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Which transcription factors participate in the negative regulation of the DELAY OF GERMINATION 1 (DOG1) gene by ABI5-BINDING PROTEIN 2 (AFP2) during seed maturation in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis thaliana, two basic helix–loop–helix transcription factors in the BR signaling pathway, BRASSINOSTEROID ENHANCED EXPRESSION 2 (BEE2) and BEE 2 INTERACTING with INCREASED LEAF INCLINATION 1 BINDING bHLH1 (HBI1), suppress DOG1 expression by recruiting the transcriptional corepressor TPR2 to carry out histone deacetylation at the DOG1 gene. In siliques, when BEE2 and HBI1 levels are low and inadequate to suppress DOG1 production, a large number of DOG1 transcripts accumulate during embryo development to maintain seed dormancy. BEE2 and HBI1transcript levels progressively rise in mature fresh or after-ripened seeds. Since AFP2 acts as an adapter, the increased BEE2 and HBI1transcripts recruit additional TPR2 and HDAC, which ultimately suppresses DOG1 expression and finally releases seed dormancy. ",
"In Arabidopsis thaliana, the transcription factor WRKY36 suppresses DOG1 expression by recruiting the transcriptional corepressor TPR2 to carry out histone deacetylation at the DOG1 gene. In siliques, when WRKY36 levels are low and inadequate to suppress DOG1 production, a large number of DOG1 transcripts accumulate during embryo development to maintain seed dormancy. WRKY36 transcript levels progressively rise in mature fresh or after-ripened seeds. Since AFP2 acts as an adapter, the increased WRKY36 recruits additional TPR2 and HDAC, which ultimately suppresses DOG1 expression and finally releases seed dormancy. ",
"In Arabidopsis thaliana, the transcription factor WRKY36 suppresses DOG1 expression by recruiting the transcriptional corepressor TPR2 to carry out histone deacetylation at the DOG1 gene. In siliques, when WRKY36 levels are high and DOG1 transcripts accumulate during embryo development to maintain seed dormancy. WRKY36 transcript levels progressively decrease in mature fresh or after-ripened seeds. AFP2 ultimately suppresses DOG1 expression and finally releases seed dormancy. "
] | Deng, G., Sun, H., Hu, Y., Yang, Y., Li, P., Chen, Y., Zhu, Y., Zhou, Y., Huang, J., Neill, S.J. and Hu, X. (2023), A transcription factor WRKY36 interacts with AFP2 to break primary seed dormancy by progressively silencing DOG1 in Arabidopsis. New Phytol, 238: 688-704. https://doi.org/10.1111/nph.18750 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1111/nph.18750 | 2,023 | 18 | 1 | New Phytologist | true |
How is the gene ETHYLENE INSENSITIVE 2 (EIN2) involved on the ABA response In Arabidopsis thaliana? | HORMONES | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis thaliana, ABA responses are largely induced by EIN2 rather than EIN3 or EIL1. This EIN2-directed ABA response enhancement depends on HLS1 function. EIN2 directly interacts with HLS1, to fine-tune ABA responses during seed germination and early seedling establishment.",
"In Arabidopsis thaliana, ABA responses are largely repressed by EIN2 rather than EIN3 or EIL1. This EIN2-directed repression depends on HLS1 function. EIN2 directly interacts with HLS1, thus repressing histone H3 acetylation at ABI5 chromatin to fine-tune ABA responses during seed germination and early seedling establishment.",
"In Arabidopsis thaliana, ABA responses are largely repressed by EIN3 rather than EIN2 or EIL1. This EIN3-directed repression depends on HLS1 function. EIN3 directly interacts with HLS1, thus repressing histone H3 acetylation at ABI5 chromatin to fine-tune ABA responses during seed germination and early seedling establishment."
] | Guo, R., Wen, X., Zhang, W., Huang, L., Peng, Y., Jin, L., Han, H., Zhang, L., Li, W. and Guo, H. (2023), Arabidopsis EIN2 represses ABA responses during germination and early seedling growth by inactivating HLS1 protein independently of the canonical ethylene pathway. Plant J, 115: 1514-1527. https://doi.org/10.1111/tpj.16335 | Model Organisms | HORMONES | 10.1111/tpj.16335 | 2,023 | 12 | 1 | The Plant Journal | true |
How are the transcription factors SISCZ and SIEXO1 involved in the lignification in the inner cortical layer in Solanum lycopersicum? | GROWTH AND DEVELOPMENT | [
"Solanum lycopersicum"
] | [
"SlEXO1 and SlSCZ regulates the polar deposition of lignin in the exodermis. As evidenced by the absence of PLC and suberin in the inner cortical layers, SlSCZ and SlEXO1 both induce PLC and most likely exodermal cell fate specification in the inner cortex layer. Exodermal lignification and suberization can likewise be enhanced by SlEXO1, possibly in a dose-dependent manner through SlMYB92.",
"Through a genetic interaction with SlEXO1, SlSCZ regulates the polar deposition of lignin in the endodermis. As evidenced by the presence of PLC and suberin in the outer cortical layers, SlSCZ and SlEXO1 both repress PLC and most likely endodermal cell fate specification in the outer cortex layer. Endodermal lignification and suberization can likewise be suppressed by SlEXO1, possibly in a dose-dependent manner through SlMYB92.",
"Through a genetic interaction with SlEXO1, SlSCZ regulates the polar deposition of lignin in the exodermis. As evidenced by the presence of PLC and suberin in the inner cortical layers, SlSCZ and SlEXO1 both repress PLC and most likely exodermal cell fate specification in the inner cortex layer. Exodermal lignification and suberization can likewise be suppressed by SlEXO1, possibly in a dose-dependent manner through SlMYB92."
] | Manzano, C., Morimoto, K.W., Shaar-Moshe, L. et al. Regulation and function of a polarly localized lignin barrier in the exodermis. Nat. Plants (2024). https://doi.org/10.1038/s41477-024-01864-z | Solanaceae & Relatives | GROWTH AND DEVELOPMENT | 10.1038/s41477-024-01864-z | 2,024 | 0 | 2 | Nature Plants | true |
How are the IncRNAs called PUPPIES involved in Arabidopsis thaliana seed germination delay upon salt stress conditions? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"The DOG1 gene represses the salt‐dependent delay of germination. DOG1 gene promoter is extensively transcribed, generating a variety of lncRNAs, called PUPPIES. Co-directional pervasive transcription of PUPPIES increases transcriptional bursts and RNA polymerase II pausing, which in turn downregulates DOG1 expression. ",
"The DOG1 gene induces the salt‐dependent delay of germination. DOG1 gene promoter is extensively transcribed, generating a variety of lncRNAs, called PUPPIES. Co-directional pervasive transcription of PUPPIES increases transcriptional bursts and RNA polymerase II pausing, which in turn stimulates DOG1 expression. ",
"The DOG1 gene induces the salt‐dependent delay of germination. DOG1 gene introns are extensively transcribed, generating a variety of lncRNAs, called PUPPIES. Co-directional pervasive transcription of PUPPIES increases transcriptional bursts and RNA polymerase II pausing, which in turn stimulates DOG1 expression. "
] | https://doi.org/10.15252/embj.2022112443 | Model Organisms | ENVIRONMENT | 10.15252/embj.2022112443 | 2,023 | 15 | 1 | The EMBO Journal | true |
How is the pyrroline-5-carboxylate synthetase (P5CS)-encoding gene (CtrP5CS1) involved in Citrus trifoliata cold response? | ENVIRONMENT - ABIOTIC STRESS | [
"Citrus trifoliata"
] | [
"Proline accumulation has been reported in plants under cold stress. The Citrus trifoliata L. gene CtrP5CS1, that encodes for the pyrroline-5-carboxylate synthetase (P5CS), is essential for cold-induced proline accumulation. CtrTGA2 bound directly to the TGACG motif of the CtrP5CS1 promoter and repress its expression. Down-regulation of CtrP5CS1 and CtrTGA2 under cold stress is dependent on salicylic acid (SA) biosynthesis. ",
"Proline accumulation has been reported in plants under cold stress. The Citrus trifoliata L. gene CtrP5CS1, that encodes for the pyrroline-5-carboxylate synthetase (P5CS), is essential for cold-induced proline accumulation. CtrTGA1 bound directly to the TGACG motif of the CtrP5CS1 promoter and activate its expression. Up-regulation of CtrP5CS1 and CtrTGA1 under cold stress is dependent on salicylic acid (SA) biosynthesis. ",
"Proline accumulation has been reported in plants under cold stress. The Citrus trifoliata L. gene CtrP5CS1, that encodes for the pyrroline-5-carboxylate synthetase (P5CS), is essential for cold-induced proline accumulation. CtrTGA2 bound directly to the TGACG motif of the CtrP5CS1 promoter and activate its expression. Up-regulation of CtrP5CS1 and CtrTGA2 under cold stress is dependent on salicylic acid (SA) biosynthesis. "
] | https://doi.org/10.1093/plcell/koae290 | Woody Perennials & Trees | ENVIRONMENT | 10.1093/plcell/koae290 | 2,024 | 2 | 2 | The Plant Cell | true |
How is the susceptibility of Arabidopsis plants to viral infections affected by a combination of heat and drought stress? | ENVIRONMENT - BIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis there are detectable differences in susceptibility to TuMV (Turnip mosaic potyvirus) when a single virus stress or a combined virus and drought stress is applied. The combination of virus infection with heat or heat and drought leads to a decrease of the level of P3, the viral gene used to quantify the level of virus accumulation, indicating that heat or combined heat and drought stress decreases the susceptibility of Arabidopsis to virus infection.",
"In Arabidopsis there are no detectable differences in susceptibility to TuMV (Turnip mosaic potyvirus) when a single virus stress or a combined virus and drought stress is applied. The combination of virus infection with heat or heat and drought leads to no change of the level of P3, the viral gene used to quantify the level of virus accumulation, indicating that heat or combined heat and drought stress does not affect the susceptibility of Arabidopsis to virus infection.",
"In Arabidopsis there are no detectable differences in susceptibility to TuMV (Turnip mosaic potyvirus) when a single virus stress or a combined virus and drought stress is applied. The combination of virus infection with heat or heat and drought leads to an increase of the level of P3, the viral gene used to quantify the level of virus accumulation, indicating that heat or combined heat and drought stress increases the susceptibility of Arabidopsis to virus infection."
] | doi: 10.1104/pp.113.221044. | Model Organisms | ENVIRONMENT | 10.1104/pp.113.221044 | 2,013 | 438 | 2 | Plant Physiology | true |
How is the evolution of Turnip mosaic potyvirus (TuMV) affected by severe drought conditions and what are the salicylic acid (SA) levels in plants infected with standard- and drought-evolved viruses? | ENVIRONMENT - BIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"Viruses evolved under drought conditions accumulate more mutations and, in contrast to viruses evolved in standard conditions, the mutations are randomly distributed across the different viral cistrons. Plants infected with standard- or drought-evolved viruses show a significant decrease in salicylic acid (SA) levels compared to non-infected plants. ",
"Viruses evolved under drought conditions accumulate the same number of mutations as viruses evolved in standard conditions, and the mutations are randomly distributed across the different viral cistrons. Plants infected with standard- or drought-evolved viruses show no changes in salicylic acid (SA) levels compared to non-infected plants. ",
"Viruses evolved under drought conditions accumulate less mutations and, as in the case of viruses evolved in standard conditions, the mutations are not randomly distributed and accumulate in the VPg cistron. Plants infected with standard- or drought-evolved viruses show a significant increase in salicylic acid (SA) levels compared to non-infected plants. "
] | doi: 10.1073/pnas.2020990118. | Model Organisms | ENVIRONMENT | 10.1073/pnas.2020990118 | 2,021 | 79 | 2 | Proceedings of the National Academy of Sciences | true |
Which is the role of the Cucumber mosaic virus (CMV) protein 2b in the response to drought stress in Arabidopsis thaliana and how does it affect abscisic acid (ABA)-mediated signaling? | ENVIRONMENT - BIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"The CMV 2b protein is responsible for the increase of drought tolerance in infected Arabidopsis plants. 2b exerts this role by interfering with the regulation of gene expression mediated by ABA, a phytohormone with a key role in regulating drought responses. ABA levels are not altered in CMV infected plants, but the expression of RD29A, an ABA- and desiccation-responsive gene, is induced in mock-treated plants but not in CMV-infected plants in response to drought stress.",
"The CMV 2b protein is responsible for the increase of drought tolerance in infected Arabidopsis plants. 2b exerts this role by interfering with the regulation of gene expression mediated by ABA, a phytohormone with a key role in regulating drought responses. ABA levels are increased in CMV infected plants, and the expression of RD29A, an ABA- and desiccation-responsive gene, is induced in mock-treated and, to less extend, in CMV-infected plants in response to drought stress.",
"The CMV 2b protein is responsible for the increase of drought tolerance in infected Arabidopsis plants. 2b exerts this role by interfering with the regulation of gene expression mediated by ABA, a phytohormone with a key role in regulating drought responses. ABA levels are reduced in CMV infected plants, and the expression of RD29A, an ABA- and desiccation-responsive gene, is induced in mock-treated plants and, to less extend, in CMV-infected plants in response to drought stress."
] | https://doi.org/10.1111/j.1364-3703.2012.00840.x | Model Organisms | ENVIRONMENT | 10.1111/j.1364-3703.2012.00840.x | 2,012 | 94 | 0 | Molecular Plant Pathology | true |
What is the role of artificial micro RNAs (amiRNAs) and synthetic trans-acting RNAs (syn-tasiRNAs), two types of artificial sRNAs (art-RNAs), in triggering systemic silencing (SS) of the magnesium chelatase subunit CHLI encoded by the Nicotiana benthamiana SULFUR gene (NbSu) and how do they move to exert their function? | PLANT BIOTECHNOLOGY | [
"Nicotiana benthamiana"
] | [
"The expression of a 21-nt long amiRNA designed to silence NbSu is able to induce SS in upper leaves. This process is characterized by a strong chlorosis near to the leaf veins. The expression of a 22-nucleotide form of the same amiRNA did not induce SS despite inducing the production of 21-nucleotide-phased small interfering RNAs (siRNAs). Transient expression of the 21-nt long syn-tasiRNbSu-2 triggers SS in a similar manner, and since the process does not requires transitivity, it is assumed that both classes of art-sRNAs are able to move to the surrounding cells via plasmodesmata and to distant tissues trough the phloem.",
"The expression of a 21-nt long amiRNA designed to silence NbSu is not able to induce SS in upper leaves, a process that is characterized by a strong chlorosis in the complete leaf. The expression of a 22-nucleotide form of the same amiRNA induces SS via inducing the production of 21-nucleotide-phased small interfering RNAs (siRNAs). Transient expression of the 21-nt long syn-tasiRNbSu-2 does not triggers SS, and since the process requires transitivity, it is assumed that only 21-nucleotide phased siRNAs are able to move to the surrounding cells via plasmodesmata and to distant tissues trough the phloem.",
"The expression of a 21-nt long amiRNA designed to silence NbSu is able to induce SS in upper leaves. This process is characterized by a mild chlorosis near to the leaf veins. The expression of a 22-nucleotide form of the same amiRNA also induces SS via inducing the production of 21-nucleotide-phased small interfering RNAs (siRNAs). Transient expression of the 21-nt long syn-tasiRNbSu-2 triggers SS in a similar manner, and since the process does requires transitivity, it is assumed that the derived secondary siRNAs are able to move to the surrounding cells via plasmodesmata and to distant tissues trough the phloem."
] | doi: 10.1111/tpj.15730. | Solanaceae & Relatives | PLANT BIOTECHNOLOGY | 10.1111/tpj.15730 | 2,022 | 10 | 0 | The Plant Journal | true |
What are the advantages and disadvantages of using a Potato virus X (PVX)-based system to induce silencing in Nicotiana benthamiana plants? | PLANT BIOTECHNOLOGY | [
"Nicotiana benthamiana"
] | [
"The use of a PVX-based viral vector makes it possible to trigger widespread silencing in Nicotiana benthamiana plants. The advantages of this system are that it is a stable and completely DNA-free approach. Crude extracts prepared from infected plants expressing the desired construct can be used for transmitting the viral vector to new plants by spraying. The system has no disadvantages, since the use of PVX-based viral vector does not induces symptoms typically present in PVX infected plants, such as mild leaf curling, even over long periods after agroinoculation.",
"The use of a PVX-based viral vector makes it possible to trigger widespread silencing in Nicotiana benthamiana plants. The advantages of this system are that it is a non-transgenic and completely DNA-free approach. Crude extracts prepared from infected plants expressing the desired construct can be used for transmitting the viral vector to new plants by spraying. A disadvantage of the use of viral vectors is that symptoms typically induced by PVX infection, such as mild leaf curling, are observed on the infected plants shortly after agroinoculation.",
"The use of a PVX-based viral vector makes it possible to trigger only local silencing in Nicotiana benthamiana leaves. The advantages of this system are that it is a non-transgenic and completely DNA-free approach. Crude extracts prepared from infected leaves expressing the desired construct can be used for transmitting the viral vector to new leaves by spraying. A disadvantage of the use of viral vectors is that symptoms typically induced by PVX infection, such as mild leaf curling, are observed on the infected plants shortly after agroinoculation."
] | doi: 10.1093/nar/gkad747. | Solanaceae & Relatives | PLANT BIOTECHNOLOGY | 10.1093/nar/gkad747 | 2,023 | 16 | 1 | Nucleic Acids Research | true |
What was the first example of a long noncoding RNA capturing a miRNA by target mimicry in any living organism and what is it involved in? Indicate the corresponding organism and describe the associated molecular mechanism. | GENE REGULATION - PTGS | [
"Arabidopsis thaliana"
] | [
"The first example of a lncRNA exerting a role as a miRNA target mimicry was INDUCED BY PHOSPHATE STARVATION 1 (IPS1) from Arabidopsis thaliana. It is a transcript recognized by miRNA166, including a mismatch in the 11th position. As a result, the miRNA remains paired to IPS2 without clivage, and miRNA166 is titered and blocked. IPS1 is induced in response to phosphate starvation, blocking miRNA and increasing the transcript levels of the miRNA166 target PHO3 gene.",
"The first example of a lncRNA exerting a role as a miRNA target mimicry was INDUCED BY PHOSPHATE STARVATION 1 (IPS1) from Arabidopsis thaliana. It is a transcript recognized by miRNA399, including a mismatch in the 11th position. As a result, the miRNA remains paired to IPS2 without clivage, and miRNA399 is titered and blocked. IPS1 is induced in response to phosphate starvation, blocking miRNA and increasing the transcript levels of the miRNA399 target PHO2 gene.",
"The first example of a lncRNA exerting a role as a miRNA target mimicry was COOLAIR from Arabidopsis thaliana. It is a transcript recognized by miRNA399, including a mismatch in the 11th position. As a result, the miRNA remains paired to COOLAIR without clivage, and miRNA399 is titered and blocked. COOLAIR is induced in response to phosphate starvation, blocking miRNA and increasing the transcript levels of the miRNA399 target PHO2 gene."
] | doi.org/10.1038/ng2079 | Model Organisms | GENE REGULATION | 10.1038/ng2079 | 2,007 | 1,702 | 1 | Nature Genetics | true |
What was the first lncRNA identified in plants, in what species and what are the molecular and the physiological mechanisms it involved in? | GENE REGULATION - EPIGENETICS AND TGS | [
"Medicago truncatula"
] | [
"The first lncRNA identified in plants was EARLY NODULIN 20 (ENOD20) from the model legume Medicago sativa. ENOD20 participates in the symbiotic interaction with nitrogen-fixing bacteria forming nodules in roots. At the molecular level, ENOD20 was described as an interactor of the nuclear speckle protein RBP1, and it can relocalize its protein partner from the nucleus to the cytoplasm. It was proposed that ENOD20 may be involved in splicing regulation, although this remains unkown. Furthermore, it was shown that ENOD20 can encode small peptides involved in carbom metabolism in the nodules.",
"The first lncRNA identified in plants was COOLAIR from the model Arabidopsis thaliana. COOLAIR participates in root development. At the molecular level, COOLAIR was described as an interactor of the nuclear factor FLD, and it can relocalize its protein partner from the nucleus to the cytoplasm. It was proposed that COOLAIR may be involved in splicing regulation, although this remains unkown. Furthermore, it was shown that COOLAIR can encode small peptides involved in carbom metabolism in roots.",
"The first lncRNA identified in plants was EARLY NODULIN 40 (ENOD40) from the model legume Medicago truncatula. ENOD40 participates in the symbiotic interaction with nitrogen-fixing bacteria forming nodules in roots. At the molecular level, ENOD40 was described as an interactor of the nuclear speckle protein RBP1, and it can relocalize its protein partner from the nucleus to the cytoplasm. It was proposed that ENOD40 may be involved in splicing regulation, although this remains unkown. Furthermore, it was shown that ENOD40 can encode small peptides involved in carbom metabolism in the nodules."
] | DOI: 10.1002/j.1460-2075.1994.tb06839.x | Model Organisms | GENE REGULATION | 10.1002/j.1460-2075.1994.tb06839.x | 1,994 | 242 | 2 | The EMBO Journal | true |
How does the lncRNA APOLO regulate the locus of the RHD6 gene in Arabidopsis thaliana in response to low temperatures? | GENE REGULATION - EPIGENETICS AND TGS | [
"Arabidopsis thaliana"
] | [
"In response to low temperatures, APOLO levels decrease, leading to effective recruitment of LHP1 from the RHD6 locus, modulating the epigenetic environment of the locus and resulting in the closing of a chromatin loop. APOLO RNA maintains the R-loop structure formed with the RHD6 locus, which has been demonstrated to directly contribute to the transcriptional repression of RHD6. In addition, APOLO participates in the decoy of WRKY42 away from the RHD6 promoter in response to cold. Consequently, RHD6 transcription is enhanced which contributes through downstream genes RSL2/4 to the promotion of root hair cell expansion. This is reflected in the root phenotype of plants overexpressing and silencing APOLO and WRK42 wherein distinct patterns of root hair are observed compared to the wildtype.",
"In response to low temperatures, APOLO levels increase, leading to effective decoying of CLF from the RHD6 locus, modulating the epigenetic environment of the locus and resulting in the opening of a chromatin loop. APOLO RNA maintains the R-loop structure formed with the RHD6 locus, which has been demonstrated to directly contribute to the transcriptional activation of RHD6. In addition, APOLO participates in the recruitment of FRIGIDA to the RHD6 promoter in response to cold. Consequently, RHD6 transcription is enhanced which contributes through downstream genes RSL2/4 to the promotion of root hair cell expansion. This is reflected in the root phenotype of plants overexpressing and silencing APOLO and FRIGIDA wherein distinct patterns of root hair are observed compared to the wildtype.",
"In response to low temperatures, APOLO levels increase, leading to effective decoying of LHP1 from the RHD6 locus, modulating the epigenetic environment of the locus and resulting in the opening of a chromatin loop. APOLO RNA maintains the R-loop structure formed with the RHD6 locus, which has been demonstrated to directly contribute to the transcriptional activation of RHD6. In addition, APOLO participates in the recruitment of WRKY42 to the RHD6 promoter in response to cold. Consequently, RHD6 transcription is enhanced which contributes through downstream genes RSL2/4 to the promotion of root hair cell expansion. This is reflected in the root phenotype of plants overexpressing and silencing APOLO and WRK42 wherein distinct patterns of root hair are observed compared to the wildtype."
] | DOI: 10.1016/j.molp.2021.03.008 | Model Organisms | GENE REGULATION | 10.1016/j.molp.2021.03.008 | 2,021 | 94 | 2 | Molecular Plant | true |
How does the lncRNA VAS1 regulate the TaVRN1 locus in wheat? | GENE REGULATION - EPIGENETICS AND TGS | [
"Triticum aestivum"
] | [
"VAS-mediated repression of the TaVRN1 locus involves the decoy of RF2b. It was shown that winter wheat overexpressing VAS lncRNA early vernalizes compared to wildtype, resulting in differences in inflorescence structures and characteristics. The lncRNA VAS is produced from an alternatively spliced mRNA of TaVRN1 locus, specially repressed during early stages of vernalization. A systematic approach allowed the identification of a range of potential VAS protein interactors, including RF2b, a bZIP TF that together with RF2a form a heterodimer to directly regulate TaVRN1 via an Sp1 motif. It was proposed that before vernalization TaVRN1 and VAS are expressed at a basal level, and the VAS locus is wrapped in a chromatin loop. This loop persists during early vernalization; but VAS transcripts are more numerous and start to associate with RF2b that together with RF2a bind to the TaVRN1 promoter and preclude its expression. Late vernalization represses the opening of the chromatin loop, which releases the Sp1 motif and the full TaVRN1 locus, making all its exons non-accessible to the transcription machinery.",
"VAS-mediated activation of the TaVRN1 locus involves the recruitment of RF2b. It was shown that winter wheat overexpressing VAS lncRNA early vernalizes compared to wildtype, resulting in differences in inflorescence structures and characteristics. The lncRNA VAS is produced from an alternatively spliced mRNA of TaVRN1 locus, specially induced during early stages of vernalization. A systematic approach allowed the identification of a range of potential VAS protein interactors, including RF2b, a bZIP TF that together with RF2a form a heterodimer to directly regulate TaVRN1 via an Sp1 motif. It was proposed that before vernalization TaVRN1 and VAS are expressed at a basal level, and the VAS locus is wrapped in a chromatin loop. This loop persists during early vernalization; but VAS transcripts are more numerous and start to associate with RF2b that together with RF2a bind to the TaVRN1 promoter and induce its expression. Late vernalization induces the opening of the chromatin loop, which releases the Sp1 motif and the full TaVRN1 locus, making all its exons accessible to the transcription machinery.",
"VAS-mediated activation of the TaVRN1 locus involves the recruitment of REF6. It was shown that winter wheat overexpressing VAS lncRNA early vernalizes compared to wildtype, resulting in differences in inflorescence structures and characteristics. The lncRNA VAS is produced from an alternatively spliced mRNA of TaVRN1 locus, specially induced during late stages of vernalization. A systematic approach allowed the identification of a range of potential VAS protein interactors, including REF6, a TF that together with REF6b form a heterodimer to directly regulate TaVRN1 via an Sp1 motif. It was proposed that before vernalization TaVRN1 and VAS are expressed at a basal level, and the VAS locus is wrapped in a chromatin loop. This loop persists during late vernalization; but VAS transcripts are more numerous and start to associate with REF6 that together with REF6b bind to the TaVRN1 promoter and induce its expression. Late vernalization induces the opening of the chromatin loop, which releases the Sp1 motif and the full TaVRN1 locus, making all its exons accessible to the transcription machinery."
] | DOI:https://doi.org/10.1016/j.molp.2021.05.026 | Cereal Grains | GENE REGULATION | 10.1016/j.molp.2021.05.026 | 2,021 | 58 | 1 | Molecular Plant | true |
What proteins have been identified as molecular partners of the Arabidopsis lncRNA ASCO? In what molecular mecanism are they all involved in? | GENE REGULATION - ALTERNATIVE SPLICING | [
"Arabidopsis thaliana"
] | [
"The proteins identified so far as interactors of the lncRNA ASCO are NSRa, PRP8 and SmD1b, which are involved in splicing.",
"The proteins identified so far as interactors of the lncRNA ASCO are LHP1 and VIM1, which are involved in epigenetics.",
"The proteins identified so far as interactors of the lncRNA ASCO are GRP7, PRP64 and SmD1a, which are involved in splicing."
] | DOI: 10.15252/embr.201948977 | Model Organisms | GENE REGULATION | 10.15252/embr.201948977 | 2,020 | 63 | 0 | EMBO reports | true |
What is the molecular mechanism that leads to nitrate-dependent regulation of transcription by the NLP7 transcription factor in Arabidopsis thaliana? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"Nitrate resupply triggers the cytosolic accumulation of NLP7 via a nuclear import mechanism. Following a nitrate signal, MAPKs phosphorylate NLP7 in the cytosol and prevent NLP7 nuclear import. In addition direct binding of nitrate to the NLP7 protein is required to inhibit NLP7.",
"Nitrate depletion triggers the nuclear accumulation of NLP7 by protein degradation. FProtein phosphate 2A dephosphorylate NLP7 in the cytosol and prevent NLP7 nuclear import. In addition direct binding of nitrate to the C-terminal of the NLP7 protein is required to stabilise NLP7",
"Nitrate resupply triggers the nuclear accumulation of NLP7 via a nuclear retention mechanism. Following a nitrate signal, CDKs phosphorylate NLP7 in the nucleus and prevent NLP7 nuclear export. In addition direct binding of nitrate to the NLP7 protein is required to activate NLP7."
] | .doi: 10.1016/j.plantsci.2023.111842. | Model Organisms | GENE REGULATION | 10.1016/j.plantsci.2023.111842 | 2,023 | 8 | 2 | Plant Science | true |
The transcription factors NLP7 and NLP2 are major players for the response of A. thaliana to nitrate availability. What are the main differences in the metabolic phenotypes of loss-of-function mutants of either of these proteins? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"Specialised metabolism is strongly modified in the nlp2-1 mutant whereas nlp7-1 mutant showed a modified central metabolism in rosettes.",
"The nlp2-1 mutant displays changes in nitrate assimilation whereas the nlp7-1 mutant is defected in amino acid degradation.",
"Central metabolism is modified in both single mutant nlp2-1 and nlp7-1. Whereas the loss of NLP2 leads to a modification of glycolysis, loss of NLP7 leads to a depletion of TCA cycle intermediates in rosettes."
] | doi: 10.1093/plcell/koad025. | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1093/plcell/koad025 | 2,023 | 28 | 2 | The Plant Cell | true |
What are the physiological and developmental processes that are regulated by NLP8 in Arabidopsis? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"NLP8 is involved in the regulation of nitrate-regulated seed abortion. In the absence of NLP8, ABA degradation by CYP701A 2 is reduced, because nitrate induction of CYP701A2 protein accumulation is regulated by NLP8.",
"NLP8 is involved in the regulation of nitrite-regulated seed germination. In the absence of NLP8, nitrite production by CYP707A 2 is modified, because nitrate induction of CYP707A2 transcript accumulation is regulated by NLP8.",
"NLP8 is involved in the regulation of nitrate-regulated seed dormancy. In the absence of NLP8, ABA degradation by CYP707A 2 is reduced, because nitrate induction of CYP707A2 transcript accumulation is regulated by NLP8."
] | DOI: 10.1038/ncomms13179 | Model Organisms | GENE REGULATION | 10.1038/ncomms13179 | 2,016 | 158 | 2 | Nature Communications | true |
x | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"x",
"x",
"x"
] | https://doi.org/10.1093/jxb/eru261 | Non-specific | GENE REGULATION | 10.1093/jxb/eru261 | 2,014 | 159 | 0 | Journal of Experimental Botany | true |
What protein domain is involved in the interaction of NLP transcription factor in plants? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"The C-terminal PB1 domain",
"The RWP-RK domain",
"The N-terminal nitrate-sensing domain"
] | doi: 10.1007/s00018-019-03164-8. | Non-specific | GENE REGULATION | 10.1007/s00018-019-03164-8 | 2,019 | 71 | 0 | Cellular and Molecular Life Sciences | true |
What is the impact of transposon activity in regulating vitamin E (tocopherols) biosynthesis in tomato fruits? | GENOME AND GENOMICS | [
"Solanum lycopersicum"
] | [
"Vitamin E contents of tomato fruits are regulated, at least in part, at the transcription level of the enzyme encoding genes implicated in its biosynthesis. An insertion of a SINE transposable element in the promotor region of the 2-methyl-6-phytylquinol methyltransferase (namely VTE3(1)) encoding gene that catalyses one of the final steps in the biosynthesis of γ- and α-tocopherols activates cytosine methylation of this DNA region and silence transcription of the gene through the RdDM mechanism. ",
"Vitamin E contents of tomato fruits are regulated, at least in part, at the transcription level of the enzyme encoding genes implicated in its biosynthesis. An insertion of a SINE transposable element in the promotor region of the 2-methyl-6-phytylquinol methyltransferase (namely VTE3(1)) encoding gene that catalyses one of the final steps in the biosynthesis of γ- and α-tocopherols repress cytosine methylation of this DNA region and repress transcription of the gene through the RdDM mechanism.",
"Vitamin E contents of tomato fruits are regulated, at least in part, at the transcription level of the enzyme encoding genes implicated in its biosynthesis. An insertion of a SINE transposable element in the promotor region of the 2-methyl-6-phytylquinol methyltransferase (namely VTE3(1)) encoding gene that catalyses one of the final steps in the biosynthesis of γ- and α-tocopherols repress cytosine methylation of this DNA region and activate transcription of the gene through the RdDM mechanism. "
] | 10.1038/ncomms5027 | Solanaceae & Relatives | GENOME AND GENOMICS | 10.1038/ncomms5027 | 2,014 | 177 | 0 | Nature Communications | true |
Which mechanism/s impact environmental conditions through on vitamin E content of tomato fruits? | GENOME AND GENOMICS | [
"Solanum lycopersicum"
] | [
"Controlled environmental conditions (i.e. greenhouse conditions) result in DNA-cytosine demethylation of a SINE TE inserted in the promoter region of the VTE3(1) gene and an activation of its transcription and a consequent increment in the tocopherol levels of the tomato fruits. ",
"Uncontrolled environmental conditions (i.e. open field conditions) result in DNA-cytosine demethylation of a SINE TE inserted in the promoter region of the VTE3(1) gene and an activation of its transcription and a consequent increment in the tocopherol levels of the tomato fruits. ",
"Uncontrolled environmental conditions (i.e. open field conditions) result in DNA-cytosine methylation of a SINE TE inserted in the promoter region of the VTE3(1) gene and an activation of its transcription and a consequent increment in the tocopherol levels of the tomato fruits. "
] | 10.1038/ncomms5027 | Solanaceae & Relatives | GENOME AND GENOMICS | 10.1038/ncomms5027 | 2,014 | 177 | 1 | Nature Communications | true |
In Arabidopsis, are TEs inserted randomly or towards distinct sets of genes and associated with specific chromatin states? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"At least three kinds of TE, the LTR-retrotransposon ATCOPIA93 and the two DNA transposon families ATENSPM3 and VANDAL21 prefer the euchromatin as substrate for their integrations and more specifically ATCOPIA93 insertions are overrepresented in genes whose body is solely enriched in H2A.Z histone variant.",
"At least three kinds of TE, the LTR-retrotransposon ATCOPIA93 and the two DNA transposon families ATENSPM3 and VANDAL21 were found to be randomly inserted across the Arabidopsis genome. ",
"At least three kinds of TE, the LTR-retrotransposon ATCOPIA93 and the two DNA transposon families ATENSPM3 and VANDAL21 prefer the heterochromatin as substrate for their integrations and more specifically ATCOPIA93 insertions are underrepresented in genes whose body is solely enriched in H2A.Z histone variant."
] | https://doi.org/10.1038/s41467-019-11385-5 | Model Organisms | GENOME AND GENOMICS | 10.1038/s41467-019-11385-5 | 2,019 | 145 | 0 | Nature Communications | true |
Which are the most abundant mobile genetic elements in the plant genomes? | GENOME AND GENOMICS | [
"non-specific"
] | [
"In general, class II (DNA TEs) are more prevalent in plant genomes.",
"Both kinds of TEs (RNA for class I (retrotransposons), and DNA for class II (DNA TEs)) can be equally distributed along plant genomes ",
"In general, class I elements (retrotransposons) are more prevalent in genomes as their ‘copy and paste’ replicative transposition leads to an increase in copy number as they transpose. Among them, Long Terminal Repeat Retrotransposons (LTR-RTs) are the most abundant in plant genomes. "
] | https://doi.org/10.1016/j.pbi.2023.102418 | Non-specific | GENOME AND GENOMICS | 10.1016/j.pbi.2023.102418 | 2,023 | 22 | 2 | Current Opinion in Plant Biology | true |
Which are the most abundant gene-proximal TE in plant genomes? | GENOME AND GENOMICS | [
"non-specific"
] | [
"Gypsy, Copia and LINE make up about 80% of all gene-proximal TEs ",
"The most abundant TE family adjacent to genes are Helitron and MuDR, summing up to about 70% of all gene-proximal TEs ",
"There is not a general pattern of TE abundancy for plant genomes. This depends on the plant species"
] | https://doi.org/10.1186/s12864-021-08215-8 | Non-specific | GENOME AND GENOMICS | 10.1186/s12864-021-08215-8 | 2,022 | 31 | 2 | BMC Genomics | true |
Which transcription factor has been found to be requiered for chromatin spatial reorganization in response to heat stress in tomato? | GENE REGULATION - TRANSCRIPTION | [
"Solanum lycopersicum"
] | [
"HSFA1A was demonstrated to be required for chromatin spatial reorganization in response to heat stress in tomato",
"TCP15 was demonstrated to be required for chromatin spatial reorganization in response to heat stress in tomato",
"HSFA1A was not demonstrated to be required for chromatin spatial reorganization in response to heat stress in tomato"
] | doi: 10.1038/s41467-023-36227-3 | Solanaceae & Relatives | GENE REGULATION | 10.1038/s41467-023-36227-3 | 2,023 | 59 | 0 | Nature Communications | true |
What is the impact of an ectopic deposition of H3K9ac on TAD-like boundaries in tomato? | GENE REGULATION - EPIGENETICS AND TGS | [
"Solanum lycopersicum"
] | [
"The ectopic deposition of H3K9ac do not impact chromatin 3D structure and TAD like boundaries",
"The ectopic deposition of H3K9ac triggered a reorganization of the 3D chromatin structure and plays a major role in the determination of TAD-like boundaries",
"The ectopic deposition of H3K123 triggered a reorganization of the 3D chromatin structure and plays a major role in the determination of TAD-like boundaries"
] | doi: 10.1073/pnas.2400737121 | Solanaceae & Relatives | GENE REGULATION | 10.1073/pnas.2400737121 | 2,024 | 0 | 1 | Proceedings of the National Academy of Sciences | true |
How is the wheat chromatin architecture organized? | GENE REGULATION - TRANSCRIPTION | [
"Triticum aestivum"
] | [
"The wheat chromatin architecture is organized around long non coding RNA",
"The wheat chromatin architecture is organized in genome territories and transcription factories ",
"The wheat chromatin architecture is organized in epigenetics territories and translation factories "
] | doi: 10.1186/s13059-020-01998-1 | Cereal Grains | GENE REGULATION | 10.1186/s13059-020-01998-1 | 2,020 | 119 | 1 | Genome Biology | true |
Which histone demethylase controls H3K27me1 homeostasis in Arabidopsis thaliana euchromatin? | GENE REGULATION - EPIGENETICS AND TGS | [
"Arabidopsis thaliana"
] | [
"REF6 controls H3K27me1 homeostasis in euchromatin",
"LHP1 controls H3K27me1 homeostasis in euchromatin",
"CLF controls H3K27me1 homeostasis in euchromatin"
] | doi: 10.7554/eLife.58533 | Model Organisms | GENE REGULATION | 10.7554/eLife.58533 | 2,020 | 41 | 0 | eLife | true |
How GCN5 modulates salicylic acid homeostasis? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana"
] | [
"GCN5 modulates salicylic acid homeostasis by regulating H3K27me3 levels at the 5' and 3' ends of its target genes ",
"GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5' and 3' ends of intron ",
"GCN5 modulates salicylic acid homeostasis by regulating H3K14ac levels at the 5' and 3' ends of its target genes "
] | doi: 10.1093/nar/gkaa369 | Model Organisms | GENE REGULATION | 10.1093/nar/gkaa369 | 2,020 | 61 | 2 | Nucleic Acids Research | true |
What are the general characteristics and architecture of the genomes of virus members of family Rhabdoviridae? | GENOME AND GENOMICS | [
"non-specific"
] | [
"The genomes of rhabdoviruses are negative-sense and single-stranded RNA of approximately 10–16 kb, including monosegmented, bi segmented and tri segmented members. Most rhabdovirus genomes have five genes encoding the structural proteins (N, P, M, G and L) with variations and additional genes and only the N and L genes are present in all rhabdoviruses.",
"The genomes of rhabdoviruses are negative-sense and double-stranded RNA of approximately 10–16 kb, including monosegmented, bi segmented and tri segmented members. Most rhabdovirus genomes have five genes encoding the structural proteins (N, P, M, G and L) with variations and additional genes and only the N and L genes are present in all rhabdoviruses.",
"The genomes of rhabdoviruses are negative-sense and single-stranded RNA of approximately 10–16 kb, including monosegmented and bi segmented members. Most rhabdovirus genomes have five genes encoding the structural proteins (N, P, M, G and L) with variations and additional genes and only the G and L genes are present in all rhabdoviruses."
] | https://doi.org/10.3390/v15122402 https://doi.org/10.1099/jgv.0.001689 | Non-specific | GENOME AND GENOMICS | 10.1099/jgv.0.001689 | 2,022 | 92 | 0 | Journal of General Virology | true |
What viruses are linked to the corn leafhopper (Dalbulus maidis)? | ENVIRONMENT - BIOTIC STRESS | [
"Zea mays"
] | [
"The corn leafhopper is the vector of two viruses: maize rayado fino virus and maize striate mosaic virus and has also been reported to be linked to five insect specific DNA viruses: a beny-like virus (Benyviridae), a bunya-like virus (Bunyaviridae), a iflavirus (Iflaviridae), a orthomyxo-like virus (Orthomyxoviridae), and a rhabdovirus (Rhabdoviridae)",
"The corn leafhopper is the vector of two viruses: maize rayado fino virus and maize striate mosaic virus and has also been reported to be linked to six insect specific RNA viruses: a beny-like virus (Benyviridae), a bunya-like virus (Bunyaviridae), two iflaviruses (Iflaviridae), a orthomyxo-like virus (Orthomyxoviridae), and a rhabdovirus (Rhabdoviridae)",
"The corn leafhopper is the vector of maize rayado fino virus and has also been reported to be linked to six insect specific RNA viruses: a beny-like virus (Benyviridae), a bunya-like virus (Bunyaviridae), a iflavirus (Iflaviridae), two orthomyxo-like viruses (Orthomyxoviridae), and a rhabdovirus (Rhabdoviridae)"
] | https://doi.org/10.3390/v16101583 | Cereal Grains | ENVIRONMENT | 10.3390/v16101583 | 2,024 | 0 | 1 | Viruses | true |
What are the hosts of ophioviruses? | ENVIRONMENT - BIOTIC STRESS | [
"non-specific"
] | [
"Ophioviruses infect both monocots and dicots, mostly trees, shrubs and some ornamentals and have recently been linked to been linked to white flies, mosses, liverworts and ferns. ",
"Ophioviruses infect both monocots and dicots, mostly trees, shrubs and some ornamentals and have recently been linked to mosses, liverworts and ferns.",
"Ophioviruses infect both monocots and dicots, mostly trees, shrubs and some ornamentals."
] | https://doi.org/10.3390/v15040840 | Non-specific | ENVIRONMENT | 10.3390/v15040840 | 2,023 | 9 | 1 | Viruses | true |
Which viruses infect the 'living fossil' gymnosperm Welwitschia mirabilis, and how are they transmitted? | ENVIRONMENT - BIOTIC STRESS | [
"Welwitschia mirabilis"
] | [
"Welwitschia mirabilis is infected with caulimoviruses and geminiviruses and we do not know how they are transmitted.",
"Welwitschia mirabilis is infected with caulimoviruses and geminiviruses which are transmitted by aphids and white flies, respectively.",
"Welwitschia mirabilis is infected with caulimoviruses which are transmitted by aphids."
] | https://doi.org/10.1016/j.gene.2022.146806 | Woody Perennials & Trees | ENVIRONMENT | 10.1016/j.gene.2022.146806 | 2,022 | 6 | 0 | Gene | true |
What are the characteristics of koshoviruses and their genomes? | GENOME AND GENOMICS | [
"non-specific"
] | [
"Koshoviruses are plant infecting viruses with long monosegmented RNA genomes of 21-23 kb with similarities to the animal linked flavoviruses. They encode two large polyproteins with a helicase and RNA-dependent RNA polymerase and several additional divergent domains, including AlkB oxygenase, trypsin-like serine protease, methyltransferase, and envelope E1 flavi-like domains.",
"Koshoviruses are plant infecting viruses with long monosegmented RNA genomes of 21-23 kb with similarities to the animal linked flaviviruses. They encode a single large polyprotein with a helicase and RNA-dependent RNA polymerase and several additional divergent domains, including AlkB oxygenase, trypsin-like serine protease, methyltransferase, and envelope E1 flavi-like domains.",
"Koshoviruses are plant infecting viruses with long bisegmented RNA genomes of 21-23 kb with similarities to the animal linked flaviviruses. They encode two large polyprotein with a helicase and RNA-dependent DNA polymerase and several additional divergent domains, including AlkB oxygenase, trypsin-like serine protease, methyltransferase, and envelope E1 flavi-like domains."
] | https://link.springer.com/article/10.1007/s00705-023-05813-7 | Non-specific | GENOME AND GENOMICS | 10.1007/s00705-023-05813-7 | 2,023 | 15 | 1 | Archives of Virology | true |
Which membrane proteins have been involved in the transport of UDP-xylose during the biosynthesis of xylan? | PLANT BIOTECHNOLOGY | [
"Arabidopsis thaliana"
] | [
"The membrane proteins involved in the biosynthesis of xylan are the xylose transporters.",
"The membrane proteins involved in the transport of UDP-xylose for the biosynthesis of xylan are the UDP-xylose transporters.",
"The sugar translocators are the membrane proteins that have been involved in the biosynthesis of xylan."
] | https://doi.org/10.1093/jxb/erx448 | Model Organisms | PLANT BIOTECHNOLOGY | 10.1093/jxb/erx448 | 2,017 | 25 | 1 | Journal of Experimental Botany | true |
How does the biosynthesis of the rhamnogalacturonan backbone structure is made in the Golgi apparatus? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"The biosynthesis of rhamnogalacturonan backbone requires the substrates UDP´galacturonic acid and UDP-rhamnose. These nucleotide sugars are utilized by the rhamnosyltransferase (RRT) and the RGI-Galacturonosyltransferase (RGGAT) to make the alternating backbone structure.",
"The biosynthesis of the rhamnogalacturonan I backbone is carried out by a glycosyltransferase that has the capacity to transfer in an alternate manner rhamnose and galacturonic acid into the elongating polymer.",
"The biosynthesis of the rhamnogalacturonan I backbone requires the sugars rhamnose and galacturonic acid. These sugars are utilized by the rhamnosyltransferase (RRT) and the RGI-Galacturonosyltransferase (RGGAT) to make the alternating backbone structure."
] | https://doi.org/10.1038/s41477-022-01270-3 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1038/s41477-022-01270-3 | 2,022 | 24 | 0 | Nature Plants | true |
Why CAM plants are becoming interesting subjects to study as climate change challenges increase? | ENVIRONMENT - ABIOTIC STRESS | [
"non-specific"
] | [
"One of the major challenges of climate change is drought. Understanding how plants can be more efficient in water use efficiency (WUE) becomes an interesting aspect. CAM plants are very efficient in WUE and can save up to 40% water. Transferring this capacity to C3 plants could result in crops that need less water to thrive.",
"CAM plants capture CO2 at night and convert it to citric acid, which is efficiently used in the Calvin cycle. In this way, CAM plants can capture more CO2 from the atmosphere, thus helping to reduce the greenhouse effect on Earth and the rise in temperature that is one of the causes of climate change.",
"Climate change is a major threat to agriculture, and the use of crops that can better cope with the challenges of climate change is emerging as a possible solution. In this regard, CAM crops have an increased capacity to cope with higher temperatures and flooding; thus, they emerge as good candidates to replace the current crops used in agriculture."
] | https://doi.org/10.1111/nph.13393 | Non-specific | ENVIRONMENT | 10.1111/nph.13393 | 2,015 | 191 | 0 | New Phytologist | true |
Softening of fruits is a trait that is highly appreciated in certain fuit such as tomatos. Understanding this process can be a way to extend shelf life of these fruits. On these regard what are the genes involved in this process that may be putative targets for creating new varieties? | PLANT BIOTECHNOLOGY | [
"Solanum lycopersicum"
] | [
"The cuticle is an important part of the tomato fruit. It is composed of complex lipids that provide a firm structure. The best way to obtain tomatoes with extended shelf life is to increase the biosynthesis of these complex lipids. Then, gene editing of the genes involved in cuticle biosynthesis should lead to extended shelf life of tomatoes.",
"The genes that code for cell wall degradation, such as expansin and polygalacturonase, appear to play an important role in the softening of tomato fruit and could be good candidates for a gene editing strategy aimed at producing tomatoes with an extended shelf life.",
"The tomato cell wall is very important in the softening process of the fruit. Cellulose and lignin are important components of the tomato fruit cell wall, therefore increasing the biosynthesis of genes coding for these structures may lead to extended shelf life in tomato fruit."
] | https://doi.org/10.1016/j.copbio.2022.102786 | Solanaceae & Relatives | PLANT BIOTECHNOLOGY | 10.1016/j.copbio.2022.102786 | 2,022 | 28 | 1 | Current Opinion in Biotechnology | true |
Plants appear to be an alternative for the massive production of N-glycoproteins of pharmaceutical interest. However, sialic acid is a critical sugar in animal N-glycoproteins that is not present in plant N-glycoproteins. Why do plants not have sialic acid in their N-glycoproteins? | PLANT BIOTECHNOLOGY | [
"Arabidopsis thaliana"
] | [
"The biosynthesis of N-glycoproteins and the incorporation of sialic acid takes place in the lumen of the Golgi apparatus, and a CMP-sialic acid transporter is required to incorporate the substrate needed for the reaction. Plants do not have this transporter; therefore, the substrate does not have access to the compartment where sialic acid incorporation takes place.",
"Plants synthesize glycoproteins and the modifications that occur in the N-glycan structure in the Golgi apparatus do not include sialic acid because the substrate is not produced in plants, therefore plant N-glycoproteins cannot receive this critical modification needed in animal cells.",
"The incorporation of sialic acid into N-glycoproteins requires a very specific enzyme that uses CMP-sialic acid to catalyze the incorporation of sialic acid into the N-glycan. The gene encoding this enzyme is missing in plants; therefore, this reaction cannot take place. "
] | https://doi.org/10.1038/nbt1104-1351 | Model Organisms | PLANT BIOTECHNOLOGY | 10.1038/nbt1104-1351 | 2,004 | 58 | 1 | Nature Biotechnology | true |
How many YTHDF proteins are there in Arabidopsis thaliana? | GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE | [
"Arabidopsis thaliana"
] | [
"There are 13 YTHDF proteins in Arabidopsis, called ECT1-ECT12 and CPSF30. ",
"There are 11 YTHDF proteins in Arabidopsis, called ECT1-ECT11. \n",
"There are 12 YTHDF proteins in Arabidopsis, called ECT1-ECT12."
] | https://doi.org/10.1105/tpc.17.00854 | Model Organisms | GENE REGULATION | 10.1105/tpc.17.00854 | 2,018 | 239 | 1 | The Plant Cell | true |
Which biological functions of m6A have been ascribed to the different YTHDF proteins in Arabidopsis thaliana? | GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE | [
"Arabidopsis thaliana"
] | [
"The best studied YTHDF protein in Arabidopsis thaliana is ECT2. Together with ECT3 and ECT4, ECT2 controls the morphogenesis of different plant organs, including leaves, trichomes, flowers, pods and roots. Additionally, ECT2, ECT3, ECT4 and ECT5 are necessary for resistance against alfalfa mosaic virus. Recent reports indicate that ECT8 is involved in the response to salinity stress and regulates SA signalling, and ECT1 is involved in stress responses mediated by the phytohormone abscisic acid.",
"The best studied YTHDF protein in Arabidopsis thaliana is ECT2. Together with ECT3 and ECT4, ECT2 controls the morphogenesis of different plant organs, including leaves, leaf hairs, flowers, fruits and roots. Additionally, ECT2, ECT3, ECT4 and ECT5 are necessary for resistance against at least one RNA virus. Recent reports indicate that ECT8 is involved in the response to salinity stress and regulates ABA signalling, and ECT1 is involved in stress responses mediated by the phytohormone salicylic acid.",
"The best studied YTHDF protein in Arabidopsis thaliana is ECT3. Together with ECT2 and ECT4, ECT3 controls the morphogenesis of different plant organs, including leaves, trichomes, flowers, siliques and roots. Additionally, ECT2, ECT3, ECT4 and ECT5 are necessary for resistance against at least one DNA virus. Recent reports indicate that ECT8 is involved in the response to cold stress and regulates ABA signalling, and ECT9 is involved in stress response mediated by the phytohormone salicylic acid."
] | https://doi.org/10.1016/j.pbi.2024.102650 | Model Organisms | GENE REGULATION | 10.1016/j.pbi.2024.102650 | 2,024 | 3 | 1 | Current Opinion in Plant Biology | true |
Which protein(s) interact with the m6A reader ECT2 in Arabidopsis thaliana? | GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE | [
"Arabidopsis thaliana"
] | [
"Arabidopsis thaliana ECT2 interacts with several members of the ALBA and poly(A)-binding protein (PABP) families.\n",
"Arabidopsis thaliana ECT2 interacts with the cleavage and polyadenylation complex factor CPSF30 through the YTH domains.\n",
"Arabidopsis thaliana ECT2 interacts with the DCP5 component of the decapping complex in phase-separated stress granules.\n"
] | https://doi.org/10.1016/j.pbi.2024.102650 | Model Organisms | GENE REGULATION | 10.1016/j.pbi.2024.102650 | 2,024 | 3 | 0 | Current Opinion in Plant Biology | true |
Is HAKAI essential for m6A deposition and development in Arabidopsis thaliana? | GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE | [
"Arabidopsis thaliana"
] | [
"Although HAKAI is one of the subunits of the m6A methyltransferase complex, its deficiency leads only to a mild reduction of m6A deposition in Arabidopsis. That is why, despite the fact that complete m6A deficiency causes arrest of embryo development, homozygous HAKAI mutants are viable and similar to wild type plants. ",
"HAKAI is one of the subunits of the m6A methyltransferase complex and, as such, it is essential for m6A deposition in Arabidopsis. Because complete m6A deficiency causes arrest of embryo development, homozygous loss of function mutation of HAKAI is lethal; the embryo cannot pass the globular stage",
"HAKAI is one of the subunits of the m6A methyltransferase complex and, as such, it is essential for m6A deposition in Arabidopsis. However, beecause m6A regulates stress responses and it is not necessary for plant development, homozygous HAKAI mutants are viable and similar to wild type plants.\n"
] | https://doi.org/10.1111/nph.14586 | Model Organisms | GENE REGULATION | 10.1111/nph.14586 | 2,017 | 377 | 0 | New Phytologist | true |
How does ECT8 regulate ABA signalling? | GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE | [
"Arabidopsis thaliana"
] | [
"ECT8 binds to the methylated site URUm6AY in the 3’UTR of the mRNA of the ABA signaling factor PYL7, thereby preventing its degradation by re-localization to p-bodies.\n",
"ECT8 binds to the methylated site RRm6ACH in the 3’UTR of the mRNA of the ABA signaling factor PYRABACTIN RESISTANCE 1-LIKE 7, thereby promoting its translation.\n",
"ECT8 binds to the methylated site ATTTm6ACGCA in the 3’UTR of the mRNA of the ABA signaling factor PYL7, thereby preventing its translation by sequestration in stress granules."
] | https://doi.org/10.1038/s41477-024-01638-7 | Model Organisms | GENE REGULATION | 10.1038/s41477-024-01638-7 | 2,024 | 32 | 2 | Nature Plants | true |
How do PME activity and OG release during homogalacturonan remodeling affect Arabidopsis thaliana defenses against Myzus persicae, and which hormone signaling pathways are involved? | ENVIRONMENT - BIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"Increased PME activity during Myzus persicae infestation promotes homogalacturonan de-methylesterification, facilitating oligogalacturonides (OG) release. OGs trigger pattern-triggered immunity (PTI) by inducing ROS accumulation, callose deposition, and salicylic acid (SA) signaling activation, reducing aphid feeding performance and reproduction. However, PME inhibition or PMEI13 upregulation reduces OG release and weakens defenses.",
"Increased PME activity during Myzus persicae infestation inhibits homogalacturonan de-methylesterification, reducing oligogalacturonides (OG) release. OGs suppress pattern-triggered immunity (PTI), including ROS accumulation, callose deposition, and salicylic acid (SA) signaling activation, increasing aphid feeding performance and reproduction. PME inhibition or PMEI13 upregulation enhances OG release and strengthens defenses",
"Decreased PME activity during Myzus persicae infestation promotes homogalacturonan de-methylesterification, facilitating oligogalacturonides (OG) release. OGs trigger pattern-triggered immunity (PTI) by inducing ROS accumulation, callose deposition, and salicylic acid (SA) signaling activation, reducing aphid feeding performance and reproduction. However, PME inhibition or PMEI13 upregulation reduces OG release and weakens defenses."
] | 10.1105/tpc.19.00136 | Model Organisms | ENVIRONMENT | 10.1105/tpc.19.00136 | 2,019 | 53 | 0 | The Plant Cell | true |
How do the dynamics of Pectin Methylesterases activity and OG-triggered defenses influence the interaction between Arabidopsis thaliana and Myzus persicae, and what molecular mechanisms mediate these effects? | ENVIRONMENT - BIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"Pectin Methylesterases activity increases during Myzus persicae infestation, driving homogalacturonan de-methylesterification, which facilitates oligogalacturonides (OG) release. OGs activate PTI by promoting ROS accumulation, callose deposition, and SA signaling, enhancing plant resistance by reducing aphid feeding efficiency and reproduction. PME inhibition or PMEI13 upregulation reduces OG-mediated defenses, increasing susceptibility to aphids.",
"Pectin Methylesterases activity decreases during Myzus persicae infestation, driving homogalacturonan de-methylesterification, which facilitates oligogalacturonides (OG) release. OGs activate PTI by promoting ROS accumulation, callose deposition, and SA signaling, enhancing plant resistance by reducing aphid feeding efficiency and reproduction. PME inhibition or PMEI13 upregulation reduces OG-mediated defenses, increasing susceptibility to aphids.",
"Pectin Methylesterases activity increases during Myzus persicae infestation, suppressing homogalacturonan de-methylesterification and oligogalacturonides (OG) release. OGs inhibit PTI by reducing ROS accumulation, callose deposition, and SA signaling, weakening plant resistance and increasing aphid feeding efficiency and reproduction. PME inhibition or PMEI13 upregulation enhances these defenses, reducing susceptibility to aphids"
] | 10.3390/ijms23179753 | Model Organisms | ENVIRONMENT | 10.3390/ijms23179753 | 2,022 | 9 | 0 | International Journal of Molecular Sciences | true |
How the transcription factors WRKY7, WRKY11 and WRKY17 act during the interaction between Arabidopsis thaliana and Pseudomonas syringae pv. tomato (Pst) DC3000 and which hormone signaling pathways are mainly involved? | ENVIRONMENT - BIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis thaliana, the transcription factors WRKY7, WRKY11 and WRKY17 act as negative defence regulators against Pseudomonas syringae pv. tomato (Pst) DC3000. These transcription factors induce genes related to the biosynthesis and signalling of the jasmonic acid (JA) pathway.",
"In Arabidopsis thaliana, the transcription factors WRKY7, WRKY11 and WRKY27 act as negative defence regulators against Pseudomonas syringae pv. tomato (Pst) DC3000. These transcription factors supress genes related to the biosynthesis and signalling of the jasmonic acid (JA) pathway.",
"In Arabidopsis thaliana, the transcription factors WRKY7, WRKY11 and WRKY17 act as negative defence regulators against Botrytis cinerea. These transcription factors induce genes related to the biosynthesis and signalling of the jasmonic acid (JA) pathway."
] | 10.1111/mpp.70044 | Model Organisms | ENVIRONMENT | 10.1111/mpp.70044 | 2,024 | 0 | 0 | Molecular Plant Pathology | true |
How the root specific syntaxin 123 (SYP123) is involved in the Arabidopsis thaliana defense response? | ENVIRONMENT - BIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"The syntaxin SYP123 is involved in the polarized localization of PRP3 protein and polysaccharides in growing root hairs and this activity contribute to the establishment of effective plant defense responses.",
"The syntaxin SYP123 is involved in the polarized localization of protein and lipids in growing root hairs and this activity contribute to the establishment of effective plant defense responses.",
"The syntaxin SYP132 is involved in the polarized localization of PRP3 protein and polysaccharides in growing root hairs and this activity contribute to the establishment of effective plant defense responses."
] | 10.3389/fpls.2016.01081 | Model Organisms | ENVIRONMENT | 10.3389/fpls.2016.01081 | 2,016 | 14 | 0 | Frontiers in Plant Science | true |
What is an oligogalacturonide and its function during the feeding performance and population of Myzus persicae over Arabidopsis thaliana? Which mechanisms are involved? | ENVIRONMENT - BIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"Oligogalacturonides (OGs) are pectin-derived molecules. OG treatments of Arabidopsis thaliana decrease their resistance to Myzus persicae infestation by reducing the number of offspring and feeding performance. Furthermore, this enhanced resistance was related to diminished callose accumulation and reactive oxygen species and activation of the salicylic acid signaling pathway.",
"Oligogalacturonides (OGs) are pectin-derived molecules. OG treatments of Arabidopsis thaliana increase their resistance to Myzus persicae infestation by reducing the number of offspring and feeding performance. Furthermore, this enhanced resistance was related to a substantial accumulation of callose and reactive oxygen species and activation of the salicylic acid signaling pathway.",
"Oligogalacturonides (OGs) are cellulose-derived molecules. OG treatments of Arabidopsis thaliana increase their resistance to Myzus persicae infestation by reducing the number of offspring and feeding performance. Furthermore, this enhanced resistance was related to diminished callose accumulation and reactive oxygen species and activation of the salicylic acid signaling pathway."
] | 10.3390/ijms23179753 | Model Organisms | ENVIRONMENT | 10.3390/ijms23179753 | 2,022 | 9 | 1 | International Journal of Molecular Sciences | true |
How does the mitochondrial protein AtOXR2 influence plant growth and biomass production in Arabidopsis thaliana? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"Constitutively overexpression of AtOXR2 in Arabidopsis plants decreases basal ROS levels, which act as signalling molecules, improve the efficiency of photosynthesis and elicit tolerance to oxidative stress, allowing improved plant growth and biomass production. ",
"Constitutively overexpression of AtOXR2 in Arabidopsis plants increases basal ROS levels, which act as signalling molecules that induce Gibberellin and auxin regulatory-growth pathways, improving the efficiency of photosynthesis and elicit tolerance to oxidative stress, allowing improved plant growth and biomass production",
"Constitutively overexpression of AtOXR2 in Arabidopsis plants increases basal ROS levels, which act as signalling molecules, improve the efficiency of photosynthesis and elicit tolerance to oxidative stress, allowing improved plant growth and biomass production."
] | 10.1093/jxb/erz147 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1093/jxb/erz147 | 2,019 | 15 | 2 | Journal of Experimental Botany | true |
How does CYTc deficiency affect mitochondrial function and TOR-pathway activation in plants? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"Plants with CYTc deficiency exhibit decreased mitochondrial membrane potential and lower ATP content, even in the presence of carbon sources. CYTc deficiency reduces target of rapamycin (TOR)-pathway activation, leading to reduced phosphorylation of S6 kinase (S6K) and RPS6A, as well as lower total S6K protein levels, due to increased protein degradation via the proteasome and autophagy. Thus, CYTc-deficient plants coordinate their metabolism and energy availability by downregulating TOR-pathway activation as a preventive signal to adjust growth in anticipation of energy exhaustion.",
"Plants with CYTc deficiency exhibit increased mitochondrial membrane potential and ATP content, even in the presence of carbon sources. CYTc deficiency induces target of rapamycin (TOR)-pathway activation, leading to reduced phosphorylation of S6 kinase (S6K) and RPS6A, as well as lower total S6K protein levels, due to increased protein degradation via the proteasome and autophagy. Thus, CYTc-deficient plants coordinate their metabolism and energy availability by upregulating TOR-pathway activation as a preventive signal to adjust growth in anticipation of energy exhaustion.",
"Plants with CYTc deficiency exhibit decreased mitochondrial membrane potential and lower ATP content, only in the presence of carbon sources. CYTc deficiency reduces target of rapamycin (TOR)-pathway activation, leading to an increment in the phosphorylation of S6 kinase (S6K) and RPS6A, as well as higher total S6K protein levels, due to reduced protein degradation via the proteasome and autophagy. Thus, CYTc-deficient plants coordinate their metabolism and energy availability by downregulating TOR-pathway activation as a preventive signal to adjust growth in anticipation of energy exhaustion."
] | 10.1111/nph.19506 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1111/nph.19506 | 2,024 | 6 | 0 | New Phytologist | true |
How does cytochrome c deficiency affect seed germination, and the sensitivity to ABA in Arabidopsis? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"Cytochrome c deficiency causes delayed seed germination and the sensitivity of germination to ABA, which negatively regulates the expression of CYTC-2, one of two CYTc-encoding genes in Arabidopsis. CYTC-2 acts downstream of the transcription factor ABSCISIC ACID INSENSITIVE 4 (ABI4), which binds to a region of the CYTC-2 promoter required for repression by ABA decreasing its expression. ",
"Cytochrome c deficiency causes delayed seed germination and the sensitivity of germination to ABA, which positively regulates the expression of CYTC-2, one of two CYTc-encoding genes in Arabidopsis. CYTC-2 acts downstream of the transcription factor ABSCISIC ACID INSENSITIVE 4 (ABI4), which binds to a region of the CYTC-2 promoter required for repression by ABA increasing its expression. ",
"Cytochrome c deficiency causes improved seed germination and the sensitivity of germination to ABA and GAs, which negatively regulate the expression of CYTC-2, one of two CYTc-encoding genes in Arabidopsis. CYTC-2 acts upstream of the transcription factor ABSCISIC ACID INSENSITIVE 4 (ABI4), which binds to a region of the CYTC-2 promoter required for repression by ABA decreasing its expression"
] | 10.1111/nph.18287 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1111/nph.18287 | 2,022 | 9 | 0 | New Phytologist | true |
How does reduced levels of CYTc in Arabidopsis affect the stability and function of mitochondrial respiratory complexes? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"Reduced level of cytochrome c increases stability of Complex IV, affecting Complexes I and III stability and function. This modifies redox metabolism and improves mitochondrial respiration.",
"Reduced level of cytochrome c decreases stability of Complex IV, affecting Complexes I and III stability and function. This modifies redox metabolism and reduces mitochondrial respiration.",
"Reduced level of cytochrome c decreases stability of Complex IV without affecting Complexes I and III stability and function. This modifies redox metabolism and reduces mitochondrial respiration."
] | 10.1016/j.bbabio.2012.04.008 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1016/j.bbabio.2012.04.008 | 2,012 | 46 | 2 | Biochimica et Biophysica Acta (BBA) - Bioenergetics | true |
What is the mechanism by which overexpression of the OXR2 protein induces a basal defense against hemibiotrophic pathogens? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"AtOXR2 affects the nuclear localization of the transcriptional coactivator NPR1. OXR2 (oeOXR2 plants) show enhanced disease resistance, have increased levels of total glutathione and a more oxidized cytosolic redox cellular environment under normal growth conditions. Resistance in these plants is accompanied by higher expression of WRKY transcription factors, induction of genes involved in salicylic acid (SA) synthesis, accumulation of free SA, and overall activation of the SA signaling pathway. ",
"AtOXR2 reduces the nuclear localization of the transcriptional coactivator NPR1. OXR2 (oeOXR2 plants) show enhanced disease resistance, have increased levels of total glutathione and a more oxidized cytosolic redox cellular environment under normal growth conditions. Resistance in these plants is accompanied by lower expression of WRKY transcription factors, reduction of genes involved in salicylic acid (SA) synthesis, reduced accumulation of free SA, and overall inactivation of the SA signaling pathway. ",
"AtOXR2 affects the nuclear localization of the transcriptional coactivator NPR1. OXR2 (oeOXR2 plants) show enhanced disease resistance, have reduced levels of total glutathione and a more reduced cytosolic redox cellular environment under normal growth conditions. Resistance in these plants is accompanied by higher expression of WRKY transcription factors, induction of genes involved in salicylic acid (SA) synthesis, accumulation of free SA, and overall activation of the SA signaling pathway. "
] | 10.1104/pp.19.01351 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1104/pp.19.01351 | 2,020 | 21 | 0 | Plant Physiology | true |
What is the role of lncRNA DANA1 in Arabidopsis thaliana responses to drought stress, and what proteins have been identified as its molecular partners? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"Drought-induced lncRNA DANA1 is a positive regulator of drought tolerance in Arabidopsis thaliana, and mediates stomata closure of Arabidopsis plants in response to drought. DIP1, a L1p/L10e family member protein, can interact with DANA1 both in vitro and in vivo. Loss of either DANA1 or DIP1, could result in the decrease of ABA content in Arabidopsis thaliana (by CYP707A1 and CYP707A2).",
"Drought-induced lncRNA DANA1 is a postive regulator of drought tolerance in Arabidopsis thaliana, and mediates root development of Arabidopsis plants in response to drought. DIP1, a transcription factor, can interact with DANA1 both in vitro and in vivo. Loss of either DANA1 or DIP1, could result in the decrease of ABA content in Arabidopsis thaliana (by CYP707A1 and CYP707A2).",
"Drought-induced lncRNA DANA1 is a negative regulator of drought tolerance in Arabidopsis thaliana, and mediates stomata closure of Arabidopsis plants in response to drought. DIP1, a L1p/L10e family member protein, can interact with DANA1 both in vitro and in vivo. Loss of either DANA1 or DIP1, could result in the increase of ABA content in Arabidopsis thaliana (by NCED3 and NCED5)."
] | 10.1038/s44319-023-00030-4 | Model Organisms | ENVIRONMENT | 10.1038/s44319-023-00030-4 | 2,024 | 4 | 0 | EMBO Reports | true |
What is the role of lncRNA DANA2 in Arabidopsis thaliana responses to drought stress, and what proteins have been identified as its molecular partners? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"LncRNA DANA2 postively regulates drought stress responses through JMJ29 in Arabidopsis thaliana, and JMJ29 can positively regulate the expression of two positve regulators of proline synthesis and drought stress response, ERF15 and GOLS2. ERF84, a chromatic epigenetic regulator, not only binds specifically to DANA2, but also promotes the transcription of JMJ29 by binding to its exon.",
"LncRNA DANA2 positively regulates drought stress responses through JMJ29 in Arabidopsis thaliana, and JMJ29 can positively regulate the expression of two positve regulators of stomatal closure and drought stress response, ERF15 and GOLS2. ERF84, an AP2/ERF transcription factor, not only binds specifically to DANA2, but also promotes the transcription of JMJ29 by binding to its promoter.\n",
"LncRNA DANA2 negatively regulates drought stress responses through JMJ29 in Arabidopsis thaliana, and JMJ29 can negatively regulate the expression of two negative regulators of stomatal closure and drought stress response, ERF15 and GOLS2. ERF84, an AP2/ERF transcription factor, not only binds specifically to DANA2, but also represses the transcription of JMJ29 by binding to its promoter."
] | 10.1016/j.molp.2023.08.001 | Model Organisms | ENVIRONMENT | 10.1016/j.molp.2023.08.001 | 2,023 | 19 | 1 | Molecular Plant | true |
What is the role of lncRNA ARTA in abscisic acid (ABA) response in Arabidopsis thaliana, and what proteins have been identified as its molecular partners? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"Abscisic acid (ABA)-induced lncRNA ARTA controls ABA responses through postively regulating ABI5 exprssion in Arabidopsis thaliana, and loss of ARTA could result in desensitization to ABA. SAD2, an importin β-like protein, interacts with ARTA to block the nuclear import of a negative regulator of ABI5, MYB7.\n",
"Abscisic acid (ABA)-induced lncRNA ARTA controls ABA responses through postively regulating ABI5 exprssion in Arabidopsis thaliana, and over-expressing ARTA could result in desensitization to ABA. SAD2, a transcription factor, interacts with ARTA to promote the nuclear export of a negative regulator of ABI5, MYB7.",
"Abscisic acid (ABA)-induced lncRNA ARTA controls ABA responses through negatively regulating ABI5 exprssion in Arabidopsis thaliana, and loss of ARTA could result in hypersensitization to ABA. SAD2, an importin β-like protein, interacts with ARTA to block the nuclear import of a positive regulator of ABI5, MYB7."
] | 10.1016/j.devcel.2023.05.003 | Model Organisms | ENVIRONMENT | 10.1016/j.devcel.2023.05.003 | 2,023 | 12 | 0 | Developmental Cell | true |
What is the role of lncRNA FRILAIR in strawberry fruit ripening, and what miRNA have been identified as its target? | PLANT BIOTECHNOLOGY | [
"Fragaria ananassa"
] | [
"Accumulation of FRILAIR can release repression of LAC11a (encoding a putative laccase-11-like protein) that is the miR408 target, which subsequently promotes expressions of genes involved in anthocyanin biosynthesis pathway, leading to the acceleration of strawberry fruit ripening. FRILAIR harbours a miR408 binding site, and its RNA can be cleaved by miR397.",
"Accumulation of FRILAIR can release repression of LAC11a (encoding a putative laccase-11-like protein) that is the miR397 target, which subsequently promotes expressions of genes involved in anthocyanin biosynthesis pathway, leading to the acceleration of strawberry fruit ripening. FRILAIR harbours a miR397 binding site, and its RNA can be cleaved by miR397.",
"Reduction of FRILAIR transcripts can release repression of LAC11a (encoding a putative laccase-11-like protein) that is the miR397 target, which subsequently represses expressions of genes involved in anthocyanin biosynthesis pathway, leading to the delay of strawberry fruit ripening. FRILAIR does not harbours a miR397 binding site, and its mRNA can be cleaved by miR397."
] | 10.1371/journal.pgen.1009461 | Woody Perennials & Trees | PLANT BIOTECHNOLOGY | 10.1371/journal.pgen.1009461 | 2,021 | 46 | 1 | PLOS Genetics | true |
What are the roles of miR396e and miR396f in controlling rice architecture? | PLANT BIOTECHNOLOGY | [
"Oryza sativa"
] | [
"Mutated miR396e and miR396f result in an altered rice architecture, with lengthened leaves but shorten internodes, especially the uppermost internode. The mir396ef mutation promotes leaf elongation by increaseing the level of a gibberellin (GA) precursor, mevalonic acid, which subsequently promotes GA biosynthesis. Internode elongation in mir396ef mutants appears to be suppressed via reduced CYP96B4 expression but not via the GA pathway.\n",
"Mutated miR396e and miR396f result in an altered rice architecture, with lengthened roots and shorten leaves, especially the uppermost internode. The mir396ef mutation represses leaf elongation by increaseing the level of auxin. Leaf elongation in mir396ef mutants appears to be suppressed via reduced CYP96B4 expression but not via the auxin pathway.\n",
"Mutated miR396e and miR396f result in an altered rice architecture, with shorten leaves but lengthened internodes, especially the uppermost internode. The mir396ef mutation promotes leaf shortening by increaseing the level of a gibberellin (GA) precursor, mevalonic acid, which subsequently promotes GA biosynthesis. Internode elongation in mir396ef mutants appears to be suppressed via the GA pathway."
] | 10.1111/pbi.13214 | Model Organisms | PLANT BIOTECHNOLOGY | 10.1111/pbi.13214 | 2,019 | 88 | 0 | Plant Biotechnology Journal | true |
Which proteins were identified as part of the Arabidopsis Target of Rapamycin (TOR) complex?
| PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"Unlike animals, plants such as Arabidopsis only possess one TOR complex which is designated as TORC1. This multiple protein complex includes the Target of Rapamycin (TOR) kinase, Rictor (rapamycin-insensitive companion of mTOR) and LST8/GβL (Lethal with Sec Thirteen 8 / G protein β subunit-like) proteins. ",
"Unlike animals, plants such as Arabidopsis only possess one TOR complex which is designated as TORC1. This multiple protein complex includes Target of Rapamycin (TOR) kinase, Raptor (Regulatory-associated protein of TOR) and SIN1 (SAPK-interacting protein 1) proteins. ",
"Unlike animals, plants such as Arabidopsis only possess one TOR complex which is designated as TORC1. This multiple protein complex includes the Target of Rapamycin (TOR) kinase, Raptor (Regulatory-associated protein of TOR) and Lst8 (Lethal with Sec Thirteen 8) proteins. "
] | 10.1016/j.tibs.2020.11.004 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1016/j.tibs.2020.11.004 | 2,021 | 57 | 2 | Trends in Biochemical Sciences | true |
How does the Arabidopsis ribosomal protein S6 Kinase (S6K) accumulate in seedlings grown in 1% sucrose plates during short day (8h light / 16h dark) and long day (16h light / 8h dark) conditions? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"When Arabidopsis seedlings are grown in vitro with 1% sucrose, the S6K protein displays different accumulation patterns both in terms of its total levels and its phosphorylated (S6K-P) form. Under short days, total S6K is minimal during the dark period (ZT9 – ZT21) and when lights are on at ZT0 (ZT means zeitgeber time, and it refers to the time passed after lights on which is ZT0). It will reach its peak levels at ZT3 and ZT6. In the case of S6K-P levels, these are maximal only at ZT3 and will decline as the day progresses. Under long days conditions, both total and phosphorylated S6K display a similar pattern of accumulation. Total S6K protein levels do show a clear peak of accumulation being present throughout the day, that is during light and dark periods. That is also the case of S6K-P levels which are high from ZT0 to ZT6 and then increase up until ZT15, being high again during the night period (ZT18 – ZT21).",
"When Arabidopsis seedlings are grown in vitro with 1% sucrose, the S6K protein displays different accumulation patterns both in terms of its total levels and its phosphorylated (S6K-P) form. Under short days, total S6K is maximal during the dark period (ZT9 – ZT21) and when lights are on at ZT0 (ZT means zeitgeber time, and it refers to the time passed after lights on which is ZT0). It will reach its trough (minimal) levels at ZT3 and ZT6. In the case of S6K-P levels, these are minimal only at ZT3 and will increase as the day progresses. Under long days conditions, both total and phosphorylated S6K display a different pattern of accumulation. Total S6K protein levels do not show a clear peak of accumulation being present throughout the day, that is during light and dark periods. That is not the case of S6K-P levels which are high from ZT0 to ZT6 and then decline up until ZT15, starting to increase again during the night period (ZT18 – ZT21).",
"When Arabidopsis seedlings are grown in vitro with 1% sucrose, the S6K protein displays different accumulation patterns both in terms of its total levels and its phosphorylated (S6K-P) form. Under short days, total S6K is minimal during the dark period (ZT9 – ZT21) and when lights are on at ZT0 (ZT means zeitgeber time, and it refers to the time passed after lights on which is ZT0). It will reach its peak levels at ZT3 and ZT6. In the case of S6K-P levels, these are maximal only at ZT3 and will decline as the day progresses. Under long days conditions, both total and phosphorylated S6K display a different pattern of accumulation. Total S6K protein levels do not show a clear peak of accumulation being present throughout the day, that is during light and dark periods. That is not the case of S6K-P levels which are high from ZT0 to ZT6 and then decline up until ZT15, starting to increase again during the night period (ZT18 – ZT21)."
] | 10.1093/plphys/kiae254 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1093/plphys/kiae254 | 2,024 | 1 | 2 | Plant Physiology | true |
What is the half life of Arabidopsis S6K protein and which regulators control its stability? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"When Arabidopsis wild type seedlings grown under short day (SD) conditions are treated with the protein synthesis inhibitor Cycloheximide (CHX) at ZT3, kept in the light and their S6K total protein levels are determined every 3h (i.e., from Time 0 until Time 6h), we observe that 50% of this protein is maintained after 3h of treatment. This means that S6K half-life under these conditions is more than 3h. However, when we do exactly the same experiment with the zeitlupe (ztl) mutant seedlings that lack the F-box protein ZTL, the half-life of S6K is extended for more than 6h. This experiment shows that S6K protein levels are regulated by the proteasome machinery of which ZTL is a component.",
"When Arabidopsis wild type seedlings grown under short day (SD) conditions are treated with the protein synthesis inhibitor Cycloheximide (CHX) at ZT3, kept in the light and their S6K total protein levels are determined every 3h (i.e., from Time 0 until Time 6h), we observe that 50% of this protein disappears after 3h of treatment. This means that S6K half-life under these conditions is approximately 3h. However, when we do exactly the same experiment with the zeitlupe (ztl) mutant seedlings that lack the F-box protein ZTL, the half-life of S6K is extended for more than 6h. This experiment shows that S6K protein levels are regulated by the proteasome machinery of which ZTL is a component.",
"When Arabidopsis wild type seedlings grown under long day (SD) conditions are treated with the protein synthesis inhibitor Cycloheximide (CHX) at ZT3, kept in the light and their S6K total protein levels are determined every 3h (i.e., from Time 0 until Time 6h), we observe that 50% of this protein disappears after 3h of treatment. This means that S6K half-life under these conditions is approximately 3h. However, when we do exactly the same experiment with the zeitlupe (ztl) mutant seedlings that lack the F-box protein ZTL, the half-life of S6K is reduced by more than 6h. This experiment shows that S6K protein levels are not regulated by the proteasome machinery of which ZTL is a component."
] | 10.1093/plphys/kiae254 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1093/plphys/kiae254 | 2,024 | 1 | 1 | Plant Physiology | true |
What are the main differences between the root extension patterns of wild type (Col-0) and raptor mutant seedlings grown under long day conditions?
| PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"Roots are considered ‘sink organs’ since they rely on Carbon to be reallocated to them from source leaves which are photosynthetically active. Therefore, when Arabidopsis wild type seedlings grow under long day (16h light / 8h dark) conditions they display a distinct pattern of root extension which is higher in the first hours of the light period (ZT0-ZT3), and it will decrease until ZT6. From then until dusk (ZT16) there will be a slight increase in root extension, but just in the first hours of dark this response is inhibited, and root extension will steadily increase during the night period. When the role of the TOR pathway in regulating plant growth responses is assessed the results show that this pattern of root extension is not affected in raptor mutants which show a similar root growth peak in the early morning. Although there is a slight lower root growth extension during the first half of the day when comparing with wild type seedlings, raptor mutants’ roots will grow more during the second half of the light period and all of the night.",
"Roots are considered ‘sink organs’ since they rely on Carbon to be reallocated to them from source leaves which are photosynthetically active. Therefore, when Arabidopsis wild type seedlings grow under long day (16h light / 8h dark) conditions they display a distinct pattern of root extension which is lower in the first hours of the light period (ZT0-ZT3) and it will increase until ZT6. From then until dusk (ZT16) there will be a slight decrease in root extension, but just in the first hours of dark this response is promoted, and root extension will steadily decrease during the night period. Confirming the importance of the TOR pathway in regulating plant growth responses, this pattern of root extension is affected in raptor mutants which show a delay in root growth peak in the early morning. Although there is a slightly higher root growth extension during the first half of the day when comparing with wild type seedlings, raptor mutants’ roots will grow less during the second half of the light period and all of the night.",
"Roots are considered ‘sink organs’ since they rely on Carbon to be reallocated to them from source leaves which are photosynthetically active. Therefore, when Arabidopsis wild type seedlings grow under long day (16h light / 8h dark) conditions they display a distinct pattern of root extension which is higher in the first hours of the light period (ZT0-ZT3), and it will decrease until ZT6. From then until dusk (ZT16) there will be a slight increase in root extension, but just in the first hours of dark this response is inhibited, and root extension will steadily increase during the night period. Confirming the importance of the TOR pathway in regulating plant growth responses, this pattern of root extension is affected in raptor mutants which show a delay in the root growth peak in the early morning. Although there is a slightly higher root growth extension during the first half of the day when comparing with wild type seedlings, the raptor mutants’ roots will grow less during the second half of the light period and all of the night. "
] | 10.1093/jxb/erac279 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1093/jxb/erac279 | 2,022 | 6 | 2 | Journal of Experimental Botany | true |
How does the TOR pathway regulate lateral root formation in Arabidopsis thaliana? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"Lateral root (LR) formation in Arabidopsis requires carbohydrate catabolism and auxin. Lateral root initiation is modulated by high gycolysis depending on sugar derived from source organs (shoots). Sugars and auxin will stimulate the TOR pathway, which acts as a positive and essential regulator of lateral root formation. Knocking down of TOR will block LR formation and this cannot be rescued either by auxin or sucrose application. This regulation does not seem to occur via transcriptional modulation of auxin-induced genes in the pericycle, suggesting that founder cells can sense and respond to auxin but are unable to initiate LR formation. In fact, TOR will attenuate the translation of several critical regulators (ARF19, ARF7, and LBD16) leading to the development of LR. These results show that TOR could integrate both auxin and metabolic (e.g., carbohydrate) signals to modulate the translation efficiency of several auxin-induced genes.",
"Lateral root (LR) formation in Arabidopsis requires carbohydrate catabolism and auxin. Lateral root initiation is modulated by high gycolysis depending on sugar derived from source organs (shoots). Sugars and auxin will inhibit the TOR pathway, which acts as a negative regulator of lateral root formation. Knocking down of TOR will promote LR formation and this can be rescued either by auxin or sucrose application. This regulation does not seem to occur via transcriptional modulation of auxin-induced genes in the pericycle, suggesting that founder cells can sense and respond to auxin but are unable to initiate LR formation. In fact, TOR will attenuate the translation of several critical regulators (ARF19, ARF7, and LBD16) leading to the development of LR. These results show that TOR could integrate both auxin and metabolic (e.g., carbohydrate) signals to modulate the translation efficiency of several auxin-induced genes.",
"Lateral root (LR) formation in Arabidopsis requires carbohydrate catabolism and auxin. Lateral root initiation is modulated by high gycolysis depending on sugar derived from source organs (shoots). Sugars and auxin will stimulate the TOR pathway, which acts as a positive and essential regulator of lateral root formation. Knocking down of TOR will block LR formation and this cannot be rescued either by auxin or sucrose application. This regulation occurs via transcriptional modulation of auxin-induced genes in the pericycle, suggesting that founder cells cannot sense and respond to auxin and are unable to initiate LR formation. In fact, TOR will attenuate the transcription of several critical regulators (ARF19, ARF7, and LBD16) leading to the development of LR. These results show that TOR could integrate both auxin and metabolic (e.g., carbohydrate) signals to modulate the translation efficiency of several auxin-induced genes."
] | https://doi.org/10.15252/embj.2022111273 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.15252/embj.2022111273 | 2,023 | 27 | 0 | The EMBO Journal | true |
What is the role of the PHANTASTICA (PHAN) gene in Antirrhinum majus leaf development? | GENE REGULATION | [
"Antirrhinum majus"
] | [
"Controlling overall plant height and flower color.",
"Establishing dorsoventral polarity and repressing KNOX genes.",
"Promoting radial symmetry and activating KNOX genes."
] | 10.1016/S1369-5266(00)00133-3 | Other Herbaceous Crops, Spices, Fibers & Weeds | GENE REGULATION | 10.1016/S1369-5266(00)00133-3 | 2,001 | 64 | 1 | COPB | false |
What is the primary role of the YABBY gene family (e.g., FIL, CRC) in Arabidopsis thaliana leaf development? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"Specifying adaxial (upper) cell identity.",
"Recruiting founder cells from the shoot apical meristem.",
"Specifying abaxial (lower) cell identity."
] | 10.1016/S1369-5266(00)00133-3 | Model Organisms | GENE REGULATION | 10.1016/S1369-5266(00)00133-3 | 2,001 | 64 | 2 | COPB | false |
What is a common consequence of ectopically expressing class I KNOX homeobox genes in developing leaves? | GENE REGULATION | [
"non-specific"
] | [
"Disruption of proximodistal axis patterning, leading to altered leaf shape and displaced structures.",
"Complete conversion of leaves into stem tissue.",
"Formation of perfectly radial, undifferentiated leaves."
] | 10.1016/S1369-5266(00)00133-3 | Non-specific | GENE REGULATION | 10.1016/S1369-5266(00)00133-3 | 2,001 | 64 | 0 | COPB | false |
What key aspect of leaf development requires interaction between the shoot apical meristem (SAM) and the incipient leaf primordium? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"Establishment of the dorsoventral (adaxial-abaxial) axis.",
"Initiation of vascular tissue differentiation within the stem.",
"Determination of final leaf size solely through cell expansion."
] | 10.1016/S1369-5266(00)00133-3 | Non-specific | GROWTH AND DEVELOPMENT | 10.1016/S1369-5266(00)00133-3 | 2,001 | 64 | 0 | COPB | false |
What is a shared function of the homologous genes ASYMMETRIC LEAVES1 (AS1) in Arabidopsis, ROUGH SHEATH2 (RS2) in maize, and PHANTASTICA (PHAN) in Antirrhinum? | GENE REGULATION | [
"non-specific"
] | [
"Promoting cell division throughout the entire shoot apical meristem.",
"Repressing the expression of KNOX class homeobox genes within developing lateral organs.",
"Activating the expression of YABBY genes to specify abaxial fate."
] | 10.1016/S1369-5266(00)00133-3 | Non-specific | GENE REGULATION | 10.1016/S1369-5266(00)00133-3 | 2,001 | 64 | 1 | COPB | false |
How do sugars and ABA influence the transition from cell division to cell enlargement and storage reserve accumulation during seed development? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"High hexose levels promote cell division, while high sucrose and ABA levels promote cell enlargement and storage reserve accumulation.",
"High sucrose levels promote cell division, while high hexose and ABA levels promote storage reserve accumulation.",
"Both high hexose and sucrose levels promote cell division, while ABA inhibits storage reserve accumulation."
] | 10.1016/s1369-5266(01)00225-4 | Non-specific | GROWTH AND DEVELOPMENT | 10.1016/s1369-5266(01)00225-4 | 2,002 | 252 | 0 | COPB | false |
Which set of transcription factors integrates ABA, light, and potentially sugar signals during Arabidopsis embryogenesis? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"SNF1, PKABA1, GARE, and GAMyb.",
"CTR1, EIN2, ETR1, and ABA2.",
"ABI3, ABI4, ABI5, DET1, FUS3, and LEC1."
] | 10.1016/s1369-5266(01)00225-4 | Model Organisms | GENE REGULATION | 10.1016/s1369-5266(01)00225-4 | 2,002 | 252 | 2 | COPB | false |
How do gibberellins (GA), abscisic acid (ABA), and sugars interact to regulate α-amylase gene expression in germinating cereal embryos? | HORMONES | [
"non-specific"
] | [
"GA represses expression, while ABA and sugars promote it.",
"GA promotes expression, while both ABA and sugars repress it, with sugar repression potentially acting downstream or independently of GA signaling.",
"GA and sugars promote expression, while ABA represses it."
] | 10.1016/s1369-5266(01)00225-4 | Non-specific | HORMONES | 10.1016/s1369-5266(01)00225-4 | 2,002 | 252 | 1 | COPB | false |
What is the role of ABA signaling in the inhibition of germination and early seedling growth by high sugar concentrations in Arabidopsis? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"High sugar concentrations inhibit growth partly by involving ABA signaling; mutants insensitive to or deficient in ABA are resistant to sugar inhibition.",
"ABA signaling counteracts the inhibitory effect of high sugar concentrations on seedling growth.",
"High sugar concentrations promote growth independently of ABA signaling."
] | 10.1016/s1369-5266(01)00225-4 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1016/s1369-5266(01)00225-4 | 2,002 | 252 | 0 | COPB | false |
What is the relationship between ethylene signaling and sensitivity to sugar during early seedling development in Arabidopsis? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"Ethylene signaling is completely independent of sugar response pathways.",
"Ethylene signaling interacts with sugar response pathways; constitutive ethylene signaling confers sugar insensitivity, while reduced ethylene sensitivity leads to sugar hypersensitivity.",
"Increased ethylene signaling leads to sugar hypersensitivity."
] | 10.1016/s1369-5266(01)00225-4 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1016/s1369-5266(01)00225-4 | 2,002 | 252 | 1 | COPB | false |
What distinguishes the function of DRE/CRT cis-acting elements from ABRE elements in Arabidopsis stress response? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"DRE/CRT mediates ABA-independent responses, while ABRE mediates ABA-dependent responses.",
"Both DRE/CRT and ABRE mediate only ABA-dependent responses.",
"DRE/CRT mediates ABA-dependent responses, while ABRE mediates ABA-independent responses."
] | 10.1016/S1369-5266(03)00092-X | Model Organisms | GENE REGULATION | 10.1016/S1369-5266(03)00092-X | 2,003 | 1,453 | 0 | COPB | false |
What effect does the overexpression of CBF/DREB1 transcription factors have on Arabidopsis thaliana? | BIOTECHNOLOGY | [
"Arabidopsis thaliana"
] | [
"Decreased tolerance to freezing but increased tolerance to drought and salt.",
"Increased sensitivity to freezing, drought, and high salt stress.",
"Increased tolerance to freezing, drought, and high salt stress."
] | 10.1016/S1369-5266(03)00092-X | Model Organisms | BIOTECHNOLOGY | 10.1016/S1369-5266(03)00092-X | 2,003 | 1,453 | 2 | COPB | false |
Which specific gene's expression is regulated by the ICE1 transcription factor in Arabidopsis during cold stress? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"All CBF/DREB1 family genes.",
"CBF3/DREB1A.",
"DREB2 genes."
] | 10.1016/S1369-5266(03)00092-X | Model Organisms | GENE REGULATION | 10.1016/S1369-5266(03)00092-X | 2,003 | 1,453 | 1 | COPB | false |
What is required for the activation of AREB/ABF transcription factors in the ABA-dependent stress response pathway in Arabidopsis? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"An ABA-mediated signal, likely involving phosphorylation.",
"Binding to DRE/CRT elements instead of ABRE.",
"Direct activation by cold stress without ABA involvement."
] | 10.1016/S1369-5266(03)00092-X | Model Organisms | GENE REGULATION | 10.1016/S1369-5266(03)00092-X | 2,003 | 1,453 | 0 | COPB | false |
What pattern of crosstalk between stress response pathways was revealed by transcriptome analyses in Arabidopsis? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"All stress pathways (drought, cold, high-salinity, ABA) show equal levels of crosstalk.",
"Significant crosstalk exists between drought, high-salinity, and ABA responses, but less with cold stress responses.",
"Significant crosstalk exists mainly between cold and drought responses."
] | 10.1016/S1369-5266(03)00092-X | Model Organisms | GENOME AND GENOMICS | 10.1016/S1369-5266(03)00092-X | 2,003 | 1,453 | 1 | COPB | false |
How are Arabidopsis Response Regulators (ARRs) primarily classified based on their structure and function? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"Into Pseudo-regulators (APRRs) and True-regulators (ARRs) based solely on phosphorylation potential.",
"Into Type-A (often negative regulators in cytokinin signaling) and Type-B (transcription factors, positive regulators).",
"Into Kinase-linked (AHKs) and Phosphotransfer-linked (AHPs)."
] | 10.1016/j.pbi.2004.07.015 | Model Organisms | GENE REGULATION | 10.1016/j.pbi.2004.07.015 | 2,004 | 79 | 1 | COPB | false |
What is the general role of Type-A Arabidopsis Response Regulators (ARRs) in the cytokinin signaling pathway? | HORMONES | [
"Arabidopsis thaliana"
] | [
"They act as the primary cytokinin receptors on the cell surface.",
"They act as positive regulators by directly activating downstream gene expression.",
"They act as negative regulators, providing a feedback loop to attenuate the signal."
] | 10.1016/j.pbi.2004.07.015 | Model Organisms | HORMONES | 10.1016/j.pbi.2004.07.015 | 2,004 | 79 | 2 | COPB | false |
Which structural feature allows Type-B Arabidopsis Response Regulators (ARRs) to function as transcription factors? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"A phospho-accepting receiver domain that directly binds RNA polymerase.",
"A transmembrane domain for sensing extracellular signals.",
"A conserved DNA-binding domain (GARP motif) in their C-terminal region."
] | 10.1016/j.pbi.2004.07.015 | Model Organisms | GENE REGULATION | 10.1016/j.pbi.2004.07.015 | 2,004 | 79 | 2 | COPB | false |
What is the role of TOC1/APRR1 in the Arabidopsis circadian clock mechanism? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"It acts solely as a photoreceptor sensing dawn and dusk signals.",
"It is a central component that participates in a negative feedback loop with CCA1 and LHY transcription factors.",
"It functions as a histidine kinase phosphorylating downstream clock proteins."
] | 10.1016/j.pbi.2004.07.015 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1016/j.pbi.2004.07.015 | 2,004 | 79 | 1 | COPB | false |
Besides cytokinin signaling and circadian rhythms, in which other process are certain Arabidopsis Response Regulators (ARRs and APRRs) implicated? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"Primary nutrient uptake regulation in the roots.",
"Ethylene perception and signaling downstream of ETR1 receptors.",
"Light-signal transduction, potentially integrating light signals with other pathways."
] | 10.1016/j.pbi.2004.07.015 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1016/j.pbi.2004.07.015 | 2,004 | 79 | 2 | COPB | false |
What is the primary mechanism maintaining the stem cell population in the Arabidopsis thaliana shoot apical meristem? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"Positive regulation where WUS directly activates CLV3 expression, leading to meristem expansion.",
"Independent specification of stem cells and organizing center cells by distinct genetic pathways without feedback.",
"A negative feedback loop involving CLV3 signaling from stem cells repressing WUS expression in the organizing center."
] | 10.1016/j.pbi.2005.09.010 | Model Organisms | GENE REGULATION | 10.1016/j.pbi.2005.09.010 | 2,005 | 115 | 2 | COPB | false |
What is the consequence of loss-of-function mutations in the WUSCHEL (WUS) gene in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"Conversion of shoot meristem identity to root meristem identity.",
"Uncontrolled proliferation of stem cells leading to an enlarged meristem.",
"Premature termination of the shoot apical meristem due to mis-specification of stem cells."
] | 10.1016/j.pbi.2005.09.010 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1016/j.pbi.2005.09.010 | 2,005 | 115 | 2 | COPB | false |
How is the stem cell-inducing signal mediated by WUSCHEL (WUS) typically restricted to the apical cells in the Arabidopsis thaliana shoot meristem? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"A secondary repressor signal from peripheral zones actively blocks WUS signaling outside the apex.",
"The WUS protein itself is physically restricted from moving beyond the apical cell layers.",
"Only the apical cells appear competent to perceive and/or respond to the WUS-derived signal, regardless of broader WUS presence."
] | 10.1016/j.pbi.2005.09.010 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1016/j.pbi.2005.09.010 | 2,005 | 115 | 2 | COPB | false |
Which type of molecular factor has been shown to directly bind the WUSCHEL (WUS) promoter in Arabidopsis thaliana and positively regulate its expression? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"The microRNA miR166.",
"The chromatin remodeling factor SPLAYED (SYD), an SNF2 class ATPase.",
"The CLAVATA1 (CLV1) receptor kinase."
] | 10.1016/j.pbi.2005.09.010 | Model Organisms | GENE REGULATION | 10.1016/j.pbi.2005.09.010 | 2,005 | 115 | 1 | COPB | false |
Which class of transcription factors in Arabidopsis thaliana, themselves regulated by microRNAs, act to restrict shoot apical meristem activity partly by downregulating WUSCHEL (WUS) transcription? | GENE REGULATION | [
"Arabidopsis thaliana"
] | [
"GATA-3-like transcription factors (like HAN).",
"WOX family homeodomain proteins (like STIP/WOX9).",
"Class III HD-ZIP proteins (like PHB, PHV, CNA)."
] | 10.1016/j.pbi.2005.09.010 | Model Organisms | GENE REGULATION | 10.1016/j.pbi.2005.09.010 | 2,005 | 115 | 2 | COPB | false |
How extensive is the representation of peptidase-encoding genes within the Arabidopsis genome? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"Fewer than 100 genes encode peptidases, primarily involved in basic nutrient recycling.",
"Approximately 300 genes encode peptidases, mostly focused on C-terminal processing.",
"Over 600 genes encode various types of peptidases, indicating significant roles in cellular processes."
] | 10.1016/j.pbi.2006.03.009 | Model Organisms | GENOME AND GENOMICS | 10.1016/j.pbi.2006.03.009 | 2,006 | 59 | 2 | COPB | false |
What is the fundamental role of the N-end rule pathway in plant protein regulation? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"It exclusively removes N-terminal signal peptides after protein import into organelles.",
"It adds specific carbohydrate modifications to N-terminal residues to determine protein localization.",
"It influences a protein's lifespan by recognizing its N-terminal amino acid, potentially targeting it for degradation."
] | 10.1016/j.pbi.2006.03.009 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1016/j.pbi.2006.03.009 | 2,006 | 59 | 2 | COPB | false |
What is the primary function of Methionine Aminopeptidases (MAPs) during protein synthesis? | CELL BIOLOGY AND CELL SIGNALING | [
"non-specific"
] | [
"They add a formyl group to the initial methionine in cytosolic proteins.",
"They cleave internal peptide bonds specifically after methionine residues.",
"They remove the initial methionine residue from nascent polypeptide chains."
] | 10.1016/j.pbi.2006.03.009 | Non-specific | CELL BIOLOGY AND CELL SIGNALING | 10.1016/j.pbi.2006.03.009 | 2,006 | 59 | 2 | COPB | false |
What critical step in meiosis is dependent on the M1 peptidase MPA1 in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"The formation of the cell plate during meiotic cytokinesis.",
"The degradation of cyclins to exit meiosis II.",
"Chromosome pairing and the completion of synapsis during prophase I."
] | 10.1016/j.pbi.2006.03.009 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1016/j.pbi.2006.03.009 | 2,006 | 59 | 2 | COPB | false |
In tomato (Solanum lycopersicum), Leucine Aminopeptidase A (LAP-A) acts as a regulator within which signaling pathway? | HORMONES | [
"Solanum lycopersicum"
] | [
"It controls the primary perception of ethylene for fruit ripening.",
"It modulates salicylic acid signaling required for systemic acquired resistance.",
"It regulates the late branch of the jasmonic acid (JA) signaling pathway involved in wound response."
] | 10.1016/j.pbi.2006.03.009 | Solanaceae & Relatives | HORMONES | 10.1016/j.pbi.2006.03.009 | 2,006 | 59 | 2 | COPB | false |
What is the primary role of the rapid reorganization of the actin cytoskeleton in plant cells during attempted pathogen penetration? | CELL BIOLOGY AND CELL SIGNALING | [
"non-specific"
] | [
"To initiate programmed cell death immediately upon pathogen contact.",
"To direct the transport of secretory vesicles and organelles towards the infection site for cell wall apposition formation.",
"To directly attack and degrade the pathogen's cell wall components."
] | 10.1016/j.pbi.2007.05.001 | Non-specific | CELL BIOLOGY AND CELL SIGNALING | 10.1016/j.pbi.2007.05.001 | 2,007 | 172 | 1 | COPB | false |
What type of protein is AtSYP121/PEN1 in Arabidopsis thaliana, and what is its key function in penetration resistance? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"A receptor kinase that directly recognizes pathogen elicitors.",
"A transcription factor that activates defense gene expression globally.",
"A plasma membrane syntaxin (t-SNARE) involved in vesicle fusion for cell wall apposition formation."
] | 10.1016/j.pbi.2007.05.001 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1016/j.pbi.2007.05.001 | 2,007 | 172 | 2 | COPB | false |
What is a primary structural component rapidly deposited in cell wall appositions during plant defense, synthesized by enzymes like PMR4/GLS5 in Arabidopsis? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"Lignin, a complex phenolic polymer.",
"Callose, a β-1,3 glucan.",
"Cellulose, a β-1,4 glucan."
] | 10.1016/j.pbi.2007.05.001 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1016/j.pbi.2007.05.001 | 2,007 | 172 | 1 | COPB | false |
Besides syntaxins, what other types of proteins, such as PEN2 and PEN3/AtPDR8 in Arabidopsis, contribute to penetration resistance at the infection site? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"Nuclear pore complex proteins and histone modifiers.",
"Chloroplast ATP synthases and photosystem components.",
"A peroxisomal glycosyl hydrolase (PEN2) and a plasma membrane ABC transporter (PEN3/AtPDR8)."
] | 10.1016/j.pbi.2007.05.001 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1016/j.pbi.2007.05.001 | 2,007 | 172 | 2 | COPB | false |
Apart from chemical elicitors, what type of signal can plant epidermal cells perceive to initiate defense responses like actin rearrangement during attempted pathogen invasion? | CELL BIOLOGY AND CELL SIGNALING | [
"non-specific"
] | [
"Physical pressure or mechanical stimuli exerted by the pathogen penetration structure.",
"Changes in ambient light intensity caused by the pathogen.",
"Electrical signals transmitted from distant infected tissues."
] | 10.1016/j.pbi.2007.05.001 | Non-specific | CELL BIOLOGY AND CELL SIGNALING | 10.1016/j.pbi.2007.05.001 | 2,007 | 172 | 0 | COPB | false |
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