Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA343034 | ENA |
REPOSITORIES: ENA
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Project description:During low temperature exposure, temperate plant species increase their freezing tolerance in a process termed cold acclimation. During deacclimation in response to warm temperatures cold acclimated plants lose freezing tolerance and resume growth and development. While considerable effort has been directed toward understanding the molecular and metabolic basis of cold acclimation, much less information is available about the regulation of deacclimation. Here, we report metabolic (GC-MS) and transcriptional (microarrays, qRT-PCR) responses underlying deacclimation during the first 24 h after a shift of cold acclimated Arabidopsis thaliana (Columbia-0) plants to warm temperature. The data revealed a faster response of the transcriptome than of the metabolome and provided evidence for tightly regulated temporal responses at both levels. Metabolically deacclimation is associated with decreasing contents of sugars, amino acids and glycolytic and TCA cycle intermediates, indicating an increased need for carbon sources and respiratory energy production associated with growth resumption under warm temperature conditions. Deacclimation also involves extensive down-regulation of protein synthesis and changes in the metabolism of lipids and cell wall components. Altered hormonal regulation appears particularly important during deacclimation, with changes in the expression of genes related to auxin, gibberellin, brassinosteroid, jasmonate and ethylene metabolisms. Several transcription factor families controlling fundamental aspects of plant development are significantly regulated during deacclimation, emphasizing that loss of freezing tolerance and growth resumption are interrelated processes that are transcriptionally highly interrelated. Expression patterns of some clock oscillator components during deacclimation resembled those under warm conditions, indicating at least partial re-activation of the circadian clock. This study provide the first comprehensive analysis of the regulation of deacclimation in cold acclimated plants. The data indicate cascades of rapidly regulated genes and metabolites that underly the developmental switch resulting in reduced freezing tolerance and the resumption of growth. They constitute a reference dataset of genes, metabolites and pathways that are crucial during the first rapid phase of deacclimation and will be useful for the further analysis of this important but under-researched plant process. We used whole genome microarrays to monitor changes in gene expression in the Arabidopsis thaliana accession Columbia-0 during the first 24 h after a shift of cold acclimated plants to warm temperature.
2017-09-18 | GSE86935 | GEO
Project description:Plants adapt to cold, non-freezing temperatures through cold acclimation and subsequently lose the acquired freezing tolerance in warmer temperatures in a process called deacclimation. By measuring the freezing tolerance of mutant lines, this study identified that the loss of HRA1, LBD41, MBF1c and JUB1 slows the rate of deacclimation in the first four days in Arabidopsis thaliana. Comparative transcriptomic (RNA-Seq) and co-expression analysis of Col-0, mbf1c and jub1 during deacclimation identified an involvement of thermoswitches, cell wall remodeler and transporters in the regulation of the rate of deacclimation. In mbf1c and jub1 a unique increase in stress responsive genes and regulation of the jasmonic acid pathway was detected and linked to the mutants’ retention of freezing tolerance during deacclimation. Hypoxia was observed to be induced in early deacclimation evidenced by an increase in ADH enzyme activity and upregulated gene expression of hypoxia markers (qRT-PCR). This work suggests that the overserved hypoxia response creates hypoxic niches within the plants and supports growth and development during deacclimation.
2022-09-30 | GSE196111 | GEO
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:To understand mRNA expression pattern during cold acclimation and deacclimation, transcriptional profiling of cold acclimation and deacclimation-treated plants were analyzed using Agilent-015059 Arabidopsis 3 Oligo Microarray 4x44K G2519F.
2014-10-02 | GSE49796 | GEO
Project description:Arabidopsis thaliana and Eutrema salsugineum show the ability to cold acclimate. However, the degree of freezing tolerance depends in both cases on the accession. To elucidate the transcriptional basis of this differencial freezing tolerance, we performed where we grew plants under control conditions (20°C/18°C day/night) or under cold conditions (additional 4°C for 2 weeks). Rosettes were harvested from non-acclimated and cold acclimated plants for RNA isolation. Expression patterns were compared between treatments, accessions and species.
2018-01-01 | GSE100108 | GEO
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 Plants from Arabidopsis thaliana accessions Columbia-0, Rschew and Tenela were cold acclimated at 4°C for two weeks. Detached leaves were then sub-zero acclimated at -3°C for 8 h, 1 d or 3 d at -3°C. Leaves of cold acclimated plants and sub-zero acclimated leaves were collected for RNA extraction and hybridization on Affymetrix ATH1 microarrays in order to explore temporal transcriptome changes during sub-zero acclimation. For each sample total RNA was isolated from a pool of three leaves from three different plants. The experiment was performed in three idenpendent biological replicates.
2014-03-12 | E-GEOD-55835 | biostudies-arrayexpress
Project description:To understand mRNA expression pattern during cold acclimation and deacclimation, transcriptional profiling of cold acclimation and deacclimation-treated plants were analyzed using Agilent-015059 Arabidopsis 3 Oligo Microarray 4x44K G2519F. Arabidopsis Col-0 were grown on MS plate for 2 weeks (16 hours light / 8 hours dark). Two week-old Arabidopsis samples (NA, non acclimation) were treated with cold (2 M-BM-:C) for 7 days (CA7d) under 12h/12h light/dark conditions. Deacclimation-treated samples (DA6h, DA12h, DA24h) were grown at normal growth temperature under long day conditions after cold treatment for 7 days. Then total RNA was prepared from the whole seedling and used for the microarray hybridization. Three replicative hybridization experiments for each array were carried out using the independent biological samples.
2014-10-02 | E-GEOD-49796 | biostudies-arrayexpress
Project description:Abscisic acid (ABA) plays crucial regulatory roles in cold acclimation and deacclimation of grapevine, making it a potential tool to be utilized in vineyards for the acquisition of preferred phenotypes in winter and spring. To understand the function of ABA , we conducted two experiments during cold acclimation and deacclimation and evaluated the impact of exogenous abscisic acid (ABA) on the grapevine transcriptome. RNA-seq data were collected periodically hours or days after ABA treatment. Transcriptomic data were analyzed using principal component analysis (PCA) , hierarchical clustering, unsupervised weighed gene co-expression network analysis (WGCNA), contrast-based differentially expressed genes (DEGs) identification and pre-ranked gene set enrichment analysis (GSEA). Our results suggest that ABA functions differently during cold acclimation and deacclimation by selectively regulating key pathways including auxin/indole acetic acid (IAA) metabolism, galactose metabolism and ribosome biogenesis. We also identified the activation of several apparent negative feedback systems that regulated ABA-induced transcriptomic changes, suggesting the existence of a balancing system in response to excessive ABA.
2022-01-25 | GSE184114 | GEO
Project description:Environmental fluctuations lead to a rapid adjustment of the physiology of Escherichia coli, necessitating changes on every level of the underlying cellular and molecular network. Thus far, the vast majority of global analyses of E. coli stress responses have been limited to just one level, gene expression. Here we incorporate the metabolite composition together with gene expression data in order to provide a more comprehensive insight on system level stress adjustments by describing detailed time-resolved E. coli response to five different perturbations (cold, heat, oxidative stress, lactose diauxie, and stationary phase). The metabolite response is more specific as compared to the general response observed on the transcript level and is reflected by much higher specificity during the early stress adaptation phase and when comparing the stationary phase response to other perturbations. Despite these differences, the response on both levels still follows the same dynamics and general strategy of energy conservation as reflected by rapid decrease of central carbon metabolism intermediates coinciding with down regulation of genes related to cell growth. Application of co-clustering and canonical correlation analysis on combined metabolite and transcript data identified a number of significant condition dependent associations between metabolites and transcripts. The results confirm and extend existing models about co-regulation between gene expression and metabolites demonstrating the power of integrated systems oriented analysis.
2010-02-13 | GSE20305 | GEO
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