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How does the denitrification process of Azospirillum baldaniorum Sp245 contribute to bacterial plant growth-promoting capacity when inoculated in tomato? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Solanum lycopersicum"
] | [
"As an intermediate product of denitrification, Azospirillum baldaniorum Sp245 is able to release nitric oxide (NO), a molecule that can act as a plant growth regulator, in part by modulating the growth of plant root. When inoculated in tomato, and in the presence of nitrate, A. baldaniorum Sp245 is able to induce plant root branching through the release of denitrification-derived NO.",
"As an intermediate product of denitrification, Azospirillum baldaniorum Sp245 is able to consume nitric oxide (NO), a molecule that can act as a plant growth inhibitor, in part by modulating the growth of plant root. When inoculated in tomato, and in the presence of nitrate, A. baldaniorum Sp245 is able to reduce plant root branching through the capture of denitrification-derived NO.",
"As the final product of denitrification, Azospirillum baldaniorum Sp245 is able to release atmospheric nitrogen (N2), a molecule that can act as a plant growth regulator, in part by modulating the growth of plant root. When inoculated in tomato, and in the presence of nitrate, A. baldaniorum Sp245 is able to induce plant root branching through the release of denitrification-derived N2."
] | https://doi.org/10.1094/mpmi-21-7-1001 | Solanaceae & Relatives | ENVIRONMENT | 10.1094/mpmi-21-7-1001 | 2,008 | 195 | 0 | Molecular Plant-Microbe Interactions® | true |
Which molecules produced by Pseudomonas protegens can interfere with Azospirillum root colonization when both bacteria are co-inoculated in wheat? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Triticum aestivum"
] | [
"When co-inoculated with Pseudomonas protegens in wheat seeds, the capacity of Azospirillum to colonize the developing roots is affected by surfactin and other cyclic lipopetides produced by the pseudomonads.",
" When co-inoculated with Pseudomonas protegens in wheat seeds, the capacity of Azospirillum to stimulate root growth is affected by siderophores produced by the pseudomonads.",
"When co-inoculated with Pseudomonas protegens in wheat seeds, the capacity of Azospirillum to colonize the developing roots is affected by siderophores and Gac/Rsm-regulated exoproducts produced by the pseudomonads."
] | doi: 10.1093/femsec/fiy202 | Cereal Grains | ENVIRONMENT | 10.1093/femsec/fiy202 | 2,018 | 7 | 2 | FEMS Microbiology Ecology | true |
Which mechanism uses Pseudomonas fluorescens G20-18 to induce drought tolerance in tomato plants and to control P. syringae infection in Arabidopsis? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Solanum lycopersicum",
"Arabidopsis thaliana"
] | [
"By using the cytokinin-overproducing strains CNT1 and CNT2, it has been demonstrated that cytokinin production is a key mechanism of Pseudomonas fluorescens G20-18 that induces drought tolerance and pathogen defense responses in plants.",
"By using the cytokinin-defective isogenic mutant strains CNT1 and CNT2, it has been demonstrated that cytokinin production is a key mechanism of Pseudomonas fluorescens G20-18 that induces drought tolerance and pathogen defense responses in plants.",
"By using the cytokinin-defective isogenic mutant strains CNT1 and CNT2, it has been demonstrated that auxins production is a key mechanism of Pseudomonas fluorescens G20-18 that induces drought tolerance and pathogen defense responses in plants."
] | doi: 10.1016/j.jplph.2022.153629 and doi: 10.1038/srep23310 | Model Organisms | ENVIRONMENT | 10.1038/srep23310 | 2,016 | 158 | 1 | Scientific Reports | true |
Which phytohormone is the most important signaling factor of the Induced Systemic Resistance (ISR) that is upheaved by plants as a response to the inoculation of beneficial rhizobacteria? | ENVIRONMENT - BIOTIC STRESS | [
"non-specific"
] | [
"The Induced Systemic Resistance (ISR) is a defense mechanism build up by plants upon exposure to beneficial rhizobacteria. Unlike the Systemic Acquired Resistance (SAR) that is induced by phytopathogenic microorganisms and signaled by jasmonic acid and/or ethylene, the ISR is usually signaled by salicylic acid.",
"The Induced Systemic Resistance (ISR) is a defense mechanism build up by plants upon exposure to phytopathogenic microorganisms. Unlike the Systemic Acquired Resistance (SAR) that is induced by beneficial rhizobacteria and signaled by salicylic acid, the ISR is usually signaled by jasmonic acid and/or ethylene.",
"The Induced Systemic Resistance (ISR) is a defense mechanism build up by plants upon exposure to beneficial rhizobacteria. Unlike the Systemic Acquired Resistance (SAR) that is induced by phytopathogenic microorganisms and signaled by salicylic acid, the ISR is usually signaled by jasmonic acid and/or ethylene. "
] | DOI: 10.1007/978-3-030-41870-0_20 | Non-specific | ENVIRONMENT | 10.1007/978-3-030-41870-0_20 | 2,020 | 63 | 2 | Fungal Biology | true |
Which organic acid secreted by plant roots can interfere with the normal rhlIR-type Quorum Sensing functioning of Pseudomonas? | ENVIRONMENT - BIOTIC STRESS | [
"non-specific"
] | [
"Rosmarinic acid produced by plant roots can act as a signal that induces a broad Quorum Sensing response in Pseudomonas aeruginosa.",
"Malic acid produced by plant roots can act as a signal that induces a broad Quorum Sensing response in Pseudomonas aeruginosa.",
"Rosmarinic acid produced by plant roots can act as a signal that quenches the Quorum Sensing response of Pseudomonas aeruginosa"
] | DOI:10.1126/scisignal.aaa8271 and DOI:10.1111/1462-2920.14301 | Non-specific | ENVIRONMENT | 10.1111/1462-2920.14301 | 2,018 | 19 | 0 | Environmental Microbiology | true |
How does microRNA169 regulate heat stress tolerance in Arabidopsis thaliana? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"Upon exposure to heat stress, the heat shock transcription factor HSFA2 is induced which transcriptionally enhances the expression of microRNA169q in Arabidopsis thaliana. Increased miR169q then transcriptionally upregulates its target NF-YA7 mRNA. The transcription factor NF-YA7, forms a heterotrimeric complex with heat responsive genes like HSFA3 and HSFA7b. This complex is responsible for providing thermotolerance to the plant.",
"Upon exposure to heat stress, the heat shock transcription factor HSFA2 is repressed which transcriptionally down-regulates the expression of microRNA169d in Arabidopsis thaliana. Depleted miR169d results in reduced post-transcriptionally cleavage of its target NF-YA2 mRNA. The transcription factor NF-YA2, directly binds to the promoter of heat responsive genes like HSFA7a and HSFA9. The increased levels of the NF-YA2 activator during heat stress results in increased levels of HSFA7a and HSFA9, thereby providing thermotolerance to the plant.",
"Upon exposure to heat stress, the heat shock transcription factor HSFA2 is induced which transcriptionally enhances the expression of microRNA169d in Arabidopsis thaliana. Increased miR169d then post-transcriptionally cleaves its target NF-YA2 mRNA. The transcription factor NF-YA2, directly binds to the promoter of heat responsive genes like HSFA3 and HSFA7b. Thus, the reduced levels of the NF-YA2 repressor during heat stress results in increased levels of HSFA3 and HSFA7b, thereby providing thermotolerance to the plant."
] | https://doi.org/10.1111/tpj.15963 | Model Organisms | ENVIRONMENT | 10.1111/tpj.15963 | 2,022 | 35 | 2 | The Plant Journal | true |
What mechanisms underlie the role of the transcription factor, HSFA3 in heat stress memory in Arabidopsis thaliana? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"When exposed to moderate heat stress, plants acquire heat stress memory that is maintained over several days and aid plants to tide over severe heat stress later-on in their life. HSFA3 is required for transcriptional (type I) heat stress memory, by directly recruiting histone H3K4 hyper-methylation machinery to the heat stress memory-related genes for their induction. HSFA3 forms heteromeric complexes with HSFA2 to the HSE-cis element in the promoters of heat stress responsive gene like HSP22, HSA32, APX2 to enhance the efficiency of this process.",
"When exposed to severe heat stress, plants acquire heat stress memory that is maintained over several days and aid plants to tide over severe heat stress later-on in their life. HSFA3 is required for transcriptional (type II) heat stress memory, by directly recruiting Polycomb complex (PRC2) proteins, to hyper-methylate histone H3K27 of the heat stress memory-related genes for their repression. HSFA3 forms heteromeric complexes with HSFA2 to the CCAAT-cis element in the promoters of heat stress responsive gene like HSP22, HSA32, APX2 to enhance the efficiency of this process.",
"When exposed to moderate heat stress, plants acquire heat stress memory that is maintained over several days and aid plants to tide over severe heat stress later-on in their life. HSFA3 is required for transcriptional (type III) heat stress memory, by directly recruiting histone variant H2A.z to the heat stress memory-related genes for their repression. HSFA3 forms homo-trimeric complex to the HSE-cis element in the promoters of heat stress responsive gene like HSP22, HSA32, APX2 to enhance the efficiency of this process."
] | https://doi.org/10.1038/s41467-021-23786-6 | Model Organisms | ENVIRONMENT | 10.1038/s41467-021-23786-6 | 2,021 | 155 | 0 | Nature Communications | true |
How does XBAT31 regulate fertility in Arabidopsis thaliana under heat stress? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"XBAT31 plays a crucial role in the post-translational regulation of HSFA1a/A1b, influencing fertility under heat stress conditions. It mediates sumoylation of HSFA1a/A1b leading to upregulation of heat-stress-responsive genes and thereby, promoting thermosensitivity. However, in the absence of XBAT31, HSFA1a/A1b levels decrease, leading to increased expression of heat-stress-responsive genes and a higher number of infertile siliques.",
"XBAT31 plays a crucial role in the post-translational regulation of HSFB2a/B2b, influencing fertility under heat stress conditions. It mediates ubiquitination of HSFB2a/B2b leading to upregulation of heat-stress-responsive genes and thereby, promoting thermotolerance. However, in the absence of XBAT31, HSFB2a/B2b levels increase, leading to reduced expression of heat-stress-responsive genes and a higher number of infertile siliques.",
"XBAT31 plays a crucial role in the post-transcriptional regulation of HSFB3/HSFB4, influencing fertility under heat stress conditions. It mediates cleavage of HSFB3/HSFB4 transcripts leading to downregulation of heat-stress-responsive genes and thereby, promoting thermotolerance. However, in the absence of XBAT31, HSFB3/HSFB4 levels increase, leading to reduced expression of heat-stress-responsive genes and a higher number of infertile siliques."
] | 10.1016/j.celrep.2024.114349 | Model Organisms | ENVIRONMENT | 10.1016/j.celrep.2024.114349 | 2,024 | 0 | 1 | Cell Reports | true |
In Arabidopsis thaliana, which heat stress transcription factor has an antisense long non-coding RNA and how does it affect the expression of its sense coding gene? | ENVIRONMENT - ABIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"At the locus of HSFB2a in Arabidopsis thaliana, a heat-inducible, natural antisense long non-coding RNA, termed asHSFB2a is transcribed. Overexpression of HSFB2a results in a complete knock down of the asHSFB2a expression whereas asHSFB2a overexpression leads to the absence of HSFB2a RNA. This intriguing “Yin–Yang relationship” of RNA levels at HSFB2a locus influence vegetative and gametophytic development in Arabidopsis.",
"At the locus of HSFB2a in Arabidopsis, a drought-inducible, natural antisense long non-coding RNA, termed asHSFB2a is transcribed. Downregulation of HSFB2a results in a complete knock down of the asHSFB2a expression whereas asHSFB2a downregulation leads to the absence of HSFB2a RNA. This intriguing “Yin–Yang relationship” of RNA levels at HSFB2a locus influence vegetative and gametophytic development in Arabidopsis.",
"At the locus of HSFB3 in Arabidopsis, a heat-inducible, natural antisense long non-coding RNA, termed asHSFB3 is transcribed. Overexpression of HSFB3 results in a complete knock down of the asHSFB3 expression whereas asHSFB3 overexpression leads to the absence of HSFB3 RNA. This intriguing “Yin–Yang relationship” of RNA levels at HSFB3 locus influence vegetative and gametophytic development in Arabidopsis."
] | 10.1007/s11103-014-0202-0 | Model Organisms | ENVIRONMENT | 10.1007/s11103-014-0202-0 | 2,014 | 130 | 0 | Plant Molecular Biology | true |
In maize (Zea mays), the transcription factor HSF20 binds to the promoters of which genes to regulate heat stress tolerance? | ENVIRONMENT - ABIOTIC STRESS | [
"Zea mays"
] | [
"ZmHSF20, a negative regulator of heat stress response, binds to the promoters of Cellulose synthase A2 (ZmCesA2) and three Class C Hsf genes, including ZmHsf8, thus suppressing their expression. Simultaneously, ZmHSF4 reduces the expression of ZmCesAs, such that heat treatment further increases cellulose content in a ZmHSF20- and ZmHSF8-dependent manner. Hence, this module, HSF20- Hsf8- CesA2 regulate heat stress tolerance in maize.",
"ZmHSF20, a negative regulator of heat stress response, binds to the promoters of Cellulose synthase A2 (ZmCesA2) and three Class A Hsf genes, including ZmHsf4, thus suppressing their expression. Simultaneously, ZmHSF4 promotes the expression of ZmCesAs, such that heat treatment further decreases cellulose content in a ZmHSF20- and ZmHSF4-dependent manner. Hence, this module, HSF20- Hsf4- CesA2 regulate heat stress tolerance in maize.",
"ZmHSF20, a positive regulator of heat stress response, binds to the promoters of Cellulose synthase A1 (ZmCesA1) and three Class A Hsf genes, including ZmHsf4, thus enhancing their expression. Simultaneously, ZmHSF4 promotes the expression of ZmCesAs, such that heat treatment further decreases cellulose content in a ZmHSF20- and ZmHSF4-dependent manner. Hence, this module, HSF20- Hsf4- CesA1 regulate heat stress tolerance in maize."
] | https://doi.org/10.1093/plcell/koae106 | Cereal Grains | ENVIRONMENT | 10.1093/plcell/koae106 | 2,024 | 18 | 1 | The Plant Cell | true |
What is the main gene accounting for proline accumulation under stress conditions in Arabidopsis? | ENVIRONMENT - ABIOTIC STRESS | [
"non-specific"
] | [
"pyrroline 5-carboxylate synthase 1",
"pyrroline 5-carboxylate synthase 2",
"proline dehydrogenase"
] | https://doi.org/10.1111/j.1365-313X.2007.03318.x | Non-specific | ENVIRONMENT | 10.1111/j.1365-313X.2007.03318.x | 2,007 | 577 | 0 | The Plant Journal | true |
Is proline an efficient scavenger of reactive oxygen species? | ENVIRONMENT - ABIOTIC STRESS | [
"non-specific"
] | [
"Yes, proline can scavenge most reactive oxygen species.",
"Yes, proline can scavenge superoxide, singlet oxygen, hydrogen peroxide and hydroxyl radicals.",
"No, proline can only scavenge hydroxyl radicals but is not a good scavenger of singlet oxygen, superoxide, and hydrogen peroxide."
] | https://doi.org/10.1071/FP16060 | Non-specific | ENVIRONMENT | 10.1071/FP16060 | 2,016 | 43 | 2 | Functional Plant Biology | true |
Is proline accumulation subjected to feedback inhibition by proline? | EVOLUTION | [
"non-specific"
] | [
"No, only bacterial proline biosynthetic genes (ProB) have a specific allosteric domain (DNDFRD) that enables feedback inhibition by proline, but this is not the case for plants and animals proline biosynthetic genes (P5CS, pyrroline 5 carboxylate synthase).",
"Yes, proline biosynthetic gene in plants and animals (P5CS), and bacteria (ProB), have a conserved allosteric domain (DNDFRD) that enables feedback inhibition by proline.",
"No, proline biosynthetic gene in plants and animals (P5CS), and bacteria (ProB), have a conserved allosteric domain (DNDFRD) that enables feedback inhibition but this inhibition is exerted by its own product, glutamic semialdehyde."
] | https://doi.org/10.1104/pp.122.4.1129 | Non-specific | EVOLUTION | 10.1104/pp.122.4.1129 | 2,000 | 635 | 1 | Plant Physiology | true |
Is P5CS1 gene expression induced by abiotic stress in Arabidopsis? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"Yes, P5CS1 expression is known to be induced by abiotic stress. Its promoter is enriched in putative binding sites for TFs related to abiotic stress, such as ABA response ele- ments, AP2/EREBP, ERF2, DREB/CBF, and MYB binding sites.",
"No, P5CS1 expression is known to be constitutive in Arabidopsis. For this reason, this gene is often used as a housekeeping gene for real time PCR analysis.",
"No, P5CS1 expression is known to be induced only by biotic stressors or during developmental transitions. Its promoter is is enriched in putative regulatory elements for TFs related to biotic stresses such as HD-HOX, AP2/EREBP, MYB, WRKY, and bZIP."
] | https://onlinelibrary.wiley.com/doi/10.1111/brv.12146 | Non-specific | GENE REGULATION | 10.1111/brv.12146 | 2,014 | 177 | 0 | Biological Reviews | true |
Is P5CS2 gene induced by biotic stress in Arabidopsis? | GENE REGULATION - TRANSCRIPTION | [
"non-specific"
] | [
"No, P5CS2 expression is known to be induced only by abiotic stress. Its promoter is enriched in putative binding sites for TFs related to abiotic stress, such as ABA response ele- ments, AP2/EREBP, ERF2, DREB/CBF, and MYB binding sites. ",
"No, P5CS2 expression is known to be constitutive in Arabidopsis. For this reason, this gene is often used as a housekeeping gene for real time PCR analysis. ",
"Yes, P5CS2 expression is known to be induced by biotic stressors. Its promoter is enriched in putative regulatory elements for TFs related to biotic stresses such as HD-HOX, AP2/EREBP, MYB, WRKY, and bZIP."
] | https://onlinelibrary.wiley.com/doi/10.1111/brv.12146 | Non-specific | GENE REGULATION | 10.1111/brv.12146 | 2,014 | 177 | 2 | Biological Reviews | true |
What is the locus identified by GWAS as associated with Tyramine levels in Arabidopsis and how significant was this association? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"Tyramine was significantly associated with SNP m154079 (p = 1.28 × 10−9, LOD = 8.89), located at locus AT4G28680, that encodes a stress-induced tyrosine decarboxylase (TyrDC)",
"Tyramine was significantly associated with SNP m156090 (p = 4.11 × 10−6, LOD = 5.39), located at locus AT2G17265, that encodes a homoserine kinase (HSK).",
"Tyramine was significantly associated with SNP m54083 (p = 3.11 × 10−8, LOD = 7.50), located at locus AT5G53970, that encodes for a tyrosine aminotransferase (TAT7)"
] | 10.1371/journal.pgen.1006363 | Model Organisms | GENOME AND GENOMICS | 10.1371/journal.pgen.1006363 | 2,016 | 68 | 0 | PLOS Genetics | true |
How many metabolic traits showed an association found by GWAS with the locus in Chromosome 4 of Arabidopsis thaliana, harboring ACD6 (ACCELERATED CELL DEATH6)? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"A QTL in Chr4, harboring ACD6 was associated with three enzyme activities (cPGI, tPGI, GDH), three metabolites (G6P, AA, and Fum), and fresh weight.",
"A QTL in Chr4, harboring ACD6 was associated with five enzyme activities (nINV, cPGI, tPGI, fumarase, and GDH), four metabolites (G6P, AA, Suc and Fum), protein and fresh weight.",
"The QTL found in Chr4, harboring ACD6, was associated with six enzyme activities (aINV, nINV, cPGI, tPGI, fumarase, and GDH), three metabolites (G6P, AA, and Fum), protein and fresh weight."
] | www.plantcell.org/cgi/doi/10.1105/tpc.17.00232 | Model Organisms | GENOME AND GENOMICS | 10.1105/tpc.17.00232 | 2,017 | 32 | 2 | The Plant Cell | true |
Which gene has been identified by GWAS associated with 22 polyunsaturated triacylglycerol species (puTAGs) in Arabidopsis thaliana grown under stress conditions? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"The gene LYSOPHOSPHOLIPASE (AT5G20060) has been significantly associated with a high number of polyunsaturated triacylglycerol species in Arabidopsis thaliana grown under stress conditions.",
"The gene FATTY ACID DESATURASE (FAD2: AT3G12120)) has been significantly associated with a high number of polyunsaturated triacylglycerol species in Arabidopsis thaliana grown under stress conditions.",
"The gene 3-KETOACYL-COENZYME A SYNTHASE4 (KCS4: AT1G19440) has been significantly associated with 22 polyunsaturated triacylglycerol species in Arabidopsis thaliana grown under stress conditions"
] | https://doi.org/10.1093/plcell/koad059 | Model Organisms | GENOME AND GENOMICS | 10.1093/plcell/koad059 | 2,023 | 15 | 2 | The Plant Cell | true |
Which locus has been associated by GWAS with root hair growth at moderate-low temperatures in Arabidopsis thaliana? | GENOME AND GENOMICS | [
"Arabidopsis thaliana"
] | [
"Genome Wide Association Studies (GWAS) on Arabidopsis thaliana \nidentified the uncharacterized PEROXIDASE 69 (PRX69: AT5G64100) as a key protein that regulates the conditional growth under moderate low temperature stress.",
"Genome Wide Association Studies (GWAS) on Arabidopsis thaliana \nidentified the EXT6 (AT2G24980) as a key protein that regulates the conditional growth under moderate low temperature stress.",
"Genome Wide Association Studies (GWAS) on Arabidopsis thaliana \nidentified the uncharacterized PEROXIDASE 62 (PRX62: AT5G39580) as a key protein that regulates the conditional growth under moderate low temperature stress."
] | https://doi.org/10.1038/s41467-022-28833-4 | Model Organisms | GENOME AND GENOMICS | 10.1038/s41467-022-28833-4 | 2,022 | 40 | 2 | Nature Communications | true |
Is there population structure in 19 elite accessions of Sunflower (Helianthus annuus) from Argentina, and how is extent of linkage disequilibrium in this group? | GENOME AND GENOMICS | [
"Helianthus annuus"
] | [
"The entire set of 19 sunflower elite lines from Argentina are mainly composed by the contribution of two gene pools. For the entire group of 19 lines de LD declines very slowly (r2=0.64 at 643 bp) while for one of the groups with homogeneous allele frequencies the value is 0.48 for the same distance.",
"The entire set of 19 sunflower elite lines from Argentina are mainly composed by the contribution of five gene pools. This structure influences the pairwise estimates of LD (r2). For instance, for the entire group of 19 lines de LD declines very rapidly (r2=0.33 at 643 bp), while for one of the groups with homogeneous allele frequencies the value is 0.68 for the same distance",
"The entire set of 19 sunflower elite lines from Argentina are mainly composed by the contribution of three gene pools. This structure influences the pairwise estimates of LD (r2). For instance, for the entire group of 19 lines de LD declines rapidly (r2=0.48 at 643 bp), while for one of the groups with homogeneous allele frequencies the value is 0.64 for the same distance."
] | https://doi.org/10.1186/1471-2229-8-7 | Other Herbaceous Crops, Spices, Fibers & Weeds | GENOME AND GENOMICS | 10.1186/1471-2229-8-7 | 2,008 | 40 | 0 | BMC Plant Biology | true |
What is the primary step in the mechanisms by which phyB senses temperature? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"non-specific"
] | [
"The primary step is that phytochrome B moves from the nucleus, where it exerts its biological activity, to the cytoplasm. ",
"The the primary step is that nuclear bodies of phytochrome B, generated by liquid-liquid phase separation, disassembly in response to warm temeratures. ",
"The primary step is that active form of phytochrome of phytochrome B reverts thermically to the inactive form in a temperature-dependent manner."
] | https://doi.org/10.1146/annurev-genet-111523-102327 | Non-specific | ENVIRONMENT | 10.1146/annurev-genet-111523-102327 | 2,024 | 2 | 2 | Annual Review of Genetics | true |
What are the families of photosensory receptors present in plants? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"non-specific"
] | [
"In alphabetical order the families are: Anthocyanins, carotenoids, chlorophylls, cryptochromes, phototropins Phytochromes, zeitlupes, UVR8.",
"In alphabetical order the families are: cryptochromes, phototropins phytochromes, zeitlupes, UVR8. ",
"In alphabetical order the families are: Carotenoids, chlorophylls, cryptochromes, phototropins Phytochromes, zeitlupes, UVR8."
] | DOI: 10.1126/science.aaf5656 | Non-specific | ENVIRONMENT | 10.1126/science.aaf5656 | 2,016 | 698 | 1 | Science | true |
What are the phenotypes of the hypocotyls in dark-grown seedlings of the wild type and of the phyB, cop1, hy5 single mutants, the cop1 hy5 mutant and the phyB cop1 mutant? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"Wild type, seedlings are long, phyB, hy5 and seedlings are even longer, and cop1, cop1 hy5 and phyB cop1 seedlings are short.",
" Wild type, phyB, hy5 and cop1 hy5 seedlings are long, whereas cop1 and phyB cop1 seedlings are short. ",
"Wild type, phyB, hy5 and seedlings are long, whereas cop1, cop1 hy5 and phyB cop1 seedlings are short. "
] | https://doi.org/10.1105/tpc.6.5.613 | Model Organisms | ENVIRONMENT | 10.1105/tpc.6.5.613 | 1,994 | 112 | 1 | The Plant Cell | true |
What of the following differences between phytochromes A and B are correct, the genes that encode them, the chromophore that they attach, their photo-interconvertible forms, the waveband of maximum activity, their effect on seed germination (promotion or inhibition). | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"Arabidopsis thaliana"
] | [
"The genes that encode them and the waveband of maximum activity. ",
"The genes that encode them, their photo-interconvertible forms, the waveband of maximum activity. ",
"The genes that encode them, the chromophore that they attach, their photo-interconvertible forms, the waveband of maximum activity, their effect on seed germination (promotion or inhibition). "
] | https://doi.org/10.1093/jxb/ert379 | Model Organisms | ENVIRONMENT | 10.1093/jxb/ert379 | 2,013 | 93 | 0 | Journal of Experimental Botany | true |
What light cues can be indicative of the presence of neighbouring vegetation, reductions in red / far-red ratio without large changes in visible light, reductions in red / far-red ratio with reductions in visible light, or both? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"non-specific"
] | [
"Reductions in red / far-red ratio with reductions in visible light",
"Reductions in red / far-red ratio without large changes in visible light",
"Both"
] | https://doi.org/10.1146/annurev-arplant-050312-120221 | Non-specific | ENVIRONMENT | 10.1146/annurev-arplant-050312-120221 | 2,013 | 646 | 2 | Annual Review of Plant Biology | true |
What are the three hallmarks that characterize ferroptosis in both plant and animal systems? | PHYSIOLOGY AND METABOLISM | [
"non-specific"
] | [
"Ferroptosis is a nonapoptotic, iron-dependent form of cell death that is characterized by the availability of redoxactive iron, the oxidation of polyunsaturated fatty acid (PUFA)-containing phospholipids and the loss of lipid peroxide repair capacity by phospholipid hydroperoxidases. ",
"Ferroptosis is a nonapoptotic, iron-dependent form of cell death that is characterized by by the availability of redoxactive iron, the oxidation of saturated fatty acid (PUFA)-containing phospholipids and an increase in the activity of phospholipid hydroperoxidases",
"Ferroptosis is a nonapoptotic, iron-dependent form of cell death that is characterized by a decrease in iron availability, the oxidation of polyunsaturated fatty acid (PUFA)-containing phospholipids and an increase in the activity of phospholipid hydroperoxidases.………………………………………………………………………………………….."
] | https://doi.org/10.1146/annurev-cancerbio-030518-055844 | Non-specific | PHYSIOLOGY AND METABOLISM | 10.1146/annurev-cancerbio-030518-055844 | 2,019 | 450 | 0 | Annual Review of Cancer Biology | true |
Which protein has been identified as a molecular marker for ferroptosis in Arabidopsis thaliana and how is its response? | PHYSIOLOGY AND METABOLISM | [
"Arabidopsis thaliana"
] | [
"Kiss of death (KOD), a gene encoding a transcription factor that induces cell death in A. thaliana roots is significantly up-regulated in response to heat stress (HS) and ROS and down-regulated in response to specific ferroptosis canonical inhibitors, acting downstream of GSH depletion and ROS accumulation in the cascade of events that lead to HS–induced ferroptotic cell death. ",
"Kiss of death (KOD), a gene encoding for a 25-aa peptide that induces cell death in A. thaliana roots is significantly up-regulated in response to heat stress (HS) and ROS and down-regulated in response to specific ferroptosis canonical inhibitors, acting downstream of GSH depletion and ROS accumulation in the cascade of events that lead to HS–induced ferroptotic cell death. ",
"Kiss of death (KOD), a gene encoding a 25-aa peptide that induces cell death in A. thaliana roots is significantly down-regulated in response to heat stress (HS) and ROS and up-regulated in response to specific ferroptosis canonical inhibitors, acting downstream of GSH depletion and ROS accumulation in the cascade of events that lead to HS–induced ferroptotic cell death. "
] | https://doi.org/10.1083/jcb.201605110 | Model Organisms | PHYSIOLOGY AND METABOLISM | 10.1083/jcb.201605110 | 2,017 | 192 | 1 | Journal of Cell Biology | true |
Which brassinosteroid is specifically found in female gametophytes and what is the proposed mechanism for its biosynthesis in Arabidopsis thaliana? | HORMONES | [
"non-specific"
] | [
"Castasterone is the brassinosteroid that is specifically found inside the female gametophytes of A. thaliana. Its biosynthesis takes place in female gametophyte mitochondria, in a pathway that involves an Adrenodoxin reductase, an Adrenodoxin and a cytochrome P450 (ADXR-ADX-P450) electron shuttle as occurs in animal systems, and whose activity is essential for female megagametophyte development and function. In this model, a precursor steroid is imported into the inner mitochondrial membrane via PBR, a peripheral-type benzodiazepine receptor. Inside mitochondria, electrons are transferred from NADPH via ADX–ADXR to one of the P450s that are able to interact with ADX1 (CYP711A1, CYP90A1, or CYP75B1), to catalyze the synthesis of homocastasterone from the steroid precursor",
"Brasinolide is the brassinosteroid that is specifically found inside the female gametophytes of A. thaliana. Its biosynthesis takes place in female gametophyte endoplasmic reticulum, in a pathway that involves an Adrenodoxin reductase, an Adrenodoxin and a cytochrome P450 (ADXR-ADX-P450) electron shuttle as occurs in animal systems, and whose activity is essential for female megagametophyte development and function. In this model, a sterol is imported into the inner mitochondrial membrane via PBR, a peripheral-type benzodiazepine receptor. Inside mitochondria, electrons are transferred from NADPH via ADX–ADXR to one of the P450s that are able to interact with ADX1 (CYP711A1, CYP90A1, or CYP75B1), to catalyze the synthesis of homocastasterone from the sterol precursor",
" Homocastasterone is the brassinosteroid that is specifically found inside the female gametophytes of A. thaliana. Its biosynthesis takes place in female gametophyte mitochondria, in a pathway that involves an Adrenodoxin reductase, an Adrenodoxin and a cytochrome P450 (ADXR-ADX-P450) electron shuttle as occurs in animal systems, and whose activity is essential for female megagametophyte development and function. In this model, a sterol is imported into the inner mitochondrial membrane via PBR, a peripheral-type benzodiazepine receptor. Inside mitochondria, electrons are transferred from NADPH via ADX–ADXR to one of the P450s that are able to interact with ADX1 (CYP711A1, CYP90A1, or CYP75B1), to catalyze the synthesis of homocastasterone from the sterol precursor.……………………………………….."
] | https://doi.org/10.1073/pnas.200048211 | Non-specific | HORMONES | null | null | null | 2 | null | true |
Which receptors of Brassinosteroids (BRs) have been identified in Arabidopsis thaliana and how are they activated in the presence of BRs? | HORMONES | [
"Arabidopsis thaliana"
] | [
"BRs are perceived outside the cell by a plasma membrane-localized receptor. Three functional BR receptors have been identified in Arabidopsis: BRASSINOSTEROID-INSENSITIVE1 (BRI1) BRL1 and BRL3. These receptors associate with a smaller LRR receptor kinase, BRI1-ASSOCIATED KINASE1 (BAK1), whose function in BR signalling is also redundant with SERK1. BL binds to the extracellular domain of the receptor, inducing heterodimerization of BRI1 and BAK1 or SERK1, which function as co-receptors of BRI1. This interaction is required for BRI1 activation. ",
"BRs are perceived outside the cell by a plasma membrane-localized receptor. Three functional BR receptors have been identified in Arabidopsis: BRASSINOSTEROID-INSENSITIVE1 (BRI1) BRL1 and BRL3. These receptors associate with a smaller LRR receptor kinase, BRI1-ASSOCIATED KINASE1 (BAK1), whose function in BR signalling is also redundant with SERK1. BL binds to the extracellular domain of the receptor, inducing homodimerization of BRI1 and its later binding with BAK1 or SERK1. This interaction is required for BRI1 activation. ",
"BRs are perceived outside the cell by a plasma membrane-localized receptor. Four functional BR receptors have been identified in Arabidopsis: BRASSINOSTEROID-INSENSITIVE1 (BRI1) BRL1, BRL2 and BRL3. These receptors associate with a smaller LRR receptor kinase, BRI1-ASSOCIATED KINASE1 (BAK1), whose function in BR signalling is also redundant with SERK1 and with SERK5. BL binds to the extracellular domain of the receptor, inducing heterodimerization of BRI1 and BAK1 or SERK1, which function as co-receptors of BRI1. This interaction is required for BRI1 activation. "
] | 10.1016/j.cub.2020.02.011 | Model Organisms | HORMONES | 10.1016/j.cub.2020.02.011 | 2,020 | 107 | 0 | Current Biology | true |
How do brassinosteroids (BRs) regulate Arabidopsis root development and how is the interaction between BRs and auxins in this process? | HORMONES | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis, BR signaling controls cell division and cell elongation by establishing a signal gradient along the longitudinal root axis. The coordinated growth of roots requires a gradient distribution of BR concentration, with higher hormone levels in the meristematic tissue and lower levels in the elongation zone, which are attributable to the spatial distribution of biosynthetic enzymes. The maintenance of the root meristematic state depends on the coordination of multiple hormone signals, with the interaction between BR and auxin playing a crucial role. BR promotes auxin signaling, but also inhibits its biosynthesis, which is essential to maintain the root meristem. ",
"In Arabidopsis, BR signaling controls cell division and cell elongation by establishing a signal gradient along the longitudinal root axis. The coordinated growth of roots requires a gradient distribution of BR concentration, with lower hormone levels in the meristematic tissue and higher levels in the elongation zone, which are attributable to the spatial distribution of biosynthetic enzymes. The maintenance of the root meristematic state depends on the coordination of multiple hormone signals, with the interaction between BR and auxin playing a crucial role. BR promotes auxin synthesis but also inhibits auxin signal output, which is essential to maintain the root meristem. ",
"In Arabidopsis, BR signaling controls cell division and cell elongation by establishing a signal gradient following the radial root axis. The coordinated growth of roots requires a gradient distribution of BRs receptors, which results in lower hormone signaling in the meristematic tissue and higher levels in the peripheral region. The maintenance of the root meristematic state depends on the coordination of multiple hormone signals, with the interaction between BR and auxin playing a crucial role. BR inhibits both auxin synthesis and auxin signal output, which is essential to maintain the root meristem. "
] | 10.3390/plants13213051 | Model Organisms | HORMONES | 10.3390/plants13213051 | 2,024 | 3 | 1 | Plants | true |
Which is the fundament behind the TRAP (Translating Ribosome Affinity Purification) methodology that allows purification of ribosome bound mRNAs? | GENE REGULATION - TRANSLATION | [
"non-specific"
] | [
"TRAP is based on the expression of a tagged version of a eukaryotic initiation factor that will be incorporated into ribosomes, providing a means for affinity purification of ribosomes containing the tagged ribosomal protein and their associated mRNAs.",
"TRAP is based on the expression of a tagged version of a ribosomal protein that will be incorporated into ribosomes, providing a means for affinity purification of ribosomes containing the tagged ribosomal protein and their associated mRNAs.",
"TRAP is based on the expression of a tagged version of a nuclear envelope protein that will be incorporated into ribosomes, providing a means for affinity purification of ribosomes containing the tagged ribosomal protein and their associated mRNAs"
] | www.plantphysiol.org/cgi/doi/10.1104/pp.105.059477. | Non-specific | GENE REGULATION | 10.1104/pp.105.059477 | 2,005 | 189 | 1 | Plant Physiology | true |
How can TRAP (Translating Ribosome Affinity Purification) methodology be applied to the generation of an atlas of the translated mRNAs within specific cell type populations? | GENE REGULATION - TRANSLATION | [
"non-specific"
] | [
"By expressing a tagged ribosomal protein under the control of cell type specific promoters",
"By expressing a tagged ribosomal protein under the control of a constitutive promoter",
"By expressing a tagged ribosomal protein under the control of a chemically induced promoter"
] | https://doi.org/10.1073/pnas.0906131106 | Non-specific | GENE REGULATION | 10.1073/pnas.0906131106 | 2,009 | 503 | 0 | Proceedings of the National Academy of Sciences | true |
Which mRNAs encoding components of the Nodulation signaling pathway are upregulated at translational level in Medicago truncatua roots upon inoculation with Sinorhizobium meliloti? | GENE REGULATION - TRANSLATION | [
"Medicago truncatula"
] | [
"mRNAs upregulated at translation levels in Medicago truncatula roots upon inoculation with Sinorhizobium meliloti include those encoding the Nod factor receptor LYK3 and the calcium calmodulin dependent protein kinase DMI3. \n\n",
"mRNAs upregulated at translation levels in Medicago truncatula roots upon inoculation with Sinorhizobium meliloti include those encoding the transcription factors NSP1, NSP2, HAP2.1/NF-YA1, HAP5. ",
"mRNAs upregulated at translation levels in Medicago truncatula roots upon inoculation with Sinorhizobium meliloti include those encoding the transcription factors NSP1, NSP2, and the interacting protein with DMI3 (IPD3). "
] | doi: 10.1111/tpj.12033 | Model Organisms | GENE REGULATION | 10.1111/tpj.12033 | 2,012 | 66 | 1 | The Plant Journal | true |
How is the Superkiller 3 (SKI3) subunit involved in the symbiosis between Medicago truncatula and Sinorhizobium meliloti? | GENE REGULATION - TRANSLATION | [
"Medicago truncatula"
] | [
"SKI3 is a component of the Superkiller complex, which threads mRNA to the exosome for 3´to 5´mRNA degradation. SKI3 is required for nodule formation, the progression of infection events and the induction of the mRNA encoding the transcription factor NF-YA1 in the Medicago truncatula-Sinorhizobium meliloti symbiosis.",
"SKI3 is a component of the Superkiller complex, which threads mRNA to the exosome for 5´to 3´mRNA degradation. SKI3 is required for the formation of infection threads, the survival of the bacterial within the nodule and the induction of the early nodulin ENOD40 in the Medicago truncatula-Sinorhizobium meliloti symbiosis.",
"SKI3 is a component of the Superkiller complex, which threads mRNA to the exosome for 3´ to 5´mRNA degradation. SKI3 is required for nodule formation, the survival of the bacterial within the nodule and the induction of the early nodulin ENOD40 in the Medicago truncatula-Sinorhizobium meliloti symbiosis."
] | https://www.plantcell.org/cgi/doi/10.1105/tpc.19.00647 | Model Organisms | GENE REGULATION | 10.1105/tpc.19.00647 | 2,019 | 31 | 2 | The Plant Cell | true |
How is the translational control of the translational control of the mRNA encoding transcription factor TL1-1 Binding Factor 1 (TBF1) in Arabidopsis thaliana in response to Pseudomonas syringae? | GENE REGULATION - TRANSLATION | [
"Arabidopsis thaliana"
] | [
"TBF1 translational control in Arabidopsis is mediated by a mechanism involving two upstream Open Reading Frames (uORF1 and uORF2) in its mRNA leader, which represses translation of the mORF under normal conditions due to stall of the ribosomes at such uORFs. Inoculation with the Pseudomonas syringae reversed this translational repression, allowing ribosomes to reinitiate translation at the mORF of TBF1. ",
"TBF1 translational control in Arabidopsis is mediated by a mechanism involving an ADC box present in its mRNA leader, which represses translation of the mORF under normal conditions due to stall of the ribosomes. Inoculation with the Ralstonia solanacearum reversed this translational repression, allowing ribosomes to reinitiate translation of TBF1. ",
"TBF1 translational control in Arabidopsis is mediated by a mechanism involving two binding sites for microRNAs in its mRNA leader, which represses translation of the mORF under normal conditions due to stall of the ribosomes. Inoculation with the Pseudomonas syringae reversed this translational repression, allowing ribosomes to reinitiate translation of TBF1. "
] | https://doi.org/10.1042/BCJ20210066 | Model Organisms | GENE REGULATION | 10.1042/BCJ20210066 | 2,021 | 2 | 0 | Biochemical Journal | true |
How is DYSFUNCTIONAL TAPETUM1 involved in pollen development in Arabidopsis thaliana? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"2 DYSFUNCTIONAL TAPETUM 1 (DYT1) is a bHLH transcription factor that serves as a master regulator of the tapetum transcriptional network. DYT1 plays a critical role in tapetal development and also determines the viability of pollen grains. It is expressed at early stages of anther development, and forms homodimers, which are localized in the nucleus and promote the expression of multiple downstream genes involved in anther development, including DLX proteins. DLX proteins can interact with cytoplasmic DYT1 and block their nuclear translocation. At later stages of anther development, DYT1 specifically localizes to the cytoplasm, forming inactive DYT1-DLX dimers.",
"DYSFUNCTIONAL TAPETUM 1 (DYT1) is a bHLH transcription factor that serves as a master regulator of the tapetum transcriptional network. DYT1 plays a critical role in tapetal development and also determines the viability of pollen grains. It is expressed during the early stages of anther development and forms homodimers, which are primarily localized in the cytoplasm. Basal levels of nuclear-localized DYT1 promote the expression of other bHLH transcription factors, which can interact with cytoplasmic DYT1 to facilitate their nuclear translocation. At later stages of anther development, DYT1 specifically localizes to the nucleus, forming various DYT1-bHLH heterodimers capable of binding to the promoters of multiple downstream genes, thereby activating complex transcriptional networks involved in anther development.",
"DYSFUNCTIONAL TAPETUM 1 (DYT1) is a NAC family transcriptional regulator that serves as a master regulator of the tapetum transcriptional network. DYT1 plays a critical role in tapetal development and also determines the viability of pollen grains. It is expressed during the early stages of anther development and forms homodimers, which are primarily localized in the cytoplasm. Basal levels of nuclear-localized DYT1 promote the expression of other NAC family transcriptional regulators, which can interact with cytoplasmic DYT1 to facilitate their nuclear translocation. At later stages of anther development, DYT1 specifically localizes to the nucleus, forming various DYT1-NAC heterodimers capable of acting as transcriptional repressors, leading to major changes in the transcriptional landscape required to complete anther development."
] | https://doi.org/10.1105/tpc.15.00986 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1105/tpc.15.00986 | 2,016 | 82 | 1 | The Plant Cell | true |
How are RALF peptides and LRX proteins involved in pollen tube growth in Arabidopsis? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"Pollen tube growth is regulated during the process of fertilization by the interactions of extracellular signaling molecules (RALF peptides) with receptors of the LRX protein family at the pollen tube surface. RALF34 peptides, secreted by the pollen tube, are sensed by LRX proteins BUPS1/2 and ANXUR1/2, RALF4 and RALF19 are required to maintain pollen tube integrity. On the other hand, female-derived RALF4/19, which competes with RALF34 peptides for the same receptors, induces pollen tube bursting, leading to pollen tube rupture and sperm release",
"Pollen tube growth is regulated during the process of fertilization by the interactions of extracellular signaling molecules (RALF peptides) with receptors of the LRX protein family at the pollen tube surface. RALF4 and RALF19 peptides, secreted by the female tissue, are sensed by LRX proteins BUPS1/2, and are required to maintain pollen tube integrity. On the other hand, pollen-derived RALF34, which is sense by and ANXUR1/2 receptors, induces pollen tube bursting, leading to pollen tube rupture and sperm release.",
"Pollen tube growth is regulated during the process of fertilization by the interactions of extracellular signaling molecules (RALF peptides) with receptors of the LRX protein family at the pollen tube surface. RALF4 and RALF19 peptides, secreted by the pollen tube, are sensed by LRX proteins BUPS1/2 and ANXUR1/2, and are required to maintain pollen tube integrity. On the other hand, female-derived RALF34, which competes with RALF4/19 peptides for the same receptors, induces pollen tube bursting, leading to pollen tube rupture and sperm release."
] | 10.1126/science.aao3642 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1126/science.aao3642 | 2,017 | 335 | 2 | Science | true |
How are RHO OF PLANT and BDR8/9 proteins involved in pollen development in Arabidopsis? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"RHO OF PLANT (ROP), BDR8 and BDR9 proteins play a crucial role in establishing polarity during pollen germination. Active ROPs associate with the plasma membrane at germination sites prior to pollen germination. ROP then can interact with two proteins from the Boundary of ROP Domain (BDR) family: BDR8 and BDR9. In mature pollen grains, BDR8 and BDR9 are distributed in the cytosol and the vegetative nucleus, but they redistribute to the plasma membrane of germination sites upon ROP recruitment.",
"RHO OF PLANT (ROP), BDR8 and BDR9 proteins play a crucial role during pollen tube rupture and sperm release. Active ROPs associate with the plasma membrane at apical side of the pollen tube prior rupture. ROP then can interact with two proteins from the Boundary of ROP Domain (BDR) family: BDR8 and BDR9. During pollen tube growth, BDR8 and BDR9 are distributed in the cytosol and the vegetative nucleus, but they redistribute to the plasma membrane at bursting sites upon ROP recruitment.",
"RHO OF PLANT (ROP), BDR8, and BDR9 proteins play a crucial role in establishing polarity during pollen germination. BDR8 and BDR9, two proteins from the Boundary of ROP Domain family, associate with the plasma membrane at germination sites prior to pollen germination. Then, BDR8 and BDR9 can recruit ROP at the germination site. In mature pollen grains, ROPs are distributed homogeneously at the plasma membrane, but they redistribute to germination sites upon BDR8 and BDR9 recruitment."
] | https://doi.org/10.1093/plphys/kiad196 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1093/plphys/kiad196 | 2,023 | 7 | 0 | Plant Physiology | true |
How is the microRNA OsmiR159 involved in pollen development in rice | GROWTH AND DEVELOPMENT | [
"Oryza sativa"
] | [
"The microRNA OsmiR159 is involved in the regulation of starch content in pollen; since starch is an indispensable energy reserve for pollen, failure of starch biosynthesis leads to male sterility. The microRNA OsmiR159 targets OsSPEAR2, which is expressed in mature pollen and localizes in the nucleus, where it interacts with multiple OsTCPs, including OsTCP14, a transcriptional repressor of the essential starch biosynthesis gene OsUGP2. The interaction between OsSPEAR2 and OsTCP14 alleviates its repressing activity on OsUGP2. \nOsmiR159 expression leads to reduced OsSPEAR2 levels and, hence, increased repression of OsUGP2 by OsTCP14, diminishing starch content in pollen and causing male sterility.",
"The microRNA OsmiR159 is involved in the regulation of starch content in pollen; since starch is an indispensable energy reserve for pollen, failure of starch biosynthesis leads to male sterility. The microRNA OsmiR159 targets OsSPEAR2, which is expressed in mature pollen and localizes in the nucleus, where it interacts with multiple OsTCPs, including OsTCP14, forming a dimer that promotes the transcription of the essential starch biosynthesis gene OsUGP2. \nOsmiR159 expression leads to reduced OsSPEAR2 levels and, hence, decreased expression of OsUGP2, diminishing starch content in pollen and causing male sterility.",
"The microRNA OsmiR159 is involved in the synthesis of sporophytic pollen coat proteins in the anther tapetum. Sporophytic pollen coat proteins derived from the anther tapetum are deposited into pollen wall cavities and fulfill key roles in pollen development. \nThe microRNA OsmiR159 targets MALE STERILITY 188, which is expressed in the anther tapetum and localizes in the nucleus, where it directly activates MALE STERILITY 1, which in turn controls the expression of genes coding for sporophytic pollen coat proteins. OsmiR159 expression leads to reduced levels of MALE STERILITY 188 and, hence, decreased expression of MALE STERILITY 1, diminishing sporophytic pollen coat proteins and causing male sterility."
] | https://doi.org/10.1093/plcell/koae324 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1093/plcell/koae324 | 2,024 | 0 | 0 | The Plant Cell | true |
How are BNP and VOZ1/2 involved in male gametophyte development in Arabidopsis? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"The DC1 domain protein BINUCLEATE POLLEN (BNP) is required to complete male gametophyte development, as its absence causes an arrest at the bicellular pollen stage. At this stage, BNP interacts with the transcription factors VOZ1 and VOZ2 in the nucleus and promotes their degradation through the ubiquitin-proteasome pathway. The degradation of VOZ1 and VOZ2 is required to complete the transition from the bicellular stage to the mature pollen stage.",
"The DC1 domain protein BINUCLEATE POLLEN (BNP) is required to complete male gametophyte development, as its absence causes an arrest at the unicellular pollen stage. At this stage, BNP interacts with the transcription factors VOZ1 and VOZ2 at the endoplasmic reticulum and facilitates their nuclear translocation, which is necessary to promote the transcriptional changes associated with the transition to the bicellular pollen stage.",
"The DC1 domain protein BINUCLEATE POLLEN (BNP) is required to complete male gametophyte development, as its absence causes an arrest at the bicellular pollen stage. At this stage, BNP interacts with the transcription factors VOZ1 and VOZ2 in prevacuolar compartments or multivesicular bodies and facilitates their nuclear translocation, which is necessary to promote the transcriptional changes associated with the transition from the bicellular stage to the mature pollen stage."
] | https://doi.org/10.1093/pcp/pcac122 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1093/pcp/pcac122 | 2,022 | 3 | 2 | Plant and Cell Physiology | true |
The plant immune system plays a central role in the social network of plants. It is generally assumed that rhizobia are first recognized by plants as intruders, and that hosts mount a defense response against these bacteria. Modulation of plant immunity plays an important role in symbiosis development. Q: Which rhizobial molecules have been related with the suppression of the defense responses in host legume? | ENVIRONMENT - PLANT-SYMBIONTS | [
"non-specific"
] | [
"Several rhizobial molecules have been related with the triggering of the plant defense responses, such as Nod factors (NFs), effectors secreted through Type III secretion system (T3SS), surface polysaccharides such as extracellular polysaccharides (EPS), plipopolysaccharides (LPS), capsular polysaccharides (KPS) cyclic β -glucans, salicylic acid (SA), flagellin and elongation factor Tu (EFTu).",
"Several rhizobial molecules have been related with the suppression of the plant defense responses, such as Nod factors (NFs), surface polysaccharides such as extracellular polysaccharides (EPS), plipopolysaccharides (LPS), capsular polysaccharides (KPS) cyclic β -glucans, salicylic acid (SA), flagellin and elongation factor Tu (EFTu).",
"Several rhizobial molecules have been related with the suppression of the plant defense responses, including Nod factors (NFs), effectors secreted through Type III secretion system (T3SS) and surface polysaccharides such as extracellular polysaccharides (EPS), lipopolysaccharides (LPS), capsular polysaccharides (KPS) and cyclic β -glucans."
] | https://doi.org/10.1007/s11104-020-04423-5. | Non-specific | ENVIRONMENT | 10.1007/s11104-020-04423-5 | 2,020 | 25 | 2 | Plant and Soil | true |
It had been demonstrated that flg22-triggered defense responses in the roots of Lotus japonicus negatively influence nodulation by inhibiting rhizobial infections and delaying the nodule organogenesis. Q: What is the impact of the mutation of conserved flagellin epitope of Mesorhizobium loti in Lotus japonicus defense response? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Lotus japonicus"
] | [
"The roots of Lotus japonicus, do not respond to purified flagellin from Mesorhizobium loti. The receptor LjFLS2 is unable to sense flagellin molecules from the symbiotic partner. Immune selective pressure exerted by the putative FLS2 orthologs of the leguminous hosts forced the emergence of escape mutations within the active flagellin epitope, hence providing the microsymbionts with an evolutionary advantage of reducing stimulation of the host’s immune system.",
"The roots of Lotus japonicus, respond to purified flagellin from Mesorhizobium loti. The receptor LjFLS2 senses flagellin molecules from the symbiotic partner. Immune selective pressure exerted by the putative FLS2 orthologs of the leguminous hosts forced the emergence of escape mutations within the active flagellin epitope, hence providing the microsymbionts with an evolutionary advantage of stimulation of the host’s immune system.",
"The roots of Lotus japonicus, do not respond to purified flagellin from Mesorhizobium loti. The receptor AtFLS2 is unable to sense flagellin molecules from the symbiotic partner. Immune selective pressure exerted by the orthologs flg22 of the symbiotic rhizobia forced the emergence of escape mutations within the active flagellin epitope, hence providing the legume with an evolutionary advantage of reducing stimulation of the symbiont ’s immune system"
] | doi:10.1093/jxb/err291 | Model Organisms | ENVIRONMENT | 10.1093/jxb/err291 | 2,011 | 128 | 0 | Journal of Experimental Botany | true |
In Arachis hypogaea (peanut) has been proved that AhNF-YA1 and the LysMRLK Ahy.IM7I4N receptors are related to the plant response to the inoculation with Nod Factors. On the other hand, AhPER7 and AhWRKY11 are related to the plant response to the inoculation with chitosan. Q: How is the AhNF-YA1, AhPER7 and AhWRKY11 gene expression profile in A. hypogaea (peanut) when NFs (symbiotic molecule signal) and chitosan (pathogenic molecule signal) are co-inoculated? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Arachis hypogaea"
] | [
"The expression patterns of symbiosis and defense-related marker genes after co- inoculation with elicitor molecules shows that defense and symbiotic responses in peanut does not influence each other. Co-inoculation of NFs and chitosan in A. hypogaea has no effect on the transcription of the symbiotic gene marker AhNF-YA1, suggesting that the symbiotic pathway is not suppressed when defense signaling pathways are activated. Meanwhile AhPER7 and AhWRKY11 expression levels are lower in co-inoculated peanut roots compared to those inoculated with chitosan, suggesting that defense signaling pathways could being synergically activated during the early steps of the interaction with both molecules.",
"The expression patterns of symbiosis and defense-related marker genes after co- inoculation with elicitor molecules shows that defense and symbiotic responses in peanut appear to influence each other. Co-inoculation of NFs and chitosan in A. hypogaea has a positive effect on the transcription of the symbiotic gene marker AhNF-YA1, suggesting that the symbiotic pathway is stimulated when defense signaling pathways are activated. Meanwhile AhPER7 and AhWRKY11 expression levels are lower in co-inoculated peanut roots compared to those inoculated with chitosan, suggesting that defense signaling pathways could being suppressed during the early steps of the interaction with both molecules.",
"The expression patterns of symbiosis and defense-related marker genes after co- inoculation with elicitor molecules shows that defense and symbiotic responses in peanut appear to influence each other. Co-inoculation of NFs and chitosan in A. hypogaea has a negative effect on the transcription of the symbiotic gene marker AhNF-YA1, suggesting that the symbiotic pathway is suppressed when defense signaling pathways are activated. Meanwhile AhPER7 and AhWRKY11 expression levels are higher in co-inoculated peanut roots compared to those inoculated with chitosan, suggesting that defense signaling pathways could being synergically activated during\nthe early steps of the interaction with both molecules.\n"
] | https://doi.org/10.1007/s13199-024-01022-1 | Legumes | ENVIRONMENT | 10.1007/s13199-024-01022-1 | 2,024 | 0 | 2 | Symbiosis | true |
It has been demonstrated that responses triggered in peanut plants by single microbial species populations are modified in presence of others. Q: What is the effect of the challenge with the phypathogen Sclerotium rolfsii on the expression of AhSymRK and the symbiotic behavior in Arachis hypogaea (peanut) plants inoculated with the microsymbiont Bradyrhizobium sp. SEMIA6144? What is the effect of the biocontrol agent Bacillus sp. CHEP5 inoculation on these symbiotic parameters? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Arachis hypogaea"
] | [
"AhSymRK gene expression is lower in plants inoculated only with the microsymbiont compared to those co-inoculated with Bacillus sp. CHEP5 and Bradyrhizobium sp. SEMIA6144. Meanwhile, this gene expression is increased in plants inoculated with Bradyrhizobium sp. SEMIA6144 and challenged with S. rolfsii. In this sense, in plants inoculated with Bradyrhizobium sp. SEMIA6144 and challenged with S. rolfsii, the number of nodules per plant, percentage of red nodules formed, percentage of nodulated plants as well as plant nitrogen content are higher. However, AhSymRK expression in plants challenges with S. rolfsii and co-inoculated the mycrosimbiont and biocontrol bacterium was reduced compared to plant-mycrosimbiont control condition as well as the nodulation parameters. \n\n",
"AhSymRK gene expression is similar both in plants inoculated only with the microsymbiont and in those co-inoculated with Bacillus sp. CHEP5 and Bradyrhizobium sp. SEMIA6144. Moreover, this gene expression is stable in plants inoculated with Bradyrhizobium sp. SEMIA6144 and challenged with S. rolfsii. In this sense, in plants inoculated with Bradyrhizobium sp. SEMIA6144 and challenged with S. rolfsii, the number of nodules per plant, percentage of red nodules formed, percentage of nodulated plants as well as plant nitrogen content are the same as in plants only inoculated with Bradyrhizobium sp. SEMIA6144. However, AhSymRK expression in plants challenges with S. rolfsii and co-inoculated the mycrosimbiont and biocontrol bacterium was lower to plant-mycrosimbiont control condition as well as the nodulation parameters.",
"AhSymRK gene expression is similar both in plants inoculated only with the microsymbiont and in those co-inoculated with Bacillus sp. CHEP5 and Bradyrhizobium sp. SEMIA6144. Meanwhile, this gene expression is reduced in plants inoculated with Bradyrhizobium sp. SEMIA6144 and challenged with S. rolfsii. In this sense, in plants inoculated with Bradyrhizobium sp. SEMIA6144 and challenged with S. rolfsii, the number of nodules per plant, percentage of red nodules formed, percentage of nodulated plants as well as plant nitrogen content are lower. However, AhSymRK expression in plants challenges with S. rolfsii and co-inoculated the mycrosimbiont and biocontrol bacterium was reverted to plant-mycrosimbiont control condition as well as the nodulation parameters. "
] | https://doi.org/10.1007/s11104-018-3846-8, http://dx.doi.org/10.1016/j.micres.2017.01.002 | Legumes | ENVIRONMENT | 10.1016/j.micres.2017.01.002 | 2,017 | 42 | 2 | Microbiological Research | true |
How is the expression profile in Arachis hypogaea (peanut) plants of the receptor genes Ahy.IM7I4N and Ahy.YTK8KP in presence of chitosan (molecule triggering defense) or Nod Factors (molecule triggering rhizobial symbiosis)? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Arachis hypogaea"
] | [
"Transcriptional activation of Ahy.IM7I4N is observed at 1 hours post inoculation (hpi) with Nod Factors and chitosan, separately, suggesting a versatile function of Ahy.IM7I4N. At later time points (from 1 to 72 hpi), Ahy.IM7I4N expression levels are significantly increased in response to Nod Factors. Instead, Ahy.YTK8KP expression is a specific transcriptional response to NF treatment (with significant expression levels increased at 1 and 8 hpi). ",
"Transcriptional activation of Ahy.IM7I4N is observed at 1 hours post inoculation (hpi) with chitosan, suggesting a specific function of Ahy.IM7I4N. At later time points (from 1 to 72 hpi), Ahy.IM7I4N expression levels are significantly repressed in response to Nod Factors. Instead, Ahy.YTK8KP expression is a specific transcriptional response to chitosan treatment (with significant expression levels increased at 1 and 8 hpi). ",
"Transcriptional repression of Ahy.IM7I4N is observed at 1 hours post inoculation (hpi) with Nod Factors and chitosan, separately, suggesting a negative signaling function of Ahy.IM7I4N. At later time points (from 1 to 72 hpi), Ahy.IM7I4N expression levels are significantly increased in response to Nod Factors. Instead, Ahy.YTK8KP expression is a specific transcriptional response to chitosan treatment (with significant expression levels increased at 1 and 8 hpi). "
] | https://doi.org/10.3390/horticulturae8111000 | Legumes | ENVIRONMENT | 10.3390/horticulturae8111000 | 2,022 | 1 | 0 | Horticulturae | true |
Which transposable element family from tomato has been shown to be activated by drought stress, abscisic acid, and which epigenetic pathway is involved in its control? | GENOME AND GENOMICS | [
"Solanum lycopersicum"
] | [
"In tomato, heat stress and abscisic acid trigger the transcriptional activation of the transposable element family Rider. Under heat and high abscisic acid treatment, Rider transcript levels increase and correlate with the accumulation of extrachromosomal RNA. Rider is under the control of DNA methylation mediated by the RNA-directed DNA methylation pathway.",
"In tomato, drought stress and gibberellic acid trigger the transcriptional activation of the transposable element family Rider. Under drought and high gibberellic acid treatment, Rider transcript levels increase and correlate with the accumulation of extrachromosomal DNA. Rider is under the control of histone methylation mediated by the RNA-directed DNA methylation pathway.",
"In tomato, drought stress and abscisic acid trigger the transcriptional activation of the transposable element family Rider. Under drought and high abscisic acid treatment, Rider transcript levels increase and correlate with the accumulation of extrachromosomal DNA. Rider is under the control of DNA methylation mediated by the RNA-directed DNA methylation pathway."
] | 10.1371/journal.pgen.1008370 | Solanaceae & Relatives | GENOME AND GENOMICS | 10.1371/journal.pgen.1008370 | 2,019 | 55 | 2 | PLOS Genetics | true |
Beyond tomato, in how many Solanaceae species has the Rider transposable element been detected, and which ones? | GENOME AND GENOMICS | [
"Solanum lycopersicum"
] | [
"Beyond tomato, the Rider transposable element has been detected in four other Solanaceae species: Solanum pimpinellifolium, Solanum arcanum, Solanum tuberosum, Capsicum annuum.",
"Beyond tomato, the Rider transposable element has been detected in four other Solanaceae species: Solanum pimpinellifolium, Solanum arcanum, Solanum pennellii, Solanum habrochaites.",
"Beyond tomato, the Rider transposable element has been detected in six other Solanaceae species: Solanum pimpinellifolium, Solanum arcanum, Solanum pennellii, Solanum habrochaites. Solanum tuberosum, Capsicum annuum."
] | 10.1371/journal.pgen.1008370 | Solanaceae & Relatives | GENOME AND GENOMICS | 10.1371/journal.pgen.1008370 | 2,019 | 55 | 1 | PLOS Genetics | true |
How many structural variants have been detected in the tomato panSV-genome and which superfamilies of transposable elements are contributing the most to structural variation? | GENOME AND GENOMICS | [
"Solanum lycopersicum"
] | [
"The tomato panSV-genome revealed 238,490 structural variants with the Copia and Gypsy superfamilies of transposable elements contributing the most to structural variation.",
"The tomato panSV-genome revealed 45,840 structural variants with the Copia and Gypsy superfamilies of transposable elements contributing the most to structural variation.",
"The tomato panSV-genome revealed 238,490 structural variants with the CACTA and Helitron superfamilies of transposable elements contributing the most to structural variation."
] | 10.1016/j.cell.2020.05.021 | Solanaceae & Relatives | GENOME AND GENOMICS | 10.1016/j.cell.2020.05.021 | 2,020 | 586 | 0 | Cell | true |
Which DNA methyltransferase is involved in the epigenetic reprogramming associated with symbiotic gene activation in the differentiation and fixation zones of Medicago truncatula nodules? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Medicago truncatula"
] | [
"The transcriptional activation of symbiotic genes in the differentiation and the fixation zones of Medicago truncatula nodules correlates with a decrease in CHH methylation. DME, the main DNA methyltransferase of the RNA-directed DNA methylation pathway, is expressed in the differentiation and the fixation zones of the nodules, and is responsible for the reduction of CHH methylation at symbiotic genes expressed in the differentiation and the fixation zones.",
"The transcriptional activation of symbiotic genes in the differentiation and the fixation zones of Medicago truncatula nodules correlates with an increase in histone methylation. DRM2, the main histone methyltransferase of the histone methylation pathway, is expressed in the differentiation and the fixation zones of the nodules, and is responsible for the hyperaccumulation of histone methylation at symbiotic genes expressed in the differentiation and the fixation zones.",
"The transcriptional activation of symbiotic genes in the differentiation and the fixation zones of Medicago truncatula nodules correlates with an increase in CHH methylation. DRM2, the main DNA methyltransferase of the RNA-directed DNA methylation pathway, is expressed in the differentiation and the fixation zones of the nodules, and is responsible for the hyperaccumulation of CHH methylation at symbiotic genes expressed in the differentiation and the fixation zone."
] | 10.1038/s41477-022-01188-w | Model Organisms | ENVIRONMENT | 10.1038/s41477-022-01188-w | 2,022 | 14 | 2 | Nature Plants | true |
Which histone post-translational marks undergo reprogramming between roots and developing nodules in Medicago truncatula? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Medicago truncatula"
] | [
"Several histone post-translational modifications are dynamically modulated during the development of nodules from roots in Medicago. Levels of tri-methylation of lysine 27 of histones H3 (H3K27me3) decrease drastically in nodules compared to roots. Conversely, levels of acetylation of lysine 9 of histones H3 (H3K9ac) are higher in nodules compared to roots.",
"Several histone post-translational modifications are dynamically modulated during the development of nodules from roots in Medicago truncatula. Levels of mono-methylation of lysine 27 of histones H3 (H3K27me1) decrease drastically in nodules compared to roots. Conversely, levels of mono-methylation of lysine 9 of histones H3 (H3K9me1) are higher in nodules compared to roots.",
"Several histone post-translational modifications are dynamically modulated during the development of nodules from roots in Medicago truncatula. Levels of tri-methylation of lysine 27 of histones H3 (H3K27me3) increase drastically in nodules compared to roots. Conversely, levels of acetylation of lysine 9 of histones H3 (H3K9ac) are lower in nodules compared to roots."
] | 10.1038/s41477-018-0286-7 | Model Organisms | ENVIRONMENT | 10.1038/s41477-018-0286-7 | 2,018 | 231 | 0 | Nature Plants | true |
What is the role of GOLVEN/Root Meristem Growth Factor peptides in modulating root architecture in Arabidopsis and in legumes? What downstream transcription factor family is involved in this process? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"In Arabidopsis, GOLVEN peptides are involved in root cap maintenance, lateral root branching, root hair elongation, the root gravitropic response and lateral organ spacing. In legumes, GOLVEN peptides can alter the number of cysts and their positioning on the root and decrease the zone of over which cysts form. The MYB family of transcription factors act as key markers of GOLVEN signaling in plants mediating changes in root architecture upon GOLVEN signal perception.",
"In Arabidopsis, GOLVEN peptides are involved in root apical meristem maintenance, lateral root initiation and emergence, root hair elongation, the root gravitropic response and lateral organ spacing. In legumes, GOLVEN peptides can alter the number of nodules and their positioning on the root and decrease the zone of over which nodules form. The PLETHORA family of transcription factors act as key markers of GOLVEN signaling in plants mediating changes in root architecture upon GOLVEN signal perception.",
"In Arabidopsis, GOLVEN peptides are involved in root cap maintenance, lateral root branching, root hair curling, the root gravitropic response and lateral organ shape. In legumes, GOLVEN peptides enhance the number of nodules and their positioning on the root and decrease the infection zone over which microcolonies form. The WRKY family of transcription factors act as key markers of GOLVEN signaling in plants mediating changes in root architecture upon GOLVEN signal perception."
] | https://doi.org/10.1111/tpj.16626 | Non-specific | GROWTH AND DEVELOPMENT | 10.1111/tpj.16626 | 2,024 | 9 | 1 | The Plant Journal | true |
What is the mechanism of strigolactone perception by the a/b hydrolase DWARF14? | HORMONES | [
"non-specific"
] | [
"The intact Strigolactone molecule binds to the preformed binding pocket of the dual-functional receptor/hydrolase DWARF14. Next, the F-box protein D53 binds to the strigolactone-DWARF14 complex. Binding of the transcriptional repressor D3 changes the DWARF14 to its catalytically active state and DWARF14 hydrolyzes the strigolactone molecule. This triggers degradation of the transcriptional activator D3 by the proteasome thereby repressing the strigolactone signaling response. DWARF14 is degraded and D53 recycled. ",
"The intact Strigolactone molecule binds to the preformed binding pocket of the dual-functional receptor/hydrolase DWARF14. Next, the F-box protein D3 binds to the strigolactone-DWARF14 complex. Binding of the transcriptional repressor D53 changes the DWARF14 to its catalytically active state and DWARF14 hydrolyzes the strigolactone molecule. This triggers degradation of the transcriptional repressor D53 by the proteasome thereby initiating the strigolactone signaling response. DWARF14 is degraded and D3 recycled. ",
"The hydrolyzed Strigolactone molecule binds to the preformed binding pocket of the dual-functional receptor/hydrolase DWARF14. Next, the F-box protein D3 is degraded by the strigolactone-DWARF14 complex. Binding of the transcriptional repressor D53 changes the DWARF14 to its catalytically inactive state and DWARF14 cannot hydrolyze the strigolactone molecule. This triggers degradation of the transcriptional repressor D53 by the proteasome thereby initiating the strigolactone signaling response. DWARF14 and D3 are both recycled subsequently. "
] | https://doi.org/10.1016/j.tplants.2019.12.009 | Non-specific | HORMONES | 10.1016/j.tplants.2019.12.009 | 2,020 | 116 | 1 | Trends in Plant Science | true |
What are NIN Like Proteins (NLPs) and what roles do they play in Nitrogen acquisition in both legumes such as Medicago and non-legumes such as Arabidopsis? | ENVIRONMENT - NUTRIENTS | [
"non-specific"
] | [
"NIN Like proteins are a group of transcription factors with an SET domain named after the founding member NIN (NODULE INITIATION). NLPs are involved in maintaining Nitrogen homeostasis in both legumes and non-legumes. In legumes, under high soil Nitrogen, NIN acts as a master regulator inhibiting both, nodule organogenesis and rhizobial infection processes ensuring the plant receives only sufficient Nitrogen. In the non-legume Arabidopsis, NLPs are responsive to nitrate and can activate transcription of several genes in N-uptake such as NRT1.1, signaling as well as Nitrogen-assimilation genes such as NITRATE REDUCTASEs to regulate their activity. These early events ultimately lead to physiological changes in root architecture in response to changes in nitrogen availability such as altering lateral root length or adventitious root number, and formation of nitrogen fixing nodules in legumes.",
"NIN Like proteins are a group of transcription factors with an RWP-RK domain named after the founding member NIN (NODULE INCEPTION). NLPs are involved in maintaining Nitrogen homeostasis in both legumes and non-legumes. In legumes, under low soil Nitrogen, NIN acts as a master regulator coordinating both, nodule organogenesis and rhizobial infection processes ensuring the plant receives sufficient Nitrogen. In the non-legume Arabidopsis, NLPs are responsive to nitrate and can activate transcription of several genes in N-uptake such as NRT1.1, signaling as well as Nitrogen-assimilation genes such as NITRATE REDUCTASEs to regulate their activity. These early events ultimately lead to physiological changes in root architecture in response to changes in nitrogen availability such as altering primary root length or lateral root number, and formation of nitrogen fixing nodules in legumes.",
"NIN Like proteins are a group of transcription factors with an LRR-RLK domain named after the founding member NIN (NODULE INCEPTION). NLPs are involved in maintaining Nitrogen homeostasis in both legumes and non-legumes. In legumes, under low soil phosphorus, NIN acts as a master regulator coordinating both, nodule organogenesis and rhizobial infection processes ensuring the plant receives sufficient Nitrogen. In the non-legume Lotus japonicus, NLPs are responsive to nitrate and can activate transcription of several genes in N-uptake such as NRT12.1, signaling as well as Phosphorus-assimilation genes such as NITRATE REDUCTASEs to regulate their activity. These early events ultimately lead to physiological changes in root architecture in response to changes in phosphorus availability such as altering primary root length or lateral root number, and formation of nitrogen fixing nodules in legumes."
] | https://doi.org/10.1038/ncomms2621 | Non-specific | ENVIRONMENT | 10.1038/ncomms2621 | 2,013 | 334 | 1 | Nature Communications | true |
What three characteristics are used to classify an open reading frame as that of a small signaling peptide? | GENOME AND GENOMICS | [
"non-specific"
] | [
"The polypeptide length should be less than 250 amino acids with no transmembrane domains and the presence of an N-terminal signal peptide directing it to the secretory pathway.",
"The polypeptide length should be more than 250 amino acids with no transmembrane domains and the presence of a C-terminal signal peptide directing it to the secretory pathway.",
"The polypeptide length should be less than 250 amino acids with multiple transmembrane domains and the presence of an N-terminal signal peptide directing it to the vacuole. "
] | https://doi.org/10.1104/pp.17.01096 | Non-specific | GENOME AND GENOMICS | 10.1104/pp.17.01096 | 2,017 | 102 | 0 | Plant Physiology | true |
What are microbial plant peptide mimics? Explains the in planta mechanism of action of CLE peptide secreting nematodes on soybean roots. | ENVIRONMENT - BIOTIC STRESS | [
"non-specific"
] | [
"Many plant associated pathogens have evolved to encode peptides within their genome which are identical in structure to host plant peptides. These peptides confer evolutionary advantage to the pathogen by increasing their virulence. These microbially encoded peptides are called peptide mimics as they are recognized by plant meristems which activates the same downstream pathways as that of the plant signaling peptide. For example, the pathogenic bacteria Agrobacterium rhizogenes encodes CLE peptide mimics that repress cell division at nematode feeding sites on the vasculature. The female larvae attached to these feeding sites derive sufficient nutrients from the plants to complete one reproductive cycle. These cyst-nematodes therefore repress the plant growth processes to improve their chances of survival. ",
"Many plant associated pathogens have evolved to encode peptides within their genome which are identical in sequence to host plant peptides. These peptides confer evolutionary advantage to the pathogen by increasing their virulence. These microbially encoded peptides are called peptide mimics as they are recognized by plant receptors which activates the same downstream pathways as that of the plant signaling peptide. For example, the cyst knot nematode Heterodera glycines encodes CLE peptide mimics that activate uncontrolled cell division or ‘cysts’ at nematode feeding sites called syncytia. The female larvae attached to these feeding sites derive sufficient nutrients from the plants to complete one reproductive cycle. These cyst-nematodes therefore exploit the plant machinery to derive nutrition and improve their chances of survival. ",
"Many plant associated pathogens have evolved to encode peptides within their genome which are identical in sequence to host plant peptides. These peptides confer evolutionary advantage to the pathogen by increasing their virulence. These microbially encoded peptides are called peptide mimics as they are recognized by plant receptors which activates the same downstream pathways as that of the plant signaling peptide. For example, the root knot nematode Meloidogyne incognita encodes CLE peptide mimics that activate cell division at nematode feeding sites called syncytia. The male larvae attached to these feeding sites derive sufficient nitrogen from the plants to complete one reproductive cycle. These root knot nematodes therefore exploit the plant machinery to improve their chances of survival. "
] | DOI: 10.1016/j.tplants.2022.02.002 | Non-specific | ENVIRONMENT | 10.1016/j.tplants.2022.02.002 | 2,022 | 34 | 1 | Trends in Plant Science | true |
What is the role of the sulfotransferase ST2a in the regulation of plant defense under conditions of competition for light (low red:far-red ratios)? | HORMONES | [
"non-specific"
] | [
"The sulfotransferase ST2a catalyzes the transformation of OH-JA into the inactive metabolite HSO4-JA. Under conditions of low red:far-red ratios, which activate phytochrome B, the transcription of the ST2a gene is up-regulated by the high levels of Pfr, and the sulfotransferase acts to reduce the pool of precursors of active forms of jasmonates. Therefore, ST2a represents a direct molecular link between photoreceptors and jasmonate signaling in plants.",
"The sulfotransferase ST2a catalyzes the transformation of inactive OH-JA into the active metabolite HSO4-JA. Under conditions of low red:far-red ratios, which inactivate phytochrome B, the transcription of the ST2a gene is down-regulated, leading to a reduction in the pool of active forms of jasmonates. Therefore, ST2a represents a direct molecular link between photoreceptors and jasmonate signaling in plants.",
"The sulfotransferase ST2a catalyzes the transformation of OH-JA into the inactive metabolite HSO4-JA. Under conditions of low red:far-red ratios, which inactivate phytochrome B, the transcription of the ST2a gene is up-regulated and the sulfotransferase ST2a acts to reduce the pool of precursors of active forms of jasmonates. Therefore, ST2a represents a direct molecular link between photoreceptors and jasmonate signaling in plants."
] | 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 |
How are the transcription factors of the PIF family involved in the regulation of jasmonate responses? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"The PIFs are growth-promoting transcription factors whose abundance and/or activity increase under conditions of low red:far-red light ratios, which are typical of dense plant canopies. They bind to the promoter region of ST2a and activate its transcription. ST2a is required for the biosynthesis of gibberellins, which antagonize jasmonate responses. Therefore, under conditions of leaf shading or in the proximity of plant competitors, the increased biosynthesis of gibberellins facilitates growth (shade avoidance) and reduces the expression of jasmonate-dependent plant defenses.",
"The PIFs are growth-promoting transcription factors whose abundance and/or activity increase under conditions of low red:far-red light ratios, which are typical of dense plant canopies. They bind to the promoter region of ST2a and repress its transcription. ST2a is required for the biosynthesis of bioactive jasmonate pools. Therefore, the repression of ST2a leads to low production of bioactive jasmonates, which facilitates growth (shade avoidance) and reduces the expression of plant defenses under conditions of leaf shading or in the proximity of plant competitors.",
"The PIFs are growth-promoting transcription factors whose abundance and/or activity increase under conditions of low red:far-red light ratios, which are typical of dense plant canopies. They bind to the promoter region of ST2a and activate its transcription. ST2a leads to the formation of inactive jasmonate pools, thereby facilitating growth (shade avoidance) and reducing the expression of plant defenses under conditions of leaf shading or the proximity of plant competitors."
] | https://doi.org/10.1038/s41477-020-0604-8 | Non-specific | GROWTH AND DEVELOPMENT | 10.1038/s41477-020-0604-8 | 2,020 | 109 | 2 | Nature Plants | true |
Why is the accumulation of chemical defenses often accompanied by reduced growth in plants attacked herbivores or pathogens? | ENVIRONMENT - BIOTIC STRESS | [
"non-specific"
] | [
"Plant defenses are costly, in terms of the resources (carbon; nutrients) that are required for their biosynthesis. Therefore, when the jasmonates activate the biosynthesis of chemical defenses, the increased investment of carbon and nutrients in the formation of defense compounds inhibits plant growth simply as a consequence of the reduction in the amount of resources available to support rapid cell division and expansion.",
"Herbivores and pathogens may reduce the amount of leaf tissue and therefore photosynthetic activity. Therefore, when the plant is under attack (and activates the biosynthesis of chemical defenses), growth is reduced simply as a consequence of the reduction in the amount photosynthetic area caused by the attackers. This results in a reduction in the pool of photo-assimilates available to support rapid cell division and expansion, which explains the negative correlation between growth and chemical defense.",
"A high rate of plant growth may be maladaptive when the plant is under attack by herbivores or pathogens, because it would expose new tissue to the consumer organisms. Therefore, growth inhibition is often an adaptive response to tissue damage, which is accompanied by the increased accumulation of chemical defenses, with both responses being triggered and orchestrated by the jasmonates."
] | https://doi.org/10.1093/jxb/erz237 | Non-specific | ENVIRONMENT | 10.1093/jxb/erz237 | 2,019 | 76 | 2 | Journal of Experimental Botany | true |
How does UV-B radiation increase Arabidopsis immunity against certain fungal pathogens? | ENVIRONMENT - BIOTIC STRESS | [
"Arabidopsis thaliana"
] | [
"UV-B radiation, acting through the photoreceptor UVR8 promotes the biosynthesis of phenolic sunscreens, including flavonoids and sinapates in Arabidopsis. In addition to their photoprotective role, genetic evidence suggests that the flavonoids also play a protective against fungal infection, presumably because they boost the activation of jasmonate-dependent defense responses, which include the biosynthesis of antimicrobial compounds.",
"UV-B radiation, acting through the photoreceptor UVR8 promotes the biosynthesis of phenolic sunscreens, including flavonoids and sinapates in Arabidopsis. In addition to their photoprotective role, genetic evidence suggests that the sinapates also play a protective against fungal infection, presumably because they serve as precursors for the synthesis of syringyl-type (‘defense’) lignin, which is involved in cell wall fortification and could prevent penetration of fungal hyphae into plant cells.",
"UV-B radiation, acting through the photoreceptor UVR8 promotes the biosynthesis of glucosinolates and camalexin in Arabidopsis. Genetic evidence indicates that mutants impaired in the production of the bioactive hydrolysis products of indolic glucosinolates or in camalexin biosynthesis do not respond to UV-B radiation with increased resistance to the fungal pathogen Botrytis cinerea, which is consistent with the postulated role of these compounds in UVR-8-induced defense."
] | https://doi.org/10.1093/mp/sss025 | Model Organisms | ENVIRONMENT | 10.1093/mp/sss025 | 2,012 | 185 | 1 | Molecular Plant | true |
Which are the light signals and photoreceptors that trigger shade avoidance responses in dense plant canopies? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"non-specific"
] | [
"Depending on the density and structure of the canopy, shade avoidance responses are triggered by photoreceptors that sense the changes in the light environment that result from the selective absorption of sunlight by chlorophylls and other leaf pigments. One of these changes is the reduction in the ratio of red to far-red light (R:FR), which is perceived by the phytochromes (particularly phyC). Other changes that are perceived by the plant as signals of shading or proximity of other plants include the increased reflection of green light, which is perceived by the chlorophylls, and the attenuation of blue light, which is perceived by the carotene-containing photoreceptors.",
"Depending on the density and structure of the canopy, shade avoidance responses are triggered by specific photoreceptors that sense the changes in the light and thermal environment that result from the absorption of sunlight by plant structures. One of these changes is the reduction in temperature, which is perceived by the phytochromes (particularly phyB). Other changes that are perceived by the plant as signals of shading or proximity of other plants include the attenuation of blue light, which is also perceived by the phytochromes, and the attenuation of UV radiation, which is perceived by the combined action of cryptochromes and the photoreceptor UVR8.",
"Depending on the density and structure of the canopy, shade avoidance responses are triggered by specific photoreceptors that sense the changes in the light environment that result from the selective absorption of sunlight by chlorophylls and other leaf pigments. One of these changes is the reduction in the ratio of red to far-red light (R:FR), which is perceived by the phytochromes (particularly phyB). Other changes that are perceived by the plant as signals of shading or proximity of other plants include the attenuation of blue light, which is perceived by the cryptochromes and phototropins, and the attenuation of UV radiation, which is perceived by the photoreceptor UVR8."
] | https://doi.org/10.1016/j.tplants.2020.12.006 | Non-specific | ENVIRONMENT | 10.1016/j.tplants.2020.12.006 | 2,021 | 97 | 2 | Trends in Plant Science | true |
Oxygenic photosynthesis can be improved and optimized to address the current climate change scenario. Strategies based on synthetic biology approaches have been tested in crops and plant model systems, such as Arabidopsis, Nicotiana tabacum, and the moss Physcomitrella patens. Which of the following statements best reflects the current consensus? | PLANT BIOTECHNOLOGY | [
"non-specific"
] | [
"Research has not yet developed strategies to achieve maximum photosynthetic capacity in plants",
"Maximum photosynthetic efficiency has been achieved in most plant model systems but not in crops",
"Maximum photosynthetic efficiency has been achieved in most species under greenhouse conditions. However, plants growing in natural environments cannot reach maximum photosynthetic capacity"
] | DOI: 10.1104/pp.18.00360, 10.1016/j.molp.2022.08.005, 10.1093/jxb/eraa075 | Non-specific | PLANT BIOTECHNOLOGY | 10.1093/jxb/eraa075 | 2,020 | 38 | 0 | Journal of Experimental Botany | true |
NPQ can improve photosynthetic yield and biomass when plants face adverse conditions. What is the most the efficient way to regulate the qE component of NPQ to augment productivity? | ENVIRONMENT - LIGHT AND TEMPERATURE | [
"non-specific"
] | [
"Increasing relaxation rates of qE",
"Increasing the induction and relaxation rates of qE",
"Increasing the amplitude of qE"
] | DOI: 10.1126/science.aai8878 | Non-specific | ENVIRONMENT | 10.1126/science.aai8878 | 2,016 | 1,048 | 1 | Science | true |
What plant physiological aspects that can be improved by engineering RubisCo using synthetic biology? | PLANT BIOTECHNOLOGY | [
"non-specific"
] | [
"Photosynthetic capacity",
"Tolerance to drought ",
"Resistance to biotic stress "
] | DOI: 10.1104/pp.18.00360 | Non-specific | PLANT BIOTECHNOLOGY | 10.1104/pp.18.00360 | 2,018 | 43 | 0 | Plant Physiology | true |
Does carboxylation rate of RubisCo influence photosynthetic yield? | PLANT BIOTECHNOLOGY | [
"non-specific"
] | [
"In the absence of O2 ",
"The photosynthetic yield is unaffected by plant growing conditions ",
"In the presence of O2"
] | DOI: 10.1093/jxb/erz029 | Non-specific | PLANT BIOTECHNOLOGY | 10.1093/jxb/erz029 | 2,019 | 93 | 2 | Journal of Experimental Botany | true |
Several synthetic biology approaches aim to adapt carbon concentrating mechanisms (CCM) to C3 plants. What are key aspects for the success of this strategy? | PLANT BIOTECHNOLOGY | [
"non-specific"
] | [
"The silencing of the endogenous RubisCo enzyme ",
"The ectopic localization of inorganic carbon transporters to homogenize the levels of CO2 inside leaves",
"The co-localization of the carboxysomes with RubisCo "
] | DOI: 10.1016/j.xplc.2020.100032, 10.1093/jxb/erz029 | Non-specific | PLANT BIOTECHNOLOGY | 10.1093/jxb/erz029 | 2,019 | 93 | 2 | Journal of Experimental Botany | true |
What is the impact of synthetically inducing a burst in phytoene production, the first committed intermediate of the carotenoid pathway, on chloroplasts in leaves? | PLANT BIOTECHNOLOGY | [
"non-specific"
] | [
"Synthetically inducing a phytoene burst triggers artificial chloroplast-to-gerontoplast differentiation in leaves.",
"Synthetically inducing a phytoene burst promotes artificial chloroplast proliferation in leaves.",
"Synthetically inducing a phytoene burst triggers artificial chloroplast-to-chromoplast differentiation in leaves."
] | https://doi.org/10.1073/pnas.2004405117 | Non-specific | PLANT BIOTECHNOLOGY | 10.1073/pnas.2004405117 | 2,020 | 88 | 2 | Proceedings of the National Academy of Sciences | true |
Which isoprenoid pathway can be exploited to supply intermediates for engineering carotenoid biosynthesis in the plant cytosol (i.e., outside chloroplasts)? | PLANT BIOTECHNOLOGY | [
"non-specific"
] | [
"The pentose phosphate pathway (PPP) can be exploited to supply intermediates for engineering carotenoid biosynthesis in the plant cytosol. This pathway operates in the vacuole and provides PPP-derived precursors that can be converted into carotenoids, enabling targeted metabolic engineering efforts to boost carotenoid production in plants.",
"The mevalonic acid (MVA) pathway can be exploited to supply intermediates for engineering carotenoid biosynthesis in the plant cytosol. This pathway operates in the cytosol and provides MVA-derived precursors that can be converted into carotenoids, enabling targeted metabolic engineering efforts to boost carotenoid production in plants.",
"The methylerythritol 4-phosphate (MEP) pathway can be exploited to supply intermediates for engineering carotenoid biosynthesis in the plant cytosol. This pathway operates in the cytosol and provides MEP-derived precursors that can be converted into carotenoids, enabling targeted metabolic engineering efforts to boost carotenoid production in plants."
] | https://doi.org/10.1111/pbi.13526 | Non-specific | PLANT BIOTECHNOLOGY | 10.1111/pbi.13526 | 2,021 | 31 | 1 | Plant Biotechnology Journal | true |
How can the methylerythritol 4-phosphate (MEP) pathway and the mevalonic acid (MVA) pathway be simultaneously exploited to engineer parallel carotenoid biosynthesis in the cytosol and plastids of plants? | PLANT BIOTECHNOLOGY | [
"non-specific"
] | [
"Both the cytosolic methylerythritol 4-phosphate (MEP) pathway and the plastidial mevalonic acid (MVA) pathway produce isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP), key isoprenoid precursors that can be harnessed to engineer parallel carotenoid biosynthesis in the cytosol and plastids of plants. Leveraging these identical pathways enables enhanced carotenoid production in both cellular compartments.",
"Both the cytosolic mevalonic acid (MVA) pathway and the plastidial methylerythritol 4-phosphate (MEP) pathway produce isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP), key isoprenoid precursors that can be harnessed to engineer parallel carotenoid biosynthesis in the cytosol and plastids of plants. Leveraging these distinct pathways enables enhanced carotenoid production in both cellular compartments.",
"Both the cytosolic methylerythritol 4-phosphate (MEP) pathway and the plastidial mevalonic acid (MVA) pathway produce isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP), key flavonoid precursors that can be harnessed to engineer parallel carotenoid biosynthesis in the cytosol and plastids of plants. Leveraging these distinct pathways enables enhanced carotenoid production in both cellular compartments."
] | https://doi.org/10.1111/tpj.16964 | Non-specific | PLANT BIOTECHNOLOGY | 10.1111/tpj.16964 | 2,024 | 0 | 1 | The Plant Journal | true |
How could relocating genes between the nuclear genome and the plastome improve plant disease resistance? | PLANT BIOTECHNOLOGY | [
"non-specific"
] | [
"Chloroplasts rely on thousands of proteins encoded by nucleus-encoded chloroplast genes (NECGs). To promote infection, pathogens deploy protein and small RNA (sRNA) effectors that enter plant cells and manipulate their physiology. Various plant pathogens—including viruses, bacteria, fungi, and oomycetes—have convergently evolved effectors to specifically target NECGs or their mRNA and protein products. Relocating NECGs targeted by pathogen effectors to the plastome could render these infection strategies more effective.",
"Chloroplasts rely on thousands of proteins encoded by plastome-encoded chloroplast genes (PECGs). To promote infection, pathogens deploy protein and small RNA (sRNA) effectors that enter plant cells and manipulate their physiology. Various plant pathogens—including viruses, bacteria, fungi, and oomycetes—have convergently evolved effectors to specifically target PECGs or their mRNA and protein products. Relocating PECGs targeted by pathogen effectors to the nuclear genome could render these infection strategies ineffective.",
"Chloroplasts rely on thousands of proteins encoded by nucleus-encoded chloroplast genes (NECGs). To promote infection, pathogens deploy protein and small RNA (sRNA) effectors that enter plant cells and manipulate their physiology. Various plant pathogens—including viruses, bacteria, fungi, and oomycetes—have convergently evolved effectors to specifically target NECGs or their mRNA and protein products. Relocating NECGs targeted by pathogen effectors to the plastome could render these infection strategies ineffective."
] | https://doi.org/10.1038/s41467-021-26975-5 | Non-specific | PLANT BIOTECHNOLOGY | 10.1038/s41467-021-26975-5 | 2,021 | 9 | 2 | Nature Communications | true |
What is the potential of plant synthetic biology to support long-term human endeavors in space? | PLANT BIOTECHNOLOGY | [
"non-specific"
] | [
"Long-duration human space endeavors will require significant self-sufficiency. Plant synthetic biology could play a pivotal role in enabling the sustainable production of food, materials, chemicals, and medicines to support human travel and habitation in space.",
"Long-duration human space endeavors will require significant self-sufficiency. Plant synthetic biology could play a pivotal role in enabling the unsustainable production of food, materials, chemicals, and medicines to support human travel and habitation in space.",
"Long-duration human space endeavors will require little self-sufficiency. Plant synthetic biology would play a minimal role in supporting human travel and habitation in space."
] | https://doi.org/10.3390/genes9070348 | Non-specific | PLANT BIOTECHNOLOGY | 10.3390/genes9070348 | 2,018 | 36 | 0 | Genes | true |
What is symbiosis and how symbiosis between leguminous plants and rhizobia leads to the formation of N2-fixing root nodules? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"Symbiosis is a mutual beneficial relationship between the nitrogen-fixing soil bacteria know as rhizobia and leguminous plants. Nitrogen is one of the major macro-nutrients required for the plant growth. Although atmosphere is predominately made up of nitrogen (79%), but this nitrogen is not available to plants, because most plants cannot directly utilize gaseous atmospheric nitrogen. Interestingly, a group of flowering plants also known as nitrogen fixing clade (NFC) have evolved an ability to form symbiotic relationship with nitrogen-fixing bacteria, which converts atmospheric nitrogen to biologically available form like ammonia (NH3). The rhizobia-legume interaction is a complex exchange of signals initiated by release of flavonoids by legumes, which are perceived by compatible rhizobia species. These bacteria secrete lipo-oligosaccharides (LCOs also known as Nod factors) and oligosaccharides and the perception of these Nod factors under low nitrogen conditions in the susceptible region of root initiates one programs which is bacterial infection at the epidermis and cell division at the cortex to develop nodules hosting rhizobial symbionts.",
"Symbiosis is a mutual beneficial relationship between all soil bacteria know and leguminous plants. Nitrogen is one of the major macro-nutrients required for the plant growth. Although atmosphere is predominately made up of nitrogen (79%), but this nitrogen is available to plants, and most plants can directly utilize gaseous atmospheric nitrogen. Interestingly, a group of flowering plants also known as nitrogen fixing clade (NFC) have evolved an ability to form symbiotic relationship with all bacteria, which converts atmospheric nitrogen to biologically available form like ammonia (NH3). The rhizobia-legume interaction is a complex exchange of signals initiated by release of flavonoids by legumes, which are perceived by compatible rhizobia species. These bacteria secrete lipo-oligosaccharides (LCOs also known as Nod factors) and the perception of these Nod factors under low nitrogen conditions in the susceptible region of root initiates two interconnected programs concurrently: bacterial infection at the epidermis and cell division at the cortex to develop nodules hosting rhizobial symbionts. Once released from the infection threads within the root nodules of legumes, these bacteria differentiate into bacteroids and helps to convert gaseous nitrogen to ammonia in the low oxygen environment inside the mature nodules. ",
"Symbiosis is a mutual beneficial relationship between the nitrogen-fixing soil bacteria know as rhizobia and leguminous plants. Nitrogen is one of the major macro-nutrients required for the plant growth. Although atmosphere is predominately made up of nitrogen (79%), but this nitrogen is not available to plants, because most plants cannot directly utilize gaseous atmospheric nitrogen. Interestingly, a group of flowering plants also known as nitrogen fixing clade (NFC) have evolved an ability to form symbiotic relationship with nitrogen-fixing bacteria, which converts atmospheric nitrogen to biologically available form like ammonia (NH3). The rhizobia-legume interaction is a complex exchange of signals initiated by release of flavonoids by legumes, which are perceived by compatible rhizobia species. These bacteria secrete lipo-oligosaccharides (LCOs also known as Nod factors) and the perception of these Nod factors under low nitrogen conditions in the susceptible region of root initiates two interconnected programs concurrently: bacterial infection at the epidermis and cell division at the cortex to develop nodules hosting rhizobial symbionts. Once released from the infection threads within the root nodules of legumes, these bacteria differentiate into bacteroids and help to convert gaseous nitrogen to ammonia in the low oxygen environment inside the mature nodules. "
] | https://doi.org/10.1016/j.pbi.2023.102478 | Non-specific | GROWTH AND DEVELOPMENT | 10.1016/j.pbi.2023.102478 | 2,023 | 12 | 2 | Current Opinion in Plant Biology | true |
What is cell layer specific role of gibberellins in root development and nodulation? | GROWTH AND DEVELOPMENT | [
"non-specific"
] | [
"Gibberellins (GA), have no role in cell layers during nodule organogenesis and infection. GA produced in the endodermis reduces nodule organogenesis and lateral root formation and also suppresses rhizobial infection via direct action or with the help of a potential mobile signal which can move from endodermis to epidermis. On the other hand, GA in epidermis have very big influence on nodule and root development but suppresses infection. ",
"Gibberellins (GA) and Auxin, both plays an important dual and opposing role in cell layers during nodule organogenesis and infection. GA produced in the endodermis enhance nodule organogenesis and lateral root formation and also suppresses rhizobial infection via direct action or with the help of a potential mobile signal which can move from endodermis to epidermis. On the other hand, GA in epidermis have little influence on nodule and root development but suppresses infection.",
"Gibberellins (GA), plays an important dual and opposing role in cell layers during nodule organogenesis and infection. GA produced in the endodermis enhance nodule organogenesis and lateral root formation and also suppresses rhizobial infection via direct action or with the help of a potential mobile signal which can move from endodermis to epidermis. On the other hand, GA in epidermis have little influence on nodule and root development but suppresses infection. "
] | https://doi.org/10.1111/nph.19623 | Non-specific | GROWTH AND DEVELOPMENT | 10.1111/nph.19623 | 2,024 | 1 | 2 | New Phytologist | true |
What are small signaling peptides and which peptide is involved in altering root development and noduletaxis in Medicago truncatula? | CELL BIOLOGY AND CELL SIGNALING | [
"Medicago truncatula"
] | [
"Small signaling peptides (SSPs) are less than 200-250 amino acids in length and are generated from prepropeptides following multiple maturation steps. SSPs are classified into two main categories viz., cysteine-rich peptides (CRPs) and post-translationally modified peptides (PTMPs). The PTMPs are smaller in length (5-30amino acids) and are characterized by post-translation modifications like tyrosine sulphation, hydroxylation and glycosylation. These modifications in PTMPs have been reported to play an important role in their activity via increasing their stability and binding. CRPs are longer in length and recognized by at least four cysteine residues responsible for forming disulfide bridges important for stable secondary structures. GOLVEN10 peptide alters the positioning of first lateral root and also nodule on the primary root called as “noduletaxis”. This response of GOLVEN10 peptide has resulted in decreased length of the total lateral organ formation zone in Medicago truncatula roots. ",
"Small signaling peptides (SSPs) are less than 200-250 amino acids in length and are generated from prepropeptides following multiple maturation steps. SSPs are classified into two main categories viz., cysteine-rich peptides (CRPs) and post-translationally modified peptides (PTMPs). The PTMPs are smaller in length (5-30amino acids) and are characterized by post-translation modifications like tyrosine sulphation, hydroxylation and glycosylation. These modifications in PTMPs have been reported to play an important role in their activity via increasing their stability and binding. CRPs are longer in length and recognized by at least four cysteine residues responsible for forming disulfide bridges important for stable secondary structures. GOLVEN4 and 6 peptide alters the positioning of first lateral root and also nodule on the primary root called as “noduletaxis”. This response of GOLVEN4 and 6 peptide has resulted in decreased length of the total lateral organ formation zone in Medicago truncatula roots.",
"Small signaling peptides (SSPs) are more than 200-250 amino acids in length and are generated from prepropeptides following one maturation steps. SSPs are classified into two main categories viz., cysteine-rich peptides (CRPs) and post-translationally modified peptides (PTMPs). The PTMPs are smaller in length (5-30amino acids) and are characterized by post-translation modifications like tyrosine sulphation, hydroxylation and glycosylation. These modifications in PTMPs have been reported to play an important role in their activity via increasing their stability and binding. CRPs are smaller in length and recognized by at least four cysteine residues responsible for forming disulfide bridges important for stable secondary structures. GOLVEN10 peptide does not alters the positioning of first lateral root and also nodule on the primary root called as “noduletaxis”. This response of GOLVEN10 peptide has resulted in increased length of the total lateral organ formation zone in Medicago truncatula roots. "
] | https://doi.org/10.1111/tpj.16626 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1111/tpj.16626 | 2,024 | 9 | 0 | The Plant Journal | true |
Which previously unidentified CLE peptide is responsible for repressing phloem differentiation in Arabidopsis thaliana? | CELL BIOLOGY AND CELL SIGNALING | [
"Arabidopsis thaliana"
] | [
"The protophloem differentiation is controlled by complex genetic circuit involving, on one side, a number of regulators like DOF transcription factors, hormonal gradients and SMXL transcriptional repressors. Additionally, BREVIS RADIX (BRX) and OCTOPUS (OPS), two membrane localized proteins which act as positive regulators of protophloem development. While the other side have negative regulators like CLAVATA3/EMBRYO SURROUNDING REGION RELATED (CLE) peptides and their receptors BARELY ANY MERISTEM (BAM) receptor-like kinases. The brx and ops mutants has displayed a discontinuous protophloem (gap cells that fail to differentiate) which results in reduced phloem sap delivery to the root meristem and inhibited root growth. This discontinuous protophloem phenotypes can be rescued by mutation in BAM3, which encodes for LRR-RLK (leucine-rich repeat receptor kinase), a receptor of CLAVATA3/EMBRYO SURROUNDING REGION 45 (CLE45) peptide but is partially rescued when all three known phloem CLE genes (CLE25/26/45) are mutated together. Therefore \nanother crucial player in protophloem formation namely CLE33 closely related to CLE45 was identified and double mutant of cle33cle45 was reported to fully suppresses brx and ops protophloem phenotype.\n",
"The protophloem differentiation is controlled by complex genetic circuit involving, on one side, a number of regulators like DOF transcription factors, hormonal gradients and SMXL transcriptional repressors. Additionally, BREVIS RADIX (BRX) and OCTOPUS (OPS), two membrane localized proteins which act as positive regulators of protophloem development. While the other side have negative regulators like CLAVATA3/EMBRYO SURROUNDING REGION RELATED (CLE) peptides and their receptors BARELY ANY MERISTEM (BAM) receptor-like kinases. The brx and ops mutants has displayed a discontinuous protophloem (gap cells that fail to differentiate) which results in reduced phloem sap delivery to the root meristem and inhibited root growth. This discontinuous protophloem phenotypes can be rescued by mutation in BAM3, which encodes for LRR-RLK (leucine-rich repeat receptor kinase), a receptor of CLAVATA3/EMBRYO SURROUNDING REGION 45 (CLE45) peptide. Therefore, crucial player in protophloem formation namely CLE25/26/45 was identified and its double mutant was reported to fully suppresses brx and ops protophloem phenotype.",
"The protophloem differentiation is controlled by simple genetic circuit involving, on one side, a number of regulators like WRKY transcription factors, hormonal gradients and SMXL transcriptional repressors. Additionally, BREVIS RADIX (BRX) and OCTOPUS (OPS), two membrane localized proteins which act as positive regulators of protophloem development. While the other side have positive regulators like CLAVATA3/EMBRYO SURROUNDING REGION RELATED (CLE) peptides and their receptors BARELY ANY MERISTEM (BAM) receptor-like kinases. The brx and ops mutants has displayed a discontinuous protophloem (gap cells that fail to differentiate) which results in increased phloem sap delivery to the root meristem and inhibited root growth. This discontinuous protophloem phenotypes can be rescued by mutation in BAM3, which encodes for LRR-RLK (leucine-rich repeat receptor kinase), a receptor of CLAVATA3/EMBRYO SURROUNDING REGION 45 (CLE45) peptide but is partially rescued when all three known phloem CEP genes (CLE25/26/45) are mutated together. Therefore \nanother crucial player in protophloem formation namely CLE33 closely related to CLE45 was identified and double mutant of cle33cle45 was reported to fully suppresses brx and ops protophloem phenotype.\n"
] | https://doi.org/10.1038/s42003-023-04972-2 | Model Organisms | CELL BIOLOGY AND CELL SIGNALING | 10.1038/s42003-023-04972-2 | 2,023 | 20 | 0 | Communications Biology | true |
How small signaling peptide CEP1 and NIN-like protein NLP1, regulate NRT2.1 expression to control root nodule formation under different nitrogen conditions? | CELL BIOLOGY AND CELL SIGNALING | [
"non-specific"
] | [
"Legumes takes nitrogen (N) from soil with endosymbiont association with all bacteria via forming N2 fixing nodules. The establishment and maintenance of these nodules is easy for the host legumes, therefore, when N is plentiful, plants increases symbiosis and increases it when N is sparse. It has been proposed that under low nitrogen conditions, MtCEP1 expression increases which systematically upregulates the expression of MtNRT2.1 in a MtCRA2-dependent manner. Simultaneously, under low nitrogen conditions, restricted nuclear localization of MtNLP1 activates low level of MtNRT2.1 expression, consequently boosting nitrate uptake to improve leaf size and plant growth. However, under high nitrogen conditions, increased migration of MtNLP1 to the chloroplast results in activation of CLE35 expression which negatively regulates nodulation via SUNN in shoot. Moreover, MtNLP1 also activates expression of MtNRT2.1 to enhance nitrate uptake to further inhibit nodulation. ",
"Legumes takes nitrogen (N) from soil with endosymbiont association with rhizobia via forming N2 fixing nodules. The establishment and maintenance of these nodules is expensive for the host legumes, therefore, when N is plentiful, plants suppress symbiosis and increases it when N is sparse. It has been proposed that under low nitrogen conditions, MtCEP1 expression increases which systematically upregulates the expression of MtNRT2.1 in a MtCRA2-dependent manner. Simultaneously, under low nitrogen conditions, restricted nuclear localization of MtNLP1 activates low level of MtNRT2.1 expression, consequently boosting nitrate uptake to improve nodulation and plant growth. However, under high nitrogen conditions, increased migration of MtNLP1 to the nucleus results in activation of CLE35 expression which negatively regulates nodulation via SUNN in shoot. Moreover, MtNLP1 also activates expression of MtNRT2.1 to enhance nitrate uptake to further inhibit nodulation. ",
"Legumes takes nitrogen (N) from soil with endosymbiont association with rhizobia via forming N2 fixing nodules. The establishment and maintenance of these nodules is expensive for the host legumes, therefore, when N is plentiful, plants suppress symbiosis and increases it when N is sparse. It has been proposed that under low nitrogen conditions, MtCEP1.1 expression increases which systematically upregulates the expression of MtNRT2.1 in a MtCRA2-dependent manner. Simultaneously, under low nitrogen conditions, restricted nuclear localization of MtNLP2 activates low level of MtNRT3.1 expression, consequently boosting nitrate uptake to improve nodulation and plant growth. However, under high nitrogen conditions, increased migration of MtNLP1 to the nucleus results in activation of CLE33 expression which negatively regulates nodulation via SUNN in shoot. Moreover, MtNLP1 also activates expression of MtNRT2.1 to enhance nitrate uptake to further inhibit nodulation. "
] | 10.1093/plcell/koac340 | Non-specific | CELL BIOLOGY AND CELL SIGNALING | 10.1093/plcell/koac340 | 2,022 | 33 | 1 | The Plant Cell | true |
What are the main differences in the secondary structural pattern from Arabidopsis thaliana miR171a compared to miR171c precursors? | GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE | [
"Arabidopsis thaliana"
] | [
"miR171c precursor has a conserved dsRNA region below the miRNA/miRNA* duplex, in contrast, the miR171a, has a conserved region above the miRNA/miRNA* duplex, which determines a dsRNA segment.",
"miR171a precursor has a conserved dsRNA region below the miRNA/miRNA* duplex, in contrast, the miR171c, has a conserved region above the miRNA/miRNA* duplex, which determines a dsRNA segment.",
"Both miR171a and miR171c precursors have a conserved dsRNA region below the miRNA/miRNA* duplex"
] | 10.1105/tpc.17.00272 | Model Organisms | GENE REGULATION | 10.1105/tpc.17.00272 | 2,017 | 59 | 1 | The Plant Cell | true |
What happens to the MIR157c precursor in Arabidopsis thaliana when you replace the terminal branched loop with a small loop of 4 nt? | GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE | [
"Arabidopsis thaliana"
] | [
"MIR157c with the small loop will be processed much more efficiently and will cause a significant decrease in leaf number upon flowering compared to the wild-type branched loop version",
"MIR157c with the small loop will be processed much less efficiently and will cause a significant decrease in leaf number upon flowering compared to the wild-type branched loop version",
"MIR157c with the small loop will be processed much more efficiently and will cause a significant increase in leaf number upon flowering compared to the wild-type branched loop version"
] | 10.1093/nar/gky853 | Model Organisms | GENE REGULATION | 10.1093/nar/gky853 | 2,018 | 15 | 2 | Nucleic Acids Research | true |
What is the impact of the C-C mismatches within miRNA/miRNA* duplexes on miRNA biogenesis in Arabidopsis thaliana? | GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE | [
"Arabidopsis thaliana"
] | [
"C-C mismatches consistently impair miRNA processing efficiency, as they disrupt DCL1-mediated cleavage, leading to reduced mature miRNA levels.",
"C-C mismatches enhance miRNA biogenesis by increasing duplex flexibility, which facilitates DCL1 cleavage.",
"C-C mismatches have no significant effect on miRNA biogenesis, as DCL1 processes precursors independently of specific mismatch identities."
] | 10.1038/s41467-020-19129-6 | Model Organisms | GENE REGULATION | 10.1038/s41467-020-19129-6 | 2,020 | 27 | 0 | Nature Communications | true |
What structural diversity is exhibited by the COOLAIR lncRNA isoforms in Arabidopsis thaliana under warm conditions? | GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis thaliana, the major distally polyadenylated COOLAIR isoform exhibits three primary structural conformations under warm conditions. These conformations involve structural changes predominantly in the hyper-variable H4-H6 region, which is complementary to the FLC transcription start site.",
"In Arabidopsis thaliana, the major distally polyadenylated COOLAIR isoform exhibits three primary structural conformations under warm conditions. These conformations involve changes primarily in the conserved 5′ region of the transcript.",
"In Arabidopsis thaliana, the major distally polyadenylated COOLAIR isoform exhibits two stable conformations under warm conditions. These conformations involve structural changes predominantly in the H5 region, which is complementary to the FLC transcription start site."
] | 10.1038/s41586-022-05135-9 | Model Organisms | GENE REGULATION | 10.1038/s41586-022-05135-9 | 2,022 | 79 | 0 | Nature | true |
Which are the most structurally stable regions of MIR319a sequential precursors in Arabidopsis thaliana? | GENE REGULATION - EPITRANSCRIPTOMICS AND RNA STRUCTURE | [
"Arabidopsis thaliana"
] | [
"DCL1 processing of sequential MIRNAs releases the miRNA/miRNA* in the last two cuts. The other small RNA duplexes produced are miRNA.1/miRNA.1* and miRNA.2/miRNA.2* according to their relative distance to the miRNA/miRNA*. The miRNA.1/miRNA.1* presents a better pairing overall and the most stable regions of miRNA/miRNA* and miRNA.2/miRNA.2* are located at the ends of the duplexes. Consequently, the structural features of these long sequential precursors rely on stable small RNA duplexes, with no mismatches that generate suitable DCL1 cleavage sites. ",
"DCL1 processing of sequential MIRNAs releases the miRNA/miRNA* in the last two cuts. The other small RNA duplexes produced are miRNA.1/miRNA.1* and miRNA.2/miRNA.2* according to their relative distance to the miRNA/miRNA*. The miRNA/miRNA* presents a better pairing overall and the most stable regions of miRNA.1/miRNA.1* and miRNA.2/miRNA.2* are located at the ends of the duplexes. Consequently, the structural features of these long sequential precursors rely on unstable small RNA duplexes, with internal mismatches and paired ends that generate suitable DCL1 cleavage sites. ",
"DCL1 processing of sequential MIRNAs releases the miRNA/miRNA* in the last two cuts. The other small RNA duplexes produced are miRNA.1/miRNA.1* and miRNA.2/miRNA.2* according to their relative distance to the miRNA/miRNA*. The miRNA/miRNA* presents a worse pairing overall and the most stable regions of miRNA.1/miRNA.1* and miRNA.2/miRNA.2* are located at the beginning of the duplexes. Consequently, the structural features of these long sequential precursors rely on stable small RNA duplexes, with no mismatches that generate suitable DCL1 cleavage sites. "
] | 10.1093/nar/gkae458 | Model Organisms | GENE REGULATION | 10.1093/nar/gkae458 | 2,024 | 4 | 1 | Nucleic Acids Research | true |
What is the primary function of gene looping, short range chromatin loops encompasing single genes, in plants? | GENE REGULATION - PTGS | [
"non-specific"
] | [
"Gene-looping promotes the deletion of introns from the gene.",
"Gene-looping prevents transcription by promoting a lineal stage of the chromatin",
"Gene-looping enhances gene transcription by allowing more efficient recycling of RNA polymerase II."
] | 10.1111/nph.16632 | Non-specific | GENE REGULATION | 10.1111/nph.16632 | 2,020 | 20 | 2 | New Phytologist | true |
How can intragenic chromatin loops regulate gene expression in plants? | GENE REGULATION - PTGS | [
"non-specific"
] | [
"Intragenic chromatin loops exclusively enhance transcription by stabilizing the promoter.",
"Intragenic chromatin loops silence genes by inducing the compactation of the nucleosomes.",
"Intragenic chromatin loops can repress transcription by blocking RNA polymerase II elongation, change splicing or transcription termination."
] | 10.1111/nph.16632 | Non-specific | GENE REGULATION | 10.1111/nph.16632 | 2,020 | 20 | 2 | New Phytologist | true |
What is the primary outcome, regarding chromatin organization, of the insertion of an inverted repeat (IR) near a gene in Plants? | GENE REGULATION - PTGS | [
"Arabidopsis thaliana"
] | [
"The IR has negligible effects on the surrounding genomic neighborhood.",
"The IR exclusively enhances transcription by acting as a distal enhancer.",
"IRs locates near genes often produce small RNAs that trigger DNA methylation changing the chromatin organization and the expresion of the neighbor genes."
] | 10.1016/j.celrep.2023.112029 | Model Organisms | GENE REGULATION | 10.1016/j.celrep.2023.112029 | 2,023 | 12 | 2 | Cell Reports | true |
How do IRs contribute to changes in gene expression through their impact on chromatin topology? | GENE REGULATION - PTGS | [
"non-specific"
] | [
"IRs uniformly repress gene expression by silencing all nearby genes.",
"IRs act as anchor points for short-range chromatin loops, which can either enhance or repress gene expression depending on the loop structure and gene region included.",
"The insertion of a TE-derived IR near genes has no evolutionary or adaptive implications for the plant."
] | 10.1016/j.celrep.2023.112029 | Non-specific | GENE REGULATION | 10.1016/j.celrep.2023.112029 | 2,023 | 12 | 1 | Cell Reports | true |
How does the Ea-IR inverted repeat regulate EFR expression in Arabidopsis thaliana? | GENE REGULATION - PTGS | [
"Arabidopsis thaliana"
] | [
"Once the DNA sequence encoding Ea-IR becomes methylated, a repressive chromatin loop is irreversibly formed.",
"The Ea-IR forms a repressive chromatin loop that suppresses EFR expression in the absence of pathogen infection, thereby preventing excessive autoimmune responses. Additionally, this loop prevents RNA Polymerase II from readthrough past the terminator of the adjacent XI-k gene.",
"The Ea-IR is concerved across plant species not representing an adaptative TE insertion."
] | 10.1038/S41594-024-01440-1 | Model Organisms | GENE REGULATION | 10.1038/S41594-024-01440-1 | 2,024 | 2 | 1 | Nature Structural & Molecular Biology | true |
In sunflower Sclerotinia head rot disease, which genes are known to be upregulated within the first week of infection in the plant's defense response? | GENE REGULATION - TRANSCRIPTION | [
"Helianthus annuus"
] | [
"Late gene expression analysis in sunflower infected with Sclerotinia head rot revealed a complex network of defense responses. All genes involved include those related to redox homeostasis (e.g., glutathione S-transferase DHAR3), photosynthesis (e.g., a chloroplastic-like gene), pathogen recognition (e.g., a leucine-rich repeat receptor-like serine/threonine kinase), and general defense responses (e.g., pathogenesis-related 1). There seems to be a lack of non-coding RNA players in the response.",
"Early gene expression analysis in sunflower infected with Sclerotinia head rot revealed a complex network of defense responses. Key genes involved include those related to redox homeostasis (e.g., glutathione S-transferase DHAR3), photosynthesis (e.g., a chloroplastic-like gene), pathogen recognition (e.g., a leucine-rich repeat receptor-like serine/threonine kinase), and general defense responses (e.g., pathogenesis-related 1). Notably, the upregulation of IBH1, a transcription factor previously implicated in growth-immunity balance in Arabidopsis thaliana, suggests a coordinated regulation of plant development and defense. Additionally, the presence of a non-coding RNA highlights the potential role of novel regulatory mechanisms in this interaction.",
"Late gene expression analysis in sunflower infected with Sclerotinia head rot revealed a complex network of defense responses. Key genes involved include those related to auxin homeostasis, photosynthesis (e.g., a chloroplastic-like gene), pathogen recognition (e.g., a leucine-rich repeat receptor-like serine/threonine kinase), and general defense responses (e.g., pathogenesis-related 1). Notably, the downregulation of IBH1, a transcription factor previously implicated in growth-immunity balance in Arabidopsis thaliana, "
] | https://doi.org/10.1038/s41598-020-70315-4 | Other Herbaceous Crops, Spices, Fibers & Weeds | GENE REGULATION | 10.1038/s41598-020-70315-4 | 2,020 | 21 | 1 | Scientific Reports | true |
……What is the current understanding of the genetic architecture of Sclerotinia head rot resistance in sunflower, and how has modern breeding influenced its evolution? | GENOME AND GENOMICS | [
"Helianthus annuus"
] | [
"The observed loci count in clusters across the sunflower genome suggest that Sclerotinia head rot resistance has been introgresed in recent years. This pattern indicates large introgression events by transgenics technology through modern breeding programs",
"The observed distribution of QTLs across the sunflower genome and the clustered DEGs suggest that Sclerotinia head rot resistance has been introgresed recently. This pattern indicates large introgression events by introduction of large genomic regions through modern breeding programs. ",
"The observed sparse distribution of QTLs across the sunflower genome and the absence of clustered DEGs suggest that Sclerotinia head rot resistance has evolved through a gradual accumulation of genetic variation from wild relatives. This pattern indicates multiple, smaller introgression events rather than the introduction of large genomic regions through modern breeding programs. "
] | https://doi.org/10.1038/s41598-020-70315-4 | Other Herbaceous Crops, Spices, Fibers & Weeds | GENOME AND GENOMICS | 10.1038/s41598-020-70315-4 | 2,020 | 21 | 2 | Scientific Reports | true |
What are the key regulatory pathways and genes involved in sunflower leaf senescence? | GENE REGULATION - TRANSLATION | [
"Helianthus annuus"
] | [
"Ethylene signaling, particularly through the action of ethylene-responsive transcription factors, plays a pivotal role in regulating leaf senescence. Notably, the NAC family of transcription factors, including the well-characterized senescence inducer ORE1 in Arabidopsis, has been implicated in this process. In sunflower, ORE1 has been established as a key biomarker for leaf senescence",
"GA signaling, particularly through the action of non ethylene-responsive transcription factors, play a pivotal role in regulating leaf senescence. Notably, the bZIP family of transcription factors have been implicated in this process",
"Jasmonate signaling, particularly through the action of ethylene-responsive transcription factors, plays a pivotal role in regulating leaf senescence. Notably, the bZIP family of transcription factors have been implicated in this process. In sunflower, ORE1 has been established as a key biomarker for leaf senescence"
] | https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-019-2021-6 | Other Herbaceous Crops, Spices, Fibers & Weeds | GENE REGULATION | 10.1186/s12870-019-2021-6 | 2,019 | 13 | 0 | BMC Plant Biology | true |
Which transcription factor families are key regulators of leaf senescence in sunflower, and how do they impact photosynthetic processes? | GROWTH AND DEVELOPMENT | [
"Helianthus annuus"
] | [
"Leaf senescence in sunflower is a complex process regulated by a diverse array of transcription factors (TFs), including NAC, AP2/ERF, WRKY, and MYB families. These TFs orchestrate senescence by controlling various cellular processes, including the upregulation of photosynthetic genes, such as those involved in chloroplast development and maintenance",
"Leaf senescence in sunflower is a process regulated by one transcription factors (TFs), bZIP. This TFs orchestrate senescence by controlling various cellular processes, including the stabalizing photosynthetic genes, such as those involved in chloroplast development and maintenance",
"Leaf senescence in sunflower is a complex process regulated by a diverse array of transcription factors (TFs), including NAC, AP2/ERF, WRKY, and MYB families. These TFs orchestrate senescence by controlling various cellular processes, including the downregulation of photosynthetic genes, such as those involved in chloroplast development and maintenance, for example, the repression of GLK genes by ORE1 and ATAF1"
] | https://bmcplantbiol.biomedcentral.com/articles/10.1186/s12870-019-2021-6 | Other Herbaceous Crops, Spices, Fibers & Weeds | GROWTH AND DEVELOPMENT | 10.1186/s12870-019-2021-6 | 2,019 | 13 | 2 | BMC Plant Biology | true |
In Arabidopsis thaliana, where in the cell does ethylene bind to its receptor? What other genes are essential for the receptor to function correctly in the ethylene signaling pathway? | HORMONES | [
"Arabidopsis thaliana"
] | [
"In Arabidopsis thaliana, the ethylene receptor ETR1, is localized to in the cytosol perceiving ethylene at its C-terminal domain. This initiates a signaling cascade involving key genes such as RTE1, CTR1, EIN2, and EIN3. RTE1, a protein that is localized to the cell membrane and possibly interacts with ETR1 is believed to modulate receptor activity.",
"In Arabidopsis thaliana, the ethylene receptor ETR1, is localized to the cell membrane, where it senses ethylene at its N-terminal transmembrane domain. This initiates a signaling cascade involving key genes such as RTE1, CTR1, EIN2, and EIN3. RTE1, a non membrane protein that colocalizes and possibly interacts with ETR1, is believed to modulate receptor activity.",
"In Arabidopsis thaliana, the ethylene receptor ETR1, is localized to both the endoplasmic reticulum and the Golgi apparatus, perceiving ethylene at its N-terminal transmembrane domain. This initiates a signaling cascade involving key genes such as RTE1, CTR1, EIN2, and EIN3. RTE1, a protein that colocalizes and possibly interacts with ETR1 at the ER, is believed to modulate receptor activity. "
] | https://onlinelibrary.wiley.com/doi/full/10.1111/j.1365-313X.2007.03339.x https://www.sciencedirect.com/science/article/pii/S0021925820850558 | Model Organisms | HORMONES | 10.1111/j.1365-313X.2007.03339.x | 2,007 | 112 | 2 | The Plant Journal | true |
What is the main cytokinin receptor regulating symbiotic nitrogen-fixing nodulation in Medicago truncatula ? | HORMONES | [
"Medicago truncatula"
] | [
"The main cytokinin receptor involved in regulating symbiotic nitrogen-fixing nodulation in Medicago truncatula is MtCRE1 (Cytokinin response 1). This receptor is notably required to promote rhizobial infections.",
"The main cytokinin receptor involved in regulating symbiotic nitrogen-fixing nodulation in Medicago truncatula is MtCHK1 (CHASE-domain containing Histidine Kinase 1). This receptor is notably required to promote nodule organogenesis.",
"The main cytokinin receptor involved in regulating symbiotic nitrogen-fixing nodulation in Medicago truncatula is MtCRE1 (Cytokinin response 1). This receptor is notably required to promote nodule organogenesis."
] | 10.1105/tpc.106.043778 | Model Organisms | HORMONES | 10.1105/tpc.106.043778 | 2,006 | 418 | 2 | The Plant Cell | true |
How many authentic cyctokinin receptor exist in the Medicago truncatula genome ? | HORMONES | [
"Medicago truncatula"
] | [
"There are four authentic cytokinin receptor that exist in the Medicago truncatula genome: MtCRE1/MtCHK4, MtCHK1, MtCHK2, MtCHK3.",
"There are five cytokinin receptor that exist in the Medicago truncatula genome: MtCRE1/MtCHK1, MtCHK2, MtCHK3, MtCHK4, MtCHK5.",
"There are four authentic cytokinin receptor that exist in the Medicago truncatula genome: MtCRE1/MtCHK1, MtCHK2, MtCHK3, MtCHK4."
] | 10.1186/s12864-019-5724-z | Model Organisms | HORMONES | 10.1186/s12864-019-5724-z | 2,019 | 17 | 2 | BMC Genomics | true |
What are the signaling peptides and their associated receptors that are involved in the systemic regulation of nitrogen-fixing symbiotic nodulation in Medicago truncatula ? | HORMONES | [
"Medicago truncatula"
] | [
"The signaling peptides and their associated receptors that are involved in the systemic regulation of nitrogen-fixing symbiotic nodulation in Medicago truncatula are: 1) the CLE (CLAVATA-LIKE / EMBRYO SURROUNDING) peptides, perceived by the CRA2 (COMPACT ROOT ARCHITECTURE 2) ; and 2) the CEP (C-TERMINALLY ENCODED PEPTIDES) peptides and the SUNN (SUPERNUMERARY NODULES) receptor.",
"The signaling peptides and their associated receptors that are involved in the systemic regulation of nitrogen-fixing symbiotic nodulation in Medicago truncatula are: 1) the CLE (CLAVATA-LIKE / EMBRYO SURROUNDING) peptides, perceived by the SUNN (SUPERNUMERARY NODULES) receptor; 2) the CEP (C-TERMINALLY ENCODED PEPTIDES) peptides and the CRA2 (COMPACT ROOT ARCHITECTURE 2) receptor; and 3) the RGF/GLV (ROOT GROWTH FACTOR/GOLVEN) peptides perceived by the RGFR (RGF RECEPTOR) receptor.",
"The signaling peptides and their associated receptors that are involved in the systemic regulation of nitrogen-fixing symbiotic nodulation in Medicago truncatula are: 1) the CLE (CLAVATA-LIKE / EMBRYO SURROUNDING) peptides, perceived by the SUNN (SUPERNUMERARY NODULES) receptor; and 2) the CEP (C-TERMINALLY ENCODED PEPTIDES) peptides and the CRA2 (COMPACT ROOT ARCHITECTURE 2) receptor."
] | 10.1016/j.tplants.2020.11.009 | Model Organisms | HORMONES | 10.1016/j.tplants.2020.11.009 | 2,021 | 51 | 2 | Trends in Plant Science | true |
Which signaling peptide pathway promotes in Medicago truncatula both root competence to rhizobium bacteria and vesiculo-arbuscular mycorrhiza fungi symbionts? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Medicago truncatula"
] | [
"The CEP/CRA2 (C-TERMINALLY ENCODED PEPTIDE/COMPACT ROOT ARCHITECTURE 2) peptide/receptor pathway promotes in Medicago truncatula both root competence to rhizobium bacteria and vesiculo-arbuscular mycorrhiza fungi symbionts.",
"The CLE/SUNN (CLAVATA-LIKE/EMBRYO SURROUNDING / SUPERNUMERARY NODULES) peptide/receptor pathway promotes in Medicago truncatula both root competence to rhizobium bacteria and vesiculo-arbuscular mycorrhiza fungi symbionts.",
"There is no peptide/receptor pathway that promotes in Medicago truncatula both root competence to rhizobium bacteria and vesiculo-arbuscular mycorrhiza fungi symbionts."
] | 10.1016/j.cub.2024.09.058 | Model Organisms | ENVIRONMENT | 10.1016/j.cub.2024.09.058 | 2,024 | 1 | 0 | Current Biology | true |
What are the main similarities between nodulation and mycorrhizal endosymbioses in Medicago truncatula? | ENVIRONMENT - PLANT-SYMBIONTS | [
"Medicago truncatula"
] | [
"The main similarities between nodulation and mycorrhizal endosymbioses in Medicago truncatula are: 1) at the microscopic level, the infection process through respectively infection threads and pre-penetration apparatus; 2) at the molecular level, the recognition of symbionts through the perception of microbial chitooligosacharidic (CO) molecules by the host plant receptor CHITIN ELICITOR RECEPTOR KINASE 1 (CERK1), to activate a COMMON SYMBIOTIC SIGNALING (SYM) pathway.",
"The main similarities between nodulation and mycorrhizal endosymbioses in Medicago truncatula are: 1) at the microscopic level, the activation of the root cortex through respectively nodule organogenesis and arbuscule differentiation; 2) at the molecular level, the recognition of symbionts through the perception of host plant lipochitooligosacharidic (LCO) molecules by microbial receptors from the LYSM DOMAIN RECEPTOR-LIKE KINASES (LysM RLK) family, to activate a COMMON SYMBIOTIC SIGNALING (SYM) pathway.",
"The main similarities between nodulation and mycorrhizal endosymbioses in Medicago truncatula are: 1) at the microscopic level, the infection process through respectively infection threads and pre-penetration apparatus; 2) at the molecular level, the recognition of symbionts through the perception of microbial lipochitooligosacharidic (LCO) molecules by host plant receptors from the LYSM DOMAIN RECEPTOR-LIKE KINASES (LysM RLK) family, to activate a COMMON SYMBIOTIC SIGNALING (SYM) pathway."
] | 10.1093/plcell/koac039 | Model Organisms | ENVIRONMENT | 10.1093/plcell/koac039 | 2,022 | 78 | 2 | The Plant Cell | true |
What is the function of the peptides of the LURE family during Arabidopsis thaliana pollen tube growth and what are the pollen genes involved in this process? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"Arabidopsis LURE peptides are cysteine-rich peptides (CRP) that function in attracting pollen tubes to guide them to the ovule where fertilization occurs. The LURE peptides are secreted by the synergid cells of the ovule and bind to the leucine-rich receptor kinase (LRR-RK) PRK6 that is in the pollen tube. Upon interaction, the pollen tube redirects its growth in the direction of the ovule. LURE peptides are specific to each plant species, which makes sure that only plants of the same species can fertilize each other.",
"LURE peptides are leucin rich repeat peptides that function in attracting pollen tubes to guide them to the ovule where fertilization occurs in gymnosperms. The LURE peptides are secreted by the egg cell of the ovule and bind to the leucine-rich receptor kinase (LRR-RK) ANXUR that is in the pollen tube. Upon interaction, the pollen tube redirects its growth in the direction of the stigma. LURE peptides are not specific to each plant species, which makes sure that only plants of different species can fertilize each other",
"Arabidopsis LURE peptides are glyco-peptides that function in repelling pollen tubes to avoid them to reach the ovule where fertilization occurs. The LURE peptides are secreted by the antipodal cells of the ovule and bind to the leucine-rich receptor kinase (LRR-RK) FERONIA that is in the pollen grain. Upon interaction, the pollen tube redirects its growth away from the ovule. LURE peptides are specific to each plant species, which makes sure that plants of the same species cannot fertilize each other."
] | https://doi.org/10.1016/j.peptides.2021.170572 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1016/j.peptides.2021.170572 | 2,021 | 24 | 0 | Peptides | true |
What is the function of ethylene during fertilization in Arabidopsis thaliana and why is important for the establishment of a pollen tube block? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"The ethylene-response cascade is repressed during fertilization, thus allowing the admission of a second pollen tube into the ovule and interfering with normal sexual fertilization. The process of fertilization activates two ethylene-activated genes, EIN1 and ETR2, that are necessary for the first synergid cell death and then the establishment of an entry of a new pollen tube.",
"The ethylene-response cascade is activated during fertilization, thus preventing the entry of a second pollen tube into the ovule and ensuring normal sexual fertilization. The process of fertilization activates two ethylene-activated genes, EIN3 and EIN2, that are necessary for the second synergid cell death and then the establishment of a pollen tube block. ",
"The ethylene-response cascade is activated during fertilization, thus preventing the entry of a third pollen tube into the ovule and ensuring normal asexual fertilization. The process of fertilization inhibits two ethylene-activated genes, CTR1 and EIN5, that are necessary for the second synergid cell death and then the establishment of a pollen tube acceptance. "
] | https://doi.org/10.1016/j.devcel.2013.04.001 | Model Organisms | GROWTH AND DEVELOPMENT | 10.1016/j.devcel.2013.04.001 | 2,013 | 130 | 1 | Developmental Cell | true |
How is negative signal transduction established as the hormonal and light signaling pathways in Arabidopsis thaliana? | HORMONES | [
"Arabidopsis thaliana"
] | [
"The process of signal transduction typically involves only the modulation of positive components, thereby ensuring best functionality of signals. Arabidopsis plants can transduce stress signals in a manner that is similar of animals. In the presence of a stimulus, proteins that typically function as repressors in the absence of a stimulus, are immediately activated. This signaling pathway is fully repressed and inhibits the final response quickly and efficiently. This peculiar way of signaling hormonal and light stimuli is energetically costly but ensures a fast and effective response, essential for mobile organisms such as plants.",
"The process of signal transduction typically involves the modulation of positive and negative components, thereby ensuring best functionality of signals. Arabidopsis plants can transduce hormonal and light signals in a manner that differs from that of animals. In the presence of a stimulus, proteins that typically function as repressors in the absence of a stimulus, are immediately degraded. This signaling pathway is fully de-repressed and produces the final response quickly and efficiently. This peculiar way of signaling hormonal and light stimuli is energetically costly but ensures a fast and effective response, essential for sessile organisms such as plants.",
"The process of signal transduction typically involves the modulation of negative components, thereby ensuring best functionality of signals. Rice plants can transduce pathogen signals in a manner that differs from that of insects. In the presence of a stimulus, proteins that typically function as activators in the absence of a stimulus, are immediately degraded. This signaling pathway is fully de-activated and stops the final response quickly and efficiently. This peculiar way of signaling hormonal and light stimuli is energetically cheap and ensures a slow response, essential for sessile organisms such as funghi."
] | https://doi.org/10.1016/j.tplants.2005.11.005 | Model Organisms | HORMONES | 10.1016/j.tplants.2005.11.005 | 2,006 | 47 | 1 | Trends in Plant Science | true |
How is S-locus receptor kinase (SRK) involved in the maintenance of the self-incompatibility response in Brassica? | PHYSIOLOGY AND METABOLISM | [
"non-specific"
] | [
"In Self-incompatibility (SI) the generation of zygotes is stimulated by self-pollination in a fertile hermaphrodite plant. This induces self-fertilization and inbreeding. In flowering plants, such as Brassica, the S-locus receptor kinase (SRK) is required for the inhibition of the SI response. The SRK protein localizes to the ovules, and interacts with the pollen determinant protein S-locus 11 (SP11).The incompatible response is triggered when the male (SP11) and female (SRK) S-locus-determinants come from different S-alleles of the S-locus.",
"In Self-incompatibility (SI) the generation of zygotes is arrested by self-pollination in a fertile hermaphrodite plant. This prevents self-fertilization and inbreeding. In flowering plants, such as Brassica, the S-locus receptor kinase (SRK) is required for the maintenance of the SI response. The SRK protein localizes to the stigmas, and interacts with the pollen determinant protein S-locus 11 (SP11).The incompatible response is triggered when the male (SP11) and female (SRK) S-locus-determinants come from the same S-alleles of the S-locus.",
"In Self-incompatibility (SI) the generation of zygotes is arrested by cross-pollination in a fertile dioecious plant. This prevents self-fertilization and inbreeding. In flowering plants, such as Brassica, the S-locus glycoprotein (SLG) is required for the maintenance of the SI response. The SLG protein localizes to the stigmas, and interacts with the pollen determinant protein S-locus SLF. The incongruous response is triggered when the male (SP11) and female (SRK) S-locus-determinants come from the same plants."
] | https://doi.org/10.1093/plphys/kiad301 | Non-specific | PHYSIOLOGY AND METABOLISM | 10.1093/plphys/kiad301 | 2,023 | 13 | 1 | Plant Physiology | true |
What is function of the homeotic genes in Arabidopsis thaliana flower development? | GROWTH AND DEVELOPMENT | [
"Arabidopsis thaliana"
] | [
"The floral organs are arranged in six concentric rings or whorls. The sepals and petals (reproductive organs) are arranged in the two outer whorls, and the stamens and carpels (structural organs) in the two inner whorls. Homeotic genes in Arabidopsis flowers have been shown to repress the development of floral organs and the identity of each organ. The presence of different homeotic genes in a specific whorl determines the fate of the organ. APETALA1 (AP1) is a key player in the development of reproductive organs, such as stamens and carpels. Meanwhile, AGAMOUS (AG) controls sepal and petal development.",
"The floral organs are arranged in four concentric rings or whorls. The sepals and petals (structural organs) are arranged in the two outer whorls, while the stamens and carpels (reproductive organs) in the two inner whorls. Homeotic genes in Arabidopsis flowers have been shown to regulate the development of floral organs and the identity of each organ. The presence of different homeotic genes in a specific whorl determines the fate of the organ. AGAMOUS (AG) is a key player in the development of reproductive organs, such as stamens and carpels. Meanwhile, APETALA1 (AP1) controls sepal and petal development.",
"The floral organs are arranged in four concentric rings or whorls. The sepals and petals (structural organs) are arranged in the two inner whorls, and the stamens and carpels (reproductive organs) in the two outer whorls. Homeotic genes in Arabidopsis fruits have been shown to regulate the development of seeds. The presence of different homeotic genes in a specific whorl determines the fate of the organ. AGAMOUS (AG) is a key player in the development of leaves, such as stamens and carpels. Meanwhile, APETALA1 (AP1) controls root development."
] | https://doi.org/10.3390/plants12051128 | Model Organisms | GROWTH AND DEVELOPMENT | 10.3390/plants12051128 | 2,023 | 7 | 1 | Plants | true |
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