source_journal":"Physiologia Plantarum", "is_expert":true }, { "question":"What are the two strategies that can be used to develop a synthetic trans-acting siRNA (syn-tasiRNA)-based system for fine-tuning the gene expression in Arabidopsis thaliana and Nicotiana benthamiana plants?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Arabidopsis thaliana", "Nicotiana benthamiana" ], "options":[ "Fine-tuning of gene expression based on syn-tasiRNAs can be achieved by two independent strategies. The first involves modifying the position from which the artificial sRNA is expressed. In this case, the accumulation and efficacy of the syn-tasiRNAs progressively decrease as they are expressed from positions more distal to the target site of the triggering microRNA. The second strategy entails modifying the degree of base pairing between the 3' end of the syn-tasiRNA and the 5' end of the target site, considering that 2-3 mismatches can reduce syn-tasiRNA activity, while 4-5 completely suppress it. These two strategies can be used in a complementary manner, offering a range of possible combinations to achieve various silencing levels", "Fine-tuning of gene expression based on syn-tasiRNAs can be achieved by two independent strategies. The first involves modifying the position from which the artificial sRNA is expressed. In this case, the accumulation and efficacy of the syn-tasiRNAs progressively decrease as they are expressed from positions more proximal to the target site of the triggering microRNA. The second strategy entails modifying the degree of base pairing between the 3' end of the syn-tasiRNA and the 5' end of the target site, considering that 7-9 mismatches can reduce syn-tasiRNA activity, while 10-12 completely suppress it. These two strategies cannot be used in a complementary manner, offering a limited range of possible combinations to achieve various silencing levels.", "Fine-tuning of gene expression based on syn-tasiRNAs can be achieved by two independent strategies. The first involves modifying the position from which the artificial sRNA is expressed. In this case, the accumulation and efficacy of the syn-tasiRNAs progressively increase as they are expressed from positions more distal to the target site of the triggering microRNA. The second strategy entails modifying the degree of base pairing between the 5' end of the syn-tasiRNA and the 3\u2019 end of the target site, considering that 2-3 mismatches can induce syn-tasiRNA activity, while 4-5 completely promote it. These two strategies can be used in a complementary manner, offering a range of possible combinations to achieve various silencing levels." ], "source":"https:\/\/doi.org\/10.1093\/nar\/gkaa343", "normalized_plant_species":"Model Organisms", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1093\/nar\/gkaa343", "Year":2020.0, "Citations":20.0, "answer":0, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"What is the shortest MIR390-based precursor designed for artificial micro-RNA (amiRNA) expression in Arabidopsis thaliana and Nicotiana benthamiana?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Arabidopsis thaliana", "Nicotiana benthamiana" ], "options":[ "The shortest artificial microRNA precursor that can produce accurately processed amiRNAs in a highly effective manner consists of a shortened chimeric MIR390-based amiRNA precursor of only 89 nucleotides. This minimal amiRNA precursor includes the basal stem region of pri-AtMIR390a without the ssRNA segments and the distal stem loop of OsMIR390 with a deletion of two nucleotides.", "The shortest artificial microRNA precursor that can produce accurately processed amiRNAs in a highly effective manner consists of a shortened chimeric MIR390-based amiRNA precursor of only 89 nucleotides. This minimal amiRNA precursor includes the complete basal stem region of pri-AtMIR390a with the ssRNA segments and the distal stem loop of NbMIR390 with a deletion of five nucleotides.", "The shortest artificial microRNA precursor that can produce inaccurately processed amiRNAs in a highly effective manner consists of a shortened chimeric MIR319-based amiRNA precursor of only 587 nucleotides. This minimal amiRNA precursor includes the basal stem region of pri-AtMIR319a without the ssRNA segments and the distal stem loop of OsMIR319 with a deletion of two nucleotides" ], "source":"https:\/\/doi.org\/10.1093\/nar\/gkad747", "normalized_plant_species":"Model Organisms", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1093\/nar\/gkad747", "Year":2023.0, "Citations":16.0, "answer":0, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"What is the shortest precursor designed for synthetic trans-active small interfering RNA (syn-tasiRNA) expression in non-Arabidopsis plants, such as Nicotiana benthamiana?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Nicotiana benthamiana" ], "options":[ "The minimal RNA precursor designed for the expression of accurately phase-processed syn-tasiRNA in non-Arabidopsis plants consists of a 21 nucleotides (nt) endogenous miRNA target site and an 21-nt Arabidopsis thaliana TAS1c-derived spacer followed by the 21-nt syn-tasiRNA sequences. In the case of Nicotiana benthamina, this minimal precursor includes the NbmiR390a (N. benthamiana endogenous 21-nt miRNA) target site and the 11-nt SlLRR1-derived spacer.", "The minimal RNA precursor designed for the expression of accurately phase-processed syn-tasiRNA in non-Arabidopsis plants consists of a 22 nucleotides (nt) endogenous miRNA target site and an 11-nt Arabidopsis thaliana TAS1c-derived spacer followed by the 21-nt syn-tasiRNA sequences. In the case of Nicotiana benthamina, this minimal precursor includes the NbmiR482a (N. benthamiana endogenous 22-nt miRNA) target site and the 11-nt AtTAS1c-derived spacer.", "The minimal RNA precursor designed for the expression of accurately phase-processed syn-tasiRNA in Arabidopsis plants consists of a 22 nucleotides (nt) endogenous miRNA target site and an 11-nt Arabidopsis thaliana TAS3a-derived spacer followed by the 24-nt syn-tasiRNA sequences. In the case of Arabidopsis thaliana, this minimal precursor includes the AtMIR173a (A. thaliana endogenous 22-nt miRNA) target site and the 11-nt AtTAS1c-derived spacer." ], "source":"https:\/\/doi.org\/10.1101\/2024.12.18.629176", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1101\/2024.12.18.629176", "Year":2024.0, "Citations":0.0, "answer":1, "source_journal":null, "is_expert":true }, { "question":"What are the advantages of using shorter artificial sRNA precursors in RNA viral vectors for plants, such as potato virus X (PVX)?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "non-specific" ], "options":[ "Short artificial sRNA precursors, such as AtMIR319a for artificial microRNAs (amiRNAs) and AtTAS3a for synthetic trans-acting small interfering RNA (syn-tasiRNAs), are not stably maintained in the viral genome over extended periods due to the limited cargo capacity of DNA viral vectors such as PVX. The use of longer precursors allows for stable maintenance in the viral genome due to their large size, as well as reducing the accumulation of mutations during viral replication, which is a significant advantage.", "Long artificial sRNA precursors, such as AtMIR390a for artificial microRNAs (amiRNAs) and AtTAS1c for synthetic trans-acting small interfering RNA (syn-tasiRNAs), are not stably maintained in the viral genome over extended periods due to the limited cargo capacity of RNA viral vectors such as PVX. The use of shorter precursors allows for stable maintenance in the viral genome due to their small size, as well as reducing the accumulation of mutations during viral replication, which is a significant advantage.", "Long artificial sRNA precursors, such as AtMIR390a for artificial microRNAs (amiRNAs) and AtTAS1c for synthetic trans-acting small interfering RNA (syn-tasiRNAs), are stably maintained in the viral genome over extended periods due to the non-limited cargo capacity of RNA viral vectors such as PVX. The use of shorter precursors prevents stable maintenance in the viral genome due to their small size, as well as inducing the accumulation of mutations during viral replication, which is a significant disadvantage." ], "source":"https:\/\/doi.org\/10.1093\/nar\/gkad747 and https:\/\/doi.org\/10.1101\/2024.12.18.629176", "normalized_plant_species":"Non-specific", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1101\/2024.12.18.629176", "Year":2024.0, "Citations":0.0, "answer":1, "source_journal":null, "is_expert":true }, { "question":"What is the transgene-free antiviral vaccination strategy for plant protection based on syn-tasiRNA-based virus-induced gene silencing (syn-tasiR-VIGS) tested in Nicotiana benthamiana?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Nicotiana benthamiana" ], "options":[ "The new generation of antiviral plant vaccines based on syn-tasiR-VIGS uses an RNA viral vector, such as Potato Virus X (PVX), into which a complete syn-tasiRNA precursor is incorporated to express antiviral syn-tasiRNAs, e.g. anti-tomato spotted wilt virus (TSWV) syn-tasiRNAs. Vaccination consists of inoculating plants with total RNA obtained from plants accumulating the viral vector with the syn-tasiRNA precursor. Inoculation of Nicotiana benthamiana plants with PVX total RNA allows the virus to spread and produce anti-TSWV syn-tasiRNAs throughout the plant. When TSWV is inoculated at the same time, the vaccinated plants are loaded with antiviral syn-tasiRNAs that target TSWV and ultimately block its infection. These antiviral vaccines can be applied transgenically and in three doses.", "The new generation of antiviral plant vaccines based on syn-tasiR-VIGS uses an RNA viral vector, such as Potato Virus X (PVX), into which a minimal syn-tasiRNA precursor is incorporated to express antiviral syn-tasiRNAs, e.g. anti-tomato spotted wilt virus (TSWV) syn-tasiRNAs. Vaccination consists of inoculating plants with infectious crude extracts obtained from plants accumulating the viral vector with the syn-tasiRNA precursor. Inoculation of Nicotiana benthamiana plants with PVX crude extract allows the virus to spread and produce anti-TSWV syn-tasiRNAs throughout the plant. When TSWV is inoculated a few days later, the vaccinated plants are loaded with antiviral syn-tasiRNAs that target TSWV and ultimately block its infection. These antiviral vaccines can be applied non-transgenically and in a single dose.", "The new generation of antiviral plant vaccines based on syn-tasiR-VIGS uses a DNA viral vector, such as Cabbage Leaf Curl Virus (CaLCuV), into which a minimal amiRNA precursor is incorporated to express antiviral amiRNA, e.g. anti-tomato spotted wilt virus (TSWV) amiRNAs. Vaccination consists of inoculating plants with infectious crude extracts obtained from plants accumulating the viral vector with the amiRNA precursor. Inoculation of Nicotiana benthamiana plants with CaLCuV crude extract allows the virus to spread and produce anti-TSWV amiRNA throughout the plant. When TSWV is inoculated a few days later, the vaccinated plants are loaded with antiviral amiRNA that target TSWV and ultimately block its infection. These antiviral vaccines can be applied non-transgenically and in a single dose." ], "source":"https:\/\/doi.org\/10.1101\/2024.12.18.629176", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1101\/2024.12.18.629176", "Year":2024.0, "Citations":0.0, "answer":1, "source_journal":null, "is_expert":true }, { "question":"What is the role of the Lotus japonicus LysM-RLK receptors LjNFR1 and LjNFR5 in the plant\u2019s ability to interact with both symbiotic and pathogenic microbes?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Lotus japonicus" ], "options":[ "In Lotus japonicus, NFR1 and NFR5 are lysin motif (LysM) receptor kinases that exclusively detect and respond to the lipochitooligosaccharides (Nod factors) produced by symbiotic rhizobia, without any role in plant defense against pathogens.", "In Lotus japonicus, NFR1 and NFR5 are leucine-rich repeat receptors (LRR) that directly activate immune responses against all types of microbes, whether symbiotic or pathogenic, without distinguishing between beneficial and harmful organisms.", "In Lotus japonicus, NFR1 and NFR5 are lysin motif (LysM) receptor kinases that play a dual role. They recognize the lipochitooligosaccharides (Nod factors) produced by symbiotic rhizobia and initiate the signaling cascade that leads to nodule organogenesis for nitrogen fixation. At the same time, they are involved in recognizing similar molecular patterns from pathogenic microbes, helping the plant balance its symbiotic association while triggering defense mechanisms when needed." ], "source":"https:\/\/doi.org\/10.1038\/nature02039", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/nature02039", "Year":2003.0, "Citations":950.0, "answer":2, "source_journal":"Nature", "is_expert":true }, { "question":"What is the role of the LjEPR3 receptor in symbiosis in Lotus japonicus and which protein interactors are involved in its function?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Lotus japonicus" ], "options":[ "In Lotus japonicus, the LjEPR3 (Epidermal Pattern Recognition Receptor 3) is a receptor kinase that recognizes the specific Myc factors produced by compatible fungi during defense responses. LjEPR3 interacts with receptors such as LjSYMRK and facilitates the activation of downstream signaling genes like LjJAZ1 and LjNPR1, suggesting that LjEPR3 plays an essential role in early defense responses against fungal pathogens.", "In Lotus japonicus, the LjEPR3 (Epidermal Pattern Recognition Receptor 3) recognizes general exopolysaccharides from soil microbes and activates immune-related genes like LjNPR1 (Nonexpressor of Pathogenesis-Related Genes) and LjWRKY45, which are unrelated to symbiotic processes. LjEPR3 interacts with other receptors, such as LjLyk20 (Symbiosis Receptor-like Kinase), and facilitates the activation of downstream signaling genes like LjJAZ1 and LjNPR1, indicating that LjEPR3 plays an essential role in the early stages of defense responses against fungal pathogens.", "In Lotus japonicus, the LjEPR3 (Epidermal Pattern Recognition Receptor 3) is a receptor kinase that recognizes the specific exopolysaccharides (EPS) produced by compatible rhizobia during symbiotic interactions. LjEPR3 interacts with other receptors such as LjSYMRK (Symbiosis Receptor-like Kinase) and facilitates the activation of downstream signaling genes, including LjCCaMK (Calcium\/Calmodulin-dependent Protein Kinase) and LjCYCLOPS (Cyclic Nucleotide-Gated Channel Interacting Protein). This indicates that LjEPR3 plays an essential role during the early stages of symbiotic interactions by enabling specific recognition of compatible rhizobia and activating the downstream symbiotic signaling pathway." ], "source":"https:\/\/doi.org\/10.1038\/ncomms14534", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/ncomms14534", "Year":2017.0, "Citations":125.0, "answer":2, "source_journal":"Nature Communications", "is_expert":true }, { "question":"What are the common components shared between the symbiotic signaling pathway and the defense response in legumes, and how do these components contribute to each process?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "non-specific" ], "options":[ "The symbiotic signaling pathway and the defense response in legumes share several key components, including LysM receptors like NFR1 and NFR5, mitogen-activated protein kinases (MAPKs), and calcium signaling components like CCaMK. However, these components are specialized and only function in symbiosis or defense, not both. In symbiosis, they mediate the recognition of general microbial patterns rather than specific molecules secreted by fungal and rhizobia symbionts. In defense, they are activated exclusively by chemical signals unrelated to PAMPs. This separation demonstrates distinct evolutionary adaptations in legumes.", "The symbiotic signaling pathway and the defense response in legumes do not share components; instead, they rely on entirely distinct mechanisms. LysM receptors like NFR1 and NFR5 and calcium signaling components like CCaMK are specific to symbiosis and have no role in defense responses. In symbiosis, these components mediate the recognition of PAMPs, while in defense, unrelated molecules are recognized by unique receptors with no overlap. This complete divergence reflects a lack of evolutionary conservation in microbial recognition mechanisms in legumes.", "The symbiotic signaling pathway and the defense response in legumes share several key components, including LysM receptors such as NFR1 and NFR5, mitogen-activated protein kinases (MAPKs), and calcium signaling components like CCaMK (Calcium\/Calmodulin-dependent Protein Kinase). These shared components play crucial roles from early signal perception to late downstream signaling. In symbiosis, these components mediate the recognition of specific molecules secreted by fungal and rhizobia symbionts. In defense, they are activated by pathogen-associated molecular patterns (PAMPs) to trigger immune responses. This overlap between symbiotic and defense pathways highlights the evolutionary conservation of microbial recognition mechanisms in legumes." ], "source":"https:\/\/nph.onlinelibrary.wiley.com\/doi\/10.1111\/nph.13117", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/nph.13117", "Year":2014.0, "Citations":93.0, "answer":2, "source_journal":"New Phytologist", "is_expert":true }, { "question":"How does the regulation of SA levels influence the balance between symbiosis and defense responses in legumes?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "non-specific" ], "options":[ "Salicylic acid (SA) plays a pivotal role in legumes as a signaling molecule in both symbiotic and pathogenic interactions. During pathogenic interactions, basal SA levels activate systemic acquired resistance (SAR), inducing the expression of pathogenesis-related genes, such as NF-1, SymRK and PR-5, strengthening cell walls, and limiting pathogen spread. In contrast, during symbiotic interactions, elevated SA can enhance symbiotic signaling, inducing the formation of nodules and arbuscular mycorrhizal associations by activating transcriptionally the downstream signaling pathways like the common symbiosis pathway (CCaMK, CYCLOPS). ", "Salicylic acid (SA) plays a pivotal role in legumes as a signaling molecule in both symbiotic and pathogenic interactions. During pathogenic interactions, elevated SA levels activate systemic acquired resistance (SAR), inducing the expression of pathogenesis-related genes such as PR-1, PR-2, and PR-5, strengthening cell walls and limiting pathogen spread. In contrast, during symbiotic interactions, SA levels must be tightly regulated. Elevated SA can suppress symbiotic signaling, inhibiting the formation of nodules and arbuscular mycorrhizal associations by disrupting downstream signaling pathways such as the common symbiosis pathway (CCaMK, CYCLOPS). However, basal levels of SA are required to fine-tune immune responses, ensuring the plant can accommodate symbionts while maintaining defense capabilities. This balance ensures effective recognition and response to both beneficial and harmful microbes.", "Salicylic acid (SA) has a specific role in legumes as a signaling molecule in both symbiotic and pathogenic interactions. During pathogenic interactions, high SA levels deactivate the systemic acquired resistance (SAR), by downregulation of the pathogenesis-related genes, such as NF-1, SymRK and PR-5, strengthening cell walls, and limiting pathogen spread. Also, during symbiotic interactions, high SA levels can enhance symbiotic signaling, by inducing the common symbiosis pathway (CCaMK, CYCLOPS) and the formation of nodules and arbuscular mycorrhizal associations." ], "source":"https:\/\/doi.org\/10.3390\/biology11060861", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.3390\/biology11060861", "Year":2022.0, "Citations":39.0, "answer":1, "source_journal":"Biology", "is_expert":true }, { "question":"How does the receptor Ahy.IM7I4N contribute to the interaction between symbionts and pathogens in peanut, and what does its transcriptional response to Nod Factors (NF) and chitosan suggest about its role in signaling pathways?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Arachis hypogaea" ], "options":[ " In peanut, the Ahy.IM7I4N receptor contributes to interactions between symbionts and pathogens by exhibiting a dual transcriptional response to both Nod Factors (NF) and Myc factors. This suggests that Ahy.IM7I4N functions as a master receptor involved in mediating the perception or activation of signaling pathways triggered by these elicitors. The late transcriptional response of Ahy.IM7I4N to either Nod Factors or Myc factors highlights the receptor\u2019s potential role in facilitating interactions with rhizobia, as well as its ability to detect chitosan, a molecule often associated with pathogenic bacteria.", "In peanut, the Ahy.IM7I4N receptor contributes only to the interaction with symbionts and not pathogens, due to its transcriptional response to Nod Factors (NF) but not chitosan. This suggests that Ahy.IM7I4N functions as a specific receptor involved solely in the perception or activation of the signaling pathway triggered by this elicitor. The early transcriptional response of Ahy.IM7I4N to Nod Factors, and not to chitosan, highlights the potential role of this receptor in facilitating interactions with rhizobia, suggesting it plays a role in peanut's response to symbiotic interactions rather than in pathogenic signaling.", "In peanut, the Ahy.IM7I4N receptor contributes to the interaction between symbionts and pathogens by exhibiting a dual transcriptional response to both Nod Factors (NF) and chitosan. This suggests that Ahy.IM7I4N functions as a versatile co-receptor involved in mediating the perception and activation of signaling pathways triggered by these elicitors. The early transcriptional response of Ahy.IM7I4N to Nod Factors and chitosan highlights the potential role of this receptor in facilitating interactions with rhizobia while also detecting chitosan, a molecule often associated with pathogens." ], "source":"https:\/\/doi.org\/10.3390\/horticulturae8111000", "normalized_plant_species":"Legumes", "normalized_area":"ENVIRONMENT", "doi":"10.3390\/horticulturae8111000", "Year":2022.0, "Citations":1.0, "answer":2, "source_journal":"Horticulturae", "is_expert":true }, { "question":"Which are the photorreceptors essential for the germinatin of Arabidopsis seeds?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The phytochromes", "The cryptochromes", "The phototropins" ], "source":"10.1073\/pnas.0910446107", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1073\/pnas.0910446107", "Year":2010.0, "Citations":151.0, "answer":0, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"Which are the proteins that interact with MED25 and promote its degradation by the Proteasome in Arabidopsis?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "MBR1 and MBR2", "MBRL1 and MBRL2", "MBR1 and MBRL2" ], "source":"10.1104\/pp.112.205500", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1104\/pp.112.205500", "Year":2012.0, "Citations":51.0, "answer":0, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"What is the mechanism known as activation by destruction in the regulation of gene expression?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "A mechanism that requires the destruction of a transcription factor before its activator role", "A mechanism that requires the destruction of a transcription factor after completing its activator role", "A mechanism that requires the destruction of a transcription factor concomitantly with its activator role" ], "source":"10.1104\/pp.112.205500", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1104\/pp.112.205500", "Year":2012.0, "Citations":51.0, "answer":2, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"Why a mutation that affects the Arabidopsis DNA Polymerase delta leads to early flowering in Arabidopsis?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Because it leads to the overexpression of CO, a promotor of flowering", "Because it leads to the overexpression of SEP3, a promotor of flowering", "Because it leads to the overexpression of FLC, a promotor of flowering" ], "source":"10.1371\/journal.pgen.1004975", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1371\/journal.pgen.1004975", "Year":2015.0, "Citations":34.0, "answer":1, "source_journal":"PLOS Genetics", "is_expert":true }, { "question":"Which subunit of the Mediator complex of Arabidopsis is essential for early embryo development while expressed in the male gametophyte?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "MED30", "MED25", "MED31" ], "source":"10.1242\/dev.175224", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1242\/dev.175224", "Year":2019.0, "Citations":12.0, "answer":0, "source_journal":"Development", "is_expert":true }, { "question":"Which transcription factors are expressed in the apical cells of the gametophytic meristem of the liverwort Marchantia polymorpha ?", "area":"EVOLUTION", "plant_species":[ "Marchantia polymorpha" ], "options":[ "MpERF20, also known as MpLAXR, is specifically expressed in the apical cell of the gametophytic meristem. ", "The auxin biosynthesis gene MpYUC2 is specifically expressed in the apical cell of the gametophytic meristem. ", "MpPLETHORA is specifically expressed in the apical cell of the gametophytic meristem. " ], "source":"https:\/\/doi.org\/10.1093\/plcell\/koae053", "normalized_plant_species":"Model Organisms", "normalized_area":"EVOLUTION", "doi":"10.1093\/plcell\/koae053", "Year":2024.0, "Citations":12.0, "answer":0, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"Which cell type is homologous to root hairs in the liverwort Marchantia polymorpha? Which genetic evidence supports this observation?", "area":"EVOLUTION", "plant_species":[ "Marchantia polymorpha", "Arabidopsis thaliana" ], "options":[ "Liverworts like Marchantia polymorpha display multicellular roots that also possess cells called rhizoids that are equivalent to root hairs and are regulated by the same genes regulatory networks GLABRA2, GLABRA3, WEREWOLF, EGL3, TTG1.", "Liverworts like Marchantia polymorpha do not have roots and non any other cell can be compared to root hairs.", "Liverworts like Marchantia polymorpha do not display roots but has tip-growing cells in the gametophyte called rhizoids that are equivalent to root hairs. The bHLH transcription factor MpRSL1 regulate both cell types, suggesting that both cell-types are homologues." ], "source":"https:\/\/10.1016\/j.cub.2015.11.042", "normalized_plant_species":"Model Organisms", "normalized_area":"EVOLUTION", "doi":"10.1016\/j.cub.2015.11.042", "Year":2016.0, "Citations":107.0, "answer":2, "source_journal":"Current Biology", "is_expert":true }, { "question":"Are the transcription factors controlling the vegetative meristem of land plants conserved among the gametophyte and the sporophyte?", "area":"EVOLUTION", "plant_species":[ "Physcomitrella patens", "Arabidopsis thaliana" ], "options":[ "Both bryophytes and vascular plants have a conserved set of transcription factors regulating the vegetative gametophyte of both the gametophyte and the sporophyte.", "Transcription factors networks show a clear pattern of conservation between the gametophyte of bryophytes and the sporophyte of vascular plants. Particularly, WOX and class I KNOX are critical to regulate the vegetative gametophyten of bryophytes and vascular plants.", "No, many transcription factors regulating the vegetative sporophyte of land plants such as WOX and class I KNOX do not seem to regulate the vegetative gametophyte of bryophytes, suggesting that gene regulatory networks are quite different between both vegetative tissues." ], "source":"https:\/\/doi.org\/10.1111\/j.1525-142X.2008.00271.x, https:\/\/doi.org\/10.1242\/dev.097444", "normalized_plant_species":"Model Organisms", "normalized_area":"EVOLUTION", "doi":"10.1242\/dev.097444", "Year":2014.0, "Citations":126.0, "answer":2, "source_journal":"Development", "is_expert":true }, { "question":"Do bryophytes form a monophyletic group?", "area":"EVOLUTION", "plant_species":[ "non-specific" ], "options":[ "Yes. This includes three divisions of non-vascular plants: Hornworts, Liverworts and Mosses.", "No. Only Liverworts and Mosses form a monophyletic clade. Hornworts are sister to vascular plants.", "No. Liverworts are the most ancestral land plants and diverge from mosses, hornworts, and vascular plants before their diversification." ], "source":"https:\/\/doi.org\/10.1016\/j.cub.2018.01.063", "normalized_plant_species":"Non-specific", "normalized_area":"EVOLUTION", "doi":"10.1016\/j.cub.2018.01.063", "Year":2018.0, "Citations":399.0, "answer":0, "source_journal":"Current Biology", "is_expert":true }, { "question":"Are abscisic acid-mediated gene regulation conserved among land plants?", "area":"EVOLUTION", "plant_species":[ "Marchantia polymorpha" ], "options":[ "Indeed, a similar regulatory network exists in both bryophytes and vascular plants, including PYL1 and ABI3, in the model liverwort Marchantia polymorpha species. However, the bioactive hormone is lunularic acid and not abscisic acid.", "Indeed, a similar regulatory network exists in both bryophytes and vascular plants, including PYL1 and ABI3 in bryophyte species. This is particularly true in the liverwort Marchantia polymorpha, where this gene regulatory network was studied more extensively.", "No, gene knock-outs homologous to PYL1 and ABI3 in the liverwort Marchantia polymorpha revealed that these genes are dispensable for stress responses, suggesting that gene regulatory networks are extensively rewired." ], "source":"https:\/\/doi.org\/10.1016\/j.cub.2018.10.018, https:\/\/doi.org\/10.1104\/pp.18.00761", "normalized_plant_species":"Model Organisms", "normalized_area":"EVOLUTION", "doi":"10.1104\/pp.18.00761", "Year":2018.0, "Citations":52.0, "answer":1, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"How are Arabidopsis thaliana long intergenic noncoding RNAs conserved among Angiosperms in term of sequences compared to other sequence type?", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Arabidopsis thaliana long intergenic noncoding RNAs are the less conserved type of sequence compared to coding genes, pseudogenes or transposable elements. The measured selection pressure through PhastCons score is higher than the other type of sequence.", "Arabidopsis thaliana long intergenic noncoding RNAs are the most conserved type of sequence compared to coding genes, pseudogenes or transposable elements. The measured selection pressure through PhastCons score is higher than the other type of sequence.", "Arabidopsis thaliana long intergenic noncoding RNAs are intermediately conserved sequence features compared and are less conserved than coding genes, but more conserved than pseudogenes or transposable elements in term of sequence. The measured selection pressure through PhastCons score is lower than the one of protein coding genes and higher than the one of pseudogenes and transposable elements." ], "source":"https:\/\/doi.org\/10.1104\/pp.20.00446 https:\/\/doi.org\/10.1093\/plphys\/kiad360", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1093\/plphys\/kiad360", "Year":2023.0, "Citations":6.0, "answer":2, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"How are long noncoding RNAs expressed between the different accessions of Arabidopsis thaliana?", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "long noncoding RNAs are expressed similarly between between Arabidopsis thaliana accessions. Among the thousands lncRNAs identified among accessions, the major part is lowly expressed, but expressed consistently in all accessions. ", "long noncoding RNAs are almost not expressed in the different Arabidopsis thaliana accessions. Among the thousands lncRNAs identified among accessions, the major part is actively silenced and only few of them are consistently expressed in all accessions.", "long noncoding RNAs are highly specifically expressed between Arabidopsis thaliana accessions. Among the thousands lncRNAs identified among accessions, the major part is actively silenced and only few and variable ones are expressed in each accession." ], "source":"https:\/\/doi.org\/10.1093\/plcell\/koad233 https:\/\/doi.org\/10.1104\/pp.20.00446", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1104\/pp.20.00446", "Year":2020.0, "Citations":30.0, "answer":2, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"Is there any bias of conservation among Arabidopsis thaliana long noncoding RNAs?", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Arabidopsis thaliana long noncoding RNAs do not present any bias of conservation for the different ages of homologs. They show a comparable selective pressure independently in which species they can be identified.", "Arabidopsis thaliana long noncoding RNAs present a bias of conservation for the ones having homologs within all Angiosperms. They show the strongest selective pressure compared to other sequence conserved long noncoding RNA.", "Arabidopsis thaliana long noncoding RNAs present a bias of conservation for the ones having homologs within Brassicacea. They show a strongest selective pressure compared to other sequence conserved long noncoding RNA." ], "source":"https:\/\/doi.org\/10.1093\/plphys\/kiad360", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1093\/plphys\/kiad360", "Year":2023.0, "Citations":6.0, "answer":2, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"Is there any bias of expression for Arabidopsis thaliana long noncoding RNAs according to specific condition or tissue?", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Long noncoding RNAs are more specifically expressed than protein coding genes among conditions and tissue. The most specifically expressed long noncoding RNA are expressed in root, suggesting they may play a role in root development. This tissue specificity is stronger than the one linked with environmental response.", "Long noncoding RNAs are more specifically expressed than protein coding genes among conditions and tissue. The most specifically expressed long noncoding RNA are expressed in response to temperature, suggesting they may play a role in adaptation to this stress. This condition specificity is stronger than the one linked with tissue or developmental stage.", "Long noncoding RNAs are more broadly expressed than protein coding genes among conditions and tissue. The most specifically expressed long noncoding RNA are expressed in leaves, suggesting they may play a role in leaf development. This tissue specificity is not strongly marked compared to other tissue or environmental response." ], "source":"https:\/\/doi.org\/10.1093\/plphys\/kiad360 https:\/\/doi.org\/10.1093\/plcell\/koac166", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1093\/plcell\/koac166", "Year":2022.0, "Citations":31.0, "answer":0, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How is the long noncoding RNA MARS involved in the control of the expression of the marneral cluster in Arabidopsis thaliana?", "area":"GENE REGULATION - EPIGENETICS AND TGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "MARS is regulating genetically the expression of the marneral gene cluster in response to Auxin. This lncRNA bind to LHP1 and recruit it to the marneral cluster. In control condition, MARS is not expressed, allowing the expression of the gene of the cluster. Upon Auxin treatment the expression of the MARS lncRNA is increased and due to its high amount recruit LHP1 to the marneral cluster loci, driving the unfolding of a chromatin loop removing an enhancer away from MRN1, inactivating the expression of the latest.", "MARS is regulating epigenetically the expression of the marneral gene cluster in response to ABA. This lncRNA bind to LHP1 and recruit it to the marneral cluster. In control condition, MARS is lowly expressed, preventing the expression of the gene of the cluster. Upon ABA treatment the expression of the MARS lncRNA is increased and due to its excessive amount remove LHP1 from the marneral cluster loci, driving the formation of a chromatin loop that bring an enhancer close to MRN1, activating the expression of the latest.", "MARS is regulating epigenetically the expression of the marneral gene cluster in response to ABA. This lncRNA bind to CLF and decoy it from the marneral cluster in control condition, activating its expression. Upon ABA treatment the expression of the MARS lncRNA is decreased and due to its low amount allow CLF and PRC2 to bind the marneral cluster loci, driving the deposition of the H3K27me3 mark on MRN1 promoter, preventing the expression of the latest." ], "source":"https:\/\/doi.org\/10.1016\/j.molp.2022.02.007", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.molp.2022.02.007", "Year":2022.0, "Citations":33.0, "answer":1, "source_journal":"Molecular Plant", "is_expert":true }, { "question":"RNA secondary structure motifs like hairpins have various regulatory functions. Which base composition in small stems (~4 bases) of hairpins positively influences translation efficiency?", "area":"GENE REGULATION - TRANSLATION", "plant_species":[ "non-specific" ], "options":[ "High guanine-cytosine (GC) base pairs like GCCG have a positive impact on translation efficiency.", "High adenine-uracil (AU) base pairs like AUUA have a positive impact on translation efficiency.", "A balanced ratio of guanine-cytosine (GC) and adenine-uracil (AU) base pairs, for example a ACGU pair has a positive impact on translation efficiency." ], "source":"https:\/\/doi.org\/10.1038\/s42256-024-00946-z", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s42256-024-00946-z", "Year":2024.0, "Citations":0.0, "answer":2, "source_journal":"Nature Machine Intelligence", "is_expert":true }, { "question":"An increase in the ambient temperature triggers alternative splicing (AS). AS also causes an enrichment of Histones with the H3K36me3 modification. Is the enrichment of H3K36me3 in differentially spliced genes restricted to a specific part of the gene?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "non-specific" ], "options":[ "H3K36me3 containing histones are prevalent at the beginning of the gene body, with a peak shortly after the transcription start site (TSS).", "H3K36me3 containing histones are evenly distributed across the whole gene body of expressed and differentially spliced genes.", "H3K36me3 containing histones are prevalent at the end of the gene body, with a peak around the transcription termination site (TTS)." ], "source":"https:\/\/doi.org\/10.1186\/s13059-017-1235-x", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1186\/s13059-017-1235-x", "Year":2017.0, "Citations":143.0, "answer":0, "source_journal":"Genome Biology", "is_expert":true }, { "question":"In a natural environment, most plants form symbioses with arbuscular mycorrhizal (AM) fungi to survive in nutrient-poor regions. The fungi secrete effector molecules to initiate the symbiosis, altering, among other things, alternative splicing in the host. How does the Glomeromycotina-specific SP7 effector family influence alternative splicing in Arabidopsis thaliana?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "SP7 and SP7-like effectors interact with RNA Polymerase II (RNAPII), thereby affecting splicing.", "SP7 and SP7-like effectors do not influence alternative splicing in Arabidopsis thaliana.", "SP7 and SP7-like effectors interact with the splicing factor SR45 and the core splicing proteins U1-70K and U2AF35." ], "source":"https:\/\/doi.org\/10.1038\/s41467-024-51512-5", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/s41467-024-51512-5", "Year":2024.0, "Citations":2.0, "answer":2, "source_journal":"Nature Communications", "is_expert":true }, { "question":"In plants, temperature changes lead to alternative splicing (AS). Which mode of alternative splicing leads to an increased formation of premature translation termination codon (PTC) and thus to the degradation of the alternatively spliced transcript by NMD?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "non-specific" ], "options":[ "Exon Skipping (ES) in particular, leads to the introduction of a premature translation termination codon (PTC) in the spliced transcript.", "Selection of an Alternative Splice Site (ASS) in particular, leads to the introduction of a premature translation termination codon (PTC) in the spliced transcript.", "Intron Retention (IR) in particular, leads to the introduction of a premature translation termination codon (PTC) in the spliced transcript." ], "source":"https:\/\/doi.org\/10.1093\/jxb\/erab232", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1093\/jxb\/erab232", "Year":2021.0, "Citations":57.0, "answer":2, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"Which statement about the influence of exonic splicing silencers (ESSs), exonic splicing enhancers (ESEs), intronic splicing silencers (ISSs) and intronic splicing enhancers (ISEs) on alternative splicing control is true?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "non-specific" ], "options":[ "The enhancing elements (ESEs & ISEs) tend to play dominant roles in alternative splicing.", "The silencers (ESSs & ISSs) are relatively more important in the control of alternative splicing.", "Both, enhancing and silencing elements play an equal role in the control of alternative splicing" ], "source":"doi: 10.3892\/br.2014.407", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.3892\/br.2014.407", "Year":2014.0, "Citations":330.0, "answer":2, "source_journal":"Biomedical Reports", "is_expert":true }, { "question":"Which EPF peptides participate in stomatal development, and what is the effect of each of them on this process in Arabidopsis? ", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "EPF1, EPF2 and EPFL9 peptides bind to leucine-rich repeat receptor kinases to regulate stomatal development through the activation ot inhibition of a downstream MAP kinase cascade. EPF1 and EPF2 are negative regulators of stomatal development but have different functions. EPF2 regulates the amount of SPEECHLESS in meristemoids, and therefore its subsequent fate, while EPF1 mainly regulates the enforcement of the one-cell spacing rule by preventing stomatal lineage ground cells from re-entering the stomatal lineage. Unlike EPF1 and EPF2, which are synthesized in epidermal cells, EPFL9 is produced in mesophyll cells and is a positive regulator of stomatal development, as it competes with them to bind to leucine-rich repeat receptor kinases.", "EPF1, EPF2 and EPFL9 peptides bind to leucine-rich repeat receptor kinases to repress stomatal development through the activation ot inhibition of a downstream MAP kinase cascade. EPF1 and EPF2 are negative regulators of stomatal development but have different functions. EPF1 regulates the amount of SPEECHLESS in meristemoids, and therefore its subsequent fate, while EPF2 mainly regulates the enforcement of the one-cell spacing rule by preventing stomatal lineage ground cells from re-entering the stomatal lineage. Like EPF1 and EPF2, which are synthesized in epidermal cells, EPFL9 is produced in mesophyll cells and is a negative regulator of stomatal development, as it also bind to the same leucine-rich repeat receptor kinases to activate a repressive cascade.", "EPF1, EPF2 and EPFL9 peptides bind to leucine-rich repeat receptor kinases to regulate stomatal development through the activation ot inhibition of a downstream MAP kinase cascade. EPF1 and EPF2 are negative regulators of stomatal development but have different functions. EPF2 regulates the amount of MUTE in meristemoids, and their subsequent conversion to guard mother cells, while EPF1 mainly regulates the enforcement of the one-cell spacing rule by recruiting a MAP kinase cascade that causes SPEECHLESS degradation. Unlike EPF1 and EPF2, which are synthesized in epidermal cells, EPFL9 is produced in mesophyll cells and is a positive regulator of stomatal development, as it competes with them to bind to leucine-rich repeat receptor kinases." ], "source":"http:\/\/dx.doi.org\/10.1016\/j.gde.2017.02.001", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1016\/j.gde.2017.02.001", "Year":2017.0, "Citations":33.0, "answer":0, "source_journal":"Current Opinion in Genetics & Development", "is_expert":true }, { "question":"How does the peptide EPF2 mediate the effect of CO2 on stomatal development in Arabidopsis?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "CO2 sensing by carbonic anhidrases 1 and 4 in stomatal precursor cells induces the transcription of the extracellular protease SDD, which degrades the pro-peptide EPF2, thus increasing the abundance of immature EPF2, which promotes stomatal development through binding to leucine-rich repeat receptor kinases which activate a MAP kinase cascade that leads to the degradation of SPEECHLESS. ", "CO2 sensing by carbonic anhidrases 1 and 4 in guard cells induces the transcription of the extracellular protease CRSP, which degrades the pro-peptide EPF1, thus increasing the abundance of mature EPF2, which represses stomatal development through binding to receptor tyrosine kinases which activate a MAP kinase cascade that leads to the degradation of SPEECHLESS. ", "CO2 sensing by carbonic anhidrases 1 and 4 in stomatal precursor cells induces the transcription of the extracellular protease CRSP, which degrades the pro-peptide EPF2, thus increasing the abundance of mature EPF2, which represses stomatal development through binding to leucine-rich repeat receptor kinases which activate a MAP kinase cascade that leads to the degradation of SPEECHLESS. " ], "source":"doi:10.1038\/nature13452", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1038\/nature13452", "Year":2014.0, "Citations":191.0, "answer":2, "source_journal":"Nature", "is_expert":true }, { "question":"How does BASL protein controls cell fate during stomatal development in Arabidopsis?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "BASL is a central regulator of cell division and fate asymmetry during stomatal development in dicots. During entry divisions leading to stomatal formation, BASL becomes polarly localized in a defined sector of the plasma membrane that guides the division plane to create cells of different size and identity: while the larger cell inherits the SPEECHLESS transcription factor and eventually differentiates into a stoma, the smaller daughter stomatal lineage ground cell inherits BASL, which helps to stabilize SPEECHLESS, thus promoting guard mother cell differentiation.", "BASL is a central regulator of cell size and fate asymmetry during stomatal development in dicots. During entry divisions leading to stomatal formation, BASL is uniformly distributed in the plasma membrane of the meristemoid, and guides the division plane to create cells of different size and identity: while the smaller cell inherits the SPEECHLESS transcription factor and eventually differentiates into a stoma, the larger stomatal lineage ground cell inherits BASL, which helps to recruit a rop GTPase that targets SPEECHLESS for degradation in the proteasome.", "BASL is a central regulator of cell size and fate asymmetry during stomatal development in dicots. During entry divisions leading to stomatal formation, BASL becomes polarly localized in a defined sector of the plasma membrane that guides the division plane to create cells of different size and identity: while the smaller cell inherits the SPEECHLESS transcription factor and eventually differentiates into a stoma, the larger stomatal lineage ground cell inherits BASL, which helps to recruit a MAP kinase cascade that phosphorylates SPEECHLESS and targets it for degradation in the proteasome. " ], "source":"https:\/\/doi.org\/10.1016\/j.cub.2021.11.013", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1016\/j.cub.2021.11.013", "Year":2022.0, "Citations":17.0, "answer":2, "source_journal":"Current Biology", "is_expert":true }, { "question":"What is the role of the transcription factors SPEECHLESS, MUTE and FAMA in stomatal development in Arabidopsis?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "SPEECHLESS, MUTE, and FAMA are basic helix-loop-helix transcription factors that coordinately regulate stomatal development. While SPEECHLESS regulates the transition of guard mother cells to guard cells, MUTE controls the transition of the latter to guard mother cells. FAMA in turn regulates the symmetric division of meristemoid mother cells into guard cells. The expression of all three transcription factors is controlled solely at the transcriptional level. ", "SPEECHLESS, MUTE, and FAMA are leucine zipper transcription factors that coordinately regulate stomatal development. While MUTE regulates the transition of protodermal cells to meristemoid mother cells, SPEECHLESS controls the transition of the latter to guard mother cells. FAMA in turn regulates the symmetric division of guard mother cells into guard cells. The expression of all three transcription factors is controlled both at the transcriptional and post-transcriptional level.", "SPEECHLESS, MUTE, and FAMA are basic helix-loop-helix transcription factors that coordinately regulate stomatal development. While SPEECHLESS regulates the transition of protodermal cells to meristemoid mother cells, MUTE controls the transition of the latter to guard mother cells. FAMA in turn regulates the symmetric division of guard mother cells into guard cells. The expression of all three transcription factors is controlled both at the transcriptional and post-transcriptional level. " ], "source":"https:\/\/doi.org\/10.3390\/plants10030432", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.3390\/plants10030432", "Year":2021.0, "Citations":3.0, "answer":2, "source_journal":"Plants", "is_expert":true }, { "question":"What is the role of receptors PANGLOSS1 and PANGLOSS2 in stomatal development in maize?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Zea mays" ], "options":[ "PANGLOSS1 and PANGLOSS2 LRR receptors are part of a polarly localized complex with PLC and BRIK to guide the polarity of subsidiary mother cells to give rise to subsidiary cells, with lie next to the stoma and helps in the opening and closure process. PANGLOSS2 also interacts with MAP kinase 3, with is required for proper subsidiary cells formation.", "PANGLOSS1 and PANGLOSS2 LRR receptors are part of a polarly localized complex with the small GTPase RHO GTPASE OF PLANTS and BRIK to guide the polarity of subsidiary mother cells to give rise to subsidiary cells, with lie next to the stoma and helps in the opening and closure process. PANGLOSS2 also interacts with WPR proteins, with are required for proper subsidiary cells formation.", "PANGLOSS1 and PANGLOSS2 LRR receptors are part of a polarly localized complex with the small GTPase RHO GTPASE OF PLANTS and TMM to guide the polarity of subsidiary mother cells to give rise to guard cells, with form a stoma. PANGLOSS2 also interacts with WPR proteins, with are required for proper subsidiary cells formation." ], "source":"https:\/\/doi.org\/10.1093\/plcell\/koac301", "normalized_plant_species":"Cereal Grains", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1093\/plcell\/koac301", "Year":2022.0, "Citations":10.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How do mutations in the LNK2 gene impact circadian rhythms and domestication in tomato?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Solanum lycopersicum" ], "options":[ "Loss of function mutations in the tomato orthologue of the Arabidopsis LNK2 gene result in a long circadian period phenotype, which appears beneficial for yield in tomato plants grown at high latitudes. This deletion is present in all cultivated tomato varieties and in some landraces. Still, it is absent in wild tomato plants, which originated in equatorial regions, suggesting the LNK2 deletion was positively selected during tomato domestication. ", "Loss of function mutations in the tomato orthologue of the Arabidopsis LNK2 gene result in a short circadian period phenotype, which appears beneficial for yield in tomato plants grown at low latitudes. This deletion is present in all cultivated tomato varieties and in some landraces. Still, it is absent in wild tomato plants, which originated in North America, suggesting the LNK2 deletion was negatively selected during tomato domestication. ", "Loss of function mutations in the tomato orthologue of the Arabidopsis LNK2 gene result in a short circadian period phenotype, which appears detrimental for yield in tomato plants grown at high latitudes. This deletion, which is absent in most cultivated tomato varieties and some landraces, is present in many wild tomato plants, which originated in equatorial regions, suggesting the LNK2 deletion was negatively selected during tomato domestication." ], "source":"DOI: 10.1073\/pnas.1808194115", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1073\/pnas.1808194115", "Year":2018.0, "Citations":1.0, "answer":0, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"How does the GEMIN2 protein affect alternative splicing and circadian rhythms in response to temperature changes in Arabidopsis?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The GEMIN2 protein is a key regulator of spliceosome assembly, which is particularly important for the proper regulation of alternative splicing under high-temperature conditions. Gemin2 mutants display short circadian rhythms and an early flowering phenotype in Arabidopsis, which is associated with enhanced intron 4 retention in the core clock gene CCA1. Alternative splicing patterns in gemin2 mutant plants grown at cold temperature conditions mimic the alternative splicing patterns of wild-type plants grown under mild temperature conditions.", "The GEMIN2 protein is a key regulator of spliceosome assembly, which is particularly important for the proper regulation of alternative splicing under low-temperature conditions. Gemin2 mutants display short circadian rhythms and an early flowering phenotype in Arabidopsis, which is associated with enhanced intron 4 retention in the core clock gene TOC1. Alternative splicing patterns in gemin2 mutant plants grown at ambient temperature conditions mimic the alternative splicing patterns of wild-type plants grown under cold conditions. ", "The GEMIN2 protein is a key regulator of spliceosome assembly, which is particularly important for the proper regulation of alternative splicing under low-temperature conditions. Gemin2 mutants display long circadian rhythms and a late flowering phenotype in Arabidopsis, which is associated with enhanced splicing of intron 4 in the core clock gene Timing of Cab Expression 1 (TOC1). Alternative splicing patterns in gemin2 mutant plants grown at high-temperature conditions mimic the alternative splicing pattern of wild-type plants grown at ambient temperature conditions." ], "source":"https:\/\/doi.org\/10.1073\/pnas.1504541112", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1073\/pnas.1504541112", "Year":2015.0, "Citations":88.0, "answer":1, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"How is PRMT5 involved in the regulation of circadian rhythms, light responses, and pre-mRNA splicing in Arabidopsis?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "PRMT5 is an asymmetric arginine dimethyl transferase that transfers methyl groups to different types of proteins, including histones and spliceosomal proteins, and plays a key role in the epigenetic regulation of gene expression as well as in the control of pre-mRNA splicing. Mutations in prmt5 shorten the period of circadian rhythms in Arabidopsis plants and display longer hypocotyls under light conditions compared to wild-type plants. These phenotypes are associated with disrupted alternative splicing of core clock genes such as TOC1 and CCA1. PRMT5 appears to regulate splicing mostly post-transcriptionally, favoring the removal of introns that are retained in mature mRNAs that remain in the nucleus after the completion of transcription. In response to certain stimuli, such as a change in the light conditions, these nuclear-detained transcripts undergo a splicing reaction that completes the removal of remaining introns, which favors the exportation of the corresponding mRNA to the cytoplasm where it can get translated. ", "PRMT5 is a symmetric dimethyl arginine transferase that transfers methyl groups to different types of proteins, including histones and spliceosomal proteins, and plays a key role in the epigenetic regulation of gene expression as well as in the control of pre-mRNA splicing. Mutations in prmt5 lengthen the period of circadian rhythms in Arabidopsis plants and display longer hypocotyls under light conditions compared to wild-type plants. These phenotypes are associated with disrupted alternative splicing of core clock genes such as PRR9 and PRR7. PRMT5 appears to regulate splicing mostly post-transcriptionally, favoring the removal of introns that are retained in mature mRNAs that remain in the nucleus after the completion of transcription. In response to certain stimuli, such as a change in the light conditions, these nuclear-detained transcripts undergo a splicing reaction that completes the removal of remaining introns, which favors the exportation of the corresponding mRNA to the cytoplasm where it can get translated. ", "PRMT5 is a symmetric dimethyl arginine transferase that transfers methyl groups to different types of proteins, including histones and spliceosomal proteins, and plays a key role in the epigenetic regulation of gene expression as well as in the control of pre-mRNA splicing. Mutations in prmt5 lengthen the period of circadian rhythms in Arabidopsis plants and display shorter hypocotyls under light conditions compared to wild-type plants. These phenotypes are associated with disrupted alternative splicing of core clock genes such as PRR9 and PRR7. PRMT5 appears to regulate splicing mostly co-transcriptionally, favoring the exportation of the corresponding mRNA to the cytoplasm where it can get translated. " ], "source":"https:\/\/doi.org\/10.1038\/nature09470 ; https:\/\/doi.org\/10.1073\/pnas.2317408121", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1073\/pnas.2317408121", "Year":2024.0, "Citations":1.0, "answer":1, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"What is the molecular function of the protein encoded by the EDS4 gene, involved in immune responses in Arabidopsis, and which other physiological processes are affected in eds4 mutant plants?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The Arabidopsis EDS4 gene encodes a MYB related transcription factor in Arabidopsis. Mutations in EDS4 result not only in enhanced disease susceptibility, as its name indicates, but also in late flowering, long hypocotyls under red light conditions, and a long circadian period phenotype for the rhythms of leaf movement and gene expression. ", "The EDS4 gene encodes Cysteine proteinases superfamily protein in Arabidopsis. Mutations in EDS4 result not only in enhanced disease susceptibility, as its name indicates, but also in early flowering, long hypocotyls under red light conditions, and a long circadian period phenotype for the rhythms of leaf movement and gene expression. ", "The EDS4 gene encodes an orthologue of Nucleoporin 205 in Arabidopsis. Mutations in EDS4 result not only in enhanced disease susceptibility, as its name indicates, but also in early flowering, long hypocotyls under red light conditions, and a long circadian period phenotype for the rhythms of leaf movement and gene expression. " ], "source":"https:\/\/doi.org\/10.1016\/j.cub.2020.02.058", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1016\/j.cub.2020.02.058", "Year":2020.0, "Citations":24.0, "answer":2, "source_journal":"Current Biology", "is_expert":true }, { "question":"How does light regulate alternative splicing in plants and what is the role of phytochrome photoreceptors in this process?", "area":"ENVIRONMENT - LIGHT AND TEMPERATURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Light appears to regulate alternative splicing in plants through at least two mechanisms. In the first mechanisms, canonical sensory photoreceptors such as phytochromes interact with transcription factors such as PIF3 and PIF4 upon light excitation, modifying somehow the properties of these proteins and indirectly impacting alternative splicing patterns of genes involved in the control of plant growth and development, including many clock genes. In this mechanism, light directly affects transcription elongation rates and indirectly modulates alternative splicing due to the co-transcriptional nature of alternative splicing and its regulation. Alternatively, light perceived by chlorophyll stimulates the photosynthetic process, and one or more molecules derived from the photosynthetic reactions, including sugars, directly affect the alternative splicing of many genes involved in the control of plant growth and development, including many genes encoding splicing factors. Although phytochrome mutants show some alterations in the regulation of a subset of alternative splicing events, since phytochromes do not interact directly with splicing factors, and strong red-light regulation of many alternative splicing events can still be observed in quintuple phytochrome mutants, the effect of phytochromes in the control of alternative splicing appears to be indirect and of secondary relevance. ", "Light regulates alternative splicing in plants through at least two mechanisms. In the first mechanism, photosynthetic photoreceptors such as phytochromes and cryptochromes interact with splicing factors upon light excitation, modifying somehow the properties of these splicing regulators and modulating the splicing of genes involved in the control of plant growth and development, including many clock genes. Alternatively, light perceived by chlorophyll stimulates the photosynthetic process, and one or more molecules derived from the photosynthetic reactions, including sugars, somehow affect the alternative splicing of many genes involved in the control of plant growth and development, including many genes encoding splicing factors. Quintuple phytochrome mutants, which are blind to red light signals controlling plant growth and development, are also blind to red light signals that modulate alternative splicing, indicating phytochromes play a predominant role in the regulation of alternative splicing in Arabidopsis plants. ", "Light regulates alternative splicing in plants through at least two mechanisms. In the first mechanism, canonical sensory photoreceptors such as phytochromes and cryptochromes interact with splicing factors upon light excitation, modifying somehow the properties of these splicing regulators and modulating the splicing of genes involved in the control of plant growth and development, including many clock genes. Alternatively, light perceived by chlorophyll stimulates the photosynthetic process, and one or more molecules derived from the photosynthetic reactions, including sugars, somehow affect the alternative splicing of many genes involved in the control of plant growth and development, including many genes encoding splicing factors. Although phytochrome mutants show some deficiencies in the light regulation of a subset of alternative splicing events, and phytochromes interact directly with splicing factors, strong red light regulation of many alternative splicing events can still be observed in quintuple phytochrome mutants that are completely blind to red light signals that control developmental processes. " ], "source":"https:\/\/doi.org\/10.3390\/cells12202447", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.3390\/cells12202447", "Year":2023.0, "Citations":3.0, "answer":2, "source_journal":"Cells", "is_expert":true }, { "question":"Which transcription factors are associated with the development of ventral identity in the snapdragon flower?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Antirrhinum majus" ], "options":[ "The ventral identity of the snapdragon flower is established through the interaction between the RAD and DRIF transcription factors, which form a heterodimer.", "The ventral identity of the snapdragon flower is established through the inhibition of dorsal genes by the DIV and DRIF transcription factors.", "The ventral identity of the snapdragon flower is established through the interaction between the DIV and DRIF transcription factors, which form a heterodimer." ], "source":"doi:10.3390\/genes11040395", "normalized_plant_species":"Other Herbaceous Crops, Spices, Fibers & Weeds", "normalized_area":"GENE REGULATION", "doi":"10.3390\/genes11040395", "Year":2020.0, "Citations":12.0, "answer":2, "source_journal":"Genes", "is_expert":true }, { "question":"Which rice HD-Zip I transcription factor changes its expression at low ABA concentrations, influencing leaf angle opening in 9-day-old plant?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Oryza sativa" ], "options":[ "Low ABA concentration induced the expression of both OsHOX22 and OsHOX24, increasing the leaf angle of 9-day-old rice plants. ", "Low ABA concentration induced the expression of OsHOX24, increasing the leaf angle of 9-day-old rice plants.", "Low ABA concentration induced the expression of OsHOX22, increasing the leaf angle of 9-day-old rice plants." ], "source":"doi.org\/10.1016\/j.envexpbot.2023.105433", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.envexpbot.2023.105433", "Year":2023.0, "Citations":0.0, "answer":1, "source_journal":"Environmental and Experimental Botany", "is_expert":true }, { "question":"Which rice HD-Zip I transcription factor appears to be involved in the brassinosteroid biosynthetic pathway?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Oryza sativa" ], "options":[ "OsHOX22 and OsHOX24 seem to play roles in the brassinosteroid response that influences leaf angle opening, although only the gene edition in OsHOX24 modified the expression of transcripts related to the brassinosteroid biosynthetic pathway.", "OsHOX22 and OsHOX24 seem to play roles in the brassinosteroid response that influences leaf angle opening, although only the gene edition in OsHOX22 modified the expression of transcripts related to the brassinosteroid biosynthetic pathway.", "OsHOX22 and OsHOX24 seem to play roles in the brassinosteroid response that influences leaf angle opening, although neither modified the expression of transcripts related to the brassinosteroid biosynthetic pathway. " ], "source":"doi.org\/10.1016\/j.envexpbot.2023.105433", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.envexpbot.2023.105433", "Year":2023.0, "Citations":0.0, "answer":0, "source_journal":"Environmental and Experimental Botany", "is_expert":true }, { "question":"How does SHY2 influence the balance between auxin and cytokinin to regulate root meristem size in Arabidopsis thaliana?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "SHY2 activation in the root influences auxin transport through the downregulation of PIN expression.", "SHY2 activation in the root influences cytokinin transport through the downregulation of PIN expression", "SHY2 activation in the root influences auxin transport through the upregulation of PIN expression" ], "source":"DOI 10.1016\/j.cub.2010.05.035", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.cub.2010.05.035", "Year":2010.0, "Citations":301.0, "answer":0, "source_journal":"Current Biology", "is_expert":true }, { "question":"What is the hypothesis regarding the mechanism by which GmCRF4a promotes epicotyl elongation in soybean plants?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Glycine max" ], "options":[ "GmCRF4a promotes epicotyl elongation primarily by increasing cell length through the regulation of auxin synthesis gene expression", "GmCRF4a promotes epicotyl elongation primarily by increasing cell width through the regulation of auxin synthesis gene expression", "GmCRF4a promotes epicotyl elongation primarily by increasing cell length through the regulation of ethylene synthesis gene expression" ], "source":"doi.org\/10.3389\/fpls.2022.983650", "normalized_plant_species":"Legumes", "normalized_area":"GENE REGULATION", "doi":"10.3389\/fpls.2022.983650", "Year":2022.0, "Citations":13.0, "answer":0, "source_journal":"Frontiers in Plant Science", "is_expert":true }, { "question":"What is the role of nitrate in plant nutrition?", "area":"ENVIRONMENT - NUTRIENTS", "plant_species":[ "non-specific" ], "options":[ "Nitrate is a chemical found in soils that organisms such as plants utilize as a source of phosphorus", "Nitrate can be used for plant nutrition to secure the nitrogen micronutrient ", "Nitrate is one of the main nitrogen sources in aerobic soils. Plants uptake nitrate from the soil, reduce it to nitrate and then ammonia. Ammonia is then incorporated into amino acids. Nitrogen is essential for biosynthesis of amino acids, proteins, nucleic acids, chlorophyll among other biomolecules in plants." ], "source":"10.1016\/j.molp.2016.05.004", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.molp.2016.05.004", "Year":2016.0, "Citations":458.0, "answer":2, "source_journal":"Molecular Plant", "is_expert":true }, { "question":"How do plants sense nitrate availability in soil?", "area":"ENVIRONMENT - NUTRIENTS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Plants sense nitrate through a specific nitrate transporter and sensor known as NITRATE TRANSPORTER 1.1 (NRT1.1) and also via NIN-like proteins (NLP). NLP7 in particular has been shown to be an important regulatory factor as well as a potential nitrate sensor.", "It is unknown how plants sense nitrate", "Plants sense nitrate through a specific sensor protein expressed in the nuclei of shoot cells." ], "source":"10.1016\/j.molp.2016.05.004", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.molp.2016.05.004", "Year":2016.0, "Citations":458.0, "answer":0, "source_journal":"Molecular Plant", "is_expert":true }, { "question":"What is the primary pathway for nitrate uptake in plants?", "area":"ENVIRONMENT - NUTRIENTS", "plant_species":[ "non-specific" ], "options":[ "Plants interact with microorganisms to acquire nutrients including nitrate from the soil", "Nitrate is absorbed from the soil through root nitrate transporters. There are two transporter families that code for high affinity (NRT2) and low affinity (NRT1) transport systems.", "Nitrate is absorbed directly from the soil by diffusion through the cell plasma membrane. " ], "source":"10.1105\/tpc.19.00748", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1105\/tpc.19.00748", "Year":2020.0, "Citations":267.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"Which plant hormone is closely linked to nitrate signaling?", "area":"ENVIRONMENT - NUTRIENTS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Ethylene is closely linked to nitrate signaling", "Auxin is the most important hormone with regards to nitrate signaling and plant responses to changes in nitrate levels in the soil", "Cytokinin is closely linked to nitrate signaling and influences root and shoot growth. Auxin is also very tightly linked, particularly shown to play a role in root developmental responses. Gibberellins and ABA have been also shown to mediate nitrate responses in plants such as flowering time (GA) and root development (ABA). " ], "source":"10.1007\/s11103-016-0463-x", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1007\/s11103-016-0463-x", "Year":2016.0, "Citations":115.0, "answer":2, "source_journal":"Plant Molecular Biology", "is_expert":true }, { "question":"How does nitrate affect plant root system architecture?", "area":"ENVIRONMENT - NUTRIENTS", "plant_species":[ "non-specific" ], "options":[ "Nitrate does not influence root system architecture. The root system in plants is genetically determined and have little or no influence by environmental changes ", "Nitrate inhibits root system growth due to the stress produced by increased salt levels", "Nitrate availability influences primary root growth, lateral root development and growth and root hair density. Changes in root system architecture are associated with optimizing nutrient uptake. High nitrate availability often stimulates the formation of lateral roots, allowing for increased surface area for nutrient and water uptake. Nitrate can also enhance the density of root hairs, which helps improve the plant\u2019s ability to absorb nutrients and water from the soil. Nitrate can influence the direction of root growth, often leading roots to grow towards higher concentrations of nitrate in the soil. Sufficient nitrate levels can promote overall root growth, leading to longer roots that can explore a larger volume of soil for nutrients. Nitrate levels can also generate signals sent from roots to shoots, affecting overall plant growth and resource allocation. Overall, nitrate availability plays a critical role in shaping the root architecture, optimizing the plant's ability to access nutrients in the soil." ], "source":"10.1016\/j.pbi.2014.06.004", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.pbi.2014.06.004", "Year":2014.0, "Citations":197.0, "answer":2, "source_journal":"Current Opinion in Plant Biology", "is_expert":true }, { "question":"What role does the protein NRT2.1 play in Arabidopsis thaliana?", "area":"ENVIRONMENT - NUTRIENTS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "NRT2.1 is involved in high-affinity nitrate uptake and helps regulate root architecture in response to nitrate levels. The protein NRT2.1 plays several roles in nitrate uptake and responses in plants. NRT2.1 is responsible for the high-affinity uptake of nitrate from the soil, allowing plants to efficiently absorb nitrate when concentrations are low. High affinity transport system typically works at concentrations below 1 mM. NRT2.1 expression is regulated by nitrate availability, typically showing rapid induction by increasing nitrate levels after starvation and repression by long exposure to high nitrate levels. This helps plants adapt to fluctuating nutrient conditions. NRT2.1 works in conjunction with NRT3.1 (or NAR) which is required for high-affinity nitrate transport. Acts as a repressor of lateral root initiation. May be involved in targeting NRT2 proteins to the plasma membrane. NRT2.1 can influence the expression of other genes involved in nitrogen metabolism and assimilation, linking nitrate uptake with broader metabolic pathways. The presence of nitrate induces root developmental changes, including lateral root formation, which NRT2.1 has been shown to be implicated. Overall, NRT2.1 is a key player in facilitating nitrate uptake and integrating nutrient availability with plant growth and development responses.", "NRT2.1 is not involved in regulating root system architecture", "NRT2.1 primarily functions as a low-affinity transporter for ammonium" ], "source":"10.1111\/j.1469-8137.2012.04094.x", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/j.1469-8137.2012.04094.x", "Year":2012.0, "Citations":142.0, "answer":0, "source_journal":"New Phytologist", "is_expert":true }, { "question":"How does phosphorylation affect NRT1.1 function in Arabidopsis thaliana?", "area":"ENVIRONMENT - NUTRIENTS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Phosphorylation has no impact on NRT1.1 function", "Studies showed that T101-phosphorylated CHL1 is a high-affinity nitrate transporter, whereas T101-dephosphorylated CHL1 is a low-affinity transporter. Primary nitrate responses in CHL1T101D and CHLT101A transgenic plants showed that phosphorylated and dephosphorylated CHL1 lead to a low- and high-level response, respectively. In vitro and in vivo studies showed that, in response to low nitrate concentrations, protein kinase CIPK23 can phosphorylate T101 of CHL1 to maintain a low-level primary response. Thus, CHL1 uses dual-affinity binding and a phosphorylation switch to sense a wide range of nitrate concentrations in the soil, thereby functioning as an ion sensor in higher plants.\u00a0", "NRT1.1 is phosphorylated in multiple locations affecting its localization in the cell" ], "source":"10.1016\/j.cell.2009.07.004", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.cell.2009.07.004", "Year":2009.0, "Citations":1051.0, "answer":1, "source_journal":"Cell", "is_expert":true }, { "question":"How does nitrate influence the expression of microRNAs (miRNAs) in plants?", "area":"ENVIRONMENT - NUTRIENTS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Nitrate has not effect on miRNA levels but rather on target gene expression.", "miRNAs alter nitrate levels in the soil through regulating gene expression in the plant", "Nitrate levels can regulate expression of specific miRNAs that modulate levels and expression of target mRNAs involved in nitrogen metabolism and growth. One of the first reported examples involved miR393 and the AFB3 target mRNA coding for an auxin receptor. This regulatory module was shown to be important to modulate root system architecture in response to external nitrate and the internal N status of the plant." ], "source":"10.1073\/pnas.0909571107", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1073\/pnas.0909571107", "Year":2010.0, "Citations":521.0, "answer":2, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"Has the crystal structure of NRT1.1 been resolved and what was the implication of knowing the structure for nitrate transport in Arabidopsis thaliana?", "area":"ENVIRONMENT - NUTRIENTS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The crystal structure is unknown for NRT1.1 and remains unknown how it transport and senses nitrate", "The crystal structure of NRT1.1 was reported in two independent scientific publications. In one study, scientists report the crystal structure of unphosphorylated NRT1.1, which reveals a homodimer in the inward-facing conformation. In this low-affinity state, the Thr 101 phosphorylation site is embedded in a pocket immediately adjacent to the dimer interface, linking the phosphorylation status of the transporter to its oligomeric state. Using a cell-based fluorescence resonance energy transfer assay, they showed that functional NRT1.1 dimerizes in the cell membrane and that the phosphomimetic mutation of Thr 101 converts the protein into a monophasic high-affinity transporter by structurally decoupling the dimer. Together with analyses of the substrate transport tunnel, these results establish a phosphorylation-controlled dimerization switch that allows NRT1.1 to uptake nitrate with two distinct affinity modes.10.1038\/nature13074.\nIn a separate study, the apo and nitrate bound crystal structures of\u00a0Arabidopsis thaliana\u00a0NRT1.1 were reported, which together with\u00a0in vitro\u00a0binding and transport data identify a key role for His356 in nitrate binding. Their data supports a model whereby phosphorylation increases structural flexibility and in turn the rate of transport. 10.1038\/nature13116", "The structure of NRT1.1 shows that it only functions as a sensor and has no role in nitrate transport" ], "source":"10.1038\/nature13074.", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/nature13074", "Year":2014.0, "Citations":264.0, "answer":1, "source_journal":"Nature", "is_expert":true }, { "question":"What is the role of protein phosphatases in nitrate signaling in Arabidopsis thaliana?", "area":"ENVIRONMENT - NUTRIENTS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Protein phosphatases add phosphate groups to proteins, thereby activating components in the nitrate signaling pathway ", "Phosphatases play a crucial role in nitrate signaling, particularly regulating expression of key transcription factors involved in signal transduction ", "Less is known about the role of phosphatases in nitrate signaling as compared to kinases in the CPK family for instance. However, phosphatases can deactivate signaling components through dephosphorylation, fine-tuning the nitrate response. Benoit Lacombe\u2019s group identified two components that regulate nitrate transport, sensing, and signaling: the calcium sensor CBL1 and protein phosphatase 2C family member ABI2, which is inhibited by the stress-response hormone abscisic acid. They used bimolecular fluorescence complementation assays and in vitro kinase assays to show that ABI2 interacted with and dephosphorylated CIPK23 and CBL1. Coexpression studies in\u00a0Xenopus\u00a0oocytes and analysis of plants deficient in ABI2 indicated that ABI2 enhanced NPF6.3-dependent nitrate transport, nitrate sensing, and nitrate signaling. These findings suggest that ABI2 may functionally link stress-regulated control of growth and nitrate uptake and utilization, which are energy-expensive processes." ], "source":"10.1126\/scisignal.aaa4829", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1126\/scisignal.aaa4829", "Year":2015.0, "Citations":159.0, "answer":2, "source_journal":"Science Signaling", "is_expert":true }, { "question":"How long non-coding RNAs can affect alternative splicing in Arabidopsis thaliana?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Long non-coding RNA interact with alternative splicing regulators such as PRP8, NSR or other splicing regulators to modify the action of these proteins on specific target mRNAs being recognized by these regulators", "Long non-coding RNA interact with chromatin regulators to affect alternative splicing of mRNA targets", "Long non-coding RNA interact with mRNA targets preventing their recognition by PRP8, NSR or other splicing regulators" ], "source":"https:\/\/doi.org\/10.1093\/pcp\/pcz086", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1093\/pcp\/pcz086", "Year":2019.0, "Citations":76.0, "answer":0, "source_journal":"Plant and Cell Physiology", "is_expert":true }, { "question":"Which technologies can be used to identify mRNA target genes whose splicing depends on long non-coding RNAs?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "non-specific" ], "options":[ "ChIRP technologies can be used to identify potential target mRNAs whose splicing is controlled by long-non-coding RNAs", "RNAseq of total RNA can be used to identify potential target mRNAs whose splicing is affected by long non-coding RNAs", "ChIP histone analysis can be used to identify mRNA targeted by long non-codign RNAs" ], "source":"10.15252\/embj.2022110921", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.15252\/embj.2022110921", "Year":2023.0, "Citations":17.0, "answer":0, "source_journal":"The EMBO Journal", "is_expert":true }, { "question":"Which splicing regulators control also post-transcriptional gene silencing in Arabidopsis thaliana?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "PRP39 and SMD1b affects small RNA biogenesis and this leads to changes in alternative splicing ", "PRP39 and SMD1b have been shown to affect Posttrascriptional gene silencing through small RNAs as well as alternative splicing patterns in the corresponding mutants ", "Mutants in PRP39 and SMD1B affect small RNA production in alternatively spliced genes" ], "source":"https:\/\/doi.org\/10.1093\/plcell\/koad091", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1093\/plcell\/koad091", "Year":2023.0, "Citations":5.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"Which stress requires inhibition of the action of a specific miRNA on systemic response in plants?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "The IPS1long non-coding RNA induces the expression of miR399 during phosphate starvation ", "Phosphate starvation induces the action of IPS2 which down regulated by miR399", "The IPS1 transcript is a long non-coding RNA that inhibits the action of miR399 during phosphate starvation" ], "source":"doi: 10.1038\/ng2079. Epub 2007 Jul 22.", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/ng2079", "Year":2007.0, "Citations":1702.0, "answer":2, "source_journal":"Nature Genetics", "is_expert":true }, { "question":"How does miR396 regulates root meristem growth and mycorrhization in Medicago truncatula?", "area":"ENVIRONMENT - PLANT-SYMBIONTS", "plant_species":[ "Medicago truncatula" ], "options":[ "A bHLH transcription factor down regulates GRF genes through activation of miR396", "MiR396 down regulates three GRF genes as well as a new legume-specific target, a bHLH transcription factor to permit the exit of stem cells towards differentiation and to modulate mycorrhization", "The GRF genes activate miR396 to down-regulate a bHLH legume-specific target to dimnish mycorrhization " ], "source":"doi: 10.1111\/tpj.12178. Epub 2013 May 3.", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/tpj.12178", "Year":2013.0, "Citations":165.0, "answer":1, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"Which transcription factors participate in the negative regulation of the DELAY OF GERMINATION 1 (DOG1) gene by ABI5-BINDING PROTEIN 2 (AFP2) during seed maturation in Arabidopsis thaliana?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis thaliana, two basic helix\u2013loop\u2013helix transcription factors in the BR signaling pathway, BRASSINOSTEROID ENHANCED EXPRESSION 2 (BEE2) and BEE 2 INTERACTING with INCREASED LEAF INCLINATION 1 BINDING bHLH1 (HBI1), suppress DOG1 expression by recruiting the transcriptional corepressor TPR2 to carry out histone deacetylation at the DOG1 gene. In siliques, when BEE2 and HBI1 levels are low and inadequate to suppress DOG1 production, a large number of DOG1 transcripts accumulate during embryo development to maintain seed dormancy. BEE2 and HBI1transcript levels progressively rise in mature fresh or after-ripened seeds. Since AFP2 acts as an adapter, the increased BEE2 and HBI1transcripts recruit additional TPR2 and HDAC, which ultimately suppresses DOG1 expression and finally releases seed dormancy. ", "In Arabidopsis thaliana, the transcription factor WRKY36 suppresses DOG1 expression by recruiting the transcriptional corepressor TPR2 to carry out histone deacetylation at the DOG1 gene. In siliques, when WRKY36 levels are low and inadequate to suppress DOG1 production, a large number of DOG1 transcripts accumulate during embryo development to maintain seed dormancy. WRKY36 transcript levels progressively rise in mature fresh or after-ripened seeds. Since AFP2 acts as an adapter, the increased WRKY36 recruits additional TPR2 and HDAC, which ultimately suppresses DOG1 expression and finally releases seed dormancy. ", "In Arabidopsis thaliana, the transcription factor WRKY36 suppresses DOG1 expression by recruiting the transcriptional corepressor TPR2 to carry out histone deacetylation at the DOG1 gene. In siliques, when WRKY36 levels are high and DOG1 transcripts accumulate during embryo development to maintain seed dormancy. WRKY36 transcript levels progressively decrease in mature fresh or after-ripened seeds. AFP2 ultimately suppresses DOG1 expression and finally releases seed dormancy. " ], "source":"Deng, G., Sun, H., Hu, Y., Yang, Y., Li, P., Chen, Y., Zhu, Y., Zhou, Y., Huang, J., Neill, S.J. and Hu, X. (2023), A transcription factor WRKY36 interacts with AFP2 to break primary seed dormancy by progressively silencing DOG1 in Arabidopsis. New Phytol, 238: 688-704. https:\/\/doi.org\/10.1111\/nph.18750", "normalized_plant_species":"Model Organisms", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1111\/nph.18750", "Year":2023.0, "Citations":18.0, "answer":1, "source_journal":"New Phytologist", "is_expert":true }, { "question":"How is the gene ETHYLENE INSENSITIVE 2 (EIN2) involved on the ABA response In Arabidopsis thaliana?", "area":"HORMONES", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis thaliana, ABA responses are largely induced by EIN2 rather than EIN3 or EIL1. This EIN2-directed ABA response enhancement depends on HLS1 function. EIN2 directly interacts with HLS1, to fine-tune ABA responses during seed germination and early seedling establishment.", "In Arabidopsis thaliana, ABA responses are largely repressed by EIN2 rather than EIN3 or EIL1. This EIN2-directed repression depends on HLS1 function. EIN2 directly interacts with HLS1, thus repressing histone H3 acetylation at ABI5 chromatin to fine-tune ABA responses during seed germination and early seedling establishment.", "In Arabidopsis thaliana, ABA responses are largely repressed by EIN3 rather than EIN2 or EIL1. This EIN3-directed repression depends on HLS1 function. EIN3 directly interacts with HLS1, thus repressing histone H3 acetylation at ABI5 chromatin to fine-tune ABA responses during seed germination and early seedling establishment." ], "source":"Guo, R., Wen, X., Zhang, W., Huang, L., Peng, Y., Jin, L., Han, H., Zhang, L., Li, W. and Guo, H. (2023), Arabidopsis EIN2 represses ABA responses during germination and early seedling growth by inactivating HLS1 protein independently of the canonical ethylene pathway. Plant J, 115: 1514-1527. https:\/\/doi.org\/10.1111\/tpj.16335", "normalized_plant_species":"Model Organisms", "normalized_area":"HORMONES", "doi":"10.1111\/tpj.16335", "Year":2023.0, "Citations":12.0, "answer":1, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"How are the transcription factors SISCZ and SIEXO1 involved in the lignification in the inner cortical layer in Solanum lycopersicum?", "area":"GROWTH AND DEVELOPMENT", "plant_species":[ "Solanum lycopersicum" ], "options":[ "SlEXO1 and SlSCZ regulates the polar deposition of lignin in the exodermis. As evidenced by the absence of PLC and suberin in the inner cortical layers, SlSCZ and SlEXO1 both induce PLC and most likely exodermal cell fate specification in the inner cortex layer. Exodermal lignification and suberization can likewise be enhanced by SlEXO1, possibly in a dose-dependent manner through SlMYB92.", "Through a genetic interaction with SlEXO1, SlSCZ regulates the polar deposition of lignin in the endodermis. As evidenced by the presence of PLC and suberin in the outer cortical layers, SlSCZ and SlEXO1 both repress PLC and most likely endodermal cell fate specification in the outer cortex layer. Endodermal lignification and suberization can likewise be suppressed by SlEXO1, possibly in a dose-dependent manner through SlMYB92.", "Through a genetic interaction with SlEXO1, SlSCZ regulates the polar deposition of lignin in the exodermis. As evidenced by the presence of PLC and suberin in the inner cortical layers, SlSCZ and SlEXO1 both repress PLC and most likely exodermal cell fate specification in the inner cortex layer. Exodermal lignification and suberization can likewise be suppressed by SlEXO1, possibly in a dose-dependent manner through SlMYB92." ], "source":"Manzano, C., Morimoto, K.W., Shaar-Moshe, L. et al. Regulation and function of a polarly localized lignin barrier in the exodermis. Nat. Plants (2024). https:\/\/doi.org\/10.1038\/s41477-024-01864-z", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"GROWTH AND DEVELOPMENT", "doi":"10.1038\/s41477-024-01864-z", "Year":2024.0, "Citations":0.0, "answer":2, "source_journal":"Nature Plants", "is_expert":true }, { "question":"How are the IncRNAs called PUPPIES involved in Arabidopsis thaliana seed germination delay upon salt stress conditions?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The DOG1 gene represses the salt\u2010dependent delay of germination. DOG1 gene promoter is extensively transcribed, generating a variety of lncRNAs, called PUPPIES. Co-directional pervasive transcription of PUPPIES increases transcriptional bursts and RNA polymerase II pausing, which in turn downregulates DOG1 expression. ", "The DOG1 gene induces the salt\u2010dependent delay of germination. DOG1 gene promoter is extensively transcribed, generating a variety of lncRNAs, called PUPPIES. Co-directional pervasive transcription of PUPPIES increases transcriptional bursts and RNA polymerase II pausing, which in turn stimulates DOG1 expression. ", "The DOG1 gene induces the salt\u2010dependent delay of germination. DOG1 gene introns are extensively transcribed, generating a variety of lncRNAs, called PUPPIES. Co-directional pervasive transcription of PUPPIES increases transcriptional bursts and RNA polymerase II pausing, which in turn stimulates DOG1 expression. " ], "source":"https:\/\/doi.org\/10.15252\/embj.2022112443", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.15252\/embj.2022112443", "Year":2023.0, "Citations":15.0, "answer":1, "source_journal":"The EMBO Journal", "is_expert":true }, { "question":"How is the pyrroline-5-carboxylate synthetase (P5CS)-encoding gene (CtrP5CS1) involved in Citrus trifoliata cold response?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Citrus trifoliata" ], "options":[ "Proline accumulation has been reported in plants under cold stress. The Citrus trifoliata L. gene CtrP5CS1, that encodes for the pyrroline-5-carboxylate synthetase (P5CS), is essential for cold-induced proline accumulation. CtrTGA2 bound directly to the TGACG motif of the CtrP5CS1 promoter and repress its expression. Down-regulation of CtrP5CS1 and CtrTGA2 under cold stress is dependent on salicylic acid (SA) biosynthesis. ", "Proline accumulation has been reported in plants under cold stress. The Citrus trifoliata L. gene CtrP5CS1, that encodes for the pyrroline-5-carboxylate synthetase (P5CS), is essential for cold-induced proline accumulation. CtrTGA1 bound directly to the TGACG motif of the CtrP5CS1 promoter and activate its expression. Up-regulation of CtrP5CS1 and CtrTGA1 under cold stress is dependent on salicylic acid (SA) biosynthesis. ", "Proline accumulation has been reported in plants under cold stress. The Citrus trifoliata L. gene CtrP5CS1, that encodes for the pyrroline-5-carboxylate synthetase (P5CS), is essential for cold-induced proline accumulation. CtrTGA2 bound directly to the TGACG motif of the CtrP5CS1 promoter and activate its expression. Up-regulation of CtrP5CS1 and CtrTGA2 under cold stress is dependent on salicylic acid (SA) biosynthesis. " ], "source":"https:\/\/doi.org\/10.1093\/plcell\/koae290", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"ENVIRONMENT", "doi":"10.1093\/plcell\/koae290", "Year":2024.0, "Citations":2.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How is the susceptibility of Arabidopsis plants to viral infections affected by a combination of heat and drought stress?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis there are detectable differences in susceptibility to TuMV (Turnip mosaic potyvirus) when a single virus stress or a combined virus and drought stress is applied. The combination of virus infection with heat or heat and drought leads to a decrease of the level of P3, the viral gene used to quantify the level of virus accumulation, indicating that heat or combined heat and drought stress decreases the susceptibility of Arabidopsis to virus infection.", "In Arabidopsis there are no detectable differences in susceptibility to TuMV (Turnip mosaic potyvirus) when a single virus stress or a combined virus and drought stress is applied. The combination of virus infection with heat or heat and drought leads to no change of the level of P3, the viral gene used to quantify the level of virus accumulation, indicating that heat or combined heat and drought stress does not affect the susceptibility of Arabidopsis to virus infection.", "In Arabidopsis there are no detectable differences in susceptibility to TuMV (Turnip mosaic potyvirus) when a single virus stress or a combined virus and drought stress is applied. The combination of virus infection with heat or heat and drought leads to an increase of the level of P3, the viral gene used to quantify the level of virus accumulation, indicating that heat or combined heat and drought stress increases the susceptibility of Arabidopsis to virus infection." ], "source":"doi: 10.1104\/pp.113.221044.", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1104\/pp.113.221044", "Year":2013.0, "Citations":438.0, "answer":2, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"How is the evolution of Turnip mosaic potyvirus (TuMV) affected by severe drought conditions and what are the salicylic acid (SA) levels in plants infected with standard- and drought-evolved viruses?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Viruses evolved under drought conditions accumulate more mutations and, in contrast to viruses evolved in standard conditions, the mutations are randomly distributed across the different viral cistrons. Plants infected with standard- or drought-evolved viruses show a significant decrease in salicylic acid (SA) levels compared to non-infected plants. ", "Viruses evolved under drought conditions accumulate the same number of mutations as viruses evolved in standard conditions, and the mutations are randomly distributed across the different viral cistrons. Plants infected with standard- or drought-evolved viruses show no changes in salicylic acid (SA) levels compared to non-infected plants. ", "Viruses evolved under drought conditions accumulate less mutations and, as in the case of viruses evolved in standard conditions, the mutations are not randomly distributed and accumulate in the VPg cistron. Plants infected with standard- or drought-evolved viruses show a significant increase in salicylic acid (SA) levels compared to non-infected plants. " ], "source":"doi: 10.1073\/pnas.2020990118.", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1073\/pnas.2020990118", "Year":2021.0, "Citations":79.0, "answer":2, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"Which is the role of the Cucumber mosaic virus (CMV) protein 2b in the response to drought stress in Arabidopsis thaliana and how does it affect abscisic acid (ABA)-mediated signaling?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The CMV 2b protein is responsible for the increase of drought tolerance in infected Arabidopsis plants. 2b exerts this role by interfering with the regulation of gene expression mediated by ABA, a phytohormone with a key role in regulating drought responses. ABA levels are not altered in CMV infected plants, but the expression of RD29A, an ABA- and desiccation-responsive gene, is induced in mock-treated plants but not in CMV-infected plants in response to drought stress.", "The CMV 2b protein is responsible for the increase of drought tolerance in infected Arabidopsis plants. 2b exerts this role by interfering with the regulation of gene expression mediated by ABA, a phytohormone with a key role in regulating drought responses. ABA levels are increased in CMV infected plants, and the expression of RD29A, an ABA- and desiccation-responsive gene, is induced in mock-treated and, to less extend, in CMV-infected plants in response to drought stress.", "The CMV 2b protein is responsible for the increase of drought tolerance in infected Arabidopsis plants. 2b exerts this role by interfering with the regulation of gene expression mediated by ABA, a phytohormone with a key role in regulating drought responses. ABA levels are reduced in CMV infected plants, and the expression of RD29A, an ABA- and desiccation-responsive gene, is induced in mock-treated plants and, to less extend, in CMV-infected plants in response to drought stress." ], "source":"https:\/\/doi.org\/10.1111\/j.1364-3703.2012.00840.x", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/j.1364-3703.2012.00840.x", "Year":2012.0, "Citations":94.0, "answer":0, "source_journal":"Molecular Plant Pathology", "is_expert":true }, { "question":"What is the role of artificial micro RNAs (amiRNAs) and synthetic trans-acting RNAs (syn-tasiRNAs), two types of artificial sRNAs (art-RNAs), in triggering systemic silencing (SS) of the magnesium chelatase subunit CHLI encoded by the Nicotiana benthamiana SULFUR gene (NbSu) and how do they move to exert their function?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Nicotiana benthamiana" ], "options":[ "The expression of a 21-nt long amiRNA designed to silence NbSu is able to induce SS in upper leaves. This process is characterized by a strong chlorosis near to the leaf veins. The expression of a 22-nucleotide form of the same amiRNA did not induce SS despite inducing the production of 21-nucleotide-phased small interfering RNAs (siRNAs). Transient expression of the 21-nt long syn-tasiRNbSu-2 triggers SS in a similar manner, and since the process does not requires transitivity, it is assumed that both classes of art-sRNAs are able to move to the surrounding cells via plasmodesmata and to distant tissues trough the phloem.", "The expression of a 21-nt long amiRNA designed to silence NbSu is not able to induce SS in upper leaves, a process that is characterized by a strong chlorosis in the complete leaf. The expression of a 22-nucleotide form of the same amiRNA induces SS via inducing the production of 21-nucleotide-phased small interfering RNAs (siRNAs). Transient expression of the 21-nt long syn-tasiRNbSu-2 does not triggers SS, and since the process requires transitivity, it is assumed that only 21-nucleotide phased siRNAs are able to move to the surrounding cells via plasmodesmata and to distant tissues trough the phloem.", "The expression of a 21-nt long amiRNA designed to silence NbSu is able to induce SS in upper leaves. This process is characterized by a mild chlorosis near to the leaf veins. The expression of a 22-nucleotide form of the same amiRNA also induces SS via inducing the production of 21-nucleotide-phased small interfering RNAs (siRNAs). Transient expression of the 21-nt long syn-tasiRNbSu-2 triggers SS in a similar manner, and since the process does requires transitivity, it is assumed that the derived secondary siRNAs are able to move to the surrounding cells via plasmodesmata and to distant tissues trough the phloem." ], "source":"doi: 10.1111\/tpj.15730.", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1111\/tpj.15730", "Year":2022.0, "Citations":10.0, "answer":0, "source_journal":"The Plant Journal", "is_expert":true }, { "question":"What are the advantages and disadvantages of using a Potato virus X (PVX)-based system to induce silencing in Nicotiana benthamiana plants?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Nicotiana benthamiana" ], "options":[ "The use of a PVX-based viral vector makes it possible to trigger widespread silencing in Nicotiana benthamiana plants. The advantages of this system are that it is a stable and completely DNA-free approach. Crude extracts prepared from infected plants expressing the desired construct can be used for transmitting the viral vector to new plants by spraying. The system has no disadvantages, since the use of PVX-based viral vector does not induces symptoms typically present in PVX infected plants, such as mild leaf curling, even over long periods after agroinoculation.", "The use of a PVX-based viral vector makes it possible to trigger widespread silencing in Nicotiana benthamiana plants. The advantages of this system are that it is a non-transgenic and completely DNA-free approach. Crude extracts prepared from infected plants expressing the desired construct can be used for transmitting the viral vector to new plants by spraying. A disadvantage of the use of viral vectors is that symptoms typically induced by PVX infection, such as mild leaf curling, are observed on the infected plants shortly after agroinoculation.", "The use of a PVX-based viral vector makes it possible to trigger only local silencing in Nicotiana benthamiana leaves. The advantages of this system are that it is a non-transgenic and completely DNA-free approach. Crude extracts prepared from infected leaves expressing the desired construct can be used for transmitting the viral vector to new leaves by spraying. A disadvantage of the use of viral vectors is that symptoms typically induced by PVX infection, such as mild leaf curling, are observed on the infected plants shortly after agroinoculation." ], "source":"doi: 10.1093\/nar\/gkad747.", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1093\/nar\/gkad747", "Year":2023.0, "Citations":16.0, "answer":1, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"What was the first example of a long noncoding RNA capturing a miRNA by target mimicry in any living organism and what is it involved in? Indicate the corresponding organism and describe the associated molecular mechanism.", "area":"GENE REGULATION - PTGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The first example of a lncRNA exerting a role as a miRNA target mimicry was INDUCED BY PHOSPHATE STARVATION 1 (IPS1) from Arabidopsis thaliana. It is a transcript recognized by miRNA166, including a mismatch in the 11th position. As a result, the miRNA remains paired to IPS2 without clivage, and miRNA166 is titered and blocked. IPS1 is induced in response to phosphate starvation, blocking miRNA and increasing the transcript levels of the miRNA166 target PHO3 gene.", "The first example of a lncRNA exerting a role as a miRNA target mimicry was INDUCED BY PHOSPHATE STARVATION 1 (IPS1) from Arabidopsis thaliana. It is a transcript recognized by miRNA399, including a mismatch in the 11th position. As a result, the miRNA remains paired to IPS2 without clivage, and miRNA399 is titered and blocked. IPS1 is induced in response to phosphate starvation, blocking miRNA and increasing the transcript levels of the miRNA399 target PHO2 gene.", "The first example of a lncRNA exerting a role as a miRNA target mimicry was COOLAIR from Arabidopsis thaliana. It is a transcript recognized by miRNA399, including a mismatch in the 11th position. As a result, the miRNA remains paired to COOLAIR without clivage, and miRNA399 is titered and blocked. COOLAIR is induced in response to phosphate starvation, blocking miRNA and increasing the transcript levels of the miRNA399 target PHO2 gene." ], "source":"doi.org\/10.1038\/ng2079", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1038\/ng2079", "Year":2007.0, "Citations":1702.0, "answer":1, "source_journal":"Nature Genetics", "is_expert":true }, { "question":"What was the first lncRNA identified in plants, in what species and what are the molecular and the physiological mechanisms it involved in?", "area":"GENE REGULATION - EPIGENETICS AND TGS", "plant_species":[ "Medicago truncatula" ], "options":[ "The first lncRNA identified in plants was EARLY NODULIN 20 (ENOD20) from the model legume Medicago sativa. ENOD20 participates in the symbiotic interaction with nitrogen-fixing bacteria forming nodules in roots. At the molecular level, ENOD20 was described as an interactor of the nuclear speckle protein RBP1, and it can relocalize its protein partner from the nucleus to the cytoplasm. It was proposed that ENOD20 may be involved in splicing regulation, although this remains unkown. Furthermore, it was shown that ENOD20 can encode small peptides involved in carbom metabolism in the nodules.", "The first lncRNA identified in plants was COOLAIR from the model Arabidopsis thaliana. COOLAIR participates in root development. At the molecular level, COOLAIR was described as an interactor of the nuclear factor FLD, and it can relocalize its protein partner from the nucleus to the cytoplasm. It was proposed that COOLAIR may be involved in splicing regulation, although this remains unkown. Furthermore, it was shown that COOLAIR can encode small peptides involved in carbom metabolism in roots.", "The first lncRNA identified in plants was EARLY NODULIN 40 (ENOD40) from the model legume Medicago truncatula. ENOD40 participates in the symbiotic interaction with nitrogen-fixing bacteria forming nodules in roots. At the molecular level, ENOD40 was described as an interactor of the nuclear speckle protein RBP1, and it can relocalize its protein partner from the nucleus to the cytoplasm. It was proposed that ENOD40 may be involved in splicing regulation, although this remains unkown. Furthermore, it was shown that ENOD40 can encode small peptides involved in carbom metabolism in the nodules." ], "source":"DOI: 10.1002\/j.1460-2075.1994.tb06839.x", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1002\/j.1460-2075.1994.tb06839.x", "Year":1994.0, "Citations":242.0, "answer":2, "source_journal":"The EMBO Journal", "is_expert":true }, { "question":"How does the lncRNA APOLO regulate the locus of the RHD6 gene in Arabidopsis thaliana in response to low temperatures?", "area":"GENE REGULATION - EPIGENETICS AND TGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In response to low temperatures, APOLO levels decrease, leading to effective recruitment of LHP1 from the RHD6 locus, modulating the epigenetic environment of the locus and resulting in the closing of a chromatin loop. APOLO RNA maintains the R-loop structure formed with the RHD6 locus, which has been demonstrated to directly contribute to the transcriptional repression of RHD6. In addition, APOLO participates in the decoy of WRKY42 away from the RHD6 promoter in response to cold. Consequently, RHD6 transcription is enhanced which contributes through downstream genes RSL2\/4 to the promotion of root hair cell expansion. This is reflected in the root phenotype of plants overexpressing and silencing APOLO and WRK42 wherein distinct patterns of root hair are observed compared to the wildtype.", "In response to low temperatures, APOLO levels increase, leading to effective decoying of CLF from the RHD6 locus, modulating the epigenetic environment of the locus and resulting in the opening of a chromatin loop. APOLO RNA maintains the R-loop structure formed with the RHD6 locus, which has been demonstrated to directly contribute to the transcriptional activation of RHD6. In addition, APOLO participates in the recruitment of FRIGIDA to the RHD6 promoter in response to cold. Consequently, RHD6 transcription is enhanced which contributes through downstream genes RSL2\/4 to the promotion of root hair cell expansion. This is reflected in the root phenotype of plants overexpressing and silencing APOLO and FRIGIDA wherein distinct patterns of root hair are observed compared to the wildtype.", "In response to low temperatures, APOLO levels increase, leading to effective decoying of LHP1 from the RHD6 locus, modulating the epigenetic environment of the locus and resulting in the opening of a chromatin loop. APOLO RNA maintains the R-loop structure formed with the RHD6 locus, which has been demonstrated to directly contribute to the transcriptional activation of RHD6. In addition, APOLO participates in the recruitment of WRKY42 to the RHD6 promoter in response to cold. Consequently, RHD6 transcription is enhanced which contributes through downstream genes RSL2\/4 to the promotion of root hair cell expansion. This is reflected in the root phenotype of plants overexpressing and silencing APOLO and WRK42 wherein distinct patterns of root hair are observed compared to the wildtype." ], "source":"DOI: 10.1016\/j.molp.2021.03.008", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.molp.2021.03.008", "Year":2021.0, "Citations":94.0, "answer":2, "source_journal":"Molecular Plant", "is_expert":true }, { "question":"How does the lncRNA VAS1 regulate the TaVRN1 locus in wheat?", "area":"GENE REGULATION - EPIGENETICS AND TGS", "plant_species":[ "Triticum aestivum" ], "options":[ "VAS-mediated repression of the TaVRN1 locus involves the decoy of RF2b. It was shown that winter wheat overexpressing VAS lncRNA early vernalizes compared to wildtype, resulting in differences in inflorescence structures and characteristics. The lncRNA VAS is produced from an alternatively spliced mRNA of TaVRN1 locus, specially repressed during early stages of vernalization. A systematic approach allowed the identification of a range of potential VAS protein interactors, including RF2b, a bZIP TF that together with RF2a form a heterodimer to directly regulate TaVRN1 via an Sp1 motif. It was proposed that before vernalization TaVRN1 and VAS are expressed at a basal level, and the VAS locus is wrapped in a chromatin loop. This loop persists during early vernalization; but VAS transcripts are more numerous and start to associate with RF2b that together with RF2a bind to the TaVRN1 promoter and preclude its expression. Late vernalization represses the opening of the chromatin loop, which releases the Sp1 motif and the full TaVRN1 locus, making all its exons non-accessible to the transcription machinery.", "VAS-mediated activation of the TaVRN1 locus involves the recruitment of RF2b. It was shown that winter wheat overexpressing VAS lncRNA early vernalizes compared to wildtype, resulting in differences in inflorescence structures and characteristics. The lncRNA VAS is produced from an alternatively spliced mRNA of TaVRN1 locus, specially induced during early stages of vernalization. A systematic approach allowed the identification of a range of potential VAS protein interactors, including RF2b, a bZIP TF that together with RF2a form a heterodimer to directly regulate TaVRN1 via an Sp1 motif. It was proposed that before vernalization TaVRN1 and VAS are expressed at a basal level, and the VAS locus is wrapped in a chromatin loop. This loop persists during early vernalization; but VAS transcripts are more numerous and start to associate with RF2b that together with RF2a bind to the TaVRN1 promoter and induce its expression. Late vernalization induces the opening of the chromatin loop, which releases the Sp1 motif and the full TaVRN1 locus, making all its exons accessible to the transcription machinery.", "VAS-mediated activation of the TaVRN1 locus involves the recruitment of REF6. It was shown that winter wheat overexpressing VAS lncRNA early vernalizes compared to wildtype, resulting in differences in inflorescence structures and characteristics. The lncRNA VAS is produced from an alternatively spliced mRNA of TaVRN1 locus, specially induced during late stages of vernalization. A systematic approach allowed the identification of a range of potential VAS protein interactors, including REF6, a TF that together with REF6b form a heterodimer to directly regulate TaVRN1 via an Sp1 motif. It was proposed that before vernalization TaVRN1 and VAS are expressed at a basal level, and the VAS locus is wrapped in a chromatin loop. This loop persists during late vernalization; but VAS transcripts are more numerous and start to associate with REF6 that together with REF6b bind to the TaVRN1 promoter and induce its expression. Late vernalization induces the opening of the chromatin loop, which releases the Sp1 motif and the full TaVRN1 locus, making all its exons accessible to the transcription machinery." ], "source":"DOI:https:\/\/doi.org\/10.1016\/j.molp.2021.05.026", "normalized_plant_species":"Cereal Grains", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.molp.2021.05.026", "Year":2021.0, "Citations":58.0, "answer":1, "source_journal":"Molecular Plant", "is_expert":true }, { "question":"What proteins have been identified as molecular partners of the Arabidopsis lncRNA ASCO? In what molecular mecanism are they all involved in?", "area":"GENE REGULATION - ALTERNATIVE SPLICING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The proteins identified so far as interactors of the lncRNA ASCO are NSRa, PRP8 and SmD1b, which are involved in splicing.", "The proteins identified so far as interactors of the lncRNA ASCO are LHP1 and VIM1, which are involved in epigenetics.", "The proteins identified so far as interactors of the lncRNA ASCO are GRP7, PRP64 and SmD1a, which are involved in splicing." ], "source":"DOI: 10.15252\/embr.201948977", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.15252\/embr.201948977", "Year":2020.0, "Citations":63.0, "answer":0, "source_journal":"EMBO reports", "is_expert":true }, { "question":"What is the molecular mechanism that leads to nitrate-dependent regulation of transcription by the NLP7 transcription factor in Arabidopsis thaliana?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Nitrate resupply triggers the cytosolic accumulation of NLP7 via a nuclear import mechanism. Following a nitrate signal, MAPKs phosphorylate NLP7 in the cytosol and prevent NLP7 nuclear import. In addition direct binding of nitrate to the NLP7 protein is required to inhibit NLP7.", "Nitrate depletion triggers the nuclear accumulation of NLP7 by protein degradation. FProtein phosphate 2A dephosphorylate NLP7 in the cytosol and prevent NLP7 nuclear import. In addition direct binding of nitrate to the C-terminal of the NLP7 protein is required to stabilise NLP7", "Nitrate resupply triggers the nuclear accumulation of NLP7 via a nuclear retention mechanism. Following a nitrate signal, CDKs phosphorylate NLP7 in the nucleus and prevent NLP7 nuclear export. In addition direct binding of nitrate to the NLP7 protein is required to activate NLP7." ], "source":".doi: 10.1016\/j.plantsci.2023.111842.", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.plantsci.2023.111842", "Year":2023.0, "Citations":8.0, "answer":2, "source_journal":"Plant Science", "is_expert":true }, { "question":"The transcription factors NLP7 and NLP2 are major players for the response of A. thaliana to nitrate availability. What are the main differences in the metabolic phenotypes of loss-of-function mutants of either of these proteins?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Specialised metabolism is strongly modified in the nlp2-1 mutant whereas nlp7-1 mutant showed a modified central metabolism in rosettes.", "The nlp2-1 mutant displays changes in nitrate assimilation whereas the nlp7-1 mutant is defected in amino acid degradation.", "Central metabolism is modified in both single mutant nlp2-1 and nlp7-1. Whereas the loss of NLP2 leads to a modification of glycolysis, loss of NLP7 leads to a depletion of TCA cycle intermediates in rosettes." ], "source":"doi: 10.1093\/plcell\/koad025.", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1093\/plcell\/koad025", "Year":2023.0, "Citations":28.0, "answer":2, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"What are the physiological and developmental processes that are regulated by NLP8 in Arabidopsis?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "NLP8 is involved in the regulation of nitrate-regulated seed abortion. In the absence of NLP8, ABA degradation by CYP701A 2 is reduced, because nitrate induction of CYP701A2 protein accumulation is regulated by NLP8.", "NLP8 is involved in the regulation of nitrite-regulated seed germination. In the absence of NLP8, nitrite production by CYP707A 2 is modified, because nitrate induction of CYP707A2 transcript accumulation is regulated by NLP8.", "NLP8 is involved in the regulation of nitrate-regulated seed dormancy. In the absence of NLP8, ABA degradation by CYP707A 2 is reduced, because nitrate induction of CYP707A2 transcript accumulation is regulated by NLP8." ], "source":"DOI: 10.1038\/ncomms13179", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1038\/ncomms13179", "Year":2016.0, "Citations":158.0, "answer":2, "source_journal":"Nature Communications", "is_expert":true }, { "question":"x", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "x", "x", "x" ], "source":"https:\/\/doi.org\/10.1093\/jxb\/eru261", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1093\/jxb\/eru261", "Year":2014.0, "Citations":159.0, "answer":0, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"What protein domain is involved in the interaction of NLP transcription factor in plants?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "non-specific" ], "options":[ "The C-terminal PB1 domain", "The RWP-RK domain", "The N-terminal nitrate-sensing domain" ], "source":"doi: 10.1007\/s00018-019-03164-8.", "normalized_plant_species":"Non-specific", "normalized_area":"GENE REGULATION", "doi":"10.1007\/s00018-019-03164-8", "Year":2019.0, "Citations":71.0, "answer":0, "source_journal":"Cellular and Molecular Life Sciences", "is_expert":true }, { "question":"What is the impact of transposon activity in regulating vitamin E (tocopherols) biosynthesis in tomato fruits?", "area":"GENOME AND GENOMICS", "plant_species":[ "Solanum lycopersicum" ], "options":[ "Vitamin E contents of tomato fruits are regulated, at least in part, at the transcription level of the enzyme encoding genes implicated in its biosynthesis. An insertion of a SINE transposable element in the promotor region of the 2-methyl-6-phytylquinol methyltransferase (namely VTE3(1)) encoding gene that catalyses one of the final steps in the biosynthesis of \u03b3- and \u03b1-tocopherols activates cytosine methylation of this DNA region and silence transcription of the gene through the RdDM mechanism. ", "Vitamin E contents of tomato fruits are regulated, at least in part, at the transcription level of the enzyme encoding genes implicated in its biosynthesis. An insertion of a SINE transposable element in the promotor region of the 2-methyl-6-phytylquinol methyltransferase (namely VTE3(1)) encoding gene that catalyses one of the final steps in the biosynthesis of \u03b3- and \u03b1-tocopherols repress cytosine methylation of this DNA region and repress transcription of the gene through the RdDM mechanism.", "Vitamin E contents of tomato fruits are regulated, at least in part, at the transcription level of the enzyme encoding genes implicated in its biosynthesis. An insertion of a SINE transposable element in the promotor region of the 2-methyl-6-phytylquinol methyltransferase (namely VTE3(1)) encoding gene that catalyses one of the final steps in the biosynthesis of \u03b3- and \u03b1-tocopherols repress cytosine methylation of this DNA region and activate transcription of the gene through the RdDM mechanism. " ], "source":"10.1038\/ncomms5027", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1038\/ncomms5027", "Year":2014.0, "Citations":177.0, "answer":0, "source_journal":"Nature Communications", "is_expert":true }, { "question":"Which mechanism\/s impact environmental conditions through on vitamin E content of tomato fruits?", "area":"GENOME AND GENOMICS", "plant_species":[ "Solanum lycopersicum" ], "options":[ "Controlled environmental conditions (i.e. greenhouse conditions) result in DNA-cytosine demethylation of a SINE TE inserted in the promoter region of the VTE3(1) gene and an activation of its transcription and a consequent increment in the tocopherol levels of the tomato fruits. ", "Uncontrolled environmental conditions (i.e. open field conditions) result in DNA-cytosine demethylation of a SINE TE inserted in the promoter region of the VTE3(1) gene and an activation of its transcription and a consequent increment in the tocopherol levels of the tomato fruits. ", "Uncontrolled environmental conditions (i.e. open field conditions) result in DNA-cytosine methylation of a SINE TE inserted in the promoter region of the VTE3(1) gene and an activation of its transcription and a consequent increment in the tocopherol levels of the tomato fruits. " ], "source":"10.1038\/ncomms5027", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1038\/ncomms5027", "Year":2014.0, "Citations":177.0, "answer":1, "source_journal":"Nature Communications", "is_expert":true }, { "question":"In Arabidopsis, are TEs inserted randomly or towards distinct sets of genes and associated with specific chromatin states? ", "area":"GENOME AND GENOMICS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "At least three kinds of TE, the LTR-retrotransposon ATCOPIA93 and the two DNA transposon families ATENSPM3 and VANDAL21 prefer the euchromatin as substrate for their integrations and more specifically ATCOPIA93 insertions are overrepresented in genes whose body is solely enriched in H2A.Z histone variant.", "At least three kinds of TE, the LTR-retrotransposon ATCOPIA93 and the two DNA transposon families ATENSPM3 and VANDAL21 were found to be randomly inserted across the Arabidopsis genome. ", "At least three kinds of TE, the LTR-retrotransposon ATCOPIA93 and the two DNA transposon families ATENSPM3 and VANDAL21 prefer the heterochromatin as substrate for their integrations and more specifically ATCOPIA93 insertions are underrepresented in genes whose body is solely enriched in H2A.Z histone variant." ], "source":"https:\/\/doi.org\/10.1038\/s41467-019-11385-5", "normalized_plant_species":"Model Organisms", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1038\/s41467-019-11385-5", "Year":2019.0, "Citations":145.0, "answer":0, "source_journal":"Nature Communications", "is_expert":true }, { "question":"Which are the most abundant mobile genetic elements in the plant genomes?", "area":"GENOME AND GENOMICS", "plant_species":[ "non-specific" ], "options":[ "In general, class II (DNA TEs) are more prevalent in plant genomes.", "Both kinds of TEs (RNA for class I (retrotransposons), and DNA for class II (DNA TEs)) can be equally distributed along plant genomes ", "In general, class I elements (retrotransposons) are more prevalent in genomes as their \u2018copy and paste\u2019 replicative transposition leads to an increase in copy number as they transpose. Among them, Long Terminal Repeat Retrotransposons (LTR-RTs) are the most abundant in plant genomes. " ], "source":"https:\/\/doi.org\/10.1016\/j.pbi.2023.102418", "normalized_plant_species":"Non-specific", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1016\/j.pbi.2023.102418", "Year":2023.0, "Citations":22.0, "answer":2, "source_journal":"Current Opinion in Plant Biology", "is_expert":true }, { "question":"Which are the most abundant gene-proximal TE in plant genomes?", "area":"GENOME AND GENOMICS", "plant_species":[ "non-specific" ], "options":[ "Gypsy, Copia and LINE make up about 80% of all gene-proximal TEs ", "The most abundant TE family adjacent to genes are Helitron and MuDR, summing up to about 70% of all gene-proximal TEs ", "There is not a general pattern of TE abundancy for plant genomes. This depends on the plant species" ], "source":"https:\/\/doi.org\/10.1186\/s12864-021-08215-8", "normalized_plant_species":"Non-specific", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1186\/s12864-021-08215-8", "Year":2022.0, "Citations":31.0, "answer":2, "source_journal":"BMC Genomics", "is_expert":true }, { "question":"Which transcription factor has been found to be requiered for chromatin spatial reorganization in response to heat stress in tomato?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Solanum lycopersicum" ], "options":[ "HSFA1A was demonstrated to be required for chromatin spatial reorganization in response to heat stress in tomato", "TCP15 was demonstrated to be required for chromatin spatial reorganization in response to heat stress in tomato", "HSFA1A was not demonstrated to be required for chromatin spatial reorganization in response to heat stress in tomato" ], "source":"doi: 10.1038\/s41467-023-36227-3", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41467-023-36227-3", "Year":2023.0, "Citations":59.0, "answer":0, "source_journal":"Nature Communications", "is_expert":true }, { "question":"What is the impact of an ectopic deposition of H3K9ac on TAD-like boundaries in tomato?", "area":"GENE REGULATION - EPIGENETICS AND TGS", "plant_species":[ "Solanum lycopersicum" ], "options":[ "The ectopic deposition of H3K9ac do not impact chromatin 3D structure and TAD like boundaries", "The ectopic deposition of H3K9ac triggered a reorganization of the 3D chromatin structure and plays a major role in the determination of TAD-like boundaries", "The ectopic deposition of H3K123 triggered a reorganization of the 3D chromatin structure and plays a major role in the determination of TAD-like boundaries" ], "source":"doi: 10.1073\/pnas.2400737121", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"GENE REGULATION", "doi":"10.1073\/pnas.2400737121", "Year":2024.0, "Citations":0.0, "answer":1, "source_journal":"Proceedings of the National Academy of Sciences", "is_expert":true }, { "question":"How is the wheat chromatin architecture organized?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Triticum aestivum" ], "options":[ "The wheat chromatin architecture is organized around long non coding RNA", "The wheat chromatin architecture is organized in genome territories and transcription factories ", "The wheat chromatin architecture is organized in epigenetics territories and translation factories " ], "source":"doi: 10.1186\/s13059-020-01998-1", "normalized_plant_species":"Cereal Grains", "normalized_area":"GENE REGULATION", "doi":"10.1186\/s13059-020-01998-1", "Year":2020.0, "Citations":119.0, "answer":1, "source_journal":"Genome Biology", "is_expert":true }, { "question":"Which histone demethylase controls H3K27me1 homeostasis in Arabidopsis thaliana euchromatin?", "area":"GENE REGULATION - EPIGENETICS AND TGS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "REF6 controls H3K27me1 homeostasis in euchromatin", "LHP1 controls H3K27me1 homeostasis in euchromatin", "CLF controls H3K27me1 homeostasis in euchromatin" ], "source":"doi: 10.7554\/eLife.58533", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.7554\/eLife.58533", "Year":2020.0, "Citations":41.0, "answer":0, "source_journal":"eLife", "is_expert":true }, { "question":"How GCN5 modulates salicylic acid homeostasis?", "area":"GENE REGULATION - TRANSCRIPTION", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "GCN5 modulates salicylic acid homeostasis by regulating H3K27me3 levels at the 5' and 3' ends of its target genes ", "GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5' and 3' ends of intron ", "GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5' and 3' ends of its target genes " ], "source":"doi: 10.1093\/nar\/gkaa369", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1093\/nar\/gkaa369", "Year":2020.0, "Citations":61.0, "answer":2, "source_journal":"Nucleic Acids Research", "is_expert":true }, { "question":"What are the general characteristics and architecture of the genomes of virus members of family Rhabdoviridae?", "area":"GENOME AND GENOMICS", "plant_species":[ "non-specific" ], "options":[ "The genomes of rhabdoviruses are negative-sense and single-stranded RNA of approximately 10\u201316 kb, including monosegmented, bi segmented and tri segmented members. Most rhabdovirus genomes have five genes encoding the structural proteins (N, P, M, G and L) with variations and additional genes and only the N and L genes are present in all rhabdoviruses.", "The genomes of rhabdoviruses are negative-sense and double-stranded RNA of approximately 10\u201316 kb, including monosegmented, bi segmented and tri segmented members. Most rhabdovirus genomes have five genes encoding the structural proteins (N, P, M, G and L) with variations and additional genes and only the N and L genes are present in all rhabdoviruses.", "The genomes of rhabdoviruses are negative-sense and single-stranded RNA of approximately 10\u201316 kb, including monosegmented and bi segmented members. Most rhabdovirus genomes have five genes encoding the structural proteins (N, P, M, G and L) with variations and additional genes and only the G and L genes are present in all rhabdoviruses." ], "source":"https:\/\/doi.org\/10.3390\/v15122402 https:\/\/doi.org\/10.1099\/jgv.0.001689", "normalized_plant_species":"Non-specific", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1099\/jgv.0.001689", "Year":2022.0, "Citations":92.0, "answer":0, "source_journal":"Journal of General Virology", "is_expert":true }, { "question":"What viruses are linked to the corn leafhopper (Dalbulus maidis)?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Zea mays" ], "options":[ "The corn leafhopper is the vector of two viruses: maize rayado fino virus and maize striate mosaic virus and has also been reported to be linked to five insect specific DNA viruses: a beny-like virus (Benyviridae), a bunya-like virus (Bunyaviridae), a iflavirus (Iflaviridae), a orthomyxo-like virus (Orthomyxoviridae), and a rhabdovirus (Rhabdoviridae)", "The corn leafhopper is the vector of two viruses: maize rayado fino virus and maize striate mosaic virus and has also been reported to be linked to six insect specific RNA viruses: a beny-like virus (Benyviridae), a bunya-like virus (Bunyaviridae), two iflaviruses (Iflaviridae), a orthomyxo-like virus (Orthomyxoviridae), and a rhabdovirus (Rhabdoviridae)", "The corn leafhopper is the vector of maize rayado fino virus and has also been reported to be linked to six insect specific RNA viruses: a beny-like virus (Benyviridae), a bunya-like virus (Bunyaviridae), a iflavirus (Iflaviridae), two orthomyxo-like viruses (Orthomyxoviridae), and a rhabdovirus (Rhabdoviridae)" ], "source":"https:\/\/doi.org\/10.3390\/v16101583", "normalized_plant_species":"Cereal Grains", "normalized_area":"ENVIRONMENT", "doi":"10.3390\/v16101583", "Year":2024.0, "Citations":0.0, "answer":1, "source_journal":"Viruses", "is_expert":true }, { "question":"What are the hosts of ophioviruses?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "Ophioviruses infect both monocots and dicots, mostly trees, shrubs and some ornamentals and have recently been linked to been linked to white flies, mosses, liverworts and ferns. ", "Ophioviruses infect both monocots and dicots, mostly trees, shrubs and some ornamentals and have recently been linked to mosses, liverworts and ferns.", "Ophioviruses infect both monocots and dicots, mostly trees, shrubs and some ornamentals." ], "source":"https:\/\/doi.org\/10.3390\/v15040840", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.3390\/v15040840", "Year":2023.0, "Citations":9.0, "answer":1, "source_journal":"Viruses", "is_expert":true }, { "question":"Which viruses infect the 'living fossil' gymnosperm Welwitschia mirabilis, and how are they transmitted?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Welwitschia mirabilis" ], "options":[ "Welwitschia mirabilis is infected with caulimoviruses and geminiviruses and we do not know how they are transmitted.", "Welwitschia mirabilis is infected with caulimoviruses and geminiviruses which are transmitted by aphids and white flies, respectively.", "Welwitschia mirabilis is infected with caulimoviruses which are transmitted by aphids." ], "source":"https:\/\/doi.org\/10.1016\/j.gene.2022.146806", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.gene.2022.146806", "Year":2022.0, "Citations":6.0, "answer":0, "source_journal":"Gene", "is_expert":true }, { "question":"What are the characteristics of koshoviruses and their genomes?", "area":"GENOME AND GENOMICS", "plant_species":[ "non-specific" ], "options":[ "Koshoviruses are plant infecting viruses with long monosegmented RNA genomes of 21-23 kb with similarities to the animal linked flavoviruses. They encode two large polyproteins with a helicase and RNA-dependent RNA polymerase and several additional divergent domains, including AlkB oxygenase, trypsin-like serine protease, methyltransferase, and envelope E1 flavi-like domains.", "Koshoviruses are plant infecting viruses with long monosegmented RNA genomes of 21-23 kb with similarities to the animal linked flaviviruses. They encode a single large polyprotein with a helicase and RNA-dependent RNA polymerase and several additional divergent domains, including AlkB oxygenase, trypsin-like serine protease, methyltransferase, and envelope E1 flavi-like domains.", "Koshoviruses are plant infecting viruses with long bisegmented RNA genomes of 21-23 kb with similarities to the animal linked flaviviruses. They encode two large polyprotein with a helicase and RNA-dependent DNA polymerase and several additional divergent domains, including AlkB oxygenase, trypsin-like serine protease, methyltransferase, and envelope E1 flavi-like domains." ], "source":"https:\/\/link.springer.com\/article\/10.1007\/s00705-023-05813-7", "normalized_plant_species":"Non-specific", "normalized_area":"GENOME AND GENOMICS", "doi":"10.1007\/s00705-023-05813-7", "Year":2023.0, "Citations":15.0, "answer":1, "source_journal":"Archives of Virology", "is_expert":true }, { "question":"Which membrane proteins have been involved in the transport of UDP-xylose during the biosynthesis of xylan?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The membrane proteins involved in the biosynthesis of xylan are the xylose transporters.", "The membrane proteins involved in the transport of UDP-xylose for the biosynthesis of xylan are the UDP-xylose transporters.", "The sugar translocators are the membrane proteins that have been involved in the biosynthesis of xylan." ], "source":"https:\/\/doi.org\/10.1093\/jxb\/erx448", "normalized_plant_species":"Model Organisms", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1093\/jxb\/erx448", "Year":2017.0, "Citations":25.0, "answer":1, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"How does the biosynthesis of the rhamnogalacturonan backbone structure is made in the Golgi apparatus?", "area":"CELL BIOLOGY AND CELL SIGNALING", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The biosynthesis of rhamnogalacturonan backbone requires the substrates UDP\u00b4galacturonic acid and UDP-rhamnose. These nucleotide sugars are utilized by the rhamnosyltransferase (RRT) and the RGI-Galacturonosyltransferase (RGGAT) to make the alternating backbone structure.", "The biosynthesis of the rhamnogalacturonan I backbone is carried out by a glycosyltransferase that has the capacity to transfer in an alternate manner rhamnose and galacturonic acid into the elongating polymer.", "The biosynthesis of the rhamnogalacturonan I backbone requires the sugars rhamnose and galacturonic acid. These sugars are utilized by the rhamnosyltransferase (RRT) and the RGI-Galacturonosyltransferase (RGGAT) to make the alternating backbone structure." ], "source":"https:\/\/doi.org\/10.1038\/s41477-022-01270-3", "normalized_plant_species":"Model Organisms", "normalized_area":"CELL BIOLOGY AND CELL SIGNALING", "doi":"10.1038\/s41477-022-01270-3", "Year":2022.0, "Citations":24.0, "answer":0, "source_journal":"Nature Plants", "is_expert":true }, { "question":"Why CAM plants are becoming interesting subjects to study as climate change challenges increase?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "non-specific" ], "options":[ "One of the major challenges of climate change is drought. Understanding how plants can be more efficient in water use efficiency (WUE) becomes an interesting aspect. CAM plants are very efficient in WUE and can save up to 40% water. Transferring this capacity to C3 plants could result in crops that need less water to thrive.", "CAM plants capture CO2 at night and convert it to citric acid, which is efficiently used in the Calvin cycle. In this way, CAM plants can capture more CO2 from the atmosphere, thus helping to reduce the greenhouse effect on Earth and the rise in temperature that is one of the causes of climate change.", "Climate change is a major threat to agriculture, and the use of crops that can better cope with the challenges of climate change is emerging as a possible solution. In this regard, CAM crops have an increased capacity to cope with higher temperatures and flooding; thus, they emerge as good candidates to replace the current crops used in agriculture." ], "source":"https:\/\/doi.org\/10.1111\/nph.13393", "normalized_plant_species":"Non-specific", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/nph.13393", "Year":2015.0, "Citations":191.0, "answer":0, "source_journal":"New Phytologist", "is_expert":true }, { "question":"Softening of fruits is a trait that is highly appreciated in certain fuit such as tomatos. Understanding this process can be a way to extend shelf life of these fruits. On these regard what are the genes involved in this process that may be putative targets for creating new varieties?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Solanum lycopersicum" ], "options":[ "The cuticle is an important part of the tomato fruit. It is composed of complex lipids that provide a firm structure. The best way to obtain tomatoes with extended shelf life is to increase the biosynthesis of these complex lipids. Then, gene editing of the genes involved in cuticle biosynthesis should lead to extended shelf life of tomatoes.", "The genes that code for cell wall degradation, such as expansin and polygalacturonase, appear to play an important role in the softening of tomato fruit and could be good candidates for a gene editing strategy aimed at producing tomatoes with an extended shelf life.", "The tomato cell wall is very important in the softening process of the fruit. Cellulose and lignin are important components of the tomato fruit cell wall, therefore increasing the biosynthesis of genes coding for these structures may lead to extended shelf life in tomato fruit." ], "source":"https:\/\/doi.org\/10.1016\/j.copbio.2022.102786", "normalized_plant_species":"Solanaceae & Relatives", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1016\/j.copbio.2022.102786", "Year":2022.0, "Citations":28.0, "answer":1, "source_journal":"Current Opinion in Biotechnology", "is_expert":true }, { "question":"Plants appear to be an alternative for the massive production of N-glycoproteins of pharmaceutical interest. However, sialic acid is a critical sugar in animal N-glycoproteins that is not present in plant N-glycoproteins. Why do plants not have sialic acid in their N-glycoproteins?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The biosynthesis of N-glycoproteins and the incorporation of sialic acid takes place in the lumen of the Golgi apparatus, and a CMP-sialic acid transporter is required to incorporate the substrate needed for the reaction. Plants do not have this transporter; therefore, the substrate does not have access to the compartment where sialic acid incorporation takes place.", "Plants synthesize glycoproteins and the modifications that occur in the N-glycan structure in the Golgi apparatus do not include sialic acid because the substrate is not produced in plants, therefore plant N-glycoproteins cannot receive this critical modification needed in animal cells.", "The incorporation of sialic acid into N-glycoproteins requires a very specific enzyme that uses CMP-sialic acid to catalyze the incorporation of sialic acid into the N-glycan. The gene encoding this enzyme is missing in plants; therefore, this reaction cannot take place. " ], "source":"https:\/\/doi.org\/10.1038\/nbt1104-1351", "normalized_plant_species":"Model Organisms", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1038\/nbt1104-1351", "Year":2004.0, "Citations":58.0, "answer":1, "source_journal":"Nature Biotechnology", "is_expert":true }, { "question":"How many YTHDF proteins are there in Arabidopsis thaliana?", "area":"GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "There are 13 YTHDF proteins in Arabidopsis, called ECT1-ECT12 and CPSF30. ", "There are 11 YTHDF proteins in Arabidopsis, called ECT1-ECT11. \n", "There are 12 YTHDF proteins in Arabidopsis, called ECT1-ECT12." ], "source":"https:\/\/doi.org\/10.1105\/tpc.17.00854", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1105\/tpc.17.00854", "Year":2018.0, "Citations":239.0, "answer":1, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"Which biological functions of m6A have been ascribed to the different YTHDF proteins in Arabidopsis thaliana?", "area":"GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The best studied YTHDF protein in Arabidopsis thaliana is ECT2. Together with ECT3 and ECT4, ECT2 controls the morphogenesis of different plant organs, including leaves, trichomes, flowers, pods and roots. Additionally, ECT2, ECT3, ECT4 and ECT5 are necessary for resistance against alfalfa mosaic virus. Recent reports indicate that ECT8 is involved in the response to salinity stress and regulates SA signalling, and ECT1 is involved in stress responses mediated by the phytohormone abscisic acid.", "The best studied YTHDF protein in Arabidopsis thaliana is ECT2. Together with ECT3 and ECT4, ECT2 controls the morphogenesis of different plant organs, including leaves, leaf hairs, flowers, fruits and roots. Additionally, ECT2, ECT3, ECT4 and ECT5 are necessary for resistance against at least one RNA virus. Recent reports indicate that ECT8 is involved in the response to salinity stress and regulates ABA signalling, and ECT1 is involved in stress responses mediated by the phytohormone salicylic acid.", "The best studied YTHDF protein in Arabidopsis thaliana is ECT3. Together with ECT2 and ECT4, ECT3 controls the morphogenesis of different plant organs, including leaves, trichomes, flowers, siliques and roots. Additionally, ECT2, ECT3, ECT4 and ECT5 are necessary for resistance against at least one DNA virus. Recent reports indicate that ECT8 is involved in the response to cold stress and regulates ABA signalling, and ECT9 is involved in stress response mediated by the phytohormone salicylic acid." ], "source":"https:\/\/doi.org\/10.1016\/j.pbi.2024.102650", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.pbi.2024.102650", "Year":2024.0, "Citations":3.0, "answer":1, "source_journal":"Current Opinion in Plant Biology", "is_expert":true }, { "question":"Which protein(s) interact with the m6A reader ECT2 in Arabidopsis thaliana?", "area":"GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Arabidopsis thaliana ECT2 interacts with several members of the ALBA and poly(A)-binding protein (PABP) families.\n", "Arabidopsis thaliana ECT2 interacts with the cleavage and polyadenylation complex factor CPSF30 through the YTH domains.\n", "Arabidopsis thaliana ECT2 interacts with the DCP5 component of the decapping complex in phase-separated stress granules.\n" ], "source":"https:\/\/doi.org\/10.1016\/j.pbi.2024.102650", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1016\/j.pbi.2024.102650", "Year":2024.0, "Citations":3.0, "answer":0, "source_journal":"Current Opinion in Plant Biology", "is_expert":true }, { "question":"Is HAKAI essential for m6A deposition and development in Arabidopsis thaliana?", "area":"GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Although HAKAI is one of the subunits of the m6A methyltransferase complex, its deficiency leads only to a mild reduction of m6A deposition in Arabidopsis. That is why, despite the fact that complete m6A deficiency causes arrest of embryo development, homozygous HAKAI mutants are viable and similar to wild type plants. ", "HAKAI is one of the subunits of the m6A methyltransferase complex and, as such, it is essential for m6A deposition in Arabidopsis. Because complete m6A deficiency causes arrest of embryo development, homozygous loss of function mutation of HAKAI is lethal; the embryo cannot pass the globular stage", "HAKAI is one of the subunits of the m6A methyltransferase complex and, as such, it is essential for m6A deposition in Arabidopsis. However, beecause m6A regulates stress responses and it is not necessary for plant development, homozygous HAKAI mutants are viable and similar to wild type plants.\n" ], "source":"https:\/\/doi.org\/10.1111\/nph.14586", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1111\/nph.14586", "Year":2017.0, "Citations":377.0, "answer":0, "source_journal":"New Phytologist", "is_expert":true }, { "question":"How does ECT8 regulate ABA signalling?", "area":"GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "ECT8 binds to the methylated site URUm6AY in the 3\u2019UTR of the mRNA of the ABA signaling factor PYL7, thereby preventing its degradation by re-localization to p-bodies.\n", "ECT8 binds to the methylated site RRm6ACH in the 3\u2019UTR of the mRNA of the ABA signaling factor PYRABACTIN RESISTANCE 1-LIKE 7, thereby promoting its translation.\n", "ECT8 binds to the methylated site ATTTm6ACGCA in the 3\u2019UTR of the mRNA of the ABA signaling factor PYL7, thereby preventing its translation by sequestration in stress granules." ], "source":"https:\/\/doi.org\/10.1038\/s41477-024-01638-7", "normalized_plant_species":"Model Organisms", "normalized_area":"GENE REGULATION", "doi":"10.1038\/s41477-024-01638-7", "Year":2024.0, "Citations":32.0, "answer":2, "source_journal":"Nature Plants", "is_expert":true }, { "question":"How do PME activity and OG release during homogalacturonan remodeling affect Arabidopsis thaliana defenses against Myzus persicae, and which hormone signaling pathways are involved?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Increased PME activity during Myzus persicae infestation promotes homogalacturonan de-methylesterification, facilitating oligogalacturonides (OG) release. OGs trigger pattern-triggered immunity (PTI) by inducing ROS accumulation, callose deposition, and salicylic acid (SA) signaling activation, reducing aphid feeding performance and reproduction. However, PME inhibition or PMEI13 upregulation reduces OG release and weakens defenses.", "Increased PME activity during Myzus persicae infestation inhibits homogalacturonan de-methylesterification, reducing oligogalacturonides (OG) release. OGs suppress pattern-triggered immunity (PTI), including ROS accumulation, callose deposition, and salicylic acid (SA) signaling activation, increasing aphid feeding performance and reproduction. PME inhibition or PMEI13 upregulation enhances OG release and strengthens defenses", "Decreased PME activity during Myzus persicae infestation promotes homogalacturonan de-methylesterification, facilitating oligogalacturonides (OG) release. OGs trigger pattern-triggered immunity (PTI) by inducing ROS accumulation, callose deposition, and salicylic acid (SA) signaling activation, reducing aphid feeding performance and reproduction. However, PME inhibition or PMEI13 upregulation reduces OG release and weakens defenses." ], "source":"10.1105\/tpc.19.00136", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1105\/tpc.19.00136", "Year":2019.0, "Citations":53.0, "answer":0, "source_journal":"The Plant Cell", "is_expert":true }, { "question":"How do the dynamics of Pectin Methylesterases activity and OG-triggered defenses influence the interaction between Arabidopsis thaliana and Myzus persicae, and what molecular mechanisms mediate these effects?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Pectin Methylesterases activity increases during Myzus persicae infestation, driving homogalacturonan de-methylesterification, which facilitates oligogalacturonides (OG) release. OGs activate PTI by promoting ROS accumulation, callose deposition, and SA signaling, enhancing plant resistance by reducing aphid feeding efficiency and reproduction. PME inhibition or PMEI13 upregulation reduces OG-mediated defenses, increasing susceptibility to aphids.", "Pectin Methylesterases activity decreases during Myzus persicae infestation, driving homogalacturonan de-methylesterification, which facilitates oligogalacturonides (OG) release. OGs activate PTI by promoting ROS accumulation, callose deposition, and SA signaling, enhancing plant resistance by reducing aphid feeding efficiency and reproduction. PME inhibition or PMEI13 upregulation reduces OG-mediated defenses, increasing susceptibility to aphids.", "Pectin Methylesterases activity increases during Myzus persicae infestation, suppressing homogalacturonan de-methylesterification and oligogalacturonides (OG) release. OGs inhibit PTI by reducing ROS accumulation, callose deposition, and SA signaling, weakening plant resistance and increasing aphid feeding efficiency and reproduction. PME inhibition or PMEI13 upregulation enhances these defenses, reducing susceptibility to aphids" ], "source":"10.3390\/ijms23179753", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.3390\/ijms23179753", "Year":2022.0, "Citations":9.0, "answer":0, "source_journal":"International Journal of Molecular Sciences", "is_expert":true }, { "question":"How the transcription factors WRKY7, WRKY11 and WRKY17 act during the interaction between Arabidopsis thaliana and Pseudomonas syringae pv. tomato (Pst) DC3000 and which hormone signaling pathways are mainly involved?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "In Arabidopsis thaliana, the transcription factors WRKY7, WRKY11 and WRKY17 act as negative defence regulators against Pseudomonas syringae pv. tomato (Pst) DC3000. These transcription factors induce genes related to the biosynthesis and signalling of the jasmonic acid (JA) pathway.", "In Arabidopsis thaliana, the transcription factors WRKY7, WRKY11 and WRKY27 act as negative defence regulators against Pseudomonas syringae pv. tomato (Pst) DC3000. These transcription factors supress genes related to the biosynthesis and signalling of the jasmonic acid (JA) pathway.", "In Arabidopsis thaliana, the transcription factors WRKY7, WRKY11 and WRKY17 act as negative defence regulators against Botrytis cinerea. These transcription factors induce genes related to the biosynthesis and signalling of the jasmonic acid (JA) pathway." ], "source":"10.1111\/mpp.70044", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1111\/mpp.70044", "Year":2024.0, "Citations":0.0, "answer":0, "source_journal":"Molecular Plant Pathology", "is_expert":true }, { "question":"How the root specific syntaxin 123 (SYP123) is involved in the Arabidopsis thaliana defense response?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "The syntaxin SYP123 is involved in the polarized localization of PRP3 protein and polysaccharides in growing root hairs and this activity contribute to the establishment of effective plant defense responses.", "The syntaxin SYP123 is involved in the polarized localization of protein and lipids in growing root hairs and this activity contribute to the establishment of effective plant defense responses.", "The syntaxin SYP132 is involved in the polarized localization of PRP3 protein and polysaccharides in growing root hairs and this activity contribute to the establishment of effective plant defense responses." ], "source":"10.3389\/fpls.2016.01081", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.3389\/fpls.2016.01081", "Year":2016.0, "Citations":14.0, "answer":0, "source_journal":"Frontiers in Plant Science", "is_expert":true }, { "question":"What is an oligogalacturonide and its function during the feeding performance and population of Myzus persicae over Arabidopsis thaliana? Which mechanisms are involved?", "area":"ENVIRONMENT - BIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Oligogalacturonides (OGs) are pectin-derived molecules. OG treatments of Arabidopsis thaliana decrease their resistance to Myzus persicae infestation by reducing the number of offspring and feeding performance. Furthermore, this enhanced resistance was related to diminished callose accumulation and reactive oxygen species and activation of the salicylic acid signaling pathway.", "Oligogalacturonides (OGs) are pectin-derived molecules. OG treatments of Arabidopsis thaliana increase their resistance to Myzus persicae infestation by reducing the number of offspring and feeding performance. Furthermore, this enhanced resistance was related to a substantial accumulation of callose and reactive oxygen species and activation of the salicylic acid signaling pathway.", "Oligogalacturonides (OGs) are cellulose-derived molecules. OG treatments of Arabidopsis thaliana increase their resistance to Myzus persicae infestation by reducing the number of offspring and feeding performance. Furthermore, this enhanced resistance was related to diminished callose accumulation and reactive oxygen species and activation of the salicylic acid signaling pathway." ], "source":"10.3390\/ijms23179753", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.3390\/ijms23179753", "Year":2022.0, "Citations":9.0, "answer":1, "source_journal":"International Journal of Molecular Sciences", "is_expert":true }, { "question":"How does the mitochondrial protein AtOXR2 influence plant growth and biomass production in Arabidopsis thaliana?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Constitutively overexpression of AtOXR2 in Arabidopsis plants decreases basal ROS levels, which act as signalling molecules, improve the efficiency of photosynthesis and elicit tolerance to oxidative stress, allowing improved plant growth and biomass production. ", "Constitutively overexpression of AtOXR2 in Arabidopsis plants increases basal ROS levels, which act as signalling molecules that induce Gibberellin and auxin regulatory-growth pathways, improving the efficiency of photosynthesis and elicit tolerance to oxidative stress, allowing improved plant growth and biomass production", "Constitutively overexpression of AtOXR2 in Arabidopsis plants increases basal ROS levels, which act as signalling molecules, improve the efficiency of photosynthesis and elicit tolerance to oxidative stress, allowing improved plant growth and biomass production." ], "source":"10.1093\/jxb\/erz147", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1093\/jxb\/erz147", "Year":2019.0, "Citations":15.0, "answer":2, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"How does CYTc deficiency affect mitochondrial function and TOR-pathway activation in plants?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Plants with CYTc deficiency exhibit decreased mitochondrial membrane potential and lower ATP content, even in the presence of carbon sources. CYTc deficiency reduces target of rapamycin (TOR)-pathway activation, leading to reduced phosphorylation of S6 kinase (S6K) and RPS6A, as well as lower total S6K protein levels, due to increased protein degradation via the proteasome and autophagy. Thus, CYTc-deficient plants coordinate their metabolism and energy availability by downregulating TOR-pathway activation as a preventive signal to adjust growth in anticipation of energy exhaustion.", "Plants with CYTc deficiency exhibit increased mitochondrial membrane potential and ATP content, even in the presence of carbon sources. CYTc deficiency induces target of rapamycin (TOR)-pathway activation, leading to reduced phosphorylation of S6 kinase (S6K) and RPS6A, as well as lower total S6K protein levels, due to increased protein degradation via the proteasome and autophagy. Thus, CYTc-deficient plants coordinate their metabolism and energy availability by upregulating TOR-pathway activation as a preventive signal to adjust growth in anticipation of energy exhaustion.", "Plants with CYTc deficiency exhibit decreased mitochondrial membrane potential and lower ATP content, only in the presence of carbon sources. CYTc deficiency reduces target of rapamycin (TOR)-pathway activation, leading to an increment in the phosphorylation of S6 kinase (S6K) and RPS6A, as well as higher total S6K protein levels, due to reduced protein degradation via the proteasome and autophagy. Thus, CYTc-deficient plants coordinate their metabolism and energy availability by downregulating TOR-pathway activation as a preventive signal to adjust growth in anticipation of energy exhaustion." ], "source":"10.1111\/nph.19506", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1111\/nph.19506", "Year":2024.0, "Citations":6.0, "answer":0, "source_journal":"New Phytologist", "is_expert":true }, { "question":"How does cytochrome c deficiency affect seed germination, and the sensitivity to ABA in Arabidopsis?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Cytochrome c deficiency causes delayed seed germination and the sensitivity of germination to ABA, which negatively regulates the expression of CYTC-2, one of two CYTc-encoding genes in Arabidopsis. CYTC-2 acts downstream of the transcription factor ABSCISIC ACID INSENSITIVE 4 (ABI4), which binds to a region of the CYTC-2 promoter required for repression by ABA decreasing its expression. ", "Cytochrome c deficiency causes delayed seed germination and the sensitivity of germination to ABA, which positively regulates the expression of CYTC-2, one of two CYTc-encoding genes in Arabidopsis. CYTC-2 acts downstream of the transcription factor ABSCISIC ACID INSENSITIVE 4 (ABI4), which binds to a region of the CYTC-2 promoter required for repression by ABA increasing its expression. ", "Cytochrome c deficiency causes improved seed germination and the sensitivity of germination to ABA and GAs, which negatively regulate the expression of CYTC-2, one of two CYTc-encoding genes in Arabidopsis. CYTC-2 acts upstream of the transcription factor ABSCISIC ACID INSENSITIVE 4 (ABI4), which binds to a region of the CYTC-2 promoter required for repression by ABA decreasing its expression" ], "source":"10.1111\/nph.18287", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1111\/nph.18287", "Year":2022.0, "Citations":9.0, "answer":0, "source_journal":"New Phytologist", "is_expert":true }, { "question":"How does reduced levels of CYTc in Arabidopsis affect the stability and function of mitochondrial respiratory complexes?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Reduced level of cytochrome c increases stability of Complex IV, affecting Complexes I and III stability and function. This modifies redox metabolism and improves mitochondrial respiration.", "Reduced level of cytochrome c decreases stability of Complex IV, affecting Complexes I and III stability and function. This modifies redox metabolism and reduces mitochondrial respiration.", "Reduced level of cytochrome c decreases stability of Complex IV without affecting Complexes I and III stability and function. This modifies redox metabolism and reduces mitochondrial respiration." ], "source":"10.1016\/j.bbabio.2012.04.008", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1016\/j.bbabio.2012.04.008", "Year":2012.0, "Citations":46.0, "answer":2, "source_journal":"Biochimica et Biophysica Acta (BBA) - Bioenergetics", "is_expert":true }, { "question":"What is the mechanism by which overexpression of the OXR2 protein induces a basal defense against hemibiotrophic pathogens?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "AtOXR2 affects the nuclear localization of the transcriptional coactivator NPR1. OXR2 (oeOXR2 plants) show enhanced disease resistance, have increased levels of total glutathione and a more oxidized cytosolic redox cellular environment under normal growth conditions. Resistance in these plants is accompanied by higher expression of WRKY transcription factors, induction of genes involved in salicylic acid (SA) synthesis, accumulation of free SA, and overall activation of the SA signaling pathway. ", "AtOXR2 reduces the nuclear localization of the transcriptional coactivator NPR1. OXR2 (oeOXR2 plants) show enhanced disease resistance, have increased levels of total glutathione and a more oxidized cytosolic redox cellular environment under normal growth conditions. Resistance in these plants is accompanied by lower expression of WRKY transcription factors, reduction of genes involved in salicylic acid (SA) synthesis, reduced accumulation of free SA, and overall inactivation of the SA signaling pathway. ", "AtOXR2 affects the nuclear localization of the transcriptional coactivator NPR1. OXR2 (oeOXR2 plants) show enhanced disease resistance, have reduced levels of total glutathione and a more reduced cytosolic redox cellular environment under normal growth conditions. Resistance in these plants is accompanied by higher expression of WRKY transcription factors, induction of genes involved in salicylic acid (SA) synthesis, accumulation of free SA, and overall activation of the SA signaling pathway. " ], "source":"10.1104\/pp.19.01351", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1104\/pp.19.01351", "Year":2020.0, "Citations":21.0, "answer":0, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"What is the role of lncRNA DANA1 in Arabidopsis thaliana responses to drought stress, and what proteins have been identified as its molecular partners?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Drought-induced lncRNA DANA1 is a positive regulator of drought tolerance in Arabidopsis thaliana, and mediates stomata closure of Arabidopsis plants in response to drought. DIP1, a L1p\/L10e family member protein, can interact with DANA1 both in vitro and in vivo. Loss of either DANA1 or DIP1, could result in the decrease of ABA content in Arabidopsis thaliana (by CYP707A1 and CYP707A2).", "Drought-induced lncRNA DANA1 is a postive regulator of drought tolerance in Arabidopsis thaliana, and mediates root development of Arabidopsis plants in response to drought. DIP1, a transcription factor, can interact with DANA1 both in vitro and in vivo. Loss of either DANA1 or DIP1, could result in the decrease of ABA content in Arabidopsis thaliana (by CYP707A1 and CYP707A2).", "Drought-induced lncRNA DANA1 is a negative regulator of drought tolerance in Arabidopsis thaliana, and mediates stomata closure of Arabidopsis plants in response to drought. DIP1, a L1p\/L10e family member protein, can interact with DANA1 both in vitro and in vivo. Loss of either DANA1 or DIP1, could result in the increase of ABA content in Arabidopsis thaliana (by NCED3 and NCED5)." ], "source":"10.1038\/s44319-023-00030-4", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1038\/s44319-023-00030-4", "Year":2024.0, "Citations":4.0, "answer":0, "source_journal":"EMBO Reports", "is_expert":true }, { "question":"What is the role of lncRNA DANA2 in Arabidopsis thaliana responses to drought stress, and what proteins have been identified as its molecular partners?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "LncRNA DANA2 postively regulates drought stress responses through JMJ29 in Arabidopsis thaliana, and JMJ29 can positively regulate the expression of two positve regulators of proline synthesis and drought stress response, ERF15 and GOLS2. ERF84, a chromatic epigenetic regulator, not only binds specifically to DANA2, but also promotes the transcription of JMJ29 by binding to its exon.", "LncRNA DANA2 positively regulates drought stress responses through JMJ29 in Arabidopsis thaliana, and JMJ29 can positively regulate the expression of two positve regulators of stomatal closure and drought stress response, ERF15 and GOLS2. ERF84, an AP2\/ERF transcription factor, not only binds specifically to DANA2, but also promotes the transcription of JMJ29 by binding to its promoter.\n", "LncRNA DANA2 negatively regulates drought stress responses through JMJ29 in Arabidopsis thaliana, and JMJ29 can negatively regulate the expression of two negative regulators of stomatal closure and drought stress response, ERF15 and GOLS2. ERF84, an AP2\/ERF transcription factor, not only binds specifically to DANA2, but also represses the transcription of JMJ29 by binding to its promoter." ], "source":"10.1016\/j.molp.2023.08.001", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.molp.2023.08.001", "Year":2023.0, "Citations":19.0, "answer":1, "source_journal":"Molecular Plant", "is_expert":true }, { "question":"What is the role of lncRNA ARTA in abscisic acid (ABA) response in Arabidopsis thaliana, and what proteins have been identified as its molecular partners?", "area":"ENVIRONMENT - ABIOTIC STRESS", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Abscisic acid (ABA)-induced lncRNA ARTA controls ABA responses through postively regulating ABI5 exprssion in Arabidopsis thaliana, and loss of ARTA could result in desensitization to ABA. SAD2, an importin \u03b2-like protein, interacts with ARTA to block the nuclear import of a negative regulator of ABI5, MYB7.\n", "Abscisic acid (ABA)-induced lncRNA ARTA controls ABA responses through postively regulating ABI5 exprssion in Arabidopsis thaliana, and over-expressing ARTA could result in desensitization to ABA. SAD2, a transcription factor, interacts with ARTA to promote the nuclear export of a negative regulator of ABI5, MYB7.", "Abscisic acid (ABA)-induced lncRNA ARTA controls ABA responses through negatively regulating ABI5 exprssion in Arabidopsis thaliana, and loss of ARTA could result in hypersensitization to ABA. SAD2, an importin \u03b2-like protein, interacts with ARTA to block the nuclear import of a positive regulator of ABI5, MYB7." ], "source":"10.1016\/j.devcel.2023.05.003", "normalized_plant_species":"Model Organisms", "normalized_area":"ENVIRONMENT", "doi":"10.1016\/j.devcel.2023.05.003", "Year":2023.0, "Citations":12.0, "answer":0, "source_journal":"Developmental Cell", "is_expert":true }, { "question":"What is the role of lncRNA FRILAIR in strawberry fruit ripening, and what miRNA have been identified as its target?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Fragaria ananassa" ], "options":[ "Accumulation of FRILAIR can release repression of LAC11a (encoding a putative laccase-11-like protein) that is the miR408 target, which subsequently promotes expressions of genes involved in anthocyanin biosynthesis pathway, leading to the acceleration of strawberry fruit ripening. FRILAIR harbours a miR408 binding site, and its RNA can be cleaved by miR397.", "Accumulation of FRILAIR can release repression of LAC11a (encoding a putative laccase-11-like protein) that is the miR397 target, which subsequently promotes expressions of genes involved in anthocyanin biosynthesis pathway, leading to the acceleration of strawberry fruit ripening. FRILAIR harbours a miR397 binding site, and its RNA can be cleaved by miR397.", "Reduction of FRILAIR transcripts can release repression of LAC11a (encoding a putative laccase-11-like protein) that is the miR397 target, which subsequently represses expressions of genes involved in anthocyanin biosynthesis pathway, leading to the delay of strawberry fruit ripening. FRILAIR does not harbours a miR397 binding site, and its mRNA can be cleaved by miR397." ], "source":"10.1371\/journal.pgen.1009461", "normalized_plant_species":"Woody Perennials & Trees", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1371\/journal.pgen.1009461", "Year":2021.0, "Citations":46.0, "answer":1, "source_journal":"PLOS Genetics", "is_expert":true }, { "question":"What are the roles of miR396e and miR396f in controlling rice architecture?", "area":"PLANT BIOTECHNOLOGY", "plant_species":[ "Oryza sativa" ], "options":[ "Mutated miR396e and miR396f result in an altered rice architecture, with lengthened leaves but shorten internodes, especially the uppermost internode. The mir396ef mutation promotes leaf elongation by increaseing the level of a gibberellin (GA) precursor, mevalonic acid, which subsequently promotes GA biosynthesis. Internode elongation in mir396ef mutants appears to be suppressed via reduced CYP96B4 expression but not via the GA pathway.\n", "Mutated miR396e and miR396f result in an altered rice architecture, with lengthened roots and shorten leaves, especially the uppermost internode. The mir396ef mutation represses leaf elongation by increaseing the level of auxin. Leaf elongation in mir396ef mutants appears to be suppressed via reduced CYP96B4 expression but not via the auxin pathway.\n", "Mutated miR396e and miR396f result in an altered rice architecture, with shorten leaves but lengthened internodes, especially the uppermost internode. The mir396ef mutation promotes leaf shortening by increaseing the level of a gibberellin (GA) precursor, mevalonic acid, which subsequently promotes GA biosynthesis. Internode elongation in mir396ef mutants appears to be suppressed via the GA pathway." ], "source":"10.1111\/pbi.13214", "normalized_plant_species":"Model Organisms", "normalized_area":"PLANT BIOTECHNOLOGY", "doi":"10.1111\/pbi.13214", "Year":2019.0, "Citations":88.0, "answer":0, "source_journal":"Plant Biotechnology Journal", "is_expert":true }, { "question":"Which proteins were identified as part of the Arabidopsis Target of Rapamycin (TOR) complex?\n", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Unlike animals, plants such as Arabidopsis only possess one TOR complex which is designated as TORC1. This multiple protein complex includes the Target of Rapamycin (TOR) kinase, Rictor (rapamycin-insensitive companion of mTOR) and LST8\/G\u03b2L (Lethal with Sec Thirteen 8 \/ G protein \u03b2 subunit-like) proteins. ", "Unlike animals, plants such as Arabidopsis only possess one TOR complex which is designated as TORC1. This multiple protein complex includes Target of Rapamycin (TOR) kinase, Raptor (Regulatory-associated protein of TOR) and SIN1 (SAPK-interacting protein 1) proteins. ", "Unlike animals, plants such as Arabidopsis only possess one TOR complex which is designated as TORC1. This multiple protein complex includes the Target of Rapamycin (TOR) kinase, Raptor (Regulatory-associated protein of TOR) and Lst8 (Lethal with Sec Thirteen 8) proteins. " ], "source":"10.1016\/j.tibs.2020.11.004", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1016\/j.tibs.2020.11.004", "Year":2021.0, "Citations":57.0, "answer":2, "source_journal":"Trends in Biochemical Sciences", "is_expert":true }, { "question":"How does the Arabidopsis ribosomal protein S6 Kinase (S6K) accumulate in seedlings grown in 1% sucrose plates during short day (8h light \/ 16h dark) and long day (16h light \/ 8h dark) conditions?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "When Arabidopsis seedlings are grown in vitro with 1% sucrose, the S6K protein displays different accumulation patterns both in terms of its total levels and its phosphorylated (S6K-P) form. Under short days, total S6K is minimal during the dark period (ZT9 \u2013 ZT21) and when lights are on at ZT0 (ZT means zeitgeber time, and it refers to the time passed after lights on which is ZT0). It will reach its peak levels at ZT3 and ZT6. In the case of S6K-P levels, these are maximal only at ZT3 and will decline as the day progresses. Under long days conditions, both total and phosphorylated S6K display a similar pattern of accumulation. Total S6K protein levels do show a clear peak of accumulation being present throughout the day, that is during light and dark periods. That is also the case of S6K-P levels which are high from ZT0 to ZT6 and then increase up until ZT15, being high again during the night period (ZT18 \u2013 ZT21).", "When Arabidopsis seedlings are grown in vitro with 1% sucrose, the S6K protein displays different accumulation patterns both in terms of its total levels and its phosphorylated (S6K-P) form. Under short days, total S6K is maximal during the dark period (ZT9 \u2013 ZT21) and when lights are on at ZT0 (ZT means zeitgeber time, and it refers to the time passed after lights on which is ZT0). It will reach its trough (minimal) levels at ZT3 and ZT6. In the case of S6K-P levels, these are minimal only at ZT3 and will increase as the day progresses. Under long days conditions, both total and phosphorylated S6K display a different pattern of accumulation. Total S6K protein levels do not show a clear peak of accumulation being present throughout the day, that is during light and dark periods. That is not the case of S6K-P levels which are high from ZT0 to ZT6 and then decline up until ZT15, starting to increase again during the night period (ZT18 \u2013 ZT21).", "When Arabidopsis seedlings are grown in vitro with 1% sucrose, the S6K protein displays different accumulation patterns both in terms of its total levels and its phosphorylated (S6K-P) form. Under short days, total S6K is minimal during the dark period (ZT9 \u2013 ZT21) and when lights are on at ZT0 (ZT means zeitgeber time, and it refers to the time passed after lights on which is ZT0). It will reach its peak levels at ZT3 and ZT6. In the case of S6K-P levels, these are maximal only at ZT3 and will decline as the day progresses. Under long days conditions, both total and phosphorylated S6K display a different pattern of accumulation. Total S6K protein levels do not show a clear peak of accumulation being present throughout the day, that is during light and dark periods. That is not the case of S6K-P levels which are high from ZT0 to ZT6 and then decline up until ZT15, starting to increase again during the night period (ZT18 \u2013 ZT21)." ], "source":"10.1093\/plphys\/kiae254", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1093\/plphys\/kiae254", "Year":2024.0, "Citations":1.0, "answer":2, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"What is the half life of Arabidopsis S6K protein and which regulators control its stability?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "When Arabidopsis wild type seedlings grown under short day (SD) conditions are treated with the protein synthesis inhibitor Cycloheximide (CHX) at ZT3, kept in the light and their S6K total protein levels are determined every 3h (i.e., from Time 0 until Time 6h), we observe that 50% of this protein is maintained after 3h of treatment. This means that S6K half-life under these conditions is more than 3h. However, when we do exactly the same experiment with the zeitlupe (ztl) mutant seedlings that lack the F-box protein ZTL, the half-life of S6K is extended for more than 6h. This experiment shows that S6K protein levels are regulated by the proteasome machinery of which ZTL is a component.", "When Arabidopsis wild type seedlings grown under short day (SD) conditions are treated with the protein synthesis inhibitor Cycloheximide (CHX) at ZT3, kept in the light and their S6K total protein levels are determined every 3h (i.e., from Time 0 until Time 6h), we observe that 50% of this protein disappears after 3h of treatment. This means that S6K half-life under these conditions is approximately 3h. However, when we do exactly the same experiment with the zeitlupe (ztl) mutant seedlings that lack the F-box protein ZTL, the half-life of S6K is extended for more than 6h. This experiment shows that S6K protein levels are regulated by the proteasome machinery of which ZTL is a component.", "When Arabidopsis wild type seedlings grown under long day (SD) conditions are treated with the protein synthesis inhibitor Cycloheximide (CHX) at ZT3, kept in the light and their S6K total protein levels are determined every 3h (i.e., from Time 0 until Time 6h), we observe that 50% of this protein disappears after 3h of treatment. This means that S6K half-life under these conditions is approximately 3h. However, when we do exactly the same experiment with the zeitlupe (ztl) mutant seedlings that lack the F-box protein ZTL, the half-life of S6K is reduced by more than 6h. This experiment shows that S6K protein levels are not regulated by the proteasome machinery of which ZTL is a component." ], "source":"10.1093\/plphys\/kiae254", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1093\/plphys\/kiae254", "Year":2024.0, "Citations":1.0, "answer":1, "source_journal":"Plant Physiology", "is_expert":true }, { "question":"What are the main differences between the root extension patterns of wild type (Col-0) and raptor mutant seedlings grown under long day conditions? \n", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Roots are considered \u2018sink organs\u2019 since they rely on Carbon to be reallocated to them from source leaves which are photosynthetically active. Therefore, when Arabidopsis wild type seedlings grow under long day (16h light \/ 8h dark) conditions they display a distinct pattern of root extension which is higher in the first hours of the light period (ZT0-ZT3), and it will decrease until ZT6. From then until dusk (ZT16) there will be a slight increase in root extension, but just in the first hours of dark this response is inhibited, and root extension will steadily increase during the night period. When the role of the TOR pathway in regulating plant growth responses is assessed the results show that this pattern of root extension is not affected in raptor mutants which show a similar root growth peak in the early morning. Although there is a slight lower root growth extension during the first half of the day when comparing with wild type seedlings, raptor mutants\u2019 roots will grow more during the second half of the light period and all of the night.", "Roots are considered \u2018sink organs\u2019 since they rely on Carbon to be reallocated to them from source leaves which are photosynthetically active. Therefore, when Arabidopsis wild type seedlings grow under long day (16h light \/ 8h dark) conditions they display a distinct pattern of root extension which is lower in the first hours of the light period (ZT0-ZT3) and it will increase until ZT6. From then until dusk (ZT16) there will be a slight decrease in root extension, but just in the first hours of dark this response is promoted, and root extension will steadily decrease during the night period. Confirming the importance of the TOR pathway in regulating plant growth responses, this pattern of root extension is affected in raptor mutants which show a delay in root growth peak in the early morning. Although there is a slightly higher root growth extension during the first half of the day when comparing with wild type seedlings, raptor mutants\u2019 roots will grow less during the second half of the light period and all of the night.", "Roots are considered \u2018sink organs\u2019 since they rely on Carbon to be reallocated to them from source leaves which are photosynthetically active. Therefore, when Arabidopsis wild type seedlings grow under long day (16h light \/ 8h dark) conditions they display a distinct pattern of root extension which is higher in the first hours of the light period (ZT0-ZT3), and it will decrease until ZT6. From then until dusk (ZT16) there will be a slight increase in root extension, but just in the first hours of dark this response is inhibited, and root extension will steadily increase during the night period. Confirming the importance of the TOR pathway in regulating plant growth responses, this pattern of root extension is affected in raptor mutants which show a delay in the root growth peak in the early morning. Although there is a slightly higher root growth extension during the first half of the day when comparing with wild type seedlings, the raptor mutants\u2019 roots will grow less during the second half of the light period and all of the night. " ], "source":"10.1093\/jxb\/erac279", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.1093\/jxb\/erac279", "Year":2022.0, "Citations":6.0, "answer":2, "source_journal":"Journal of Experimental Botany", "is_expert":true }, { "question":"How does the TOR pathway regulate lateral root formation in Arabidopsis thaliana?", "area":"PHYSIOLOGY AND METABOLISM", "plant_species":[ "Arabidopsis thaliana" ], "options":[ "Lateral root (LR) formation in Arabidopsis requires carbohydrate catabolism and auxin. Lateral root initiation is modulated by high gycolysis depending on sugar derived from source organs (shoots). Sugars and auxin will stimulate the TOR pathway, which acts as a positive and essential regulator of lateral root formation. Knocking down of TOR will block LR formation and this cannot be rescued either by auxin or sucrose application. This regulation does not seem to occur via transcriptional modulation of auxin-induced genes in the pericycle, suggesting that founder cells can sense and respond to auxin but are unable to initiate LR formation. In fact, TOR will attenuate the translation of several critical regulators (ARF19, ARF7, and LBD16) leading to the development of LR. These results show that TOR could integrate both auxin and metabolic (e.g., carbohydrate) signals to modulate the translation efficiency of several auxin-induced genes.", "Lateral root (LR) formation in Arabidopsis requires carbohydrate catabolism and auxin. Lateral root initiation is modulated by high gycolysis depending on sugar derived from source organs (shoots). Sugars and auxin will inhibit the TOR pathway, which acts as a negative regulator of lateral root formation. Knocking down of TOR will promote LR formation and this can be rescued either by auxin or sucrose application. This regulation does not seem to occur via transcriptional modulation of auxin-induced genes in the pericycle, suggesting that founder cells can sense and respond to auxin but are unable to initiate LR formation. In fact, TOR will attenuate the translation of several critical regulators (ARF19, ARF7, and LBD16) leading to the development of LR. These results show that TOR could integrate both auxin and metabolic (e.g., carbohydrate) signals to modulate the translation efficiency of several auxin-induced genes.", "Lateral root (LR) formation in Arabidopsis requires carbohydrate catabolism and auxin. Lateral root initiation is modulated by high gycolysis depending on sugar derived from source organs (shoots). Sugars and auxin will stimulate the TOR pathway, which acts as a positive and essential regulator of lateral root formation. Knocking down of TOR will block LR formation and this cannot be rescued either by auxin or sucrose application. This regulation occurs via transcriptional modulation of auxin-induced genes in the pericycle, suggesting that founder cells cannot sense and respond to auxin and are unable to initiate LR formation. In fact, TOR will attenuate the transcription of several critical regulators (ARF19, ARF7, and LBD16) leading to the development of LR. These results show that TOR could integrate both auxin and metabolic (e.g., carbohydrate) signals to modulate the translation efficiency of several auxin-induced genes." ], "source":"https:\/\/doi.org\/10.15252\/embj.2022111273", "normalized_plant_species":"Model Organisms", "normalized_area":"PHYSIOLOGY AND METABOLISM", "doi":"10.15252\/embj.2022111273", "Year":2023.0, "Citations":27.0, "answer":0, "source_journal":"The EMBO Journal", "is_expert":true } ]