RNA-seq analysis of ABA-treated Nicotiana benthamiana seedlings
Ontology highlight
ABSTRACT:
ORGANISM(S): Nicotiana benthamiana
PROVIDER: GSE255725 | GEO | 2024/08/13
REPOSITORIES: GEO
Similar Datasets
Project description:Abscisic acid (ABA) is a key hormone for plant growth, development and stress adaptation. Perception of ABA through four types of receptors has been reported. We show here that impairment of ABA perception through the PYR/PYL/RCAR branch reduces vegetative growth and seed production, and leads to a severely open stomata and dramatic ABA insensitive phenotype, even though other branches for ABA perception remain functional. Arabidopsis sextuple mutant impaired in 6 PYR/PYL receptors, namely PYR1, PYL1, PYL2, PYL4, PYL5 and PYL8, was able to germinate and grow even on 100 mM ABA. Whole-rosette stomatal conductance (Gst) measurements revealed that leaf transpiration in the sextuple pyr/pyl mutant was higher than in the ABA-deficient aba3-1 or ABA-insensitive snrk2.6 mutants. The gradually increasing Gst values of plants lacking three, four, five and six PYR/PYLs indicate quantitative regulation of stomatal aperture by this family of receptors. The sextuple mutant lacked ABA-mediated activation of SnRK2s and ABA-responsive gene expression was dramatically impaired as was reported in snrk2.2/2.3/2.6. In summary, these results show that ABA perception by PYR/PYLs plays a major role to regulate seed germination and establishment, basal ABA signaling required for vegetative and reproductive growth, stomatal aperture and transcriptional response to the hormone.
2012-11-30 | GSE36692 | GEO
Project description:Abscisic acid (ABA) is a key hormone for plant growth, development and stress adaptation. Perception of ABA through four types of receptors has been reported. We show here that impairment of ABA perception through the PYR/PYL/RCAR branch reduces vegetative growth and seed production, and leads to a severely open stomata and dramatic ABA insensitive phenotype, even though other branches for ABA perception remain functional. Arabidopsis sextuple mutant impaired in 6 PYR/PYL receptors, namely PYR1, PYL1, PYL2, PYL4, PYL5 and PYL8, was able to germinate and grow even on 100 mM ABA. Whole-rosette stomatal conductance (Gst) measurements revealed that leaf transpiration in the sextuple pyr/pyl mutant was higher than in the ABA-deficient aba3-1 or ABA-insensitive snrk2.6 mutants. The gradually increasing Gst values of plants lacking three, four, five and six PYR/PYLs indicate quantitative regulation of stomatal aperture by this family of receptors. The sextuple mutant lacked ABA-mediated activation of SnRK2s and ABA-responsive gene expression was dramatically impaired as was reported in snrk2.2/2.3/2.6. In summary, these results show that ABA perception by PYR/PYLs plays a major role to regulate seed germination and establishment, basal ABA signaling required for vegetative and reproductive growth, stomatal aperture and transcriptional response to the hormone. Four biological replicates were generated for the 3 genotypes, pyr1pyl1pyl2pyl4pyl5pyl8 sextuple mutant, snrk2.2/2.3/2.6 triple mutant, and Col-0. All the samples were treated with ABA for 3 hours before harvesting. The four Col-0 samples were mix to create an unique reference Col-0 sample. Two comparasion were made, fisrt one, PYR/PYL sextuple mutant versus Col-0 reference sample and second one, SnRK2 triple mutant versus Col-0 reference sample. In each comparasion four biological replicates were made. Replicas number 1 and 2 were labeled with Cy5 for the mutant sample and Cy3 for the Col-0 reference sample, while the other two replicas,#3 and #4, were reversed-labeled.
2012-11-30 | E-GEOD-36692 | biostudies-arrayexpress
Project description:Unveiling the signal transduction of phytohormone abscisic acid (ABA) will be greatly helpful to improve plant responses to stressful environment. ABA signaling is perceived and mediated by multi-member receptor PYR/PYLs, while whose post-translational modification, especially phosphorylation, is largely unknown. Here we demonstrated that Arabidopsis EL1-like (AEL), a casein kinase that regulates various physiological processes, phosphorylates PYR/PYLs and stimulates whose ubiquitination and degradation, leading to the suppressed ABA responses. Arabidopsis ael triple mutants display hypersensitive responses to ABA treatment, which is consistent with the suppressed degradation of PYR/PYL proteins. PYR/PYLs are phosphorylated in vivo and mutation of the conserved AEL-phosphorylation sites results in the reduced phosphorylation, ubiquitination, and degradation of PYR/PYLs, and hence the enhanced ABA responses. Our studies demonstrate the crucial roles of AEL-mediated phosphorylation in regulating the stability and function of PYR/PYLs and provide informative clues for elucidating the functional mechanism of ABA through regulating PYR/PYL receptors.
2022-02-23 | PXD008565 | Pride
Project description:ABA signaling relies on the perception of the hormone by 14 different members of the PYR/PYL/RCAR family of ABA receptors. Upon ABA binding, receptors become active in inhibiting a family of type 2C protein phosphatases that usually function as negative regulators on protein kinases of the SnRK2 family. Previous physiological and genetic data supporting a negative role exerted by nitric oxide (NO) on ABA signaling have been reported. Our preliminary data suggested that negative regulation exerted by NO on ABA signaling may involve direct effects of NO on ABA receptors. Here we explore whether the effects of NO on ABA signaling are due to post-translational modifications (PTMs) on ABA receptors. Two main PTMs are functionally related to NO, the S-nitrosylation of C residues and the nitration of Y residues and they have been studied in this work. Because our data suggest that NO can also modulate the stability of the receptor proteins, we have also analyzed another PTM, the ubiquitination of K residues. A double approach based on in vitro nitration of recombinant PYR/PYL/RCAR proteins as well as in planta expression of HA-tagged versions of the receptors, followed by immunopurification strategies based on anti-3-nitroY-coated magnetic beads, and LC-MS/MS analyses of the immunopurified proteins under non-reducing conditions allowed us to identify peptides containing nitroY (mass shifts of +45), S-nitrosylated C (mass shifts of +29), and K-GG tags resulting from the trypsin digestion of ubiquitin tails (mass shift of + 114). Our data suggest that S-nitrosylation of cysteines from PYR/PYL receptors occur in planta but has not effect on receptor function as tested in vitro. By contrast, the nitration of several Y residues of PYR/PYL receptors completely inactivates them, promotes also their polyubiquitination and marks them for subsequent proteasomal degradation, thus representing a rapid mechanism for lowering ABA sensitivity when required in the plant.
2015-09-09 | PXD002396 | Pride
Project description:The plant hormone abscisic acid (ABA) is best known for its role as a regulator of the responses to abiotic stressors. Components of ABA signaling pathway are thus considered as promising targets for securing yield under stress. ABA levels rise in response to abiotic stress, mounting a number of physiological and metabolic responses that promote plant survival under unfavorable conditions. ABA elicits its effects by binding to a family of soluble receptors called PYR/PYL/RCAR. Arabidopsis genome encodes 14 PYL proteins, knowledge on differential biological functions of these members is scarce. In this work, we took a gain-of-function approach to predict receptor-specific functionality. We introduced a set of activating mutations in the mobile gate and α-helix of sub family II ABA receptors. These mutations constitutively enforce the active ABA-bound conformation. We then transformed ABA deficient mutants with the constitutive receptors and monitored suppression of ABA deficiency phenotype. Our findings suggest that subfamily II receptors have differential activity in regulating transpiration and transcription of oxidation and stress response genes. These differences partly derived from differential accumulation of PYLs in the guard cells. Data mining revealed that only a small subset of PYL receptors are transcribed in the guard cells in a steady state. Because the guard cell specific receptors have different affinity to ABA and to the PP2C co-receptor we propose that, a combined partial receptor redundancy facilitate a gradual activation of the ABA output signal as its cellular concentration rises via biochemically different receptors.
2023-08-15 | GSE181260 | GEO
Project description:This model is from the article:
A thermodynamic switch modulates abscisic acid receptor sensitivity.
Dupeux F, Santiago J, Betz K, Twycross J, Park SY, Rodriguez L, Gonzalez-Guzman M, Jensen MR, Krasnogor N, Blackledge M, Holdsworth M, Cutler SR, Rodriguez PL, Márquez JA EMBO J.
[2011 Oct; Volume: 30 (Issue: 20 )] Page info: 4171-84 21847091
,
Abstract:
Abscisic acid (ABA) is a key hormone regulating plant growth, development and the response to biotic and abiotic stress. ABA binding to pyrabactin resistance (PYR)/PYR1-like (PYL)/Regulatory Component of Abscisic acid Receptor (RCAR) intracellular receptors promotes the formation of stable complexes with certain protein phosphatases type 2C (PP2Cs), leading to the activation of ABA signalling. The PYR/PYL/RCAR family contains 14 genes in Arabidopsis and is currently the largest plant hormone receptor family known; however, it is unclear what functional differentiation exists among receptors. Here, we identify two distinct classes of receptors, dimeric and monomeric, with different intrinsic affinities for ABA and whose differential properties are determined by the oligomeric state of their apo forms. Moreover, we find a residue in PYR1, H60, that is variable between family members and plays a key role in determining oligomeric state. In silico modelling of the ABA activation pathway reveals that monomeric receptors have a competitive advantage for binding to ABA and PP2Cs. This work illustrates how receptor oligomerization can modulate hormonal responses and more generally, the sensitivity of a ligand-dependent signalling system.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2005-01-01 | MODEL1202030000 | BioModels
Project description:Phytohormone abscisic acid (ABA) regulates key aspects of plant development such as seed germination, as well as responses to important environmental stresses, including drought, salinity and cold temperatures. The ABA signaling pathway is tightly controlled by the ubiquitin proteasome system. CULLIN4-RING E3 ubiquitin ligases use the substrate receptor module COP10-DDB1-DET1-DDA1 (CDDD) to target PYL8, one of the ABA receptors of the PYR/PYL/RCAR (pyrabactin resistance/pyrabactin resistance-like/regulatory components of ABA) family. Therefore, CRL4-CDDD complexes are negative regulators of ABA-mediated stress responses. Conversely, ABA treatments attenuate PYL8 receptor degradation, although the precise molecular details of this mechanism remained unknown. Here, we show that ABA promotes the disruption of CRL4-CDDD complexes, leading to PYL8 stabilization. ABA-mediated CRL4-CDDD dissociation likely involves altered association between DDA1-containing complexes and the CSN, a master regulator of the assembly of cullin-based E3 ligases, including CRL4-CDDD. Indeed, treatments with CSN5i-3, an inhibitor of the CSN activity, suppressed the ABA effect on CRL4-CDDD assembly. Altogether, our findings indicate that ABA stabilizes PYL8 by altering the dynamics of the CRL4-CDDD-CSN complex association, unveiling a regulatory mechanism by which a plant hormone inhibits an E3 ubiquitin ligase to protect its own receptors from degradation.
2024-09-11 | PXD055735 | Pride
Project description:Phytohormone abscisic acid (ABA) regulates key aspects of plant development such as seed germination, as well as responses to important environmental stresses, including drought, salinity and cold temperatures. The ABA signaling pathway is tightly controlled by the ubiquitin proteasome system. CULLIN4-RING E3 ubiquitin ligases use the substrate receptor module COP10-DDB1-DET1-DDA1 (CDDD) to target PYL8, one of the ABA receptors of the PYR/PYL/RCAR (pyrabactin resistance/pyrabactin resistance-like/regulatory components of ABA) family. Therefore, CRL4-CDDD complexes are negative regulators of ABA-mediated stress responses. Conversely, ABA treatments attenuate PYL8 receptor degradation, although the precise molecular details of this mechanism remained unknown. Here, we show that ABA promotes the disruption of CRL4-CDDD complexes, leading to PYL8 stabilization. ABA-mediated CRL4-CDDD dissociation likely involves altered association between DDA1-containing complexes and the CSN, a master regulator of the assembly of cullin-based E3 ligases, including CRL4-CDDD. Indeed, treatments with CSN5i-3, an inhibitor of the CSN activity, suppressed the ABA effect on CRL4-CDDD assembly. Altogether, our findings indicate that ABA stabilizes PYL8 by altering the dynamics of the CRL4-CDDD-CSN complex association, unveiling a regulatory mechanism by which a plant hormone inhibits an E3 ubiquitin ligase to protect its own receptors from degradation.
2024-09-11 | PXD055583 | Pride
Project description:This model is from the article:
A thermodynamic switch modulates abscisic acid receptor sensitivit
y.
Dupeux F, Santiago J, Betz K, Twycross J, Park SY, Rodriguez L, Gonzalez-
Guzman M, Jensen MR, Krasnogor N, Blackledge M, Holdsworth M, Cutler SR, Rodrigue
z PL, Márquez JA EMBO J.
[2011 Oct; Volume: 30 (Issue: 20 )] Page info: 4171-84 21847091
,
Abstract:
Abscisic acid (ABA) is a key hormone regulating plant growth, development and the
response to biotic and abiotic stress. ABA binding to pyrabactin resistance (PYR
)/PYR1-like (PYL)/Regulatory Component of Abscisic acid Receptor (RCAR) intracell
ular receptors promotes the formation of stable complexes with certain protein ph
osphatases type 2C (PP2Cs), leading to the activation of ABA signalling. The PYR/
PYL/RCAR family contains 14 genes in Arabidopsis and is currently the largest pla
nt hormone receptor family known; however, it is unclear what functional differen
tiation exists among receptors. Here, we identify two distinct classes of recepto
rs, dimeric and monomeric, with different intrinsic affinities for ABA and whose
differential properties are determined by the oligomeric state of their apo forms
. Moreover, we find a residue in PYR1, H60, that is variable between family membe
rs and plays a key role in determining oligomeric state. In silico modelling of t
he ABA activation pathway reveals that monomeric receptors have a competitive adv
antage for binding to ABA and PP2Cs. This work illustrates how receptor oligomeri
zation can modulate hormonal responses and more generally, the sensitivity of a l
igand-dependent signalling system.
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication
for more information.
In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.
2005-01-01 | MODEL1202030001 | BioModels
Project description:To compare the genome-wide transcriptional effect of ABA and iSB09 in tomato plants, we performed RNA-seq analysis of mock-, 10 uM ABA- or 20 uM iSB09-treated plants. Differential gene expression analysis between mock- and ABA-treated or iSB09-treated seedlings was done with DESeq2 and genes with an absolute value of log2 fold change (log2FC) > 1 or (log2FC) < -1 and p-adjusted value (padj) < 0.05 were selected. iSB09 upregulated and downregulated genes represent a subset of the ABA-responsive genes, which reflects the activation of PYL1-like and PYL4-like ABA receptors in tomato seedlings.
2024-07-22 | GSE256238 | GEO