Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole genome tiling arrays
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE13584 | GEO | 2008/11/14
SECONDARY ACCESSION(S): PRJNA110687
REPOSITORIES: GEO
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Project description:Plants physiological mechanisms are affected by Abscisic acid (ABA) via changing gene expression and empowers plants to adapt in numerous environments. Plants have evolved their protection mechanisms for seed germination and abiotic environments to deal with critical harsh conditions. Here, we have explored those changes in Arabidopsis thaliana plants subjected to multiple abiotic stresses. AtBro1 transcripts showed up-regulation in the presence of salt, ABA and mannitol stress conditions. AtBRO1 over-expression lines exhibited robust tolerance to drought and salt stress. Further, ABA elicits resistance responses in loss-of-function bro1-1 mutant plants and AtBro1 positively regulates drought resistance in Arabidopsis. Promoter of AtBro1 fused with GUS showed GUS expression mainly in the rosette leaves and floral clusters, especially in anthers. AtBro1 protein was found to be localized in the plasma membrane of Arabidopsis at the subcellular level by using AtBro1::GFP fusion. Using a broad RNA-sequencing analysis, we observed that early transcriptional responses prompted by ABA induction exhibit specific quantitative differences at different time points, suggesting that ABA stimulates resistance responses in bro1-1 mutant plants. Additionally, transcripts levels of MOP9.5, MRD1, HEI10, and MIOX4 were altered in loss-of-function mutant plants which are involved in different stress conditions. Collectively, our results have shown that AtBro1 is involved in a significant role by regulating plant transcriptional response to ABA and induction of resistance response against abiotic stress.
2023-04-18 | GSE225062 | GEO
Project description:Multiple transcription factors (TFs) play essential roles in plants under abiotic stress, one of the most challenging conditions of plant survival. However, how these multiple TFs cooperate in abiotic stress responses still remains largely unknown. In this study, we provide evidence that a novel NAC (NAM, ATAF1/2, and CUC2) transcription factor (ANAC096) cooperates with bZIP-type TFs [ABRE-binding factor/ABRE-binding protein (ABF/AREB)] in ensuring survival under dehydration and osmotic stress conditions. Intriguingly, ANAC096 directly interacted with ABF2 and ABF4, but not with ABF3, both in vitro and in vivo. ANAC096 and ABF2 synergistically activated RD29A transcription. The genome-wide gene expression analysis revealed that a major proportion of ABA-responsive genes are under the transcriptional regulation of ANAC096.An Arabidopsis mutant, anac096, was hyposensitive to exogenous abscisic acid (ABA), and showed impaired ABA-induced stomatal closure and increased water loss under dehydration stress conditions. Furthermore, the anac096 abf2 abf4 triple mutant was much more sensitive to dehydration and osmotic stresses than the anac096 single mutant or the abf2 abf4 double-mutant. Based on these results, we propose that ANAC096 is involved in a synergistic relationship with a subset of ABFs for the transcriptional activation of ABA-inducible genes in response to dehydration and osmotic stresses.
2014-01-02 | GSE51218 | GEO
Project description:The signaling pathway of the phytohormone abscisic acid (ABA) regulates responses towards abiotic stress such as drought and high osmotic conditions. The multitude of functionally redundant components involved in ABA signaling, poses a major challenge for elucidating the largely unresolved response selectivity. We decided rebuilding single linear ABA signaling pathways in yeast for combinatoric permutation of ABA receptors and coreceptors, as well as the response-mediating SnRK2 protein kinases and their targeted transcription factors to drive luciferase expression in a heterologous host. We show that SnRK2s differ in the regulation by ABA receptor complexes, affect ABA responsiveness of the pathway, and differ in their transactivation activity but have similar preferences for ABA-responsive transcription factors. SnRK2s thought to act ABA-independently and known to be activated under osmotic stress in plants were regulated by ABA receptor complexes in yeast and competed with ABA receptor components in an ABA-dependent manner in plant tissue. The study reveals the suitability of the yeast system for analysis of ABA signaling factors and allowing the future dissection of ligand-receptor specificities in a functional response pathway. The analysis provides new insights into SnRK2 regulation indicating that four SnRK2 members of the osmotic stress response are tightly embedded into the ABA signaling pathway.
2019-07-30 | PXD013669 | Pride
Project description:bHLH122 could be induced by salt, osmotic and drought stress except ABA, the transgentic Arabidopsis were more tolerant to abiotic stresses, such as drought and salt. What's more, in the overexpression plants, the endogenesis ABA contents were higher than WT. We found there existed an interaction between bHLH122 and CYP707A3 by virtue of EMSA and ChIP assays. We wanted to learn more about the molecular mechanism of bHLH122 and to explore what had changed in the over-expression plant through Genechips.
2013-05-07 | GSE46661 | GEO
Project description:Plant homeodomain (PHD) finger proteins affect growth and development by regulating transcription and reading epigenetic modifications of histones, but their functions in abiotic stress responses remain largely unclear. Here we characterize seven Arabidopsis thaliana Alfin1-like PHD finger proteins (ALs) in the response to abiotic stresses. ALs localize to the nucleus and repress transcription. Except AL6, all the ALs bind to G-box element. Changes of the amino acids at positions 34 and 35 in AL6 cause the loss of G-box binding ability. Expression of the ALs responded differently to osmotic stress, salt, cold and abscisic acid treatments. AL5 was induced by multiple stresses, and AL5-overexpressing plants showed higher tolerance to salt, drought and freezing stress than Col-0. Also, al5 mutants showed reduced stress tolerance. ChIP-Seq assay helps find the direct targets of AL5.
2014-04-12 | GSE56706 | GEO
Project description:Multiple transcription factors (TFs) play essential roles in plants under abiotic stress, one of the most challenging conditions of plant survival. However, how these multiple TFs cooperate in abiotic stress responses still remains largely unknown. In this study, we provide evidence that a novel NAC (NAM, ATAF1/2, and CUC2) transcription factor (ANAC096) cooperates with bZIP-type TFs [ABRE-binding factor/ABRE-binding protein (ABF/AREB)] in ensuring survival under dehydration and osmotic stress conditions. Intriguingly, ANAC096 directly interacted with ABF2 and ABF4, but not with ABF3, both in vitro and in vivo. ANAC096 and ABF2 synergistically activated RD29A transcription. The genome-wide gene expression analysis revealed that a major proportion of ABA-responsive genes are under the transcriptional regulation of ANAC096.An Arabidopsis mutant, anac096, was hyposensitive to exogenous abscisic acid (ABA), and showed impaired ABA-induced stomatal closure and increased water loss under dehydration stress conditions. Furthermore, the anac096 abf2 abf4 triple mutant was much more sensitive to dehydration and osmotic stresses than the anac096 single mutant or the abf2 abf4 double-mutant. Based on these results, we propose that ANAC096 is involved in a synergistic relationship with a subset of ABFs for the transcriptional activation of ABA-inducible genes in response to dehydration and osmotic stresses. pTA plants (12-day-old) cultured in liquid medium were treated with 30 uM Dex alone for 1 h (Control) or 30 uM Dex alone for 30 min followed by an additional treatment of 30 min with both 30 uM Dex and 2 uM ABA (ABA). For pTA-ANAC096 plants, 12-day-old seedlings were treated with 30 uM Dex for 1 h (ANAC096) or with 30 uM Dex only for 0.5 h followed by additional 0.5 h incubation with both 2 uM ABA and 30 uM Dex (ANAC096+ABA). Total RNAs were isolated from two biological replicates at each condition and used to measure gene expression level.
2014-01-02 | E-GEOD-51218 | biostudies-arrayexpress
Project description:Plant homeodomain (PHD) finger proteins affect growth and development by regulating transcription and reading epigenetic modifications of histones, but their functions in abiotic stress responses remain largely unclear. Here we characterize seven Arabidopsis thaliana Alfin1-like PHD finger proteins (ALs) in the response to abiotic stresses. ALs localize to the nucleus and repress transcription. Except AL6, all the ALs bind to G-box element. Changes of the amino acids at positions 34 and 35 in AL6 cause the loss of G-box binding ability. Expression of the ALs responded differently to osmotic stress, salt, cold and abscisic acid treatments. AL5 was induced by multiple stresses, and AL5-overexpressing plants showed higher tolerance to salt, drought and freezing stress than Col-0. Also, al5 mutants showed reduced stress tolerance. ChIP-Seq assay helps find the direct targets of AL5. Polyclonal antibody of AL5 protein was used to perform ChIP experiment. Two samples were analyzed, AL5 OE sample and its knock out mutant. Data was analyzed as OE sample Vs mutant sample and help find targets of AL5 protein.
2014-04-12 | E-GEOD-56706 | biostudies-arrayexpress
Project description:The signaling pathway of the phytohormone abscisic acid (ABA) regulates responses towards abiotic stress such as drought and high osmotic conditions. The multitude of functionally redundant components involved in ABA signaling, poses a major challenge for elucidating the largely unresolved response selectivity. We decided rebuilding single linear ABA signaling pathways in yeast for combinatoric permutation of ABA receptors and coreceptors, as well as the response-mediating SnRK2 protein kinases and their targeted transcription factors to drive luciferase expression in a heterologous host. We show that SnRK2s differ in the regulation by ABA receptor complexes, affect ABA responsiveness of the pathway, and differ in their transactivation activity but have similar preferences for ABA-responsive transcription factors. SnRK2s thought to act ABA-independently and known to be activated under osmotic stress in plants were regulated by ABA receptor complexes in yeast and competed with ABA receptor components in an ABA-dependent manner in plant tissue. The study reveals the suitability of the yeast system for analysis of ABA signaling factors and allowing the future dissection of ligand-receptor specificities in a functional response pathway. The analysis provides new insights into SnRK2 regulation indicating that four SnRK2 members of the osmotic stress response are tightly embedded into the ABA signaling pathway.
2019-08-13 | PXD013849 | panorama
Project description:Hyperosmotic stress caused by drought and salinity is a significant environmental threat that limits plant growth and agricultural productivity. Osmotic stress induces diverse responses in plants including Ca2+ signaling, accumulation of the stress hormone abscisic acid (ABA), reprogramming of gene expression, and altering growth. Despite intensive investigation, no global regulators of all of these responses have been identified. Here, we show that the Ca2+-responsive phospholipid binding BONZAI (BON) proteins are critical for all of these osmotic stress responses. A Ca2+-imaging-based forward genetic screen identified a loss-of-function bon1 mutant with a reduced cytosolic Ca2+ signal in response to hyperosmotic stress. The loss-of-function mutants of the BON1 gene family, bon1bon2bon3, are impaired in the induction of gene expression and ABA accumulation in response to osmotic stress. In addition, the bon mutants are hypersensitive to osmotic stress in growth inhibition. BON genes have been shown to negatively regulate plant immune responses mediated by intracellular immune receptor NLR genes including SNC1. We found that the defects of the bon mutants in osmotic stress responses were suppressed by mutations in the NLR gene SNC1 or the immunity regulator PAD4. Our findings indicate that NLR signaling represses osmotic stress responses and that BON proteins suppress NLR signaling to enable global osmotic stress responses in plants.
2020-09-04 | GSE157435 | GEO
Project description:High salinity is one of the major environmental factors, which hampers plant growth, development and productivity. To better understand the regulatory mechanisms by which plants cope with salt stress, we used genetic approaches to identify salt hypersensitive mutant 9 (sahy9), a new allele of apum23, in Arabidopsis thaliana. The sahy9/apum23 mutant seedlings display postgemination developmental arrest and later become bleached under agar plates supplemented with various salt stressors. Transcriptomic and proteomic analyses of the salt-treated sahy9/apum23 and wild-type seedlings revealed differential expression of genes with similar functional categories, primarily including cellular and metabolic processes, and abiotic and biotic stress responses. However, the consistency of gene expression at both transcript and protein levels is low (), suggesting the involvement of posttranscriptional processing in salt response. Furthermore, the altered gene/protein expression mediated by SAHY9/APUM23 in salt sensitivity is involved in several functional groups, particularly in ABA biosynthesis and signaling, abiotic stress response, LEA proteins, and ribosome biogenesis-related genes. Importantly, NCED3, a key gene involved in ABA biosynthesis, and major ABA responsive marker genes, such as RD20 and RD29B, are down-regulated at both transcript and protein levels in sahy9/apum23 under salt stress. Consistently, lower contents of ABA and proline, and expression changes of a subset of LEA proteins also support the nature of sahy9/apum23 showing salt hypersensitivity. Collectively, these data suggest that SAHY9/APUM23-mediated salt response is associated with ABA signaling pathway and its downstream stress responsive or tolerant genes.
2018-02-20 | GSE99664 | GEO