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What is the difference between the conventional bootstrap method and the transfer bootstrap expectation method as measures of branch support in phylogenomic trees? | EVOLUTION | [
"non-specific"
] | [
"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´s bootstrap values by identifying and removing unstable terminals, thereby increasing overall branch support and node robustness. "
] | https://doi.org/10.1038/s41586-018-0043-0 | Non-specific | EVOLUTION | 10.1038/s41586-018-0043-0 | 2,018 | 582 | 0 | Nature | true |
What are the main discrepancies between plastome-based and nuclear phylogenomic studies in the systematics of rosids? | EVOLUTION | [
"non-specific"
] | [
"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."
] | https://doi.org/10.1038/s41586-024-07324-0 | Non-specific | EVOLUTION | 10.1038/s41586-024-07324-0 | 2,024 | 108 | 0 | Nature | true |
How can introgression be distinguished from incomplete lineage sorting in phylogenomic datasets? | EVOLUTION | [
"non-specific"
] | [
"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."
] | https://doi.org/10.1093/genetics/iyab173 | Non-specific | EVOLUTION | 10.1093/genetics/iyab173 | 2,021 | 110 | 1 | Genetics | true |
Which gene families are associated with rubber production in seed plants, and how does gene copy variation influence this trait? | EVOLUTION | [
"non-specific"
] | [
"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—significantly 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—significantly 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—significantly 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. "
] | https://doi.org/10.1038/s41467-024-51031-3 | Non-specific | EVOLUTION | 10.1038/s41467-024-51031-3 | 2,024 | 4 | 2 | Nature Communications | true |
What connections have been identified between the convergence of floral traits and the evolution of regulatory genes in Asteraceae? | EVOLUTION | [
"non-specific"
] | [
"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–CYC2e 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–CYC3e 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–CYC2e 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."
] | https://doi.org/10.1016/j.xplc.2024.100851 | Non-specific | EVOLUTION | 10.1016/j.xplc.2024.100851 | 2,024 | 1 | 2 | Plant Communications | true |
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? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"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"
] | doi: 10.1016/j.pbi.2016.10.002 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1016/j.pbi.2016.10.002 | 2,016 | 44 | 2 | Current Opinion in Plant Biology | true |
What are the composition and functions of the phragmoplast and preprophase band involved in plant organ growth? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"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"
] | doi: 10.1093/plcell/koac069 | Non-specific | GROWTH AND DEVELOPMENT | 10.1093/plcell/koac069 | 2,022 | 19 | 1 | The Plant Cell | true |
There are 2 families of cyclin-dependent kinase inhibitor proteins in plants. Name both of them and describe their function during plant organ growth. | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"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."
] | DOI: 10.3389/fpls.2024.1362460 | Non-specific | GROWTH AND DEVELOPMENT | 10.3389/fpls.2024.1362460 | 2,024 | 0 | 2 | Frontiers in Plant Science | true |
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. | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"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."
] | doi: 10.1111/nph.18650 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1111/nph.18650 | 2,022 | 4 | 0 | New Phytologist | true |
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? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"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"
] | DOI: 10.1093/jxb/erad235 | Non-specific | GROWTH AND DEVELOPMENT | 10.1093/jxb/erad235 | 2,023 | 14 | 2 | Journal of Experimental Botany | true |
Which are the roles of REM proteins in plants? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"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."
] | http://dx.doi.org/10.1016/B978-0-12-800854-6.00004-X | Non-specific | GENE REGULATION | 10.1016/B978-0-12-800854-6.00004-X | 2,016 | 1 | 0 | Plant Transcription Factors | true |
Which are the SEPALLATA family genes identified and studied in grasses? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"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."
] | https://doi.org/10.3390/plants11212934 | Non-specific | GENE REGULATION | 10.3390/plants11212934 | 2,022 | 9 | 0 | Plants | true |
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). | PLANT BIOTECHNOLOGY | [
"non-specific"
] | [
"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"
] | DOI 10.1074/jbc.REV120.013572 | Non-specific | PLANT BIOTECHNOLOGY | 10.1074/jbc.REV120.013572 | 2,020 | 449 | 0 | Journal of Biological Chemistry | true |
What enzymes does AsA-GSH pathway require in plant species? | PHYSIOLOGY AND METABOLISM | [
"non-specific"
] | [
"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."
] | doi: 10.3389/fenvs.2015.00025 | Non-specific | PHYSIOLOGY AND METABOLISM | 10.3389/fenvs.2015.00025 | 2,015 | 113 | 0 | Frontiers in Environmental Science | true |
Which are the main families of transcription factors involved in the development of the response to water stress in plants? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"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."
] | doi: 10.3389/fpls.2016.01029 | Non-specific | GENE REGULATION | 10.3389/fpls.2016.01029 | 2,016 | 608 | 2 | Frontiers in Plant Science | true |
Which clade of green algae is sister to the embryophytes? | EVOLUTION | [
"non-specific"
] | [
"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"
] | 10.1371/journal.pone.0029696 / 10.1073/pnas.1323926111 / 10.1038/s41586-019-1693-2 | Non-specific | EVOLUTION | 10.1038/s41586-019-1693-2 | 2,019 | 1,354 | 2 | Nature | true |
How has the evo-devo concept to be applied to test the conservation of a biological process within the embryophytes? | EVOLUTION | [
"non-specific"
] | [
"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."
] | 10.1016/j.cub.2019.09.044 | Non-specific | EVOLUTION | 10.1016/j.cub.2019.09.044 | 2,019 | 62 | 2 | Current Biology | true |
What are the plant proteins with a demonstrated conserved function in the arbuscular mycorrhizal symbiosis across land plants? | EVOLUTION | [
"non-specific"
] | [
"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. "
] | 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 | Non-specific | EVOLUTION | 10.1016/j.cub.2024.03.063 | 2,024 | 6 | 0 | Current Biology | true |
What are the evidence that the first embryophytes had already evolved cuticle? | EVOLUTION | [
"non-specific"
] | [
"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. "
] | 10.1038/s44318-024-00181-7 / 10.1038/ncomms14713. | Non-specific | EVOLUTION | 10.1038/ncomms14713 | 2,017 | 168 | 0 | Nature Communications | true |
What is the bryophyte cell-type homologous to the tracheophyte root hairs? | EVOLUTION | [
"non-specific"
] | [
"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. "
] | 10.1126/science.1142618 / 10.1016/j.cub.2015.11.042 | Non-specific | EVOLUTION | 10.1016/j.cub.2015.11.042 | 2,016 | 107 | 1 | Current Biology | true |
Arabidopsis thaliana coiled-coil (CC)–NLR 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? | ENVIRONMENT - BIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"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."
] | DOI: 10.1126/science.aav5870 | Model Organisms | ENVIRONMENT | 10.1126/science.aav5870 | 2,019 | 662 | 1 | Science | true |
What is the meaning of the term “two-speed genome” as applied to describe the genome architecture of filamentous plant pathogens like Phytophthora infestans? | GENOME AND GENOMICS | [
"non-specific"
] | [
"The term “two-speed genome” 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 “two-speed genome” 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 “two-speed genome” 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."
] | DOI: 10.1016/j.gde.2015.09.001 | Non-specific | GENOME AND GENOMICS | 10.1016/j.gde.2015.09.001 | 2,015 | 461 | 1 | Current Opinion in Genetics & Development | true |
How does the bacterial effector proteins HopM1 and AvrE1 induce water-soaking lesions in Arabidopsis thaliana during Pseudomonas syringae infection? | ENVIRONMENT - BIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"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."
] | DOI: 10.1016/j.chom.2022.02.006 | Model Organisms | ENVIRONMENT | 10.1016/j.chom.2022.02.006 | 2,022 | 91 | 2 | Cell Host & Microbe | true |
Which nucleotide-binding, leucine-rich repeat receptors (NLR) from Nicotiana benthamiana are suppressed in their responses by the cyst nematode effector protein SPRYSEC15 (SS15)? | ENVIRONMENT - BIOTIC STRESS | [
"Nicotiana benthamiana"
] | [
"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."
] | DOI: 10.1371/journal.pbio.3001136 | Solanaceae & Relatives | ENVIRONMENT | 10.1371/journal.pbio.3001136 | 2,021 | 91 | 1 | PLOS Biology | true |
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? | ENVIRONMENT - BIOTIC STRESS | [
"Nicotiana benthamiana"
] | [
"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."
] | 10.7554/eLife.10856 | Solanaceae & Relatives | ENVIRONMENT | 10.7554/eLife.10856 | 2,016 | 181 | 2 | eLife | true |
What is the role of DDM1 in tomato ? | GENOME AND GENOMICS | [
"Solanum lycopersicum"
] | [
"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."
] | https://doi.org/10.1105/tpc.18.00167 | Solanaceae & Relatives | GENOME AND GENOMICS | 10.1105/tpc.18.00167 | 2,018 | 77 | 1 | The Plant Cell | true |
What is the extent of natural epigenetic variation in plants ? | GENE REGULATION - EPIGENETICS AND TGS | [
"non-specific"
] | [
"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."
] | https://doi.org/10.1016/j.pbi.2022.102297 https://onlinelibrary.wiley.com/doi/10.1111/eva.13730 | Non-specific | GENE REGULATION | 10.1111/eva.13730 | 2,024 | 0 | 1 | Evolutionary Applications | true |
What is the role of IBM1 in plants ? | GENE REGULATION - EPIGENETICS AND TGS | [
"Arabidopsis thaliana"
] | [
"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."
] | https://doi.org/10.1104/pp.18.01106 | Model Organisms | GENE REGULATION | 10.1104/pp.18.01106 | 2,019 | 23 | 2 | Plant Physiology | true |
Can epialleles and transgenerational epigenetic memory contribute to plant adaptation ? | GENE REGULATION - EPIGENETICS AND TGS | [
"non-specific"
] | [
"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."
] | https://doi.org/10.1146/annurev-arplant-070122-025047 | Non-specific | GENE REGULATION | 10.1146/annurev-arplant-070122-025047 | 2,023 | 29 | 1 | Annual Review of Plant Biology | true |
Is there a link between DNA methylation, meiotic recombination and crossovers in plant species ? | GENE REGULATION - EPIGENETICS AND TGS | [
"non-specific"
] | [
"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."
] | https://doi.org/10.1186/s13059-024-03163-4 | Non-specific | GENE REGULATION | 10.1186/s13059-024-03163-4 | 2,024 | 19 | 1 | Genome Biology | true |
What is the link between TCP15, auxins and cytokinins (CK) during gynoecium development in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"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 – 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."
] | https://doi.org/10.1111/tpj.12992 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1111/tpj.12992 | 2,015 | 90 | 1 | The Plant Journal | true |
Which is the role of Class I TCP transcription factors in the stamen filament elongation in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"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."
] | https://doi.org/10.1104/pp.19.01501 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1104/pp.19.01501 | 2,020 | 49 | 0 | Plant Physiology | true |
What is the mechanism by which strigolactones (SL) regulate flowering time in Arabidopsis thaliana? | HORMONES | [
"Arabidopsis thaliana"
] | [
"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."
] | https://doi.org/10.1093/plcell/koae248 | Model Organisms | HORMONES | 10.1093/plcell/koae248 | 2,024 | 3 | 2 | The Plant Cell | true |
What is the main gene regulated by strigolactones (SL) to control shoot branching in Arabidopsis thaliana and how does it regulate it? | HORMONES | [
"Arabidopsis thaliana"
] | [
"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."
] | https://doi.org/10.1016/j.xplc.2019.100014 | Model Organisms | HORMONES | 10.1016/j.xplc.2019.100014 | 2,020 | 48 | 1 | Plant Communications | true |
How is D14 receptor stability regulated in the strigolactone (SL) signalling pathway? | HORMONES | [
"Arabidopsis thaliana"
] | [
"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."
] | https://doi.org/10.1093/jxb/erae365 | Model Organisms | HORMONES | 10.1093/jxb/erae365 | 2,024 | 0 | 1 | Journal of Experimental Botany | true |
What is the subcellular localization of plant phytochromes? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"non-specific"
] | [
"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."
] | https://doi.org/10.1038/s41467-019-13045-0 | Non-specific | ENVIRONMENT | 10.1038/s41467-019-13045-0 | 2,019 | 312 | 0 | Nature Communications | true |
Can phytochrome B function as a thermosensor in the presence of light, or is this function limited to darkness in Arabidopsis? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"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."
] | https://www.science.org/doi/10.1126/science.aaf5656 | Model Organisms | ENVIRONMENT | 10.1126/science.aaf5656 | 2,016 | 698 | 1 | Science | true |
Which photoreceptors phosphorylate the protein PHYTOCHROME KINASE SUBSTRATE 4 in response to blue light in Arabidopsis? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"Phototropins",
"Phytochromes",
"Phytochromes and phototropins"
] | doi: 10.1038/emboj.2012.186 | Model Organisms | ENVIRONMENT | 10.1038/emboj.2012.186 | 2,012 | 75 | 0 | The EMBO Journal | true |
Do plant phytochromes have histidine kinase activity? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"non-specific"
] | [
"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."
] | https://doi.org/10.1038/s41467-019-13045-0 | Non-specific | ENVIRONMENT | 10.1038/s41467-019-13045-0 | 2,019 | 312 | 2 | Nature Communications | true |
Which are the hormonal and cellular mechanisms linking unilateral light perception and positive phototropism in Arabidopsis hypocotyls? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"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. "
] | DOI: 10.1111/ppl.13098 | Model Organisms | ENVIRONMENT | 10.1111/ppl.13098 | 2,020 | 24 | 2 | Physiologia Plantarum | true |
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? | PLANT BIOTECHNOLOGY | [
"Arabidopsis thaliana",
"Nicotiana benthamiana"
] | [
"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’ 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."
] | https://doi.org/10.1093/nar/gkaa343 | Model Organisms | PLANT BIOTECHNOLOGY | 10.1093/nar/gkaa343 | 2,020 | 20 | 0 | Nucleic Acids Research | true |
What is the shortest MIR390-based precursor designed for artificial micro-RNA (amiRNA) expression in Arabidopsis thaliana and Nicotiana benthamiana? | PLANT BIOTECHNOLOGY | [
"Arabidopsis thaliana",
"Nicotiana benthamiana"
] | [
"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"
] | https://doi.org/10.1093/nar/gkad747 | Model Organisms | PLANT BIOTECHNOLOGY | 10.1093/nar/gkad747 | 2,023 | 16 | 0 | Nucleic Acids Research | true |
What is the shortest precursor designed for synthetic trans-active small interfering RNA (syn-tasiRNA) expression in non-Arabidopsis plants, such as Nicotiana benthamiana? | PLANT BIOTECHNOLOGY | [
"Nicotiana benthamiana"
] | [
"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."
] | https://doi.org/10.1101/2024.12.18.629176 | Solanaceae & Relatives | PLANT BIOTECHNOLOGY | 10.1101/2024.12.18.629176 | 2,024 | 0 | 1 | null | true |
What are the advantages of using shorter artificial sRNA precursors in RNA viral vectors for plants, such as potato virus X (PVX)? | PLANT BIOTECHNOLOGY | [
"non-specific"
] | [
"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."
] | https://doi.org/10.1093/nar/gkad747 and https://doi.org/10.1101/2024.12.18.629176 | Non-specific | PLANT BIOTECHNOLOGY | 10.1101/2024.12.18.629176 | 2,024 | 0 | 1 | null | true |
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? | PLANT BIOTECHNOLOGY | [
"Nicotiana benthamiana"
] | [
"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."
] | https://doi.org/10.1101/2024.12.18.629176 | Solanaceae & Relatives | PLANT BIOTECHNOLOGY | 10.1101/2024.12.18.629176 | 2,024 | 0 | 1 | null | true |
What is the role of the Lotus japonicus LysM-RLK receptors LjNFR1 and LjNFR5 in the plant’s ability to interact with both symbiotic and pathogenic microbes? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Lotus japonicus"
] | [
"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."
] | https://doi.org/10.1038/nature02039 | Model Organisms | ENVIRONMENT | 10.1038/nature02039 | 2,003 | 950 | 2 | Nature | true |
What is the role of the LjEPR3 receptor in symbiosis in Lotus japonicus and which protein interactors are involved in its function? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Lotus japonicus"
] | [
"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."
] | https://doi.org/10.1038/ncomms14534 | Model Organisms | ENVIRONMENT | 10.1038/ncomms14534 | 2,017 | 125 | 2 | Nature Communications | true |
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? | ENVIRONMENT - PLANT-SYMBIONTS | [
"non-specific"
] | [
"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."
] | https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.13117 | Non-specific | ENVIRONMENT | 10.1111/nph.13117 | 2,014 | 93 | 2 | New Phytologist | true |
How does the regulation of SA levels influence the balance between symbiosis and defense responses in legumes? | ENVIRONMENT - PLANT-SYMBIONTS | [
"non-specific"
] | [
"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."
] | https://doi.org/10.3390/biology11060861 | Non-specific | ENVIRONMENT | 10.3390/biology11060861 | 2,022 | 39 | 1 | Biology | true |
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? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Arachis hypogaea"
] | [
" 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’s 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."
] | https://doi.org/10.3390/horticulturae8111000 | Legumes | ENVIRONMENT | 10.3390/horticulturae8111000 | 2,022 | 1 | 2 | Horticulturae | true |
Which are the photorreceptors essential for the germinatin of Arabidopsis seeds? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"The phytochromes",
"The cryptochromes",
"The phototropins"
] | 10.1073/pnas.0910446107 | Model Organisms | ENVIRONMENT | 10.1073/pnas.0910446107 | 2,010 | 151 | 0 | Proceedings of the National Academy of Sciences | true |
Which are the proteins that interact with MED25 and promote its degradation by the Proteasome in Arabidopsis? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"MBR1 and MBR2",
"MBRL1 and MBRL2",
"MBR1 and MBRL2"
] | 10.1104/pp.112.205500 | Model Organisms | GENE REGULATION | 10.1104/pp.112.205500 | 2,012 | 51 | 0 | Plant Physiology | true |
What is the mechanism known as activation by destruction in the regulation of gene expression? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"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"
] | 10.1104/pp.112.205500 | Non-specific | GENE REGULATION | 10.1104/pp.112.205500 | 2,012 | 51 | 2 | Plant Physiology | true |
Why a mutation that affects the Arabidopsis DNA Polymerase delta leads to early flowering in Arabidopsis? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"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"
] | 10.1371/journal.pgen.1004975 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1371/journal.pgen.1004975 | 2,015 | 34 | 1 | PLOS Genetics | true |
Which subunit of the Mediator complex of Arabidopsis is essential for early embryo development while expressed in the male gametophyte? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"MED30",
"MED25",
"MED31"
] | 10.1242/dev.175224 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1242/dev.175224 | 2,019 | 12 | 0 | Development | true |
Which transcription factors are expressed in the apical cells of the gametophytic meristem of the liverwort Marchantia polymorpha ? | EVOLUTION | [
"Marchantia polymorpha"
] | [
"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. "
] | https://doi.org/10.1093/plcell/koae053 | Model Organisms | EVOLUTION | 10.1093/plcell/koae053 | 2,024 | 12 | 0 | The Plant Cell | true |
Which cell type is homologous to root hairs in the liverwort Marchantia polymorpha? Which genetic evidence supports this observation? | EVOLUTION | [
"Marchantia polymorpha",
"Arabidopsis thaliana"
] | [
"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."
] | https://10.1016/j.cub.2015.11.042 | Model Organisms | EVOLUTION | 10.1016/j.cub.2015.11.042 | 2,016 | 107 | 2 | Current Biology | true |
Are the transcription factors controlling the vegetative meristem of land plants conserved among the gametophyte and the sporophyte? | EVOLUTION | [
"Physcomitrella patens",
"Arabidopsis thaliana"
] | [
"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."
] | https://doi.org/10.1111/j.1525-142X.2008.00271.x, https://doi.org/10.1242/dev.097444 | Model Organisms | EVOLUTION | 10.1242/dev.097444 | 2,014 | 126 | 2 | Development | true |
Do bryophytes form a monophyletic group? | EVOLUTION | [
"non-specific"
] | [
"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."
] | https://doi.org/10.1016/j.cub.2018.01.063 | Non-specific | EVOLUTION | 10.1016/j.cub.2018.01.063 | 2,018 | 399 | 0 | Current Biology | true |
Are abscisic acid-mediated gene regulation conserved among land plants? | EVOLUTION | [
"Marchantia polymorpha"
] | [
"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."
] | https://doi.org/10.1016/j.cub.2018.10.018, https://doi.org/10.1104/pp.18.00761 | Model Organisms | EVOLUTION | 10.1104/pp.18.00761 | 2,018 | 52 | 1 | Plant Physiology | true |
How are Arabidopsis thaliana long intergenic noncoding RNAs conserved among Angiosperms in term of sequences compared to other sequence type? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"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."
] | https://doi.org/10.1104/pp.20.00446 https://doi.org/10.1093/plphys/kiad360 | Model Organisms | GENOME AND GENOMICS | 10.1093/plphys/kiad360 | 2,023 | 6 | 2 | Plant Physiology | true |
How are long noncoding RNAs expressed between the different accessions of Arabidopsis thaliana? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"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."
] | https://doi.org/10.1093/plcell/koad233 https://doi.org/10.1104/pp.20.00446 | Model Organisms | GENOME AND GENOMICS | 10.1104/pp.20.00446 | 2,020 | 30 | 2 | Plant Physiology | true |
Is there any bias of conservation among Arabidopsis thaliana long noncoding RNAs? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"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."
] | https://doi.org/10.1093/plphys/kiad360 | Model Organisms | GENOME AND GENOMICS | 10.1093/plphys/kiad360 | 2,023 | 6 | 2 | Plant Physiology | true |
Is there any bias of expression for Arabidopsis thaliana long noncoding RNAs according to specific condition or tissue? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"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."
] | https://doi.org/10.1093/plphys/kiad360 https://doi.org/10.1093/plcell/koac166 | Model Organisms | GENOME AND GENOMICS | 10.1093/plcell/koac166 | 2,022 | 31 | 0 | The Plant Cell | true |
How is the long noncoding RNA MARS involved in the control of the expression of the marneral cluster in Arabidopsis thaliana? | GENE REGULATION - EPIGENETICS AND TGS | [
"Arabidopsis thaliana"
] | [
"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."
] | https://doi.org/10.1016/j.molp.2022.02.007 | Model Organisms | GENE REGULATION | 10.1016/j.molp.2022.02.007 | 2,022 | 33 | 1 | Molecular Plant | true |
RNA secondary structure motifs like hairpins have various regulatory functions. Which base composition in small stems (~4 bases) of hairpins positively influences translation efficiency? | GENE REGULATION - TRANSLATION | [
"non-specific"
] | [
"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."
] | https://doi.org/10.1038/s42256-024-00946-z | Non-specific | GENE REGULATION | 10.1038/s42256-024-00946-z | 2,024 | 0 | 2 | Nature Machine Intelligence | true |
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? | GENE REGULATION - ALTERNATIVE SPLICING | [
"non-specific"
] | [
"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)."
] | https://doi.org/10.1186/s13059-017-1235-x | Non-specific | GENE REGULATION | 10.1186/s13059-017-1235-x | 2,017 | 143 | 0 | Genome Biology | true |
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? | ENVIRONMENT - BIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"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."
] | https://doi.org/10.1038/s41467-024-51512-5 | Model Organisms | ENVIRONMENT | 10.1038/s41467-024-51512-5 | 2,024 | 2 | 2 | Nature Communications | true |
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? | GENE REGULATION - ALTERNATIVE SPLICING | [
"non-specific"
] | [
"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."
] | https://doi.org/10.1093/jxb/erab232 | Non-specific | GENE REGULATION | 10.1093/jxb/erab232 | 2,021 | 57 | 2 | Journal of Experimental Botany | true |
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? | GENE REGULATION - ALTERNATIVE SPLICING | [
"non-specific"
] | [
"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"
] | doi: 10.3892/br.2014.407 | Non-specific | GENE REGULATION | 10.3892/br.2014.407 | 2,014 | 330 | 2 | Biomedical Reports | true |
Which EPF peptides participate in stomatal development, and what is the effect of each of them on this process in Arabidopsis? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"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."
] | http://dx.doi.org/10.1016/j.gde.2017.02.001 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1016/j.gde.2017.02.001 | 2,017 | 33 | 0 | Current Opinion in Genetics & Development | true |
How does the peptide EPF2 mediate the effect of CO2 on stomatal development in Arabidopsis? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"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. "
] | doi:10.1038/nature13452 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1038/nature13452 | 2,014 | 191 | 2 | Nature | true |
How does BASL protein controls cell fate during stomatal development in Arabidopsis? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"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. "
] | https://doi.org/10.1016/j.cub.2021.11.013 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1016/j.cub.2021.11.013 | 2,022 | 17 | 2 | Current Biology | true |
What is the role of the transcription factors SPEECHLESS, MUTE and FAMA in stomatal development in Arabidopsis? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"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. "
] | https://doi.org/10.3390/plants10030432 | Model Organisms | GROWTH AND DEVELOPMENT | 10.3390/plants10030432 | 2,021 | 3 | 2 | Plants | true |
What is the role of receptors PANGLOSS1 and PANGLOSS2 in stomatal development in maize? | GROWTH AND DEVELOPMENT | [
"Zea mays"
] | [
"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."
] | https://doi.org/10.1093/plcell/koac301 | Cereal Grains | GROWTH AND DEVELOPMENT | 10.1093/plcell/koac301 | 2,022 | 10 | 1 | The Plant Cell | true |
How do mutations in the LNK2 gene impact circadian rhythms and domestication in tomato? | GROWTH AND DEVELOPMENT | [
"Solanum lycopersicum"
] | [
"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."
] | DOI: 10.1073/pnas.1808194115 | Solanaceae & Relatives | GROWTH AND DEVELOPMENT | 10.1073/pnas.1808194115 | 2,018 | 1 | 0 | Proceedings of the National Academy of Sciences | true |
How does the GEMIN2 protein affect alternative splicing and circadian rhythms in response to temperature changes in Arabidopsis? | GENE REGULATION - ALTERNATIVE SPLICING | [
"Arabidopsis thaliana"
] | [
"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."
] | https://doi.org/10.1073/pnas.1504541112 | Model Organisms | GENE REGULATION | 10.1073/pnas.1504541112 | 2,015 | 88 | 1 | Proceedings of the National Academy of Sciences | true |
How is PRMT5 involved in the regulation of circadian rhythms, light responses, and pre-mRNA splicing in Arabidopsis? | GENE REGULATION - ALTERNATIVE SPLICING | [
"Arabidopsis thaliana"
] | [
"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. "
] | https://doi.org/10.1038/nature09470 ; https://doi.org/10.1073/pnas.2317408121 | Model Organisms | GENE REGULATION | 10.1073/pnas.2317408121 | 2,024 | 1 | 1 | Proceedings of the National Academy of Sciences | true |
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? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"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. "
] | https://doi.org/10.1016/j.cub.2020.02.058 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1016/j.cub.2020.02.058 | 2,020 | 24 | 2 | Current Biology | true |
How does light regulate alternative splicing in plants and what is the role of phytochrome photoreceptors in this process? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"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. "
] | https://doi.org/10.3390/cells12202447 | Model Organisms | ENVIRONMENT | 10.3390/cells12202447 | 2,023 | 3 | 2 | Cells | true |
Which transcription factors are associated with the development of ventral identity in the snapdragon flower? | GENE REGULATION - TRANSCRIPTION | [
"Antirrhinum majus"
] | [
"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."
] | doi:10.3390/genes11040395 | Other Herbaceous Crops, Spices, Fibers & Weeds | GENE REGULATION | 10.3390/genes11040395 | 2,020 | 12 | 2 | Genes | true |
Which rice HD-Zip I transcription factor changes its expression at low ABA concentrations, influencing leaf angle opening in 9-day-old plant? | GENE REGULATION - TRANSCRIPTION | [
"Oryza sativa"
] | [
"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."
] | doi.org/10.1016/j.envexpbot.2023.105433 | Model Organisms | GENE REGULATION | 10.1016/j.envexpbot.2023.105433 | 2,023 | 0 | 1 | Environmental and Experimental Botany | true |
Which rice HD-Zip I transcription factor appears to be involved in the brassinosteroid biosynthetic pathway? | GENE REGULATION - TRANSCRIPTION | [
"Oryza sativa"
] | [
"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. "
] | doi.org/10.1016/j.envexpbot.2023.105433 | Model Organisms | GENE REGULATION | 10.1016/j.envexpbot.2023.105433 | 2,023 | 0 | 0 | Environmental and Experimental Botany | true |
How does SHY2 influence the balance between auxin and cytokinin to regulate root meristem size in Arabidopsis thaliana? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"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"
] | DOI 10.1016/j.cub.2010.05.035 | Model Organisms | GENE REGULATION | 10.1016/j.cub.2010.05.035 | 2,010 | 301 | 0 | Current Biology | true |
What is the hypothesis regarding the mechanism by which GmCRF4a promotes epicotyl elongation in soybean plants? | GENE REGULATION - TRANSCRIPTION | [
"Glycine max"
] | [
"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"
] | doi.org/10.3389/fpls.2022.983650 | Legumes | GENE REGULATION | 10.3389/fpls.2022.983650 | 2,022 | 13 | 0 | Frontiers in Plant Science | true |
What is the role of nitrate in plant nutrition? | ENVIRONMENT - NUTRIENTS | [
"non-specific"
] | [
"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."
] | 10.1016/j.molp.2016.05.004 | Non-specific | ENVIRONMENT | 10.1016/j.molp.2016.05.004 | 2,016 | 458 | 2 | Molecular Plant | true |
How do plants sense nitrate availability in soil? | ENVIRONMENT - NUTRIENTS | [
"Arabidopsis thaliana"
] | [
"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."
] | 10.1016/j.molp.2016.05.004 | Model Organisms | ENVIRONMENT | 10.1016/j.molp.2016.05.004 | 2,016 | 458 | 0 | Molecular Plant | true |
What is the primary pathway for nitrate uptake in plants? | ENVIRONMENT - NUTRIENTS | [
"non-specific"
] | [
"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. "
] | 10.1105/tpc.19.00748 | Non-specific | ENVIRONMENT | 10.1105/tpc.19.00748 | 2,020 | 267 | 1 | The Plant Cell | true |
Which plant hormone is closely linked to nitrate signaling? | ENVIRONMENT - NUTRIENTS | [
"Arabidopsis thaliana"
] | [
"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). "
] | 10.1007/s11103-016-0463-x | Model Organisms | ENVIRONMENT | 10.1007/s11103-016-0463-x | 2,016 | 115 | 2 | Plant Molecular Biology | true |
How does nitrate affect plant root system architecture? | ENVIRONMENT - NUTRIENTS | [
"non-specific"
] | [
"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’s 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."
] | 10.1016/j.pbi.2014.06.004 | Non-specific | ENVIRONMENT | 10.1016/j.pbi.2014.06.004 | 2,014 | 197 | 2 | Current Opinion in Plant Biology | true |
What role does the protein NRT2.1 play in Arabidopsis thaliana? | ENVIRONMENT - NUTRIENTS | [
"Arabidopsis thaliana"
] | [
"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"
] | 10.1111/j.1469-8137.2012.04094.x | Model Organisms | ENVIRONMENT | 10.1111/j.1469-8137.2012.04094.x | 2,012 | 142 | 0 | New Phytologist | true |
How does phosphorylation affect NRT1.1 function in Arabidopsis thaliana? | ENVIRONMENT - NUTRIENTS | [
"Arabidopsis thaliana"
] | [
"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. ",
"NRT1.1 is phosphorylated in multiple locations affecting its localization in the cell"
] | 10.1016/j.cell.2009.07.004 | Model Organisms | ENVIRONMENT | 10.1016/j.cell.2009.07.004 | 2,009 | 1,051 | 1 | Cell | true |
How does nitrate influence the expression of microRNAs (miRNAs) in plants? | ENVIRONMENT - NUTRIENTS | [
"Arabidopsis thaliana"
] | [
"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."
] | 10.1073/pnas.0909571107 | Model Organisms | ENVIRONMENT | 10.1073/pnas.0909571107 | 2,010 | 521 | 2 | Proceedings of the National Academy of Sciences | true |
Has the crystal structure of NRT1.1 been resolved and what was the implication of knowing the structure for nitrate transport in Arabidopsis thaliana? | ENVIRONMENT - NUTRIENTS | [
"Arabidopsis thaliana"
] | [
"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 Arabidopsis thaliana NRT1.1 were reported, which together with in vitro binding 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"
] | 10.1038/nature13074. | Model Organisms | ENVIRONMENT | 10.1038/nature13074 | 2,014 | 264 | 1 | Nature | true |
What is the role of protein phosphatases in nitrate signaling in Arabidopsis thaliana? | ENVIRONMENT - NUTRIENTS | [
"Arabidopsis thaliana"
] | [
"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’s 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 Xenopus oocytes 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."
] | 10.1126/scisignal.aaa4829 | Model Organisms | ENVIRONMENT | 10.1126/scisignal.aaa4829 | 2,015 | 159 | 2 | Science Signaling | true |
How long non-coding RNAs can affect alternative splicing in Arabidopsis thaliana? | GENE REGULATION - ALTERNATIVE SPLICING | [
"Arabidopsis thaliana"
] | [
"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"
] | https://doi.org/10.1093/pcp/pcz086 | Model Organisms | GENE REGULATION | 10.1093/pcp/pcz086 | 2,019 | 76 | 0 | Plant and Cell Physiology | true |
Which technologies can be used to identify mRNA target genes whose splicing depends on long non-coding RNAs? | GENE REGULATION - ALTERNATIVE SPLICING | [
"non-specific"
] | [
"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"
] | 10.15252/embj.2022110921 | Non-specific | GENE REGULATION | 10.15252/embj.2022110921 | 2,023 | 17 | 0 | The EMBO Journal | true |
Which splicing regulators control also post-transcriptional gene silencing in Arabidopsis thaliana? | GENE REGULATION - ALTERNATIVE SPLICING | [
"Arabidopsis thaliana"
] | [
"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"
] | https://doi.org/10.1093/plcell/koad091 | Model Organisms | GENE REGULATION | 10.1093/plcell/koad091 | 2,023 | 5 | 1 | The Plant Cell | true |
Which stress requires inhibition of the action of a specific miRNA on systemic response in plants? | ENVIRONMENT - ABIOTIC STRESS | [
"non-specific"
] | [
"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"
] | doi: 10.1038/ng2079. Epub 2007 Jul 22. | Non-specific | ENVIRONMENT | 10.1038/ng2079 | 2,007 | 1,702 | 2 | Nature Genetics | true |
How does miR396 regulates root meristem growth and mycorrhization in Medicago truncatula? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Medicago truncatula"
] | [
"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 "
] | doi: 10.1111/tpj.12178. Epub 2013 May 3. | Model Organisms | ENVIRONMENT | 10.1111/tpj.12178 | 2,013 | 165 | 1 | The Plant Journal | true |
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