Brassinosteroids participate in the control of basal and acquired freezing tolerance of plants
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE86605 | GEO | 2016/09/10
SECONDARY ACCESSION(S): PRJNA342464
REPOSITORIES: GEO
Similar Datasets
Project description:We conducted microarray analysis to study comprehensive changes of gene expression profile under long-term low-temperature (LT) treatment and to identify other LT-responsive genes related with cold acclimation in seedling leaves and crown tissues (shoots containing apical meristems) of a synthetic hexaploid wheat line. The microarray analysis revealed marked up-regulation of a number of Cor/Lea genes and fructan biosynthesis-related genes under the long-term LT treatment. For validation of the microarray data, we selected four synthetic wheat lines, which contained the A and B genomes from a tetraploid wheat cultivar Langdon and the diverse D genomes originating from the different Ae. tauschii accessions, with distinct levels of freezing tolerance after cold acclimation. Quantitative RT-PCR analyses showed that the transcription accumulated levels of the Cor/Lea, CBF, and fructan biosynthesis-related genes were higher in more freezing-tolerant lines than those in the sensitive lines. The fructan biosynthesis pathway would be associated with cold acclimation to develop wheat freezing tolerance and related with diversity of the freezing tolerance level in addition to the CBF-mediated Cor/Lea expression pathway.
2014-10-10 | GSE61621 | GEO
Project description:We conducted microarray analysis to study comprehensive changes of gene expression profile under long-term low-temperature (LT) treatment and to identify other LT-responsive genes related with cold acclimation in seedling leaves and crown tissues (shoots containing apical meristems) of a synthetic hexaploid wheat line. The microarray analysis revealed marked up-regulation of a number of Cor/Lea genes and fructan biosynthesis-related genes under the long-term LT treatment. For validation of the microarray data, we selected four synthetic wheat lines, which contained the A and B genomes from a tetraploid wheat cultivar Langdon and the diverse D genomes originating from the different Ae. tauschii accessions, with distinct levels of freezing tolerance after cold acclimation. Quantitative RT-PCR analyses showed that the transcription accumulated levels of the Cor/Lea, CBF, and fructan biosynthesis-related genes were higher in more freezing-tolerant lines than those in the sensitive lines. The fructan biosynthesis pathway would be associated with cold acclimation to develop wheat freezing tolerance and related with diversity of the freezing tolerance level in addition to the CBF-mediated Cor/Lea expression pathway. Expression patterns were compared between a synthetic wheat line which treated 24M-bM-^DM-^C and 4M-bM-^DM-^C. Total RNA samples were respectively isolated from leaves and crown tissues of the synthetic line grown at normal temperature for 3 weeks and then at 4M-BM-0C for 12 and 6 weeks. Two independent experiments were conducted in each exprement.
2014-10-10 | E-GEOD-61621 | biostudies-arrayexpress
Project description:Brassinosteroids (BRs) are steroid hormones that are essential for the development of plants. A tight control of BR homeostasis is vital for modulating their impact on various growth responses. However, whilst it is recognized that the rapid adaptation of de novo synthesis plays a key role in adjusting required BR levels, our knowledge of the mechanisms governing feedback control is limited. We identified the transcription factor CESTA as a novel regulator of BR biosynthesis. ces-D was isolated in a screen of Arabidopsis mutants by BR over-accumulation phenotypes. Loss-of-function analysis and the use of a dominant repressor version revealed functional overlap among CESTA and its homologues and confirmed the role of these basic helix-loop-helix proteins in the positive control of BR biosynthetic gene expression. In this experiment we compare the transcriptome of the CESTA mutant to wild-type plants using the Affymetrix ATH1 array.
2010-07-12 | GSE20225 | GEO
Project description:Plants possess a cold acclimation system to acquire freezing tolerance through pre-exposure to non-freezing low temperatures. The transcriptional cascade of C-repeat binding factors (CBFs)/dehydration response element-binding factors (DREBs) is considered a major transcriptional regulatory pathway during cold acclimation. However, little is known regarding the functional significance of mRNA stability regulation in the response of gene expression to cold stress. The actual level of individual mRNAs is determined by a balance between mRNA synthesis and degradation. Therefore, it is important to assess the regulatory steps to increase our understanding of gene regulation. Here, we analyzed temporal changes in mRNA amounts and half-lives in response to cold stress in Arabidopsis cell cultures based on genome-wide analysis. In this mRNA decay array method, mRNA half-life measurements and microarray analyses were combined. In addition, temporal changes in the integrated value of transcription rates were estimated from the above two parameters using a mathematical approach. Our results showed that several cold-responsive genes, including Cold-regulated 15a, were relatively destabilized, whereas the mRNA amounts were increased during cold treatment by accelerating the transcription rate to overcome the destabilization. Considering the kinetics of mRNA synthesis and degradation, this apparently contradictory result supports that mRNA destabilization is advantageous for the swift increase in CBF-responsive genes in response to cold stress.
2017-05-02 | GSE81477 | GEO
Project description:Brassinosteroids (BRs) are steroid hormones that are essential for the development of plants. A tight control of BR homeostasis is vital for modulating their impact on various growth responses. However, whilst it is recognized that the rapid adaptation of de novo synthesis plays a key role in adjusting required BR levels, our knowledge of the mechanisms governing feedback control is limited. We identified the transcription factor CESTA as a novel regulator of BR biosynthesis. ces-D was isolated in a screen of Arabidopsis mutants by BR over-accumulation phenotypes. Loss-of-function analysis and the use of a dominant repressor version revealed functional overlap among CESTA and its homologues and confirmed the role of these basic helix-loop-helix proteins in the positive control of BR biosynthetic gene expression. In this experiment we compare the transcriptome of the CESTA mutant to wild-type plants using the Affymetrix ATH1 array. 4 samples were used in this experiment.
2010-07-12 | E-GEOD-20225 | biostudies-arrayexpress
Project description:Plants in temperate regions have evolved mechanisms to survive sudden temperature drops. Previous reports have indicated that the cold acclimation mechanism is light-dependent and does not fully operate under a low light intensity. In these studies, plants were grown under a long-day photoperiod and were more sensitive to freezing stress. However, winter annuals like Arabidopsis thaliana Col-0 germinate in the fall, overwinter as rosettes, and therefore must acclimate under short photoperiods and low irradiance. The role of light intensity was analysed in plants grown under a short-day photoperiod at the growth stage 1.14. Plants were acclimated at 4 °C for seven days under 100 and 20 μmol m-2s-1 PPFD for control and limited-light conditions, respectively. All cold acclimated plants accumulated molecular markers reportedly associated with acquired freezing tolerance, including proline, sucrose, CBFs, and COR gene protein products dehydrins and low-temperature-responsive proteins LTIs. Observed changes indicated that low PPFD did not inhibit the cold acclimation process, and the freezing stress experiment confirmed similar survival rates. The molecular analysis found distinct PPFD-specific adaptation mechanisms that were manifested in contrasting content of anthocyanins, cytokinin conjugates, abundances of proteins forming photosystems, and enzymes of protein, energy, and ROS metabolism pathways. Finally, this study led to the identification of putative proteins and metabolite markers correlating with susceptibility to freezing stress of non-acclimated plants grown under low PPFD. Our data show that Arabidopsis plants grown under short-day photoperiod can be fully cold-acclimated under limited light conditions, employing standard and PPFD-specific pathways.
2021-07-08 | PXD025234 | Pride
Project description:Chromosome 5A of wheat is a major regulator of freezing tolerance. It harbours gene loci controlling freezing tolerance (Fr-A1 and Fr-A2) and vernalization requirement (Vrn-A1). The number of cold-responsive genes and their functional classification was studied by cDNA macroarray-based transcript profiling in the moderately freezing-sensitive wheat (Triticum aestivum L.) variety Chinese Spring and two derived chromosome 5A substitution lines exhibiting lower or higher levels of freezing tolerance, respectively. During 21-days of cold acclimation at 2 °C the transcript level changed significantly for 681 (6.6%) out of 10,297 studied unigenes. The freezing-tolerant substitution line exhibited about 1.5-fold higher number of differentially expressed genes compared to the sensitive one. Transcript levels of several genes were altered by cold treatment only in one of the three genotypes. For 78 genes regulation by factors hosted on chromosome 5A was determined and postulated. These genes encoded proteins involved in transcriptional regulation, defence processes and carbohydrate metabolism. Three of the chromosome 5A-affected genes, having especially strong and rapid cold-induced changes of transcript level, namely Tacr7 (Triticum aesticum cold-responsive gene 7 homolog), Cab (Ca2+-binding), and Dem (deficient embryo and meristems) were genetically mapped and characterized in further detail. Only the gene Cab was located on chromosome 5A, whereas Tacr7 and Dem resided on other chromosomes. Although chromosome 5A-affected genes are also found to be localised on the same chromosome, the present findings indicate that chromosome 5A is strongly involved in trans-regulation of genes potentially due to the presence of regulatory loci, like Fr-A2, which is harboring numerous CBF transcription factors.
2009-06-22 | E-IPKG-10 | biostudies-arrayexpress
Project description:During cold acclimation plants increase their freezing tolerance in response to low non-freezing temperatures. This is accompanied by many physiological, biochemical and molecular changes that have been extensively investigated. In addition, many cold acclimated plants become more freezing tolerant during exposure to mild, non-damaging sub-zero temperatures. There is hardly any information available about the molecular basis of this adaptation. However, Arabidopsis thaliana is among the species that acclimate to sub-zero temperatures. This makes it possible to use the molecular and genetic tools available in this species to identify components of sub-zero signal transduction and acclimation. Here, we have used microarrays and a qRT-PCR primer platform covering 1880 genes encoding transcription factors to monitor changes in gene expression in the accessions Columbia-0, Rschew and Tenela during the first three days of sub-zero acclimation at -3°C. The results indicate that gene expression during sub-zero acclimation follows a tighly controlled time-course. Especially AP2/EREBP and WRKY transcription factors may be important regulators of sub-zero acclimation, although the CBF signal transduction pathway seems to be less important during sub-zero than during cold acclimation. Globally, we estimate that approximately 5% of all Arabidopsis genes are regulated during sub-zero acclimation. Particularly photosynthesis-related genes were down-regulated and genes belonging to the functional classes of cell wall biosynthesis, hormone metabolism and RNA regulation of transcription were up-regulated. Collectively, these data provide the first global analysis of gene expression during sub-zero acclimation and allow the identification of candidate genes for forward and reverse genetic studies into the molecular mechanisms of sub-zero acclimation. We used whole genome microarrays to monitor changes in gene expression in the Arabidopsis thaliana accessions Columbia-0, Rschew and Tenela during three days of acclimation to sub-zero temperature at -3°C after cold acclimation
2014-03-12 | GSE55835 | GEO
Project description:Brassinosteroids (BRs) are a class of class of phytohormones with important roles in regulating physiological and developmental processes. Small RNAs, including small interfering RNAs and microRNAs (miRNAs), are non-protein coding RNAs that regulate gene expression at the transcriptional and post-transcriptional levels. However, the roles of small RNAs in BR response have not been studied well. In this study, we aimed to identify BR-responsive small RNA clusters and miRNAs in Arabidopsis. In addition, the effect of BR-responsive small RNAs on their transcripts and target genes were examined. Small RNA libraries were constructed from control and epibrassinolide-treated seedlings. After sequencing the small RNA libraries, differentially expressed small RNA clusters were identified by examining the expression levels of small RNAs in 100-nt bins of Arabidopsis genome. To identify the BR-responsive miRNAs, the expression levels of all the annotated mature miRNAs, registered in miRBase, were analyzed. Previously published RNA-seq data were utilized to monitor the BR-responsive expression patterns of differentially expressed small RNA clusters and miRNA target genes. In results, 38 BR-responsive small RNA clusters, including 30 down-regulated and eight up-regulated clusters, were identified. These differentially expressed small RNA clusters were from miRNA loci, transposons, protein-coding genes, pseudo genes and others. Of these, a transgene, BRI1, accumulates small RNAs, which are not found in the wild type. Small RNAs in this transgene are up-regulated by BRs while BRI1 mRNA is down-regulated by BRs. By analyzing the expression patterns of mature miRNAs, we have identified BR-repressed miR398a-5p and BR-induced miR156g. Although miR398a-5p is down-regulated by BRs, its predicted targets were not responsive to BRs. However, SPL3, a target of BR-inducible miR156g, is down-regulated by BRs. BR-responsive small RNAs and miRNAs identified in this study will provide an insight into the role of small RNAs in BR responses in plants. Especially, we suggest that miR156g/SPL3 module might play a role in BR-mediated growth and development in Arabidopsis.
2020-04-27 | GSE149360 | GEO
Project description:The C-REPEAT-BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. Previous research documented that constitutively expressed upstream transcription factors are activated by cold stress to induce the expression of CBF genes and the resulting CBF proteins trigger the expression of downstream cold responsive genes that confer freezing tolerance. In the present study, we found that dysfunction of RNA-DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol IV and Pol V as well as Pol II, and is required for RNA-directed DNA methylation (RdDM) and proper plant development in Arabidopsis, reduced chilling and freezing tolerance in Arabidopsis as evidenced by decreased survival and increased electrolyte leakage under cold stress conditions. CBFs and CBF regulon genes were down-regulated in rdm4 but not nrpe1 (the largest subunit of PolV) mutant plants, suggesting that the role of RDM4 in cold stress responses is independent of the RdDM pathway. Overexpression of RDM4 increased the expression of CBFs and CBF regulon genes and decreased cold-induced membrane injury. The rdm4 mutants exhibited decreased antioxidant enzyme activities and increased accumulation of reactive oxygen species. Microarray analysis indicated that a great proportion of genes affected by rdm4 overlapped with those affected by CBF2 and CBF3 in Arabidopsis. Chromatin immunoprecipitation (ChIP) results suggested that RDM4 is important for Pol II occupancy at the promoters of CBF genes but not the promoters of up-stream regulators of CBFs. Together, these data indicate that RDM4 acts as a component of a Pol II transcription complex that regulates CBF gene expression and cold stress resistance in Arabidopsis.
2016-06-30 | GSE63184 | GEO