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What stages characterize the development of drupes and what are the main processes taking place in each one? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"The double sigmoid growth rate of drupe development as a function of time is characterized by four stages. The first exponential growth stage is characterized by endocarp cell division and expansion. The second phase, where there is practically no increase in fruit size, is characterized by mesocarp lignification, pit hardening, and stone formation. The third phase is characterized by exponential fruit growth sustained mainly by cell duplication. During the fourth stage, fruit growth is slow; the final fruit size is reached, followed by the ripening process, in which metabolic changes and softening prepare the fruit for consumption.",
"The sigmoid growth rate of drupe development as a function of time is characterized by four stages. The first logarithmic growth stage is characterized by cell division and expansion. In the second phase, the increase in fruit size is accompanied by endocarp lignification, pit hardening, and stone formation. The third phase is characterized by the exponential fruit growth sustained mainly by cell expansion. During the fourth stage, fruit growth is fast, the final fruit size is reached, followed by the ripening process, in which metabolic changes and softening prepare the fruit for consumption.",
"The double sigmoid growth rate of drupe development as a function of time is characterized by four stages. The first exponential growth stage is characterized by cell division and expansion. The second phase, where there is practically no increase in fruit size, is characterized by endocarp lignification, pit hardening, and stone formation. The third phase is characterized by exponential fruit growth sustained mainly by cell expansion. During the fourth stage, fruit growth is slow; the final fruit size is reached, followed by the ripening process, in which metabolic changes and softening prepare the fruit for consumption. "
] | doi:10.1093/jxb/erm213 | Non-specific | GROWTH AND DEVELOPMENT | 10.1093/jxb/erm213 | 2,007 | 73 | 2 | Journal of Experimental Botany | true |
What are the main physiological and biochemical processes occurring during climacteric fruit ripening? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"Ripening, which occurs after reaching the fruit maturation stage, is a complex syndrome that transforms the fruit into an edible organ for seed dispersal organisms. Climacteric fruit ripening is characterized by: i) ethylene biosynthesis and respiration increase; ii) loss of flesh firmness and pulp structural changes due to the depolymerization and solubilization of cell wall components and cell turgor decrease; iii) changes in taste and overall flavor due to the increase of mono- and disaccharides and volatile compounds and modification of organic acid levels; iv) changes in flesh and skin color due to chlorophyll degradation and accumulation of carotenoid and/or flavonoids; v) increase of susceptibility to pathogens.",
"Ripening, which occurs after reaching the fruit maturation stage, is a complex syndrome that transforms the fruit into an edible organ for seed dispersal organisms. Climacteric fruit ripening is characterized by: i) ethylene biosynthesis and respiration increase; ii) loss of flesh firmness and pulp structural changes due to the depolymerization and solubilization of cell wall components and cell turgor decrease; iii) changes in taste and overall flavor due to the increase of mono- and disaccharides and volatile compounds and modification of organic acid levels; iv) changes in flesh and skin color due to chlorophyll synthesis and decrease of carotenoid and/or flavonoids; v) decrease of susceptibility to pathogens.",
"Ripening, which occurs after reaching the fruit maturation stage, is a complex syndrome that transforms the fruit into an edible organ for seed dispersal organisms. Climacteric fruit ripening is characterized by: i) ethylene biosynthesis and respiration inhibition; ii) loss of flesh firmness and pulp structural changes due to the polymerization and solubilization of cell wall components and cell turgor increase; iii) changes in taste and overall flavor due to the decrease of mono- and disaccharides and volatile compounds and modification of organic acid levels; iv) changes in flesh and skin color due to chlorophyll degradation and accumulation of carotenoid and/or flavonoids; v) increase of susceptibility to pathogens."
] | https://doi.org/10.1016/j.pbi.2021.102042 | Non-specific | GROWTH AND DEVELOPMENT | 10.1016/j.pbi.2021.102042 | 2,021 | 71 | 0 | Current Opinion in Plant Biology | true |
What are the differences between peaches and nectarines and what are the genes involved in these differences? | GROWTH AND DEVELOPMENT | [
"Prunus persica"
] | [
"The absence of skin pubescence fruit trichomes characterizes nectarines. The development of epidermal hairs on fruit peach skin is controlled by a MYB transcription factor (MYB25). In nectarines, the expression of this gene is impaired by the insertion of a LTR retroelement. This unique mutation discriminates between peach and nectarine plants and is used as a tool for seedling selection in peach breeding programs. MYB transcription factors also control the synthesis of anthocyanins, which are important in determining fruit the color peach skin, and other flavonoids, such as flavonols and catechins.",
"The presence of skin pubescence fruit trichomes characterizes nectarines. The development of epidermal hairs on fruit peach skin is controlled by a MYB transcription factor (MYB25). In nectarines, the expression of this gene is induced by the insertion of a LTR retroelement. This unique mutation discriminates between peach and nectarine plants and is used as a tool for seedling selection in peach breeding programs. MYB transcription factors also control the synthesis of anthocyanins, which are important in determining the color peach skin, and other flavonoids, such as flavonols and catechins.",
"The absence of skin pubescence fruit trichomes characterizes nectarines. The development of epidermal hairs on fruit peach skin is controlled by a MYB transcription factor (MYB25). In nectarines, the expression of this gene is impaired by the insertion of a LTR retroelement. This is one of the mutations that discriminates between peach and nectarine plants and may be used as a tool for seedling selection in peach breeding programs. MYB transcription factors also control the synthesis of anthocyanins, which are important in determining the color peach mesocarp, and other flavonoids, such as flavonols and catechins."
] | e90574. doi:10.1371/journal.pone.0090574 | Woody Perennials & Trees | GROWTH AND DEVELOPMENT | 10.1371/journal.pone.0090574 | 2,014 | 84 | 0 | PLoS ONE | true |
What are the main effects of cold stress in plants, and which genes mediate the plant response to low temperature? | ENVIRONMENT - ABIOTIC STRESS | [
"non-specific"
] | [
"Cold stress inhibits plant growth and productivity by direct inhibition of enzymatic reactions, decreasing cell membrane fluidity, and altering protein structure, gene expression, and protein biosynthesis. Freezing temperatures (less than 0 °C) induce cell dehydration and membrane disruption, mainly because of ice crystal formation in the apoplast. To cope with cold stress, plant cells activate a complex defense system, including the induction of reactive oxygen species scavenging systems, the modification of lipid composition to maintain membrane fluidity, and the increase of cryoprotective biomolecules, such as soluble sugars or proline, and antifreeze proteins. These changes are the results of the induction of a set of regulatory networks dependent on the induction of key transcription factors, like C-repeat Binding Factors (CBFs). The cold signaling pathways are integrated with other light signaling, the circadian clock, hormone signaling, and biotic defense.",
"Cold stress inhibits plant growth and productivity by direct inhibition of enzymatic reactions, decreasing cell membrane fluidity, and altering protein structure, gene expression, and protein biosynthesis. Freezing temperatures (less than 0 °C) induce cell dehydration and cell membrane disruption, mainly because of ice crystal formation in the apoplast. To cope with cold stress, plant cells activate a complex defense system, including the decrease of reactive oxygen species scavenging systems, the modification of lipid composition to decrease membrane fluidity, and the decrease of biomolecules, such as soluble sugars or proline, and antifreeze proteins. These changes are the results of the induction of a set of regulatory networks dependent on the induction of key transcription factors, like C-repeat Binding Factors (CBFs). The cold signaling pathways are integrated with other light signaling, the circadian clock, hormone signaling, and biotic defense.",
"Cold stress inhibits plant growth and productivity by direct activation of enzymatic reactions, increasing cell membrane fluidity, and altering protein structure, gene expression, and protein biosynthesis. Freezing temperatures (less than 0 °C) induce cell hydration and membrane disruption, mainly because of ice crystal formation in the cytosol. To cope with cold stress, plant cells activate a complex defense system, including the induction of reactive oxygen species scavenging systems, the modification of lipid composition to maintain membrane fluidity, and the increase of cryoprotective biomolecules, such as soluble sugars or proline, and antifreeze proteins. These changes are the results of the induction of a set of regulatory networks dependent on the induction of key transcription factors, like C-repeat Binding Factors (CBFs). The cold signaling pathways are integrated with other light signaling, the circadian clock, hormone signaling, and biotic defense."
] | doi.org/10.1146/annurev-genet-111523-102226 | Non-specific | ENVIRONMENT | 10.1146/annurev-genet-111523-102226 | 2,024 | 24 | 0 | Annual Review of Genetics | true |
What are the advantages and disadvantages of cold storage of fleshy fruits after harvest, and which postharvest treatments prevent cold damage? | ENVIRONMENT - ABIOTIC STRESS | [
"non-specific"
] | [
"Postharvest cold storage of fleshy fruits is essential for commercialization because it delays ripening, softening, and decay. However, cold storage also induces fruit damage, including symptoms such as surface pitting or discoloration or internal disorders such as browning or mealiness. Besides, cold storage produces several metabolic reconfigurations in the fruit, impairing ripening, organoleptic properties, and overall fruit flavor. The application of chemical compounds after harvest, such as antioxidants or hormones, and pre-conditioned treatments, such as heat treatment or incubation at moderate temperature before cold storage, are successful in preventing fleshy fruits' cold damage. ",
"Postharvest cold storage of fleshy fruits is essential for commercialization because it delays ripening, softening, and decay. However, cold storage also induces fruit damage, including symptoms such as surface pitting or discoloration or internal disorders such as browning or mealiness. Besides, cold storage inhibits metabolic reconfigurations in the fruit, increasing organoleptic properties, and overall fruit flavor. The application of chemical compounds after harvest, such as antioxidants or hormones, and pre-conditioned treatments, such as heat treatment or incubation at moderate temperature before cold storage, are not successful in preventing fleshy fruits' cold damage.",
"Postharvest cold storage of fleshy fruits is essential for commercialization because it accelerates ripening, softening, and decay. However, cold storage also prevents fruit damage, including symptoms such as surface pitting or discoloration or internal disorders such as browning or mealiness. Besides, cold storage produces several metabolic reconfigurations in the fruit, impairing ripening, organoleptic properties, and overall fruit flavor. The application of chemical compounds after harvest, such as antioxidants or hormones, and pre-conditioned treatments, such as heat treatment or incubation at moderate temperature before cold storage, are successful in preventing fleshy fruits' cold damage."
] | https://doi.org/10.1016/j.fochx.2023.101080 | Non-specific | ENVIRONMENT | 10.1016/j.fochx.2023.101080 | 2,024 | 8 | 0 | Food Chemistry: X | true |
Which lipid-derived second messengers are produced during the recognition of pathogen-associated molecular patterns (PAMPs)? | PHYSIOLOGY AND METABOLISM | [
"non-specific"
] | [
"Nitric Oxide",
"AMPc",
"Phosphatidic acid"
] | https://doi.org/10.1016/S1369-5266(02)00268-6 | Non-specific | PHYSIOLOGY AND METABOLISM | 10.1016/S1369-5266(02)00268-6 | 2,002 | 202 | 2 | Current Opinion in Plant Biology | true |
Which of the following is a lipid-derived signaling molecule involved in plant defense? | ENVIRONMENT - BIOTIC STRESS | [
"non-specific"
] | [
"Abscisic acid",
"Salicylic acid",
"Jasmonic acid"
] | https://doi.org/10.1016/S1369-5266(02)00268-6 | Non-specific | ENVIRONMENT | 10.1016/S1369-5266(02)00268-6 | 2,002 | 202 | 2 | Current Opinion in Plant Biology | true |
The phospholipase C and diacylglycerol kinase pathway produces phosphatidic acid during PAMP perception. Phosphatidic acid has been shown to participate in ROS production by regulating the activity of: | ENVIRONMENT - BIOTIC STRESS | [
"non-specific"
] | [
"Phospholipase D",
"NADPH oxidase",
"MAPK"
] | 10.1016/j.cell.2023.12.030 | Non-specific | ENVIRONMENT | 10.1016/j.cell.2023.12.030 | 2,024 | 39 | 1 | Cell | true |
Which of the following enzymes is involved in the jasmonic acid biosynthesis pathway? | ENVIRONMENT - BIOTIC STRESS | [
"non-specific"
] | [
"Phospholipase A2",
"Phospholipase C",
"Phospholipase D"
] | https://doi.org/10.1016/S1369-5266(02)00268-6 | Non-specific | ENVIRONMENT | 10.1016/S1369-5266(02)00268-6 | 2,002 | 202 | 0 | Current Opinion in Plant Biology | true |
Which of the following processes is NOT directly linked to lipid biosynthesis in plants? | PHYSIOLOGY AND METABOLISM | [
"non-specific"
] | [
"Cuticle formation",
"Cellulose biosynthesis",
"Jasmonate signaling"
] | non-specific | Non-specific | PHYSIOLOGY AND METABOLISM | null | null | null | 1 | null | true |
What structural features make mRNAs more susceptible to translational regulation during rhizobial infection in Medicago truncatula? | GENE REGULATION - TRANSLATION | [
"Medicago truncatula"
] | [
"Translationally regulated mRNAs exhibit no distinct structural features, relying entirely on transcriptional control.",
"mRNAs with shorter coding sequences and UTRs are more susceptible to translational regulation.",
"mRNAs with elongated coding sequences and unstructured UTRs are preferentially translated during infection."
] | doi: 10.1105/tpc.19.00647 | Model Organisms | GENE REGULATION | 10.1105/tpc.19.00647 | 2,019 | 31 | 1 | The Plant Cell | true |
How does the ALT TAS3 transcript affect the miR390/TAS3 pathway during rhizobial infection in Medicago truncatula? | GENE REGULATION - TRANSLATION | [
"Medicago truncatula"
] | [
"ALT TAS3 functions as an endogenous target mimic, sequestering miR390 and reducing tasiARF production, thereby modulating nodule formation.",
"ALT TAS3 degrades miR390, increasing tasiARF levels and repressing auxin-related pathways critical for nodule formation.",
"ALT TAS3 enhances tasiARF production by increasing miR390 stability, leading to suppression of auxin signaling and reduced nodulation."
] | doi: 10.1105/tpc.19.00647 | Model Organisms | GENE REGULATION | 10.1105/tpc.19.00647 | 2,019 | 31 | 0 | The Plant Cell | true |
How does Superkiller3 influence nodule morphology in Medicago truncatula? | GENE REGULATION - PTGS | [
"Medicago truncatula"
] | [
"Superkiller3 promotes the formation of oversized nodules with excessive bacterial growth.",
"Superkiller3 prevents nodule formation, prioritizing root growth over symbiotic interactions.",
"Superkiller3 ensures the formation of properly structured and functional nodules by regulating mRNA decay pathways during infection."
] | doi: 10.1105/tpc.19.00647 | Model Organisms | GENE REGULATION | 10.1105/tpc.19.00647 | 2,019 | 31 | 2 | The Plant Cell | true |
What advantage does TRAP-SEQ offer when studying cell-type-specific translation? | GENE REGULATION - TRANSLATION | [
"non-specific"
] | [
"It measures protein abundance directly rather than RNA translation.",
"It provides a global overview of transcriptional changes across the entire organism.",
"It enables the analysis of ribosome-associated RNAs in specific cell types by expressing a tagged ribosomal protein in targeted tissues."
] | doi.org/10.1007/978-1-0716-0712-1_26 | Non-specific | GENE REGULATION | 10.1007/978-1-0716-0712-1_26 | 2,020 | 3 | 2 | Methods in Molecular Biology | true |
How does TRAP-SEQ differ from traditional RNA extraction methods? | GENE REGULATION - TRANSLATION | [
"non-specific"
] | [
"TRAP-SEQ specifically isolates RNAs associated with actively translating ribosomes, avoiding contamination from other ribonucleoprotein complexes.",
"TRAP-SEQ isolates all cellular RNAs indiscriminately, including those not involved in translation",
"TRAP-SEQ purifies only small RNAs such as miRNAs and siRNAs."
] | doi.org/10.1007/978-1-0716-0712-1_26 | Non-specific | GENE REGULATION | 10.1007/978-1-0716-0712-1_26 | 2,020 | 3 | 0 | Methods in Molecular Biology | true |
Angiosperms have multiple phytochrome photoreceptors (phyA, phyB, ...). Do their functions differ during seedling de-etiolation? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana",
"Solanum lycopersicum"
] | [
"phyA and phyB equally contribute to de-etiolation in response to far-red light. They have additive effects.",
"phyB is the only phytochrome that significantly contributes to seedling de-etiolation",
"phyA is the primary phytochrome triggering de-etiolation in response to far-red light, while phyB is the primary phytochrome triggering de-etiolation in response to red light."
] | https://doi.org/10.1093/jxb/erp304 | Model Organisms | ENVIRONMENT | 10.1093/jxb/erp304 | 2,009 | 635 | 2 | Journal of Experimental Botany | true |
Where is the major site of action of phytochromes in angiosperms? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana",
"Marchantia polymorpha"
] | [
"Phytochromes primarily act in the cytosol upon light excitation",
"Light activated phytochromes act at the cell surface",
"The primary site of action of light activated phyA and phyB is in the nucleus"
] | DOI: 10.1016/j.tplants.2008.08.007 | Model Organisms | ENVIRONMENT | 10.1016/j.tplants.2008.08.007 | 2,008 | 84 | 2 | Trends in Plant Science | true |
Which of the following events is a key for subsequent signalling following cryptochrome light activation? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"Cryptochromes dimerise or multimerise following light activation",
"Cryptochromes translocate from the cytosol to the nucleus",
"Light excitation elicits monomerisation of cryptochromes"
] | DOI: 10.1016/j.tplants.2011.09.002 | Model Organisms | ENVIRONMENT | 10.1016/j.tplants.2011.09.002 | 2,011 | 250 | 0 | Trends in Plant Science | true |
What is the primary event following light activation of the UVR8 UV-B photoreceptor? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"non-specific"
] | [
"UV-B photo-excitation dimerizes UVR8",
"UV-B photo-excitation monomerizes UVR8",
"UV-B photo-excitation activates an enzymatic activity of UVR8"
] | DOI: 10.1146/annurev-arplant-050718-095946 | Non-specific | ENVIRONMENT | 10.1146/annurev-arplant-050718-095946 | 2,021 | 108 | 1 | Annual Review of Plant Biology | true |
How do plant phototropins initiate light signalling cascades? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"light activated phototropins interact with transcription factors from the PIF family.",
"phototropins are light activated Ser/Thr protein kinases",
"phototropins translocate from the cytosol to the nucleus where they initiate signaling"
] | DOI: 10.1016/j.cub.2015.03.020 | Model Organisms | ENVIRONMENT | 10.1016/j.cub.2015.03.020 | 2,015 | 133 | 1 | Current Biology | true |
What is the impact of 1 μM bioactive gibberellin (GA) application on epidermal infection by symbiotic rhizobia in Medicago truncatula? | HORMONES | [
"Medicago truncatula"
] | [
"Application of 1 μM bioactive GA increases epidermal infection by symbiotic rhizobia in Medicago truncatula",
"Application of 1µM bioactive GA reduces epidermal infection by symbiotic rhizobia in Medicago truncatula",
"Application of 1 μM bioactive GA has no impact on epidermal infection by symbiotic rhizobia in Medicago truncatula "
] | https://doi.org/10.1038/ncomms12636 and https://doi.org/10.1038/ncomms12433 | Model Organisms | HORMONES | 10.1038/ncomms12433 | 2,016 | 192 | 1 | Nature Communications | true |
In Medicago truncatula, GA suppression of infection involves the degradation of which proteins acting in the GA signaling pathway? | HORMONES | [
"Medicago truncatula"
] | [
"In Medicago truncatula, GA suppression of infection involves the degradation of DELLA proteins",
"In Medicago truncatula, GA suppression of infection involves the degradation of GID proteins",
"In Medicago truncatula, GA suppression of infection involves the degradation of PIF proteins"
] | https://doi.org/10.1038/ncomms12636 and https://doi.org/10.1038/ncomms12433 | Model Organisms | HORMONES | 10.1038/ncomms12433 | 2,016 | 192 | 0 | Nature Communications | true |
In Medicago truncatula, the promoter of which gene encoding an important transcription factor regulating the progression of the infection thread is directly bound by GFP-della1-Delta18 protein? | HORMONES | [
"Medicago truncatula"
] | [
"In Medicago truncatula, GFP-della1-Delta18 directly binds to NF-YA1 promoter",
"In Medicago truncatula, GFP-della1-Delta18 directly binds to ENOD11 promoter ",
"In Medicago truncatula, GFP-della1-Delta18 directly binds to ERN1 promoter"
] | https://doi.org/10.1038/ncomms12636 | Model Organisms | HORMONES | 10.1038/ncomms12636 | 2,016 | 111 | 2 | Nature Communications | true |
In Lotus japonicus, what is the impact of 1 μM bioactive gibberellin (GA) application on root hair deformation in response to Nod Factors (NF)? | HORMONES | [
"Lotus japonicus"
] | [
"In Lotus japonicus, with 1 μM bioactive GA treatment, root hair deformation is increased compared with Nod Factors alone",
"In Lotus japonicus, with 1 μM bioactive GA treatment, root hair deformation is completely abolished, even though Nod Factors were present",
"In Lotus japonicus, with 1 μM bioactive GA treatment, root hair deformation is not affected compared with Nod Factors alone"
] | https://doi.org/10.1111/j.1365-313X.2008.03774.x | Model Organisms | HORMONES | 10.1111/j.1365-313X.2008.03774.x | 2,009 | 143 | 1 | The Plant Journal | true |
What is the infection thread formation phenotype of DELLA-deficient pea la cry-s double mutants compared with wild-type? | HORMONES | [
"Pisum sativum"
] | [
"Infection thread formation was significantly reduced in DELLA-deficient pea la cry-s double mutants compared with wild-type plants",
"Infection thread formation was similar in DELLA-deficient pea la cry-s double mutants compared with wild-type plants",
"Infection thread formation was significantly increased in DELLA-deficient pea la cry-s double mutants compared with wild-type plants"
] | https://doi.org/10.1093/jxb/ery046 | Legumes | HORMONES | 10.1093/jxb/ery046 | 2,018 | 61 | 0 | Journal of Experimental Botany | true |
Which gene is the master regulator of heat stress response in tomato, how is it maintained inactive under control conditions, and to which cis-elements does it bind during heat stress? | ENVIRONMENT - ABIOTIC STRESS | [
"Solanum lycopersicum"
] | [
"In tomato, the master regulator of heat stress response is HSFA1a. Under control conditions it is maintained inactive through interactions with HSP70 and HSP90 proteins. In response to heat stress, HSFA1a is released from HSP70 and HSP90, makes homo-oligomeric complexes which translocate to the nucleus. In the nucleus it binds to cis-elements called Heat Shock Elements (HSEs) which are typically found in the promoters of many heat stress induced genes. ",
"In tomato, the master regulator of heat stress response is HSFA2. Under control conditions it is maintained inactive through interactions with small heat shock proteins (sHSPs). In response to heat stress, HSF2 in complex with sHSPs translocate to the nucleus. In the nucleus it binds to cis-elements called Heat Shock Elements (HSEs) which are typically found in the promoters of many heat stress induced genes. ",
"In tomato, the master regulator of heat stress response is HSFA1a. Under control conditions it is maintained inactive in the nucleus through interactions with HSP70 and HSP90. In response to heat stress, HSFA1a is released from HSP70 and HSP90, makes hetero-oligomeric complexes which translocate to the nucleus. In the nucleus it binds to cis-elements called Stress Responsive Elements (SREs) which are typically found in the promoters of many heat stress induced genes. "
] | 10.1105/tpc.110.076018 | Solanaceae & Relatives | ENVIRONMENT | 10.1105/tpc.110.076018 | 2,011 | 289 | 0 | The Plant Cell | true |
Which ethylene-related factors are involved in the induction of HSFA2 in Arabidopsis thaliana and how does this mechanism affect thermotolerance | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis thaliana, the induction of HSFA2 in response to ethylene signalling involves the transcription factors ERF95 and ERF97, which are regulated by the ethylene response master regulator ETHYLENE INSENSITIVE 3 (EIN3). This mechanism plays a critical role in enhancing thermotolerance",
"In Arabidopsis thaliana, the induction of HSFA2 in response to ethylene signalling involves the transcription factors ERF95 and ERF97, which are regulated by the ethylene response master regulator EIN2 (ETHYLENE INSENSITIVE 2). This mechanism plays a critical role in enhancing thermosensitivity.",
"In Arabidopsis thaliana, the activation of HSFA3 in response to ethylene signalling involves the transcription factors ERF91 and ERF97, which are regulated by the ethylene response master regulator ETHYLENE INSENSITIVE 3 (EIN3). This mechanism plays a significant role in enhancing thermotolerance."
] | 10.1093/plcell/koaa026 | Model Organisms | ENVIRONMENT | 10.1093/plcell/koaa026 | 2,020 | 110 | 0 | The Plant Cell | true |
How does alternative splicing of the second intron of tomato HSFA2 affect the function, localization, and stability of its protein isoforms during heat stress, and what role do these isoforms play in acquired thermotolerance? | ENVIRONMENT - ABIOTIC STRESS | [
"Solanum lycopersicum"
] | [
"Alternative splicing in the second intron of tomato HSFA2 results in two protein isoforms, HSFA2-I and HSFA2-II, with distinct roles in the heat stress response. HSFA2-II lacks a nuclear export signal (NES), resulting in strong nuclear retention. It is transcriptionally active but rapidly degraded in the nucleus by the 26S proteasome, limiting its activity during heat stress. HSFA2-I contains an NES and is sequestered in cytosolic heat stress granules (HSGs) during heat stress through interactions with class CI and CII small heat shock proteins (sHSPs). In the case of repeated heat stress, HSFA2-I is released from HSGs and interacts with HSFA1a to form superactivator complexes, which enhance acquired thermotolerance.",
"Alternative splicing in the second intron of tomato HSFA2 results in two protein isoforms, HSFA2-I and HSFA2-II, with distinct roles in the heat stress response. HSFA2-I lacks a nuclear export signal (NES), resulting in strong nuclear retention. It is transcriptionally active but rapidly degraded in the nucleus by the 26S proteasome, limiting its activity during heat stress. HSFA2-II contains an NES and is sequestered in cytosolic heat stress granules (HSGs) during heat stress through interactions with HSFA1a. In the case of repeated heat stress, HSFA2-II is released from HSGs and interacts with HSFA1a to form repressor complexes, which suppress acquired thermotolerance.",
"Alternative splicing in the second intron of tomato HSFA2 results in two protein isoforms, HSFA2-I and HSFA2-II, with distinct roles in the heat stress response. HSFA2-II lacks a nuclear export signal (NES), resulting in strong nuclear retention. It is transcriptionally active but rapidly degraded in the nucleus by autophagy, limiting its activity during heat stress. HSFA2-I contains an NES and is sequestered in cytosolic P-bodies (PBs) during heat stress through interactions with class CI and CII small heat shock proteins (sHSPs). During recovery, it is released from HSGs and interacts with HSFA1a to form superactivator complexes, which enhance acquired thermotolerance."
] | 10.1111/nph.16221 | Solanaceae & Relatives | ENVIRONMENT | 10.1111/nph.16221 | 2,019 | 61 | 0 | New Phytologist | true |
How does HSFA2 regulate thermomemory in Arabidopsis thaliana, which HSF does it interact with, what histone modification is associated with this process, and which memory genes are regulated by this mechanism? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"HSFA2 in Arabidopsis thaliana is a central factor for thermomemory. It interacts with HSFA3, and the HSFA2/HSFA3 complexes bind to the promoters of memory genes, triggering histone 3 lysine 9 (H3K9) acetylation, a modification that is associated with the genes the sustained expression of memory genes during recovery from a priming treatment, such as HSFA1a and HSP70-1.",
"HSFA2 in Arabidopsis thaliana is a central factor for thermomemory. It interacts with HSFA4, and the HSFA2/HSFA4 complexes bind to the promoters of memory genes, triggering histone 3 lysine 27 (H3K27) methylation, a modification that is associated with the sustained expression of memory genes during recovery from a priming treatment, such as APX3 and Hsa32.",
"HSFA2 in Arabidopsis thaliana is a central factor for thermomemory. It interacts HSFA3 and HSFA2/HSFA3 complexes bind to the promoters of memory genes triggers histone 3 lysine 4 (H3K4) methylation, a modification that is associated with the sustained expression of memory genes during recovery from a priming treatment, such as APX3 and HSA32. "
] | 10.1038/s41467-021-23786-6 | Model Organisms | ENVIRONMENT | 10.1038/s41467-021-23786-6 | 2,021 | 155 | 2 | Nature Communications | true |
Which are the two core transcription factors regulating the unfolded protein response (UPR) in Arabidopsis thaliana, and what are the key activation mechanisms for each transcription factor? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"bZIP60 and bZIP28 regulate the unfolded protein response (UPR) in Arabidopsis thaliana. Upon ER stress, bZIP60 mRNA is spliced by IRE1, producing an active form that translocates to the nucleus to activate UPR genes. bZIP28, an ER membrane-bound protein, is cleaved by S1P and S2P proteases in Golgi, releasing its cytosolic domain, which moves to the nucleus to promote UPR gene expression.",
"bZIP60 and bZIP38 regulate the unfolded protein response (UPR) in Arabidopsis thaliana. Upon ER stress, bZIP60 protein is spliced by IRE1, producing an active form that translocates to the nucleus to activate UPR genes. bZIP28, a mitochondrial membrane-bound protein, is cleaved by S1P and S2P proteases, releasing its cytosolic domain, which moves to the nucleus to promote UPR gene expression.",
"bZIP60 and bZIP28 regulate the unfolded protein response (UPR) in Arabidopsis thaliana. Upon ER stress, bZIP28 mRNA is spliced by the spliceosome, producing an active form that translocates to the nucleus to activate UPR genes. bZIP60, an ER membrane-bound protein, is cleaved by S1P and S2P proteases in Golgi, releasing its transmembrane domain, which moves to the nucleus to promote UPR gene expression."
] | 10.1111/pce.14063 | Model Organisms | ENVIRONMENT | 10.1111/pce.14063 | 2,021 | 31 | 0 | Plant, Cell & Environment | true |
What is the gene identified as key molecular player in the jasmonate insensitivity induced by far-red light? | HORMONES | [
"non-specific"
] | [
"ERF11 and MYC2",
"All JAZ genes",
"JAZ10"
] | https://www.pnas.org/doi/full/10.1073/pnas.0900701106 | Non-specific | HORMONES | 10.1073/pnas.0900701106 | 2,009 | 233 | 2 | Proceedings of the National Academy of Sciences | true |
What are the physiological mechanisms behind the ability of Arabidopsis thaliana to promote growth and repress the induction of defenses under light signals of competition? | HORMONES | [
"Arabidopsis thaliana"
] | [
"Jasmonate desensitization of plant tissues mediated by upregulation of JAZ proteins and the inactivation of the bioactive JA-Ile through sulfotransferases.",
"Jasmonate inactivation through degradation.",
"Jasmonate synthesis is suppressed."
] | https://www.pnas.org/doi/full/10.1073/pnas.0900701106 | Model Organisms | HORMONES | 10.1073/pnas.0900701106 | 2,009 | 233 | 0 | Proceedings of the National Academy of Sciences | true |
What is the ligand of the MpCOI1 of the jasmonate phytohormone in Marchantia polymorpha? | HORMONES | [
"Marchantia polymorpha"
] | [
"JA-Ile",
"(+)-7-iso-JA-Ile (JA-Ile)",
"dinor-OPDA"
] | https://doi.org/10.1038/s41589-018-0033-4 | Model Organisms | HORMONES | 10.1038/s41589-018-0033-4 | 2,018 | 192 | 2 | Nature Chemical Biology | true |
What is the gene identified as molecular switch inducing jasmonate insensitivity upong signals of competition? | HORMONES | [
"non-specific"
] | [
"PIF (Phytochrome Interacting Factors)",
"Phytochrome B",
"sulfotransferase (ST2a) "
] | https://doi.org/10.1038/s41477-020-0604-8 | Non-specific | HORMONES | 10.1038/s41477-020-0604-8 | 2,020 | 109 | 2 | Nature Plants | true |
What is the chemical origin for the bioactive jasmonic acid in Marchantia polymorpha? | HORMONES | [
"Marchantia polymorpha"
] | [
"C20 and C22",
"C18, C16, C20 and C22",
"C18 and C16"
] | https://www.pnas.org/doi/10.1073/pnas.2202930119?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmed | Model Organisms | HORMONES | 10.1073/pnas.2202930119 | 2,022 | 31 | 1 | Proceedings of the National Academy of Sciences | true |
What is the role of CRISPR-based systems in epigenetic regulation, and what strategies have been used to achieve transcriptional regulation in plants? | PLANT BIOTECHNOLOGY | [
"non-specific"
] | [
"The CRISPR/dCas9 system can only function to silence or repress gene expression, and any efforts to activate genes through CRISPR are inherently limited by the inability of dCas9 to recruit the necessary transcriptional activators. This makes it impractical for applications that require the upregulation of specific genes for traits such as enhanced stress tolerance, growth, or metabolic changes in plants. Additionally, despite the existence of various regulatory domains, the CRISPR/dCas9 system does not provide sufficient specificity or strength to achieve significant gene activation. As a result, this system is considered mostly ineffective for driving any form of substantial gene expression in plant systems.",
"CRISPR-based systems, particularly the use of dCas9 (dead Cas9) proteins, have been adapted to epigenetic regulation by fusing them to various epigenetic domains. These strategies allow for precise, reversible modifications of chromatin marks such as DNA methylation and histone modifications. In plants, different strategies have been employed, such as the direct fusion of the regulation, SAM (Synergistic Activation Mediator) and scRNA (scaffolding RNAs), which include regulatory domains to the CRISPR/dCas9 complex, and the SunTag strategy, which uses multi-epitope tags for efficient recruitment of multiple regulation domains. ",
"CRISPR-based systems are solely limited to gene editing applications, as they rely on creating targeted double-strand breaks in DNA to introduce genetic modifications, which directly alters the genomic sequence and cannot be used for reversible modifications of epigenetic markers. "
] | doi: 10.1007/s11248-021-00252-z. | Non-specific | PLANT BIOTECHNOLOGY | 10.1007/s11248-021-00252-z | 2,021 | 14 | 1 | Transgenic Research | true |
What was the physiological impact of using the dCas9-Suntag-DRM2 strategy on Arabidopsis thaliana, targeting genes involved in flowering time (FWA)? | PLANT BIOTECHNOLOGY | [
"Arabidopsis thaliana"
] | [
"The dCas9-Suntag-DRM2 strategy induced DNA methylation at the FWA gene promoter, leading to early flowering in Arabidopsis. This epigenetic modification was stable and passed on to the next generation, resulting in a consistent early flowering phenotype.",
"The dCas9-Suntag-DRM2 strategy delayed flowering in Arabidopsis by reducing DNA methylation at the FWA gene promoter.",
"The dCas9-Suntag-DRM2 strategy had no effect on flowering time or DNA methylation in Arabidopsis."
] | doi: 10.1007/s11248-021-00252-z. | Model Organisms | PLANT BIOTECHNOLOGY | 10.1007/s11248-021-00252-z | 2,021 | 14 | 0 | Transgenic Research | true |
What was the physiological impact of using the dCas9-Suntag-TET1 strategy on Arabidopsis thaliana, targeting genes involved in flowering time (FWA) and what epigenetic modification was responsible for this effect? | PLANT BIOTECHNOLOGY | [
"Arabidopsis thaliana"
] | [
"The dCas9-Suntag-TET1 strategy caused early flowering in Arabidopsis by increasing DNA methylation at the FWA gene promoter.",
"The dCas9-Suntag-TET1 strategy induced specific DNA demethylation of the FWA gene promoter, which led to late flowering phenotypes in Arabidopsis. The demethylation was responsible for the altered flowering time, which was inherited by subsequent plant generations.",
"The dCas9-Suntag-TET1 strategy had no effect on flowering time, as there were no changes in DNA methylation at the FWA gene."
] | doi: 10.1007/s11248-021-00252-z. | Model Organisms | PLANT BIOTECHNOLOGY | 10.1007/s11248-021-00252-z | 2,021 | 14 | 1 | Transgenic Research | true |
What role do Jasmonates (JAs) play in plant stress response and how are they involved in regulating specialized metabolites? | HORMONES | [
"non-specific"
] | [
"Jasmonates are primarily involved in regulating primary metabolic processes such as carbon assimilation and nitrogen fixation, and do not significantly influence specialized metabolism or plant defense mechanisms. They are mostly limited to controlling plant growth and reproductive processes, with minimal involvement in stress response or the production of specialized compounds.",
"Jasmonates (JAs) are oxylipin-type hormones that are key regulators of plant stress responses. The bioactive form, JA-Ile, regulates the production of specialized metabolites by activating a set of transcription factors (TFs). These TFs control the expression of genes involved in the synthesis of compounds that help the plant defend against stressors such as herbivores and pathogens. JA signaling is crucial for balancing defense mechanisms with other physiological processes like growth.",
"Jasmonates play no significant role in regulating plant stress responses. Their primary function is limited to the regulation of seed germination and flowering time, with little to no effect on specialized metabolism. Plants can defend themselves against biotic and abiotic stressors through other hormones like auxins and cytokinins, while jasmonates are not involved in such processes."
] | doi: 10.1016/j.pbi.2022.102197 | Non-specific | HORMONES | 10.1016/j.pbi.2022.102197 | 2,022 | 72 | 1 | Current Opinion in Plant Biology | true |
How does the interaction between Jasmonate signaling and light signaling pathways contribute to plant development, particularly in terms of photosynthesis and growth? | HORMONES | [
"non-specific"
] | [
"While Jasmonate signaling does play a role in defense responses, it actually represses light signaling to inhibit photosynthesis under high light conditions. This prevents the plant from engaging in efficient carbon fixation and growth, particularly under stress, by directly limiting the activation of light-dependent processes such as chlorophyll synthesis and the electron transport chain in photosynthesis.",
"The interaction between Jasmonate and light signaling has no significant impact on photosynthesis or carbon metabolism. Instead, the two pathways function independently, with JA solely focusing on growth inhibition during stress and light signaling mainly affecting chlorophyll biosynthesis. There is no integration between these pathways to regulate photosynthetic efficiency or carbon flux in response to external environmental factors.",
"The interaction between Jasmonate signaling and light signaling pathways plays a key role in regulating plant development. Specifically, JA signaling and light-regulated processes work together to maintain photosynthetic activity, enhance metabolic rate, and control carbon flow towards specialized metabolites. JA signaling modulates photomorphogenesis by regulating MYC2, which in turn promotes the expression of HY5, a transcription factor that coordinates light-regulated processes such as photosynthesis, carbon metabolism, and nutrient assimilation."
] | doi: 10.1016/j.pbi.2022.102197 | Non-specific | HORMONES | 10.1016/j.pbi.2022.102197 | 2,022 | 72 | 2 | Current Opinion in Plant Biology | true |
What is the role of the transcription factor FaRIF in the regulation of strawberry fruit ripening? | GENE REGULATION - TRANSCRIPTION | [
"Fragaria ananassa"
] | [
"FaRIF negatively regulates strawberry fruit ripening, repressing different processes such as anthocyanin and sugar biosynthesis, cell wall degradation, ABA biosynthesis and signaling, and aerobic/anaerobic metabolism",
"FaRIF positively regulates strawberry fruit ripening promoting different processes such as anthocyanin and sugar biosynthesis, cell wall degradation, ABA biosynthesis and signaling, and aerobic/anaerobic metabolism",
"FaRIF positively regulates strawberry fruit ripening promoting different processes such as anthocyanin and sugar degradation, cell wall biosynthesis, ABA degradation, and aerobic/anaerobic metabolism "
] | doi:10.1093/plcell/koab070 | Woody Perennials & Trees | GENE REGULATION | 10.1093/plcell/koab070 | 2,021 | 138 | 1 | The Plant Cell | true |
What is the role of the MADS-box transcription factor FaTM6 in strawberry development? | GENE REGULATION - TRANSCRIPTION | [
"Fragaria ananassa"
] | [
"FaTM6 plays a key role in the final stages of strawberry fruit ripening",
"FaTM6 contributes positively to the formation of the strawberry gynoecium and the promotion of fruit set",
"FaTM6 promotes strawberry anther and flower development"
] | doi:10.1093/jxb/ery400 | Woody Perennials & Trees | GENE REGULATION | 10.1093/jxb/ery400 | 2,018 | 87 | 2 | Journal of Experimental Botany | true |
During the early stages of strawberry fruit development, auxin and gibberellic acid (GA) drive fruit growth. What mechanisms delay the onset of ripening in this stage? | GROWTH AND DEVELOPMENT | [
"Fragaria ananassa"
] | [
"At the early stages of fruit development, auxin and GA induce the expression of FvCYP7070A4a, which is involved in the abscisic acid catabolism and maintains its endogenous content at a minimum",
"At the early stages of fruit development, ethylene biosynthesis is tightly suppressed by the antagonistic regulation of auxin and GA, maintaining its levels extremely low",
"At the early stages of fruit development, critical crosstalk between auxin and ethylene regulates the delay of ripening. This interaction involves the inhibition of ethylene biosynthesis, thereby preventing the activation of ripening-related genes"
] | doi/10.1073/pnas.1812575115 | Woody Perennials & Trees | GROWTH AND DEVELOPMENT | 10.1073/pnas.1812575115 | 2,018 | 170 | 0 | Proceedings of the National Academy of Sciences | true |
The transcription factor FvMYB117a in the diploid species Fragaria vesca exhibits high expression in the shoot apical meristem. What specific role does it play in the plant growth and development of strawberry plants? | HORMONES | [
"Fragaria ananassa"
] | [
"FvMYB117a binds to the promoters of FvIPT2 (isopentenyl-transferase) and FvCKX1 (cytokinin oxidase), negatively regulates their expression and acts as a repressor of crown outgrowth inhibiting cytokinin accumulation. ",
"FvMYB117a binds to the promoters of FvIPT2 (isopentenyl-transferase) and FvCKX1 (cytokinin oxidase) and positively regulates their expression, acting as an activator of runner formation inhibiting cytokinin accumulation.",
"FvMYB117a binds to the promoters of FvIPT2 (isopentenyl-transferase) and FvCKX1 (cytokinin oxidase) and positively regulates their expression, acting as an activator of crown outgrowth inhibiting cytokinin accumulation."
] | doi.org/10.1093/plcell/koae097 | Woody Perennials & Trees | HORMONES | 10.1093/plcell/koae097 | 2,024 | 3 | 0 | The Plant Cell | true |
The transcription factor BARE RECEPTACLE (FvBRE) in the diploid species Fragaria vesca shows high expression in the floral meristem and floral organ primordia. What is its specific role in regulating the growth and development process in strawberry plants? | GROWTH AND DEVELOPMENT | [
"Fragaria ananassa"
] | [
"FvBRE is essential for carpel initiation in strawberry and functions through the regulation of the auxin signaling pathway ",
"FvBRE is essential for carpel initiation in strawberry and functions through the regulation of the cytokinin signaling pathway",
"FvBRE is essential for leaf formation in strawberry and functions through the regulation of the auxin signaling pathway"
] | doi.org/10.1093/plcell/koae270 | Woody Perennials & Trees | GROWTH AND DEVELOPMENT | 10.1093/plcell/koae270 | 2,024 | 2 | 0 | The Plant Cell | true |
What is the subcellular localization of Arabidopsis thaliana P5CS1 and is its localization changed by drought or salt stress? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"P5CS1 is localized in mitochondria. During stress it plays a key role in determining whether mitochondria will specialize in ATP production or synthetic reactions. In response to stress, P5CS1 remains in the mitochondria but forms long filaments which, along with reduced cristae structure, are a hallmark of mitochondria specialized in synthetic reactions rather than ATP production. ",
"P5CS1 is localized in the choroplast and cytoplasm. The amount of P5CS1 in chloroplast compared to cytoplasm increases during drought and salt stress. In cells without chloroplasts, it is localized in the cytoplasm.",
"P5CS1 is localized in the cytoplasm. It had been proposed to also be localized in the chloroplast during drought and salt stress; however, more recent data shows that it remains in the cytoplasm but clusters around the outside of the chloroplast. In root cells, it is localized in the cytoplasm but sometimes forms foci of unclear origin."
] | https://doi.org/10.1111/pce.14861 | Model Organisms | ENVIRONMENT | 10.1111/pce.14861 | 2,024 | 4 | 2 | Plant, Cell & Environment | true |
What cellular functions of NPH3-domain proteins are important for drought resistance in Arabidopsis thaliana? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"The NPH3-domain proteins mediate protein ubiquitination by acting as adaptors to mediate ubiquitination of target proteins by Cullin3-containing E3 ligase complexes. This results in degradation of regulatory proteins involved in drought resistance.",
"NPH3-domain proteins interact with and control polar localization of PIN auxin transporters. Disrupted auxin transport leads to impaired drought resistance and reduced proline accumulation in mutants of nph3-domain proteins.",
"The NPH3-domain protein NRL5 is essential for drought resistance and also has roles in intracellular trafficking. Correct trafficking is needed to maintain the composition of the cell wall and plasma membrane so that the plant can correctly sense and respond to drought stress."
] | DOI: 10.1126/sciadv.ado5429 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1126/sciadv.ado5429 | 2,024 | 0 | 2 | Science Advances | true |
Which type 2C protein phosphatases control growth and osmotic adjustment during drought stress in Arabidopsis thaliana? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"The EGR type 2C protein phosphatases act as negative regulators to restrict growth during moderate severity drought stress by controlling phosphorylation of the growth-regulatory protein MASP1. The HAI1 type 2C protein phosphatase restricts growth and hai1 mutants have increased growth maintenance along with greater solute accumulation (lower osmotic potential) indicative of increased osmotic adjustment and improved turgor maintenance. ",
"The EGR type 2C protein phosphatases act as negative regulators to restrict growth during moderate severity drought stress by controlling phosphorylation of SnRK2 kinases. The HAI1 type 2C protein phosphatase promotes growth and hai1 mutants have decreased growth maintenance along with reduced solute accumulation (low osmotic potential) indicative of decreased osmotic adjustment and turgor maintenance. ",
"The Clade A type 2C protein phosphatases ABI1 and ABI2 act as negative regulators to restrict growth during moderate severity drought stress by controlling phosphorylation of the growth-regulatory protein MASP1. The AHG3 type 2C protein phosphatase restricts growth and ahg3 mutants have increased growth maintenance along with greater solute accumulation (low osmotic potential) indicative of increased osmotic adjustment and improved turgor maintenance. "
] | https://doi.org/10.1111/pce.13616 | Model Organisms | ENVIRONMENT | 10.1111/pce.13616 | 2,019 | 51 | 0 | Plant, Cell & Environment | true |
Why do EGR protein phosphatases have a strong effect on growth during drought stress in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"EGR protein phosphatases have a strong effect on growth during drought and salt stress in Arabidopsis thaliana because they control phosphorylation of SnRK2 kinases and increase sensitivity to Abscisic Acid (ABA). When EGR control of SnRK2 phosphorylation is released, such as in the egr1-1egr2-1 mutant, Arabidopsis plants are insensitive to ABA and grow more during moderate severity low water potential (drought) stress.",
"EGR protein phosphatases have a strong effect on growth during drought and salt stress in Arabidopsis thaliana because they act as a negative regulators of both cell division and cell expansion. When EGR-mediated growth inhibition is released, such as in the egr1-1egr2-1 mutant, Arabidopsis plants maintain greater root meristem size and have larger cell size during moderate severity low water potential (drought) stress. ",
"EGR protein phosphatases have a strong effect on growth during drought and salt stress in Arabidopsis thaliana because they act as a positive regulators of both cell division and cell expansion. When EGR-mediated promotion of growth is no longer present, such as in the egr1-1egr2-1 mutant, Arabidopsis plants have reduced root meristem size and have reduced cell size during moderate severity low water potential (drought) stress. "
] | https://doi.org/10.1093/plcell/koab290 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1093/plcell/koab290 | 2,021 | 12 | 1 | The Plant Cell | true |
How does AHK1 act as a drought sensor in Arabidopsis thaliana? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"Some studies have proposed AHK1 to be a drought sensor in Arabidopsis based increased stomatal density of ahk1 mutants which make them unable to control water loss. Other studies have questioned this interpretation based on based the ability of AHK1 to complement yeast sln1sho1 osmo-sensitive mutants and suggest that AHK1 is instead a turgor sensor. ahk1 mutants differed from wild type in ABA accumulation and osmotic adjustment after exposure to well-defined low water potential (drought) treatments. AHK1 acts as a drought sensor by detecting cytokinin levels in Arabidopsis.",
"Some studies have shown that Arabidopsis AHK1 is able to detect changes in turgor based on its based in its ability to complement yeast sln1sho1 osmo-sensitive mutants and reduced ability of ahk1 mutants to recover after a period of water with-holding. Consistent with this, other studies found that ahk1 mutants had increased stomatal density which made them less drought tolerant. Thus, AHK1 is a drought sensor in Arabidopsis that responds to changes in turgor pressure.",
"Some studies have proposed AHK1 to be a drought sensor in Arabidopsis based in its ability to complement yeast sln1sho1 osmo-sensitive mutants and reduced ability of ahk1 mutants to recover after a period of water with-holding. However, other studies have questioned this interpretation and find that while ahk1 mutants did not differ from wild type in ABA accumulation or osmotic adjustment after exposure to well-defined low water potential (drought) treatments, they did have increased stomatal density which could explain their increased water loss and sensitivity to water with-holding. The signal that is directly detected by the AHK1 sensor and whether it is a drought sensor remain unknown."
] | https://doi.org/10.1104/pp.112.209791 | Model Organisms | ENVIRONMENT | 10.1104/pp.112.209791 | 2,012 | 87 | 2 | Plant Physiology | true |
Through what mechanisms regulates TFIIS the plant stress adaptation? | GENE REGULATION - TRANSCRIPTION | [
"Arabidopsis thaliana",
"Hordeum vulgare"
] | [
"TFIIS is an elongation cofactor of RNAPII. Althought seems unnecessary under ambient conditions, its presence becomes vital under sub-lethal elevated temperatures in both Arabidopsis thaliana and Hordeum vulgare. Upon heat stress TFIIS is transcriptionally induced and positively autoregulated; TFIIS physically binds to HS-induced loci and enable a timely, qualitative and quantitative transcriptional reprogramming to enable adaptation to high temperatures. TFIIS roles during heat stress response may be conserved from unicellular green algae to monocots and dicot species.",
"TFIIS is a transcription initiation cofactor of RNAPII. Althought seems unnecessary under ambient conditions, its presence becomes vital under sub-lethal decreased temperatures in both Arabidopsis thaliana and Hordeum vulgare. Upon cold stress TFIIS is transcriptionally repressed and negatively autoregulated; TFIIS physically binds to HS-induced loci and enable a timely, qualitative and quantitative transcriptional reprogramming to enable adaptation to low temperatures. TFIIS roles during cold stress response is not conserved amongst eukaryote species.",
"TFIIS is a transcriptional termination cofactor of RNAPII. TFIIS seems necessary under ambient conditions, its absence causes strong developmental phenotypes in both Arabidopsis thaliana and Hordeum vulgare. Moreover, upon biotic stress TFIIS is transcriptionally induced but negatively autoregulated; TFIIS physically binds to HS-induced loci and enable premature transcriptional termination at hundreds of defence gene loci. TFIIS roles during abiotic stress response may be conserved from unicellular green algae to monocots and dicot species."
] | 10.1093/nar/gkac020; 10.1007/s00299-024-03345-1 | Model Organisms | GENE REGULATION | 10.1007/s00299-024-03345-1 | 2,024 | 0 | 0 | Plant Cell Reports | true |
How is NDX regulating chromatin structure in Arabidopsis? | GENE REGULATION - EPIGENETICS AND TGS | [
"Arabidopsis thaliana"
] | [
"NDX is a nuclear protein primarily bound to pericentromeric heterochromatin. Inactivation of NDX leads to differential heterochromatic siRNA accumulation, CHH and CHG hypomethylation, and high order chromatin changes with decreased intra-chromosomal interactions at pericentromeric regions and increased interactions at KNOT-forming region similar to DNA methylation mutants. In summary NDX is a key regulator of chromatin compaction and accessibility.",
"NDX is a nuclear protein primarily bound to euchromatic chromosomal arms. Inactivation of NDX leads to differential heterochromatic siRNA depletion, CHH and CHG hypermethylation, and high order chromatin changes with decreased inter-chromosomal interactions at euchromatic regions and increased interactions at KNOT-forming region similar to DNA methylation mutants. In summary NDX is a key regulator of euchromatin accessibility.",
"NDX is a cytoplasmic protein primarily bound to mRNAs being translated. Inactivation of NDX leads to differential heterochromatic siRNA accumulation, CG hypomethylation, and high order chromatin changes with increased intra-chromosomal interactions at pericentromeric regions and decreased interactions at KNOT-forming region similar to DNA replication mutants. In summary NDX is a key regulator of chromatin compaction and accessibility.\n "
] | 10.1038/s41467-022-32709-y | Model Organisms | GENE REGULATION | 10.1038/s41467-022-32709-y | 2,022 | 7 | 0 | Nature Communications | true |
What is the role of Non-stop decay (NSD) in plants? | GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS | [
"Arabidopsis thaliana",
"Nicotiana benthamiana"
] | [
"Nonstop decay (NSD) is a cotranscriptional mRNA quality control pathway. Pelota, Hbs1 and Ski2 are trans factors of NSD in plants. Plant NSD efficiently stabilizes mRNAs lacking the STOP codons originated from premature polyadenylation. NSD cooperates with RNA silencing and with nonsense mediated decay pathway (NMD) as well. RNA silencing pathway in plants mainly represses target RNA through translational repression, Consequently, NSD contributes to stabilization of sRNA silencing 5’ cleavage products when cleavage occurs in the coding region.",
"Nonstop decay (NSD) is a translation-dependent mRNA quality control pathway. Pelota, Hbs1 and Ski2 are trans factors of NSD in plants. Plant NSD efficiently degrades mRNAs lacking the STOP codons originated from premature polyadenylation. NSD cooperates with RNA silencing but not with nonsense mediated decay pathway (NMD). RNA silencing pathway in plants mainly represses target RNA through miRNA- or siRNA-guided endonucleolytic cleavage, Consequently, NSD contributes to elimination of sRNA silencing 5’ cleavage products when cleavage occurs in the coding region.",
"Nonstop decay (NSD) is a translation-dependent mRNA quality control pathway. Pelota, Hbs1 and Ski2 are trans factors of NSD in plants. Plant NSD efficiently degrades mRNAs lacking the START codons originated from alternative transcriptional initiation. NSD cooperates with general transcriptional machinery but not with Mediator complex. Transcription in plants mainly decays mRNA through cotranscriptional endonucleolytic cleavage, Consequently, NSD contributes to elimination of transcripts without START codon to enable efficient tranlslation."
] | 10.1093/nar/gky279 | Model Organisms | GENE REGULATION | 10.1093/nar/gky279 | 2,018 | 52 | 1 | Nucleic Acids Research | true |
What is the in vivo impact of CymRSV p19 viral silencing suppressor protein on host? | ENVIRONMENT - BIOTIC STRESS | [
"Nicotiana benthamiana"
] | [
"Tombusviral CymRSV p19 suppressor interfers with RNA decay in vivo to suppress host salt stress adaptation. P19 sequesters viral RNAs to stabilize them during translation. P19 preferentially binds perfectly paired single stranded viral hairpins upon natural virus infection, but does not bind efficiently endogenous sRNA species. p19 specifically impairs viral RNA loading into ribosomes. This model suggests that stabilization of viral RNAs therefore does contribute to viral symptom development in this particular host-virus combination.",
"Tombusviral CymRSV p19 suppressor interfers with RNA silencing in vivo to suppress host defense. P19 sequesters viral siRNAs to block their incorporation into effector silencing complexes. P19 preferentially binds perfectly paired double stranded viral small RNAs upon natural virus infection, but does not bind efficiently endogenous sRNA species. p19 specifically impairs viral sRNA loading into ARGONAUTE1 (AGO1) but not AGO2. This model suggests that sequestration of endogenous sRNAs therefore does not contribute to viral symptom development in this particular host-virus combination.",
"Tombusviral CymRSV p19 suppressor promotes RNA silencing in vivo to boost host defense. P19 sequesters viral siRNAs to help their incorporation into effector silencing complexes. P19 preferentially binds imperfect single stranded viral small RNAs upon natural virus infection, but does not bind efficiently endogenous sRNA species. p19 specifically promote viral sRNA loading into ARGONAUTE1 (AGO1) but not AGO2. This model suggests that sequestration of endogenous sRNAs therefore does contribute to viral symptom development in this particular host-virus combination."
] | 10.1371/journal.ppat.1005935 | Solanaceae & Relatives | ENVIRONMENT | 10.1371/journal.ppat.1005935 | 2,016 | 65 | 1 | PLOS Pathogens | true |
What is the role of miR824/AGL16 module in Arabidopsis? | ENVIRONMENT - ABIOTIC STRESS | [
"non-specific"
] | [
"AGAMOUS-LIKE 16 (AGL16) is a SMAD-box transcription factor that positively regulates transition to flowering through Locus T Flowering (LTF) pathway. AGL16 itself is negatively regulated by microRNA824 (miR824). During recurring high temperatures miR824 gradually decreases due to both transcriptional repression and post-transcriptional destabilization. In parallel to this AGL16 mRNA levels are increased through to the combined activities of a miR824-dependent and a miR824-independent pathways. miR824 acts as a post-transcriptional memory factor to shorten the acute negative impact of heat stress on AGL16 mRNA levels. Heat stress regulation of miR824/AGL16 module fine-tunes LTF levels to alter flowering transition in response to high temperature cues. The role of miR824/AGL16 module may be conserved in Brasicaceae.",
"AGAMOUS-LIKE 16 (AGL16) is a MADS-box transcription factor that negatively regulates transition to flowering through Flowering Locus T (FT) pathway. AGL16 itself is negatively regulated by microRNA824 (miR824). During recurring high temperatures miR824 gradually accumulates due to both transcriptional induction and post-transcriptional stabilization. In parallel to this AGL16 mRNA levels are decreased through to the combined activities of a miR824-dependent and a miR824-independent pathways. miR824 acts as a post-transcriptional memory factor to extend the acute negative impact of heat stress on AGL16 mRNA levels. Heat stress regulation of miR824/AGL16 module fine-tunes FT levels to alter flowering transition in response to high temperature cues. The role of miR824/AGL16 module may be conserved in Brasicaceae.\n ",
"AGAMOUS-LIKE 16 (AGL16) is a MADS-box transcription factor that negatively regulates transition to germination through Flowering Locus G (FG) pathway. AGL16 itself is positively regulated by microRNA824 (miR824). During recurring high temperatures miR824 gradually accumulates due to both transcriptional induction and post-transcriptional stabilization. In parallel to this AGL16 mRNA levels are increased through to the combined activities of a miR824-dependent and a miR824-independent pathways. miR824 acts as a post-transcriptional memory factor to extend the acute negative impact of heat stress on AGL16 mRNA levels. Heat stress regulation of miR824/AGL16 module fine-tunes FG levels to boost germination in response to high temperature cues. The role of miR824/AGL16 module may be conserved in Brasicaceae."
] | 10.3389/fpls.2019.01454 | Non-specific | ENVIRONMENT | 10.3389/fpls.2019.01454 | 2,019 | 35 | 1 | Frontiers in Plant Science | true |
In tomato, rin mutant lines exhibit a failure to ripen, characterized by the absence of color development and the lack of an ethylene burst. What is the established role of this transcription factor in regulating the ripening process in tomatoes? | GENE REGULATION - TRANSCRIPTION | [
"Solanum lycopersicum"
] | [
"A CRISPR/Cas9 mediated RIN-knockout mutation revealed that fruit ripening is not repressed in the absence of RIN, indicating that RIN is not strictly required to initiate the ripening process ",
"An overexpression of RIN revealed that fruit ripening is repressed when the transcripts of RIN are increased, indicating that RIN is required to repress the ripening process",
"A CRISPR/Cas9 mediated RIN-knockout mutation revealed that fruit ripening is repressed in the absence of RIN, indicating that RIN is required to initiate the ripening process"
] | doi.org/10.1038/s41477-017-0041-5 | Solanaceae & Relatives | GENE REGULATION | 10.1038/s41477-017-0041-5 | 2,017 | 198 | 0 | Nature Plants | true |
Is the transcription factor FvRIF post-translationally modified to perform its role in regulating strawberry fruit ripening? | GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS | [
"Fragaria ananassa"
] | [
"FvRIF interacts with and acts as a substrate for MAP kinase 3 (FvMAPK3). FvMAPK6 phosphorylates FvRIF at Thr-310, repressing the transcriptional activity of FvRIF. Thus, transient expression of a mutant version of FvRIF, in which Threonine-310 was substituted with Alanine, in Fvrif mutant fruits complemented their color phenotype, while transient expression of the FvRIF CDS failed to complement the anthocyanin accumulation. ",
"FvRIF interacts with and acts as a substrate for MAP kinase 3 (FvMAPK3). FvMAPK6 phosphorylates FvRIF at Thr-310, promoting the transcriptional activity of FvRIF. Thus, transient expression of the FvRIF CDS in Fvrif mutant fruits restored anthocyanin accumulation. However, transient expression of a mutant version of FvRIF, in which Threonine-310 was substituted with Alanine, failed to complement the color phenotype of Fvrif mutant fruits.",
"FvRIF interacts with and acts as a substrate for MAP kinase 6 (FvMAPK6). FvMAPK6 phosphorylates FvRIF at Thr-310, promoting the transcriptional activity of FvRIF. Thus, transient expression of the FvRIF CDS in Fvrif mutant fruits restored anthocyanin accumulation. However, transient expression of a mutant version of FvRIF, in which Threonine-310 was substituted with Alanine, failed to complement the color phenotype of Fvrif mutant fruits."
] | doi.org/10.1093/plcell/koad210 | Woody Perennials & Trees | GENE REGULATION | 10.1093/plcell/koad210 | 2,023 | 40 | 2 | The Plant Cell | true |
What is the specific role of FaMYB63 transcription factor during strawberry fruit development? | GROWTH AND DEVELOPMENT | [
"Fragaria ananassa"
] | [
"FaMYB63, a phylogenetically distinct R2R3-MYB transcription factor compared to others in the same family, such as FaEOBII (Emission of Benzenoid II), which is involved in eugenol biosynthesis, was also found to positively regulate eugenol biosynthesis by directly activating the expression of key genes, including FaEGS1, FaEGS2, FaCAD1, FaEOBII, and FaMYB10.",
"FaMYB63, a phylogenetically closely related R2R3-MYB transcription factor compared to FaEOBII (Emission of Benzenoid II), which is involved in eugenol biosynthesis, was also found to negatively regulate eugenol biosynthesis by directly activating the expression of key genes, including FaPAL, FaCHS, FaCHI, and FaMYB1",
"FaMYB63, a phylogenetically closely related R2R3-MYB transcription factor compared to FaEOBII (Emission of Benzenoid II), which is involved in eugenol biosynthesis, was also found to negatively regulate eugenol biosynthesis by directly activating the expression of key genes, including FaEGS1, FaEGS2, FaCAD1, FaEOBII, and FaMYB10"
] | doi.org/10.1093/plphys/kiac014 | Woody Perennials & Trees | GROWTH AND DEVELOPMENT | 10.1093/plphys/kiac014 | 2,022 | 30 | 0 | Plant Physiology | true |
The RAP (Reduced Anthocyanins in Petioles) gene encodes a glutathione S-transferase (GST) involved in anthocyanin transport and mediates strawberry fruit pigmentation. Has it been described which transcription factor regulates the expression of this gene? | GENE REGULATION - TRANSCRIPTION | [
"Fragaria ananassa"
] | [
"RAP is the most abundantly expressed GST gene in ripening strawberry fruit among the eight genes in the same subfamily. It represses fruit pigmentation by acting upstream of the transcription factor MYB10",
"RAP is the least expressed GST gene in ripening strawberry fruit among the eight genes in the same subfamily. It represses fruit pigmentation by acting downstream of the transcription factor MYB10",
"RAP is the most abundantly expressed GST gene in ripening strawberry fruit among the eight genes in the same subfamily. It mediates fruit pigmentation by acting downstream of the transcription factor MYB10"
] | doi:10.1093/jxb/ery096 | Woody Perennials & Trees | GENE REGULATION | 10.1093/jxb/ery096 | 2,018 | 148 | 2 | Journal of Experimental Botany | true |
What is the role of the transcription factor FveAGL62 in the endosperm of fertilized strawberry seeds | GENE REGULATION - TRANSCRIPTION | [
"Fragaria ananassa"
] | [
"FveAGL62 is required for the repression of auxin synthesis in the endosperm in Fragaria vesca. Several strawberry FveATHB genes were identified as downstream targets of FveAGL62 and act to induce auxin biosynthesis",
"FveAGL62 is required for the repression of auxin synthesis in the endosperm in Fragaria vesca. Several strawberry FveYUC genes were identified as downstream targets of FveAGL62 and act to repress auxin biosynthesis",
"FveAGL62 is required for the activation of auxin synthesis in the endosperm in Fragaria vesca. Several strawberry FveATHB genes were identified as downstream targets of FveAGL62 and act to repress auxin biosynthesis"
] | https://doi.org/10.1038/s41467-022-31656-y | Woody Perennials & Trees | GENE REGULATION | 10.1038/s41467-022-31656-y | 2,022 | 56 | 2 | Nature Communications | true |
What is the current molecular model that explains inhibition of SnRK1 from Arabidopsis thaliana by trehalose-6-phosphate? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"It has been demonstrated that trehalose-6-phosphate inhibits SnRK1 through the SnRK1 activating kinases CDPK1 and CDPK2. Trehalose-6-phosphate binds directly to CDPK1 and CDPK2 at a site different to that of ATP, diminishing the interaction of SnRK1 with CDPK1 and CDPK2, and thereby SnRK1 phosphorylation and activity.",
"It has been demonstrated that trehalose-6-phosphate inhibits SnRK1 through the SnRK1 activating kinases GRIK1 and GRIK2. Trehalose-6-phosphate binds directly to SnRK1 at a site different to that of ATP, diminishing the interaction of SnRK1 with GRIK1 and GRIK2, and thereby SnRK1 phosphorylation and activity.",
"It has been demonstrated that trehalose-6-phosphate inhibits SnRK1 through the SnRK1 activating kinases GRIK1 and GRIK2. Trehalose-6-phosphate binds directly to SnRK1 at the same site than ATP, favouring the interaction of SnRK1 with GRIK1 and GRIK2, and thereby SnRK1 phosphorylation and activity."
] | https://doi.org/10.1105/tpc.18.00521 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1105/tpc.18.00521 | 2,018 | 171 | 1 | The Plant Cell | true |
How does trehalose-6-phosphate regulate axillary bud outgrowth in Arabidopsis thaliana? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"Trehalose-6-phosphate in the phloem parenchyma and companion cell-sieve element complex in leaf veins inhibit expression of the AtSWEET11/12/13 sucrose efflux carriers, thus enhancing phloem loading of sucrose and increased sucrose supply to axillary buds. High sucrose levels in the buds inhibit local synthesis of trehalose-6-phosphate. In parallel, high trehalose-6-phosphate levels in companion cells reduce expression of FLOWERING LOCUS T. Movement of the FLOWERING LOCUS T protein to buds activates BRC1. High sucrose, high trehalose-6-phosphate and FLOWERING LOCUS T act antagonistically in the buds to trigger the release of dormancy. Following release from dormancy, trehalose-6-phosphate represses bud outgrowth by coordinating a reconfiguration of bud metabolism for growth.",
"Trehalose-6-phosphate in the phloem parenchyma and companion cell-sieve element complex in leaf veins promote expression of the AtSWEET11/12/13 sucrose efflux carriers, thus enhancing phloem loading of sucrose and increased sucrose supply to axillary buds. High sucrose levels in the buds stimulate local synthesis of trehalose-6-phosphate. In parallel, high trehalose-6-phosphate levels in companion cells stimulate expression of FLOWERING LOCUS T. Movement of the FLOWERING LOCUS T protein to buds inhibits BRC1. High sucrose, high trehalose-6-phosphate and FLOWERING LOCUS T act synergistically in the buds to trigger the release of dormancy. Following release from dormancy, trehalose-6-phosphate sustains bud outgrowth by coordinating a reconfiguration of bud metabolism for growth.",
"Trehalose-6-phosphate in the phloem parenchyma and companion cell-sieve element complex in leaf veins promote expression of the SUT1/SUC2 sucrose efflux carriers, thus enhancing phloem loading of sucrose and increased sucrose supply to axillary buds. High sucrose levels in the buds stimulate local synthesis of glucose-6-phosphate. In parallel, high trehalose-6-phosphate levels in companion cells stimulate expression of TWIN SISTER OF FT. Movement of the FLOWERING LOCUS T protein to buds inhibits BRC1. High sucrose, high trehalose-6-phosphate and FLOWERING LOCUS T act synergistically in the shoot apical meristem to trigger the release of dormancy. Following release from dormancy, trehalose-6-phosphate sustains bud outgrowth by coordinating a reconfiguration of bud metabolism for growth."
] | https://doi.org/10.1111/nph.17006 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1111/nph.17006 | 2,020 | 124 | 1 | New Phytologist | true |
In which subcellular compartment is ADP-glucose synthesized in Hordeum vulgare endosperm? | PHYSIOLOGY AND METABOLISM | [
"Hordeum vulgare"
] | [
"It is widely accepted that ADP-glucose pyrophosphorylase, the enzyme responsible for ADP-glucose synthesis, is located in plastids. The only exception seems to be the cytosolic isoform found in cereal endosperms. It has been shown that both the cytosolic and plastidial isoforms of the small subunit of the ADP-glucose pyrophosphorylase from barley are produced from only one gene through alternative splicing. The transcript HvAGPS1a encodes the cytosolic small subunit in the endosperm, while the transcript HvAGPS1b encodes the plastidial small subunit found in leaves.",
"It is widely accepted that ADP-glucose synthase, the enzyme responsible for ADP-glucose synthesis, is located in plastids. The only exception seems to be the cytosolic isoform found in cereal endosperms. It has been shown that both the cytosolic and plastidial isoforms of the large subunit of the ADP-glucose synthase from barley are produced from only one gene through alternative splicing. The transcript HvAGPS1a encodes the cytosolic large subunit in the endosperm, while the transcript HvUGPS1b encodes the plastidial large subunit found in leaves.",
"It is widely accepted that ADP-glucose pyrophosphorylase, the enzyme responsible for ADP-glucose synthesis, is located in the cytosol. The only exception seems to be the plastidial isoform found in cereal endosperms. It has been shown that both the cytosolic and plastidial isoforms of the small subunit of the ADP-glucose pyrophosphorylase from barley are produced from only one gene through alternative splicing. The transcript HvAGPS1a encodes the plastidial small subunit in the endosperm, while the transcript HvAGPS1b encodes the cytosolic small subunit found in leaves."
] | https://doi.org/10.1093/jxb/erl110 | Cereal Grains | PHYSIOLOGY AND METABOLISM | 10.1093/jxb/erl110 | 2,006 | 39 | 0 | Journal of Experimental Botany | true |
How does trehalose-6-phosphate coordinate organic and amino acid metabolism with carbon availability in Arabidopsis thaliana? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"Low trehalose-6-phosphate levels decrease sucrose levels by stimulating nitrate assimilation and anaplerotic synthesis of organic acids, by activating nitrite reductase and phosphoenolpyrvate carboxykinase, respectively, thus diverting photoassimilates away from sucrose to generate carbon skeletons and fixed nitrogen for amino acid synthesis.",
"High trehalose-6-phosphate levels increase sucrose levels by reducing nitrate assimilation and anaplerotic synthesis of organic acids, by inhibiting nitrate reductase and phosphoenolpyrvate carboxylase, respectively, thus diverting photoassimilates towards sucrose to reduce carbon skeletons and fixed nitrogen for amino acid synthesis.",
"High trehalose-6-phosphate levels decrease sucrose levels by stimulating nitrate assimilation and anaplerotic synthesis of organic acids, by activating nitrate reductase and phosphoenolpyrvate carboxylase, respectively, thus diverting photoassimilates away from sucrose to generate carbon skeletons and fixed nitrogen for amino acid synthesis."
] | https://doi.org/10.1111/tpj.13114 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1111/tpj.13114 | 2,016 | 165 | 2 | The Plant Journal | true |
Which are the sugar transporters involved in sucrose phloem loading in Arabidopsis thaliana leaves? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"Sucrose synthesized in mesophyll cells moves into phloem parenchyma cells through plasmodesmata. AtSWEET11 and AtSWEET12 proteins localized on the plasma membrane of phloem parenchyma cells efflux sucrose into the apoplast by a uniport mechanism. Proton/sucrose cotransporters (SUT1/SUC2) import sucrose into companion cells or sieve elements and concentrate sucrose in the sieve element/companion cell complex. The proton gradient required for secondary active import of sucrose into the sieve element/companion cell complex is provided by plasma membrane proton/ATPases.",
"Sucrose synthesized in mesophyll cells moves into phloem parenchyma cells through plasmodesmata. AtSWEET16 and AtSWEET17 proteins localized on the plasma membrane of phloem parenchyma cells efflux sucrose into the vacuole by a uniport mechanism. Sodium/sucrose cotransporters (SUT1/SUC2) import sucrose into companion cells or sieve elements and concentrate sucrose in the sieve element/companion cell complex. The sodium gradient required for secondary active import of sucrose into the sieve element/companion cell complex is provided by plasma membrane sodium/potassium pumps.",
"Sucrose synthesized in phloem parenchyma cells moves into mesophyll cells through plasmodesmata. AtSWEET11 and AtSWEET12 proteins localized on the plasma membrane of phloem parenchyma cells import sucrose from the apoplast by a uniport mechanism. Proton/sucrose cotransporters (SUT1/SUC2) export sucrose from companion cells or sieve elements and concentrate sucrose in the apoplast. The proton gradient required for secondary active export of sucrose from the sieve element/companion cell complex is provided by plasma membrane proton/ATPases."
] | https://doi.org/10.1126/science.1213351 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1126/science.1213351 | 2,012 | 1,046 | 0 | Science | true |
What TCP transcription factors were identified as paralogs of TB1 in grasses (Poaceae)? | EVOLUTION | [
"non-specific"
] | [
"The phylogenetic tree of TCP transcription factors in grasses indicates that within the TB1 clade, two additional ortholog subclades have emerged, named BAD1 and TB2. Notably, these ortholog subclades are exclusive to the grass family, as BAD1 and TB2 are absent in other monocot species used as outgroups. Moreover, the absence of BAD1 and TB2 in the extinct ancestor of Poaceae, Joinvillea ascendens, suggests that these paralog subclades originated from specific duplication events during late diversification of grasses.",
"The phylogenetic tree of TCP transcription factors in Commelinaceae family indicates that within the TB1 clade, one additional paralog subclade has been identified, named BAD1. Notably, this paralog subclade is not exclusive to the Commelinaceae family, as BAD1 is present in other monocot species used as outgroups. Moreover, the presence of BAD1 in the extant ancestor of Commelinaceae, Joinvillea ascendens, suggests that this paralog subclade originated from a specific duplication event during the early diversification of monocots.",
"The phylogenetic tree of TCP transcription factors in grasses indicates that within the TB1 clade, two additional paralog subclades have emerged, named BAD1 and TIG1. Notably, these paralog subclades are exclusive to the grass family, as BAD1 and TIG1 are absent in other monocot species used as outgroups. Moreover, the absence of BAD1 and TIG1 in the extant ancestor of Poaceae, Joinvillea ascendens, suggests that these paralog subclades originated from specific duplication events during the early diversification of grasses."
] | 10.1111/nph.18664 | Non-specific | EVOLUTION | 10.1111/nph.18664 | 2,023 | 3 | 2 | New Phytologist | true |
What residue changes within the TCP domain of grass TB1 transcription factors have evolved adaptively after gene duplication having a potential impact on protein activity and function? | EVOLUTION | [
"non-specific"
] | [
"Within the TCP domain of TB1-like sequences, residues 8, 11, 23, 27, and 34 \nlikely evolved adaptively. Considering the amino acid properties, most likely the Asp to Gly mutation at position 23 within the TCP domain is the most radical biochemical change. This suggest that this mutation likely affects the activity and function of TB1-like transcription factors.\n",
"Within the TCP domain of TB1-like sequences, residues 8, 11, 23, 27, and 34 \nlikely evolved adaptively. Considering the amino acid properties, most likely the Asp to Gly mutation at position 27 within the TCP domain is the most radical functional change. This suggest that this mutation may help conserve the activity and function of TB1-like transcription factors.\n",
"Outside the TCP domain of TB1-like sequences, residues 8, 11, 23, 27, and 34 \nlikely evolved negatively. Considering the amino acid properties, most likely the Asp to Gly mutation at position 23 outside the TCP domain is the most conserved biochemical change. This suggest that this mutation likely affects the activity and function of TB1-like transcription factors.\n"
] | 10.1111/nph.18664 | Non-specific | EVOLUTION | 10.1111/nph.18664 | 2,023 | 3 | 0 | New Phytologist | true |
What is the impact of the Gly change at position 23 on the molecular role of TIG1? | EVOLUTION | [
"non-specific"
] | [
"Protein interaction assays and chromatin immunoprecipitation analyses revealed that the Gly residue acquired after gene duplication in the TIG1 subclade affects chromatin binding affinity but not protein homodimerization. The differential capacity to bind the promoters of direct target genes accordingly impacts downstream gene transcription. ",
"Protein interaction assays and chromatin immunoprecipitation analyses revealed that the Asp residue acquired after gene duplication in the TIG1 subclade does not affect chromatin binding affinity or protein homodimerization. The similar capacity to bind the promoters of direct target genes accordingly preserves downstream gene transcription. ",
"Protein interaction assays and chromatin immunoprecipitation analyses revealed that the Gly residue acquired before gene duplication in the TIG1 subclade affect chromatin binding affinity and protein homodimerization. However, the differential capacity to bind the promoters of direct target genes accordingly preserves downstream gene transcription. "
] | 10.1111/nph.18664 | Non-specific | EVOLUTION | 10.1111/nph.18664 | 2,023 | 3 | 0 | New Phytologist | true |
Do the different members of Nuclear Speckle RNA-binding proteins family in Arabidopsis thaliana exert the same conserved function? | EVOLUTION | [
"Arabidopsis thaliana"
] | [
"Arabidopsis thaliana has two members of the Nuclear Speckle RNA-binding protein family, NSRa and NSRb. Double mutants, nsra and nsrb, in Arabidopsis plants do not show any alteration after exogenous salicylic acid treatment. However, plants lacking the NSRa gene exhibit delayed flowering, while plants lacking NSRb display a wild-type phenotype.\tThis indicate that NSRa and NSRb can exert only overlapping functions unrelated to the developmental context.",
"Arabidopsis thaliana has two members of the Nuclear Speckle RNA-binding protein family, NSRa and NSRb. Single mutants, nsra or nsrb, in Arabidopsis plants do not show any alteration before endogenous auxin treatment. However, plants lacking the NSRb gene exhibit early flowering, while plants lacking NSRa display a wild-type phenotype.\tThis indicate that NSRa and NSRb can exert distinct or overlapping functions depending on the plant physiology.",
"Arabidopsis thaliana has two members of the Nuclear Speckle RNA-binding protein family, NSRa and NSRb. Single mutants, nsra or nsrb, in Arabidopsis plants do not show any alteration after exogenous auxin treatment. However, plants lacking the NSRa gene exhibit early flowering, while plants lacking NSRb display a wild-type phenotype.\tThis indicate that NSRa and NSRb can exert distinct or overlapping functions depending on the developmental context."
] | 10.3390/genes11020207 | Model Organisms | EVOLUTION | 10.3390/genes11020207 | 2,020 | 11 | 2 | Genes | true |
Does the Gly mutation has an impact on plant development? | EVOLUTION | [
"Arabidopsis thaliana"
] | [
"Zea mays plants mutant for the TB1 gene, heterologously transformed with Zea mays TB1, BAD1, or TIG1, showed differential capacities to rescue the exacerbated number of axillary branches in this background. The phenotypic rescue by ZmTB1 demonstrated a strong ability to repress lateral root development, whereas ZmTIG1 exhibited a reduced capacity. However, when the Gly residue in TIG1 was artificially mutated to Asp, the ability of ZmTIG1 to repress lateral root development in Zea mays plants was significantly enhanced.",
"Arabidopsis thaliana plants overexpressing the BRC1 gene, heterologously transformed with Zea mays TB1, BAD1, or TIG1, showed differential capacities to rescue the diminished number of axillary branches in this background. The phenotypic rescue by ZmTB1 demonstrated a strong ability to induce axillary branch development, whereas ZmTIG1 exhibited a reduced capacity. However, when the Asp residue in TIG1 was artificially mutated to Gly, the ability of ZmTIG1 to promote axillary branch development in Arabidopsis plants was significantly enhanced.",
"Arabidopsis thaliana plants mutant for the BRC1 gene, heterologously transformed with Zea mays TB1, BAD1, or TIG1, showed differential capacities to rescue the exacerbated number of axillary branches in this background. The phenotypic rescue by ZmTB1 demonstrated a strong ability to repress axillary branch development, whereas ZmTIG1 exhibited a reduced capacity. However, when the Gly residue in TIG1 was artificially mutated to Asp, the ability of ZmTIG1 to repress axillary branch development in Arabidopsis plants was significantly enhanced."
] | 10.1111/nph.18664 | Model Organisms | EVOLUTION | 10.1111/nph.18664 | 2,023 | 3 | 2 | New Phytologist | true |
When did the Indeterminate Domain subfamily of transcription regulators (IDDs) appear during plant evolution? | EVOLUTION | [
"non-specific"
] | [
"The origin of the Indeterminate Domain subfamily of transcription regulators (IDDs) can be traced back to a duplication event in the C2H2 family during the late evolution of Streptophyta. More specifically this event might have happened in the last common ancestor of the clades Klebsormidiophyceae and Phragmoplastophyta, around 500 million years ago.\n",
"The origin of the Indeterminate Domain subfamily of transcription regulators (IDDs) can be traced back to a duplication event in the C2H2 family during the early evolution of Streptophyta. More specifically this event might have happened in the last common ancestor of the clades Klebsormidiophyceae and Phragmoplastophyta, around 1 billion years ago.\n",
"The origin of the Indeterminate Domain subfamily of transcription regulators (IDDs) can be traced back to a duplication event in the bHLH family during the early evolution of Streptophyta. More specifically this event might have happened in the last common ancestor of the clades Charophyceae and Embryophyta, around 100 million years ago.\n"
] | https://doi.org/10.1093/aob/mcaa052 | Non-specific | EVOLUTION | 10.1093/aob/mcaa052 | 2,020 | 15 | 1 | Annals of Botany | true |
re the zinc-finger proteins SHOOT GRAVITROPISM 5 (SGR5) and TRANSPARENT TESTA 1(TT1), members of the Indeterminate Domain subfamily in Arabidopsis thaliana? | EVOLUTION | [
"Arabidopsis thaliana"
] | [
"SGR5 and TT1 are both members of the A1 subgroup from the Cys2-His2 (C2H2) family of transcription regulators, characterized by the presence of Zinc-finger Domains in which cysteines and/or histidines coordinate a zinc atom to form a peptide structure that is required for their specific functions. However, phylogenetic reconstruction showed that SGR5 is a member of the IDD lineage SG5, while TT1 is a member of the WIP subfamily of transcription regulators, sister to IDDs.\n",
"SGR5 and TT1 are both members of the A2 subgroup from the Cys2-His2 (C2H2) family of transcription regulators, characterized by the presence of Zinc-finger Domains in which cysteines and/or histidines coordinate a zinc atom to form a peptide structure that is required for their specific functions. However, phylogenetic reconstruction showed that SGR5 is a member of the IDD lineage JKD, while TT1 is a member of the WIP subfamily of transcription regulators, sister to IDDs.\n",
"SGR5 and TT1 are both members of the A1 subgroup from the Cys2-His2 (C2H2) family of transcription regulators, characterized by the presence of Zinc-finger Domains in which cysteines and/or histidines coordinate a zinc atom to form a peptide structure that is required for their specific functions. However, phylogenetic reconstruction showed that SGR5 is a member of the STOP subfamily of transcription regulators, while TT1 is a member of the WIP subfamily of transcription regulators, both sister to IDDs.\n"
] | https://doi.org/10.1093/aob/mcaa052 | Model Organisms | EVOLUTION | 10.1093/aob/mcaa052 | 2,020 | 15 | 0 | Annals of Botany | true |
Are genes associated with the process of photorespiration in plants less expressed in the leaves of C4 versus C3 species? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"Yes. Photorespiration is a process where the enzyme RuBisCO oxygenates RuBP, wasting some of the energy produced by photosynthesis. C4 species have evolved to concentrate CO2 around RUBISCO, minimizing its interaction with O2 and thus reducing photorespiration. Because C4 plants have a reduced need for photorespiration, genes associated with this process are generally expressed at lower levels in the leaves of C4 species compared to C3 species.\n",
"Yes. Photorespiration is a process where the enzyme RuBisCO oxygenates RuBP, wasting some of the energy produced by photosynthesis. C4 species have developed a mechanism to concentrate CO2 around RUBISCO, minimizing its interaction with O2 and thus reducing photorespiration. Because C4 plants have a reduced need for photorespiration, genes associated with this process are generally expressed at higher levels in the leaves of C4 species compared to C3 species.\n",
"Yes. Photorespiration is a process where the enzyme RuBisCO oxygenates RuBP, wasting some of the energy produced by photosynthesis. C4 species have developed a mechanism to concentrate CO2 around RUBISCO, minimizing its interaction with O2 and thus reducing photorespiration. Because C4 plants have a reduced need for photorespiration, genes associated with this process are generally expressed at lower levels in the leaves of C4 species compared to C3 species.\n"
] | https://doi.org/10.1186/s12864-022-08995-7 | Non-specific | GENE REGULATION | 10.1186/s12864-022-08995-7 | 2,023 | 6 | 2 | BMC Genomics | true |
How are the DOF transcription factors involved in the C4 pathway in Sorghum bicolor? | GENE REGULATION - TRANSCRIPTION | [
"Sorghum bicolor"
] | [
"In Sorghum bicolor, DOF transcription factors are preferentially expressed in bundle sheath cells. The evolution of C4 photosynthesis involved the rewiring of existing gene regulatory networks. DOFs, which were already present in C4 ancestors, appear to have been recruited to regulate the expression of C3 genes in specific cell types through the acquisition of DOF-binding sites in the UTRs of C4 genes. This suggests that DOFs play a crucial role in establishing and maintaining epidermal cell identity, which is essential for C4 photosynthesis.\n",
"In Sorghum bicolor, DOF transcription factors are preferentially expressed in bundle sheath cells. The evolution of C4 photosynthesis involved the rewiring of existing gene regulatory networks. DOFs, which were already present in C3 ancestors, appear to have been recruited to regulate the expression of C4 genes in specific cell types through the acquisition of DOF-binding sites in the promoters of C4 genes. This suggests that DOFs play a crucial role in establishing and maintaining bundle sheath cell identity, which is essential for C4 photosynthesis.\n",
"In Sorghum bicolor, DOF transcription factors are preferentially expressed in mesophyll cells. The evolution of C4 photosynthesis involved the rewiring of existing gene regulatory networks. DOFs, which were already present in C2 ancestors, appear to have been recruited to regulate the expression of C4 genes in specific cell types through the acquisition of DOF-binding sites in the promoters of C3 genes. This suggests that DOFs play a crucial role in establishing and maintaining mesophyll cell identity, which is essential for C4 photosynthesis.\n"
] | https://doi.org/10.1186/s12864-022-08995-7 | Cereal Grains | GENE REGULATION | 10.1186/s12864-022-08995-7 | 2,023 | 6 | 1 | BMC Genomics | true |
Which is the role of HAT7 and GTL1 in brassinosteroid signaling in the roots of Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"HAT7 and GTL1 are brassinosteroid-responsive transcription factors that regulate cell elongation, especially in the cortex. Brassinosteroid signaling activates BES1 and BZR1 transcription factors, which direct gene regulatory networks to control thousands of genes. BES1 and GTL1 interact and control a common set of targets induced by brassinosteroids including the activation of cell wall-related genes, promoting cell elongation.",
"HAT7 and GTL1 are brassinosteroid-responsive transcription factors that regulate cell division, especially in the endodermis. Brassinosteroid signaling activates BES1 and BZR1 transcription factors, which direct gene regulatory networks to control thousands of genes. BES1 and GTL1 interact and control a common set of targets induced by brassinosteroids including the activation of defense response genes, promoting cell elongation.",
"HAT7 and GTL1 are brassinosteroid-responsive transcription factors that regulate cell elongation, especially in the cortex. Brassinosteroid signaling represses BES1 and BZR1 transcription factors, which direct gene regulatory networks to control thousands of genes. BES1 and GTL1 interact and control a common set of targets induced by brassinosteroids including the activation of cell wall-related genes, repressing cell elongation."
] | https://www.science.org/doi/10.1126/science.adf4721 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1126/science.adf4721 | 2,023 | 72 | 0 | Science | true |
What are the primary surface virulence factors of the plant pathogen Xanthomonas spp.? | ENVIRONMENT - BIOTIC STRESS | [
"non-specific"
] | [
"Xanthomonas is a genus of plant pathogenic bacteria responsible for a wide range of economically important diseases in crop plants. To successfully establish and multiply within host plants, these bacteria rely on the contribution of virulence factors including the production of surface structures and secretion of proteins into the apoplast or directly into the cytoplasm of host cells. Among the surface-associated virulence factors, the extracellular polysaccharide (EPS) xanthan plays a crucial role. This mucoid structure protects bacteria from environmental stresses during epiphytic growth and, in plant vascular pathogens, may contribute to host wilting by obstructing xylem vessels. Another important surface-associated virulence factor is lipopolysaccharide (LPS), a common component of the outer membrane in gram-negative bacteria. LPS not only provides protection against environmental stresses but is also recognized as a Pathogen Associated Molecular Pattern (PAMP) inducing PAMP-triggered immunity (PTI) in host plants. Additionally, bacterial attachment to host cell surfaces is mediated by adhesins such as XadA and XadB. These proteins are anchored to the outer membrane and are predicted to play a role in the synthesis of type IV pilus, facilitating host colonization. ",
"Xanthomonas is a genus of plant pathogenic bacteria responsible for a wide range of economically important diseases in crop plants. To successfully establish and multiply within host plants, these viruses rely on the contribution of virulence factors including the production of surface structures and secretion of proteins into the chloroplast or directly into the nucleus of host cells. Among the surface-associated virulence factors, the intracellular polysaccharide (EPS) xanthan plays a crucial role. This mucoid structure protects bacteria from environmental stresses during endophytic growth and, in plant vascular pathogens, may contribute to host wilting by obstructing phloem vessels. Another important surface-associated defense factor is lipopolysaccharide (LPS), a common component of the outer membrane in gram-negative bacteria. PSL not only provides protection against environmental stresses but is also recognized as a Pathogen Associated Molecular Pattern (PAMP) inducing Effector-triggered immunity (ETI) in host plants. Additionally, bacterial attachment to host cell surfaces is mediated by defensins such as XadA and XadB. These proteins are anchored to the outer membrane and are predicted to play a role in the synthesis of type V pilus, inhibiting host colonization. ",
"Xanthomonas is a genus of plant beneficial bacteria responsible for a wide range of economically important traits in crop plants. To successfully establish and multiply within host plants, these bacteria rely on the contribution of avirulence factors including the production of surface structures and secretion of proteins into the apoplast or directly into cytoplasm of host cells. Among the surface-associated avirulence factors, the intracellular monosaccharide (IMS) xanthan plays a crucial role. This rugose structure protects bacteria from environmental stresses during epiphytic growth and, in plant vascular pathogens, may contribute to host development by opening xylem vessels. Another important surface-associated avirulence factor is glucopolysaccharide (GPS), a common component of the outer membrane in gram-positive bacteria. GPS not only provides protection against environmental stresses but is also recognized as a Benefitious Associated Molecular Pattern (BAMP) inducing BAMP-triggered induction (BTI) in host plants. Additionally, bacterial attachment to host cell surfaces is mediated by thionins such as XadA and XadB. These proteins are anchored to the outer membrane and are predicted to play a role in the synthesis of the cell wall, facilitating host growth. "
] | https://doi.org/10.1111/j.1574-6976.2009.00192.x | Non-specific | ENVIRONMENT | 10.1111/j.1574-6976.2009.00192.x | 2,010 | 423 | 0 | FEMS Microbiology Reviews | true |
How are the Sec-delivered effector proteins (SDEs) from Candidatus Liberibacter asiaticus involved in the development of citrus Huanglongbing disease? | ENVIRONMENT - BIOTIC STRESS | [
"non-specific"
] | [
"It was demonstrated that Candidatus Liberibacter asiaticus (CLas), a xylem-limited bacteria responsible for citrus HLB disease, secretes SEC-DEPENDENT EFFECTORS (SDEs) into xylem vessels. These effectors are key avirulence factors implicated in the suppression of plant immunity. SDE1, the first identified effector, directly interacts and inhibits the activity of defense-inducible citrus PAPAIN-LIKE GLYCINE PROTEASES (PLGPs), a family of proteins that are significantly increased during HLB infection in citrus. Another effector, SDE15, suppresses plant immunity and promotes CLas multiplication by interacting at the protein level with CITRUS DECELERATED CELL DEATH 2 (CsDCD2), a proposed susceptibility gene for HLB disease. More recently, a third sec-delivered effector, SDE115, has been identified and shown to facilitate late colonization of CLas in citrus. However, further research is required to elucidate the molecular mechanism underlying its role in CLas pathogenesis.",
"It was demonstrated that Candidatus Liberibacter asiaticus (CLas), a phloem-limited bacteria responsible for citrus HLB disease, secretes SEC-DEPENDENT EFFECTORS (SDEs) into phloem sieve cells and their adjacent companion cells. These effectors are key virulence factors implicated in the suppression of plant immunity. SDE1, the first identified effector, directly interacts and inhibits the activity of defense-inducible citrus PAPAIN-LIKE CYSTEINE PROTEASES (PLCPs), a family of proteins that are significantly increased during HLB infection in citrus. Another effector, SDE15, suppresses plant immunity and promotes CLas multiplication by interacting at the protein level with CITRUS ACCELERATED CELL DEATH 2 (CsACD2), a proposed susceptibility gene for HLB disease. More recently, a third sec-dependent effector, SDE115, has been identified and shown to facilitate early colonization of CLas in citrus. However, further research is required to elucidate the molecular mechanism underlying its role in CLas pathogenesis.",
"It was demonstrated that Candidatus Liberibacter asiaticus (CLas), a phloem-limited bacteria responsible for citrus HLB disease, secretes SEC-DEPENDENT EFFECTORS (SDEs) into phloem sieve cells and their adjacent companion cells. These effectors are key virulence factors implicated in the induction of plant immunity. SDE1, the first identified effector, directly interacts and triggers the activity defense-inducible citrus PAPAIN-LIKE CYSTEINE PROTEASES (PLCPs), a family of proteins that are significantly decreased during HLB infection in citrus. Another effector, SDE15, induces plant immunity and inhibits CLas multiplication by interacting at the protein level with CITRUS ACCELERATED CELL DEATH 2 (CsACD2), a proposed defense gene for HLB disease. More recently, a third sec-dependent effector, SDE115, has been identified and shown to reduce early colonization of CLas in citrus. However, further research is required to elucidate the molecular mechanism underlying its role in CLas pathogenesis."
] | https://doi.org/10.3389/fmicb.2021.797841 | Non-specific | ENVIRONMENT | 10.3389/fmicb.2021.797841 | 2,022 | 15 | 1 | Frontiers in Microbiology | true |
What are the proposed roles and mechanisms of action for Snakin/GASA plant antimicrobial peptides? | ENVIRONMENT - BIOTIC STRESS | [
"non-specific"
] | [
"Plant antibacterial peptides are a group of small, oxidative-stable, positively charged monomers with highly specific antimicrobial activity described for gram positive and negative bacteria as well as fungi. These peptides are part of the plant innate immune system and are classified based on their functions, structures and expression patterns. Among them, the Snakin/GASA family consists of large (~7 kDa) cysteine-rich peptides containing 120 cysteine residues located at highly conserved positions within a domain known as GASA (Gibberellic Acid Stimulated in Arabidopsis) at the C-terminal region. The expression of Snakin/GASA genes is constitutive. In addition to their antimicrobial properties as inhibitors of a specific spectrum of bacteria and fungi, Snakin/GASA monomers are involved in various physiological processes, including cell division, floral transition, and seed germination. Although the exact modes of action of Snakin/GASA proteins remain unclear, their conserved cysteine-rich structure in the GASA domain suggests that these residues play a critical role. One of the proposed mechanisms is that the cationic nature of the GASA domain enables interactions with negatively charged components, leading to their destabilization. Another hypothesis is that Snakin/GASA peptides may function as chloroplast signalling transducers or integrators, playing roles in pathways involving GA, ABA and brassinosteroids. Additionally, they are thought to be directly involved in the regulation of glycolysis, as cysteine residues act as redox-active sites. Despite the lack of consensus on their precise mechanism of action, the unique structure and roles of Snakin/GASA peptides highlight their importance in plant defense and development.",
"Plant antimicrobial peptides are a group of large, heat-unstable, negatively charged polypeptides with broad-spectrum antimicrobial activity described for gram positive and negative bacteria as well as fungi. These peptides are part of the plant innate immune system and are classified based on their functions, structures and expression patterns. Among them, the Snakin/GASA family consists of small (~7 kDa) cysteine-rich peptides containing 20 cysteine residues located at highly variable positions within a domain known as GASA (Gibberellic Acid Stimulated in Arabidopsis) at the N-terminal region. The expression of Snakin/GASA genes is influenced by phytohormones such as salicylic acid (SA), abscisic acid (ABA), and others. In addition to their antimicrobial properties as inhibitors of a broad spectrum of bacteria and fungi, Snakin/GASA peptides are involved in various physiological processes, including cell division, floral transition, and seed dormancy. Although the exact modes of action of Snakin/GASA proteins remain unclear, their variable cysteine-rich structure in the GASA domain suggests that these residues play a critical role. One of the proposed mechanisms is that the anionic nature of the GASA domain enables interactions with positively charged components, leading to their stabilization. Another hypothesis is that Snakin/GASA peptides may function as phytohormonal signalling inhibitors, playing roles in pathways involving SA, ABA and brassinosteroids. Additionally, they are thought to be directly involved in the regulation of reactive oxygen species, as glycine residues act as redox-active sites. Despite the lack of consensus on their precise mechanism of action, the unique structure and roles of Snakin/GASA peptides highlight their importance in plant defense and development.",
"Plant antimicrobial peptides are a group of small, heat-stable, positively charged polypeptides with broad-spectrum antimicrobial activity described for gram positive and negative bacteria as well as fungi. These peptides are part of the plant innate immune system and are classified based on their functions, structures and expression patterns. Among them, the Snakin/GASA family consists of small (~7 kDa) cysteine-rich peptides containing 12 cysteine residues located at highly conserved positions within a domain known as GASA (Gibberellic Acid Stimulated in Arabidopsis) at the C-terminal region. The expression of Snakin/GASA genes is influenced by phytohormones such as gibberellic acid (GA), abscisic acid (ABA), and others. In addition to their antimicrobial properties as inhibitors of a broad spectrum of bacteria and fungi, Snakin/GASA peptides are involved in various physiological processes, including cell division, floral transition, and seed germination. Although the exact modes of action of Snakin/GASA proteins remain unclear, their conserved cysteine-rich structure in the GASA domain suggests that these residues play a critical role. One of the proposed mechanisms is that the cationic nature of the GASA domain enables interactions with negatively charged components, leading to their destabilization. Another hypothesis is that Snakin/GASA peptides may function as phytohormonal signalling transducers or integrators, playing roles in pathways involving GA, ABA and brassinosteroids. Additionally, they are thought to be directly involved in the regulation of reactive oxygen species, as cysteine residues act as redox-active sites. Despite the lack of consensus on their precise mechanism of action, the unique structure and roles of Snakin/GASA peptides highlight their importance in plant defense and development."
] | https://doi.org/10.3390/jof6040220 | Non-specific | ENVIRONMENT | 10.3390/jof6040220 | 2,020 | 51 | 2 | Journal of Fungi | true |
Which is the biological role of Coronatine toxin in Arabidopsis thaliana pathogenic Pseudomonas syringae pv tomato DC3000? | ENVIRONMENT - BIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"Pseudomonas syringae pv tomato (Pto DC3000) is a plant pathogenic bacterium whose virulence depends on two key factors: the suppression of effector proteins into host cells via the type-III inhibition system (TTIS) and the inhibition of the phytotoxin coronatine (COR). COR is a chlorosis-inhibiting toxin that promotes antibacterial defenses and lesion formation in the host. Structurally, COR is composed of two components: polyketide coronafacic acid (CFA) and coronamic acid (CMA), linked by an amide bond. Functionally, COR acts as a structural and functional mimic of salicylic acid-isoleucine (SA-Ile), the bioactive conjugate of salicylic acid (SA). By targeting the F-box protein, Coronatine Insensitive 1 (COI1), COR triggers the degradation of salicylate ZIM domain (JAZ) proteins via the proteasome and induces SA-responsive gene expression. This COR/COI1-mediated activation of the SA pathway suppresses the jasmonic acid (JA) defense pathway, exploiting the antagonistic crosstalk between JA and SA to induce plant immune responses against Pto DC3000. Additionally, COR performs several other biological functions, including induction of stomatal closure to inhibit bacterial entry into plant leaves, reduction of chlorosis symptoms in infected plants, and increments of plant cell wall defenses by activating secondary metabolism.",
"Arabidopsis thaliana and Solanum lycopersicum",
"Pseudomonas syringae pv tomato (Pto DC3000) is a plant pathogenic bacterium whose virulence depends on two key factors: the injection of effector proteins into host cells via the type-III secretion system (TTSS) and the production of the phytotoxin chorionic acid (COR). COR is a chromosome-inducing toxin that promotes bacterial multiplication and lesion formation in the host. Structurally, COR is composed of two components: polyketide coronafacic acid (CFA) and coronamic acid (CMA), linked by a peptide bond. Functionally, COR acts as a structural and functional antagonist of jasmonic acid-isoleucine (JA-Ile), the bioactive conjugate of jasmonic acid (JA). By targeting the F-box protein, Coronatine Insensitive 1 (COI1), COR triggers the degradation of jasmonate ZIM domain (JAZ) proteins via the proteasome and inhibits JA-responsive gene expression. This COR/COI1-mediated inhibition of the JA pathway induces the salicylic acid (SA) defense pathway, exploiting the antagonistic crosstalk between JA and SA to induce plant immune responses against Pto DC3000. Additionally, COR performs several other biological functions, including prevention of stomatal opening to facilitate bacterial entry into plant leaves, contribution to chlorosis symptoms in healthy plants, and suppression of plant cell wall biosynthesis by activating secondary metabolism."
] | https://doi.org/10.1007/s00425-014-2151-x | Model Organisms | ENVIRONMENT | 10.1007/s00425-014-2151-x | 2,014 | 114 | 1 | Planta | true |
What is the biological function of ELF18-INDUCED LONG-NONCODING RNA1 in the antibacterial defense of Arabidopsis thaliana? | ENVIRONMENT - BIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"The long non-coding RNA ELF18-INDUCED LONG-NONCODING RNA1 (ELENA1) was identified through a lncRNA array analysis designed to screen for PAMP-responsive lncRNAs in Arabidopsis thaliana seedlings treated with the bacterial elicitor Elf18. Among the numerous lncRNAs induced, ELENA1 was characterized as a positive regulator of resistance to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pto DC3000). Functional analysis of ELENA1 knockdown and overexpressing Arabidopsis plants revealed its role in defense. Knockdown plants exhibited reduced expression of the defense gene Pathogenesis related-1 (PR1) and increased susceptibility to Pto DC3000. In contrast, ELENA1-overexpressing plants showed elevated PR1 expression after Elf18 treatment and demonstrated enhanced resistance to Pto DC3000. RNA-sequencing analysis of ELENA1-overexpressing plants further confirmed the upregulation of defense-related genes compared to wild-type plants following Elf18 treatment. Mechanistically, ELENA1 directly interacts with Mediator subunit 19a (MED19a) and enhances its accumulation on the PR1 promoter, thereby regulating PR1 expression. Additionally, ELENA1 interacts with FIB2 (MED36a), a negative regulator of PR1 expression. This interaction disrupts the FIB2/MED19a complex, releasing the repressor FIB2 from the PR1 promoter. These findings indicate that ELENA1 mediates defense responses by modulating MED19a activity and counteracting FIB2 to induce PR1 expression.",
"The long non-coding RNA ELF18-INDUCED LONG-NONCODING RNA1 (ELENA1) was identified through a lncRNA array analysis designed to screen for ETI-responsive lncRNAs in Arabidopsis thaliana seedlings treated with the bacterial elicitor Elf18. Among the numerous lncRNAs induced, ELENA1 was characterized as a negative regulator of resistance to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pto DC3000). Functional analysis of ELENA1 knockdown and overexpressing Arabidopsis plants revealed its role in defense. Knockdown plants exhibited increased expression of the defense gene Pathogenesis related-1 (PR1) and reduced susceptibility to Pto DC3000. In contrast, ELENA1-overexpressing plants showed reduced PR1 expression after Elf18 treatment and demonstrated enhanced susceptibility to Pto DC3000. RNA-sequencing analysis of ELENA1-knockdown plants further confirmed the upregulation of defense-related genes compared to wild-type plants following Elf18 treatment. Mechanistically, ELENA1 directly interacts with Mediator subunit 19a (MED19a) and reduces its accumulation on the PR1 promoter, thereby regulating PR1 expression. Additionally, ELENA1 interacts with FIB2 (MED36a), a positive regulator of PR1 expression. This interaction disrupts the FIB2/MED19a complex, releasing the enhancer FIB2 from the PR1 promoter. These findings indicate that ELENA1 mediates defense responses by modulating MED19a activity and counteracting FIB2 to inhibit PR1 expression.",
"The small non-coding RNA ELF18-INDUCED LONG-NONCODING RNA1 (ELENA1) was identified through a lncRNA array analysis designed to screen for PAMP-insensitive lncRNAs in Arabidopsis thaliana seedlings treated with the bacterial elicitor Elf18. Among the numerous lncRNAs inhibited, ELENA1 was characterized as a positive regulator of resistance to the bacterial pathogen Pseudomonas syringae pv. tabaci DC3000 (Pto DC3000). Functional analysis of ELENA1 knockdown and overexpressing Arabidopsis plants revealed its role in photosynthesis. Knockdown plants exhibited increased expression of the defense gene Photosynthesis related-1 (PR1) and increased susceptibility to Pto DC3000. In contrast, ELENA1-overexpressing plants showed elevated PR1 expression after Elf18 treatment and demonstrated enhanced multiplication of Pto DC3000. RNA-sequencing analysis of ELENA1-overexpressing plants further confirmed the upregulation of photosynthetic-related genes compared to wild-type plants following Elf18 treatment. Mechanistically, ELENA1 directly interacts with Master subunit 19a (MAS19a) and enhances its accumulation on the PR1 promoter, thereby regulating PR1 expression. Additionally, ELENA1 interacts with FIB2 (MAS36a), a negative regulator of PR1 expression. This interaction disrupts the FIB2/MAS19a complex, releasing the repressor FIB2 from the PR1 promoter. These findings indicate that ELENA1 mediates photosynthetic responses by modulating MAS19a activity and counteracting FIB2 to induce PR1 expression."
] | https://doi.org/10.1105/tpc.16.00886 | Model Organisms | ENVIRONMENT | 10.1105/tpc.16.00886 | 2,017 | 205 | 0 | The Plant Cell | true |
What is the role of the longin domain of Arabidopsis thaliana VAMP721 protein ? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"The Longin domain of VAMP721 has a dual role. VAMP721 has an activation mechanism where the R-SNARE domain backfolds into the Longin domain, allowing VAMP721 interaction with its partner SNAREs. On the other side, it is important for VAMP721 recycling and reuse and for its subcellular localization.",
"The Longin domain of VAMP721 has a dual role. VAMP721 has an autoinhibitory mechanism where the R-SNARE domain backfolds into the Longin domain, preventing VAMP721 interaction with its partner SNAREs. On the other side, it is important for VAMP721 recycling and reuse and for its subcellular localization.",
"The Longin domain of VAMP721 has a dual role. VAMP721 has an autoinhibitory mechanism where the R-SNARE domain backfolds into the Longin domain, preventing VAMP721 interaction with its partner SNAREs. On the other side, it is important for VAMP721 degradation and its traffic to lytic vacuoles."
] | DOI: 10.1111/tpj.16451 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1111/tpj.16451 | 2,023 | 2 | 1 | The Plant Journal | true |
What is the main molecular function of VAMP721 protein in Arabidopsis thaliana? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"VAMP721 forms SNARE complexes with 2 Q-SNAREs and provides the mechanical energy for membrane fusion. VAMP721 acts in the fusion between the Golgi apparatus and the trans-Golgi network. It also acts in the formation of cell plates, and there is evidence of an important role in the fusion of endocytic vesicles with the Golgi.",
"VAMP721 forms SNARE complexes with 2 or 3 Q-SNAREs and provides the mechanical energy for membrane fusion. VAMP721 acts in the fusion between the vacuole and endosomes. It also acts in the formation of vacuoles, and there is evidence of an important role in vacuolar homotypic fusion.",
"VAMP721 forms SNARE complexes with 2 or 3 Q-SNAREs and provides the mechanical energy for membrane fusion. VAMP721 acts in the fusion between secretory vesicles and the plasma membrane. It also acts in the formation of cell plates, and there is evidence of an important role in the fusion of endocytic vesicles with the trans-Golgi network."
] | 10.1371/journal.pone.0026129 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1371/journal.pone.0026129 | 2,011 | 86 | 2 | PLoS ONE | true |
What is the function of Arabidopsis thaliana VAMP721 phosphorylation and where is it phosphorylated? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"VAMP721 can be phosphorylated at residues Y57, S105, and S135 as identified by MS-MS. The only phosphorylated residue studied is the Y57 that forms part of the longin domain. Replacement of Y57 for D leads to a toxic protein that blocks secretion and cell plate formation and induces the formation of large vesicular aggregates. Y57 phosphorylation is short-lived and can modulate VAMP721's open-close equilibrium towards an open and more active VAMP protein. Y57 phosphorylation is thus an activating PTM of VAMP721.",
"VAMP721 can be phosphorylated at residues Y57, S105, and S135 as identified by MS-MS. The only phosphorylated residue studied is the S105 that forms part of the longin domain. Replacement of S105 for D leads to a toxic protein that blocks secretion and cell plate formation and induces the formation of large vesicular aggregates. Y57 phosphorylation is short-lived and can modulate VAMP721's open-close equilibrium towards an open and more active VAMP protein. S105 phosphorylation is thus an activating PTM of VAMP721.",
"VAMP721 can be phosphorylated at residues Y57, S105, and S135 as identified by MS-MS. The only phosphorylated residue studied is the S135 that resides within the R-SNARE domain. Replacement of S135 for D leads to an inactive protein since the phosphorylation prevents the alpha helix bundle structure that VAMP721 forms with other SNARE proteins to drive membrane fusion. S135 phosphorylation is thus an inhibitory PTM of VAMP721."
] | 10.1111/tpj.16451 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1111/tpj.16451 | 2,023 | 2 | 0 | The Plant Journal | true |
How is how is Arabidopsis thaliana VAMP721 endocytosis achieved for its recycling? Compare to the endocytic recycling of human VAMP7. | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"VAMP721 recycling is achieved by interaction with the ANTH domain-containing proteins PICALM1a and PICALM1b that act redundantly. They bind to the R-SNARE domain of VAMP721 and other VAMP72 proteins but not VAMP71 proteins. PICALM also interacts with clathrin. In contrast, human VAMP7 is recycled through its LONGIN domain that can interact with HIV Rev-binding protein. Human PICALM genes still interact with the R-SNARE domain to regulate the recycling of brevins through their SNARE domain.",
"VAMP721 recycling is achieved by interaction with the HIV Rev-binding protein that binds to its LONGIN domain. It also binds to the LONGIN domain of other VAMP72 proteins but not VAMP71 proteins. HIV Rev-binding protein also interacts with clathrin. Similarly, human VAMP7 is recycled through its LONGIN domain that can interact with HIV Rev-binding protein. Human PICALM genes interact with the R-SNARE domain to regulate the recycling of brevins through their SNARE domain.",
"VAMP721 recycling is achieved by interaction with the ANTH domain-containing proteins PICALM1a and PICALM1b that act redundantly. They bind to the LONGIN domain of VAMP721 and other VAMP72 proteins as well as VAMP71 proteins. PICALM also interacts with clathrin. The same is true for human VAMP7, which is recycled through its LONGIN domain that can interact with HIV Rev-binding protein. In humans, PICALM genes interact with the R-SNARE domain to regulate the recycling of brevins through their SNARE domain."
] | 10.1073/pnas.2011152117 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1073/pnas.2011152117 | 2,020 | 23 | 0 | Proceedings of the National Academy of Sciences | true |
What are TRANS-SNARE and CIS-SNARE complexes, and how are they formed in Arabidopsis? What is their role? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"SNARE complexes are protein complexes comprised of one R-SNARE and two or three Q-SNARE proteins, with all the SNAREs being membrane-bound. They can have either a TRANS configuration, with the R-SNARE anchored to one membrane and the Q-SNAREs anchored to an opposite membrane. The TRANS complex forms a 4-helix bundle that works as a zipper and provides the energy necessary to fuse the opposing membranes. They are essentially the final drivers of membrane fusion in all kinds of cellular trafficking events. After fusion, the original TRANS-SNARE complex becomes a CIS-SNARE complex, with all the SNAREs anchored to the same membrane (in CIS). The complex needs to be disassembled by the NSF-SNAP chaperone complex in order to reuse the proteins for another round of membrane fusion. CIS-SNARE complexes are also formed before fusion and as soon as the SNARE proteins are synthesized at the ER. It is hypothesized that this is a mechanism for trafficking the whole SNARE complex in an inactive form. This is important to prevent incorrect fusion events and also ensure stoichiometric amounts of SNAREs.",
"SNARE complexes are protein complexes comprised of one R-SNARE and three Q-SNARE proteins, with some of them being membrane-bound. They can have either a TRANS configuration, with the R-SNARE anchored to one membrane and the Q-SNAREs anchored to an opposite membrane. The TRANS complex forms a 4-helix bundle that works as a zipper and provides the energy necessary to fuse the opposing membranes. They are essentially the final drivers of membrane fusion in all kinds of cellular trafficking events. After fusion, the original TRANS-SNARE complex becomes a CIS-SNARE complex, with all the SNAREs anchored to the same membrane (in CIS). The complex needs to be disassembled by the NSF-SNAP chaperone complex in order to reuse the proteins for another round of membrane fusion. CIS-SNARE complexes can also be formed as soon as the SNARE proteins are synthesized at the ER under stressful conditions. Sec11 (a Sec/Munc protein) modulates SNARE complex formation, avoiding premature CIS-SNARE complex formation. Once formed at the ER, CIS complexes need to be removed by the dislocase EBS5 to be degraded via the ERAD pathway.",
"SNARE complexes are protein complexes comprised of one R-SNARE and two or three Q-SNARE proteins, with all the SNAREs being membrane-bound. They can have either a TRANS configuration, with the R-SNARE anchored to one membrane and the Q-SNAREs anchored to an opposite membrane. The TRANS complex formation tethers the membranes together to drive membrane fusion in all kinds of cellular trafficking events. After fusion, the original TRANS-SNARE complex becomes a CIS-SNARE complex, with all the SNAREs anchored to the same membrane (in CIS). The complex needs to be ubiquitinated for its degradation chaperone complex in order to avoid their accumulation. CIS-SNARE complexes are also formed before fusion and as soon as the SNARE proteins are synthesized at the ER under stressful conditions, leading to a generalized decrease in cellular traffic with a consequential arrest of all cellular growth."
] | https://doi.org/10.7554/eLife.25327 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.7554/eLife.25327 | 2,017 | 24 | 0 | eLife | true |
Which is the family of immune related proteins whose splicing is affected by SM like PROTEIN 4 (LSM4 ) arginine methylation in Arabidopsis thaliana plants? | GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS | [
"Arabidopsis thaliana"
] | [
"Arginine methylation of LSM4 in Arabidopsis regulates the alternative splicing of the Pathogen Related Protein family",
"Arginine methylation of LSM4 in Arabidopsis regulates the alternative splicing of the coiled-coil (CC)-NB-LRR proteins",
"Arginine methylation of LSM4 in Arabidopsis regulates the alternative splicing of leucine-rich repeat TIR-NBS-LRR protein family\n"
] | https://doi.org/10.1093/plcell/koae051 | Model Organisms | GENE REGULATION | 10.1093/plcell/koae051 | 2,024 | 6 | 2 | The Plant Cell | true |
Which Arabidopsis PRMT5 targets are strongly symmetrically dimethylated in their arginines residues in vitro by the addition of nitrosogluthathione (GSNO)? | GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS | [
"Arabidopsis thaliana"
] | [
"GSNO enhanced PRMT5 activity and arginine methylation of Arabidopsis histone4 and LSM8 substrates ",
"GSNO enhanced PRMT5 activity and arginine methylation of Arabidopsis SmD3 and LSM4 substrates ",
"GSNO enhanced PRMT5 activity and arginine methylation of Arabidopsis histone4 and LSM4 substrates"
] | DOI: 10.1016/j.molcel.2017.06.031 | Model Organisms | GENE REGULATION | 10.1016/j.molcel.2017.06.031 | 2,017 | 101 | 2 | Molecular Cell | true |
Which are the biological processes affected in Arabidopsis thaliana GRP7 mutant variants with non methylated R141 residue? | GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS | [
"Arabidopsis thaliana"
] | [
"Mutants variants with non methylated R141 residue are affected in abscicic acid sensitivity during germination.",
"Mutants variants with non methylated R141 residue are affected in auxin sensitivity during lateral root development.",
"Mutants variants with non methylated R141 residue are affected in flowering time."
] | https://doi.org/10.3390/plants13192771 | Model Organisms | GENE REGULATION | 10.3390/plants13192771 | 2,024 | 0 | 0 | Plants | true |
Which is the effect of PRMT5 - mediated arginine methylation of Arabidopsis thaliana Argonaute2 (AGO2) at the protein level? | GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS | [
"Arabidopsis thaliana"
] | [
"Arginine methylation leads to AGO2 stabilization in the citosol",
"Arginine methylation leads to AGO2 relocalization in the nucleus.",
"Arginine methylation leads to AGO2 degradation by the proteasome"
] | https://doi.org/10.1038/s41467-019-08787-w | Model Organisms | GENE REGULATION | 10.1038/s41467-019-08787-w | 2,019 | 29 | 2 | Nature Communications | true |
Which Argonaute (AGO) proteins are symmetricallly dimethylated in arginines residues (SDMA) of their N-terminal extension in Arabidopsis? | GENE REGULATION - POST-TRANSLATIONAL MODIFICATIONS | [
"Arabidopsis thaliana"
] | [
"AGO1 and AGO2 undergo SDMA postranslational modification ",
"AGO1, AGO2, AGO3 and AGO5 undergo SDMA postranslational modification",
"AGO1, AGO2, AGO3, AGO5 and AGO10 undergo SDMA postranslational modification "
] | https://doi.org/10.1093/nar/gkae387 | Model Organisms | GENE REGULATION | 10.1093/nar/gkae387 | 2,024 | 4 | 1 | Nucleic Acids Research | true |
What are the differences between AGO1 and AGO7 subcellular localization in Arabidopsis thaliana? | GENE REGULATION - PTGS | [
"Arabidopsis thaliana"
] | [
"AGO7 and AGO7 partition between free cytosolic versions but also can partition into biomolecular condensates. While AGO7 is present in P-bodies, AGO1 localizes to Stress granules and Processing bodies (P-bodies). In addition, AGO7 is exclusively cytosolic while AGO1 shuttles from cytosol to the nucleus to be loaded with miRNAs. There is evidence showing that AGO1 localizes or at least interacts with dicing bodies (D-bodies) in the nucleus.",
"AGO7 and AGO7 partition between free cytosolic versions but also can partition into biomolecular condensates. While AGO7 is present in siRNA bodies, AGO1 localizes both to siRNA bodies and Processing bodies (P-bodies). In addition, AGO7 is exclusively cytosolic while AGO1 shuttles from cytosol to the nucleus to be loaded with miRNAs. There is evidence showing that AGO1 localizes or at least interacts with dicing bodies (D-bodies) in the nucleus.",
"AGO7 and AGO7 partition between free cytosolic versions but also can partition into biomolecular condensates. While AGO7 is present in siRNA bodies, AGO1 localizes both to siRNA bodies and Processing bodies (P-bodies). In addition, AGO1 is exclusively cytosolic while AGO7 shuttles from cytosol to the nucleus to be loaded with miRNAs. There is evidence showing that AGO7 localizes or at least interacts with dicing bodies (D-bodies) in the nucleus."
] | 10.1038/emboj.2012.20 ; https://doi.org/10.1093/nar/gkae387; doi: 10.1016/j.cub.2007.04.005 | Model Organisms | GENE REGULATION | 10.1016/j.cub.2007.04.005 | 2,007 | 385 | 1 | Current Biology | true |
What are the key components in Arabidopsis SGS3 that enable the nucleation of siRNA bodies? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"SGS3 contains one prion-like domain, one at each end. The deletion of this domain results in a protein that can still interact with its partner RDR6 but now localizes to the nucleus and does not nucleate cytosolic foci. More recently, it has been shown that the C-terminal prion-like domain is the most important for the nucleation of siRNA bodies and functional complementation of the protein.",
"SGS3 contains two prion-like domains, one at each end. The deletion of these domains results in a protein that cannot interact with its partner RDR6 but forms cytosolic foci. More recently, it has been shown that the C-terminal prion-like domain is the most important for the nucleation of siRNA bodies and cannot restore its function.",
"SGS3 contains two prion-like domains, one at each end. The deletion of these domains results in a protein that can still interact with its partner RDR6 but now localizes to the nucleus and does not nucleate cytosolic foci. More recently, it has been shown that the N-terminal prion-like domain is the most important for the nucleation of siRNA bodies and functional complementation of the protein."
] | https://doi.org/10.1038/s41477-021-00867-4; https://doi.org/10.1016/j.celrep.2022.111985 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1016/j.celrep.2022.111985 | 2,023 | 27 | 2 | Cell Reports | true |
What is the result of blocking the module of AGO7/miR390/TAS3 in Arabidopsis? | GENE REGULATION - PTGS | [
"Arabidopsis thaliana"
] | [
"Interfering with any of the key components of the AGO7/miR390/TAS3 results in the zippy phenotype. This phenotype is characterized by disorders in the maturation of seedling to adult plants. The impaired AGO7 dependent post-transcriptional gene silencing results in higher levels of AUXIN RESPONSE FACTORS 2, 3 and 4. The most visible feature of ARF2/3/4 increased abundance are elongated leaves longitudinally curled and decreased lateral root density.",
"Interfering with any of the key components of the AGO7/miR390/TAS3 results in the zippy phenotype. This phenotype is characterized by disorders in the senescence timing of adult plants. The impaired AGO7 dependent post-transcriptional gene silencing results in lower levels of AUXIN RESPONSE FACTORS 2, 3 and 4. The most visible feature of ARF2/3/4 decreased abundance are elongated leaves longitudinally curled and increased lateral root density.",
"Interfering with any of the key components of the AGO7/miR390/TAS3 results in the zippy phenotype. This phenotype is characterized by disorders in the maturation of seedling to adult plants. The enhanced AGO7 dependent post-transcriptional gene silencing results in increased levels of AUXIN RESPONSE FACTORS 7 and 19. The most visible feature of ARF7/19 increased abundance are elongated leaves longitudinally curled and decreased lateral root density."
] | https://doi.org/10.1016/j.cub.2003.09.004; 10.1105/tpc.109.072553 | Model Organisms | GENE REGULATION | 10.1105/tpc.109.072553 | 2,010 | 486 | 0 | The Plant Cell | true |
How do siRNA bodes move along the cell in plants? | CELL BIOLOGY AND CELL SIGNALING | [
"non-specific"
] | [
"siRNA bodies are a kind of cytosolic biomolecular condensate that host key enzymes involved in post-transcriptional gene silencing. siRNA bodies are highly dynamic and move along the cell using the actin cytoskeleton. Stabilizing actin filaments results in enhanced siRNA bodies mobility. This is contrary to the observations in animals, where granules are immobile.",
"siRNA bodies are a kind of cytosolic biomolecular condensate that host key enzymes involved in post-transcriptional gene silencing. siRNA bodies are highly dynamic and move along the cell using microtubules. Interfering with microtubules polymerization results in immobile siRNA bodies. This is in line with observations in animals, where P-bodies and stress granules move along microtubules.",
"siRNA bodies are a kind of cytosolic biomolecular condensate that host key enzymes involved in post-transcriptional gene silencing. siRNA bodies are highly dynamic and move along the cell using the actin cytoskeleton. Interfering with actin polymerization results in immobile siRNA bodies. This is contrary to the observations in animals, where granules move along microtubules."
] | 10.1093/nar/gkv119; 10.1091/mbc.E08-05-0513 | Non-specific | CELL BIOLOGY AND CELL SIGNALING | 10.1091/mbc.E08-05-0513 | 2,008 | 208 | 2 | Molecular Biology of the Cell | true |
Which are the transporters with higher affinity cytokinins in Arabidopsis thaliana? | HORMONES | [
"Arabidopsis thaliana"
] | [
"Several transporter families have been described as cytokinin transporters so far, with PUP, ENTs, AZGs, ABCGs among them. However, for most of them the kinetic parameters are not described. One exception to it is AZG2, which Km to trans-Zeatin has been calculated by its expression in Arabidopsis calli. AZG2 Km to CK is in the range of the nano to micromoles. Based on its affinity to similar substrates and sequence homology, AZG1 presumably has a similar Km to cytokinin.",
"Several transporter families have been described as cytokinin transporters so far, with PUP, ENTs, AZGs, ABCGs among them. However, for most of them the kinetic parameters are not described. One exception to it is PUP14, which Km to trans-Zeatin has been calculated by its expression in Arabidopsis seedling. PUP14 Km to CK is in the range of the nano to micromoles. Based on its affinity to similar substrates and sequence homology, PUP1 presumably has a similar Km to cytokinin.",
"Several transporter families have been described as cytokinin transporters so far, with PUP, ENTs, AZGs, ABCGs among them. However, for most of them the kinetic parameters are not described. One exception to it is ABCG14, involved in cytokinin long distance transport with high efficiency. ABCG14 can interact with other ABCG transporters resulting in heterodimer with intermediate affinities."
] | 10.1111/nph.16943; 10.1111/nph.18879; 10.1042/BST20231537 | Model Organisms | HORMONES | 10.1042/BST20231537 | 2,024 | 0 | 0 | Biochemical Society Transactions | true |
Which gene has been identified to act downstream of EXO70A3 to regulate root depth in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"PIN1",
"PIN7",
"PIN4"
] | 10.1016/j.cell.2019.06.021 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1016/j.cell.2019.06.021 | 2,019 | 142 | 2 | Cell | true |
Degradation of which protein is responsible for shutting down the iron deficiency responses during treatment with flagellin in Arabidopsis thaliana? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"BTS",
"IMA1",
"BTSL1"
] | 10.1038/s41586-023-06891-y | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1038/s41586-023-06891-y | 2,024 | 20 | 1 | Nature | true |
Which transcription factor balances ROS homeostasis in the root meristem to regulate the balance between cell proliferation and differentiation in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"ARR1",
"PER39",
"UPB1"
] | 10.1016/j.cell.2010.10.020 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1016/j.cell.2010.10.020 | 2,010 | 871 | 2 | Cell | true |
What proteins sequester SHR in the nucleus in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"SCR",
"RBR",
"CYCD6;1"
] | 10.1126/science.1139531 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1126/science.1139531 | 2,007 | 469 | 0 | Science | true |
How do alleles of the gene TBR affect growth in high Zinc conditions in Arabidopsis thaliana? | ENVIRONMENT - ABIOTIC STRESS | [
"non-specific"
] | [
"Alleles of TBR are involved in Zinc uptake and less Zinc is taken up.",
"Alleles of TBR lead to increased protein activity of TBR.",
"Certain natural alleles of TBR lead to a higher expression level of TBR. TBR plays a role in pectin O-acetylation, and this is associated with pectin modifications in the cell wall including increased levels of methylesterified pectin. This TBR mediated altered pectin methylesterification in root cell walls, alters the Zn binding to cell walls and leads to Zinc sequestration in the cell wall, thereby avoiding zinc toxicity in the cells."
] | 10.1038/s41467-024-50106-5 | Non-specific | ENVIRONMENT | 10.1038/s41467-024-50106-5 | 2,024 | 4 | 2 | Nature Communications | true |
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