Physiological and transcriptomic characterization of cold acclimation in endodormant grapevine under different temperature regimes
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ABSTRACT:
ORGANISM(S): Vitis vinifera
PROVIDER: GSE232062 | GEO | 2024/11/06
REPOSITORIES: GEO
Similar Datasets
Project description:Physiological and transcriptomic characterization of cold acclimation in endodormant grapevine under different temperature regimes
| PRJNA970724 | ENA
Project description:Earlier findings indicated that light plays a critical role in the development of frost tolerance in winter cereals. However, the exact mechanism is still poorly understood. In the present work the effects of light during the cold acclimation period were studied in chilling-sensitive maize plants. The results show that although exposure to relatively high light intensities during cold acclimation at 15 °C causes various stress symptoms, it enhances the effectiveness of acclimation to chilling conditions (5 °C in the light). Interestingly, certain stress responses were light-dependent not only in the leaves, but also in the roots. A microarray study was also conducted to achieve a better understanding of the interaction of low temperature and light intensity during the cold hardening period. Numerous genes significantly differentially expressed were observed in almost all assimilation and metabolic pathways. Acclimation at moderately low temperature and low light intensity reduced the level of soluble sugars, while chilling increased it. Greater accumulation during hardening was detected at relatively high light intensity. It seems that the photoinhibition induced by low temperature is a necessary evil for cold acclimation processes in plants.
2020-12-31 | GSE107913 | GEO
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:The REIL proteins are required for late ribosomal biogenesis and accumulation of the 60S large ribosome subunit in mature leaves of Arabidopsis thaliana upon acclimation to low temperature. To validate these functions in roots, we conducted a multi-level system analysis targeted at understanding defects and compensations responses of reil mutants before acclimation to low temperature and following temperature shift. Hydroponic root tissue enabled analysis of eukaryotic ribosome complexes with negligible interference of organelle ribosomes. Hydroponic cultivation attenuated the growth defect of reil mutants at low temperature and provided new insights into the primary functions of Arabidopsis REIL proteins. Arabidopsis tightly controls the balance of non-translating 40S and 60S subunits. Reil mutants initially deplete both non-translating subunits upon shift to 10°C and subsequently replenish these pools slowly. Reil mutations compensate the 60S biosynthesis defect by increased baseline levels of non-translating 40S and 60S subunits and depletion of a likely non-translating, KCl-sensitive 80S sub-fraction in the cold. We infer that Arabidopsis buffers fluctuating translation demands following temperature cues by activating non-translating ribosome fractions before de novo synthesis meets temperature-induced demands. Reil1 reil2 double mutants accumulate 43S-preinitiation complexes and pre-60S-maturation complexes and affect the paralog composition of non-translating ribosome fractions. With few exceptions, e.g. RPL3B and RPL24C, these changes were not under transcriptional control. Our study suggests requirement of de novo synthesis of eukaryotic ribosomes for long-term cold acclimation. Double mutant analysis indicates feedback control of REIL-mediated 60S maturation on NUC2 and eIF3C2 transcription and implies functions of two so far non-described proteins in late plant ribosome biogenesis. We propose that Arabidopsis requires biosynthesis of specialized ribosomes for successful cold acclimation.
2021-02-03 | GSE144916 | GEO
Project description:Purpose: We aimed at i) obtaining insight into how a thermophile organism reacts to cold stress, and ii) evaluating the impact of HGT candidates on the acclimation process to temperature decrease. Methods: The experimental design followed a temperature shift timeline: after two weeks of cultivation at 42°C, constant illumination (90 μE) and constant shaking (160 rpm) in photoautotrophic conditions the first sampling took place (Hot_T48_1) and the cultures of G.sulphuraria were swiftly moved to 28°C ( = cold temperature). "Cold" samples were taken after 3h (Cold_T3_2), 12h (Cold_T12_3) and 48h (Cold_T48_4). After cold treatment at 28°C for 48 hours, the G. sulphuraria was then switched to 46°C for 48 hours (="Hot"). Again, samples were taken after 3h (Hot_T3_5), 12h (Hot_T12_6) and 48h (Hot_T48_7). Altogether, a 48h temperature timeshift at 28°C and successive recovery at 46°C were targeted for sampling. Results: Galdieria sulphuraria is a unicellular red alga that lives in hot, acidic, toxic metal-rich, volcanic environments, where few other organisms survive. Its genome harbours up to 5% of genes most likely acquired through horizontal gene transfer. These genes probably contributed to G. sulphuraria’s adaptation to its extreme habitats, resulting in today’s polyextremophilic traits. Here, we applied RNA-sequencing to obtain insights into the acclimation of a thermophilic organism towards temperatures below its growth optimum and to study how horizontally acquired genes contribute to cold acclimation. A decrease in growth temperature from 42 °C/46 °C to 28 °C resulted in an upregulation of ribosome biosynthesis, while excreted proteins, probably components of the cell wall, were downregulated. Photosynthesis was suppressed at cold temperatures, and transcript abundances indicated that C-metabolism switched from gluconeogenesis to glycogen degradation. Folate cycle and S-adenosylmethionine cycle (one-carbon metabolism) were transcriptionally upregulated, probably to drive the biosynthesis of betaine. All these cold-induced changes in gene expression were reversible upon temperature increase. Numerous genes acquired by horizontal gene transfer displayed pronounced temperature-dependent expression changes, corroborating the view that these genes contributed to adaptive evolution in G. sulphuraria.
2018-12-31 | GSE118890 | GEO
Project description:Ambient temperature affects organisms comprehensively, however cold responses are different among tissues. Here, we adopt a transcript screening approach to explore and compare the cold responses in zebrafish gills and brain. Zebrafish were exposed to cold and the oligonucleotide-based microarray was used to identify cold-induced genes. Principle component analysis (PCA) of the gene expression profiles indicated that gills develop different strategies for the increasing of exposure period while brain relatively remained stable. Combining statistic and clustering methods, we found that gills showed higher protein metabolism and cell activity while brain showed higher stress responses and detoxification during cold acclimation. According to the microarray data sets, we extended the study on ionocyte- and isotocin neuron-related genes in gills and brain, respectively, and found these genes were broadly stimulated by cold. These data suggest that cold activates specific physiological functions in different tissues. Taken together, our results provide molecular evidences to elucidate the cold acclimation in zebrafish gills and brain. Keywords: Time course, Tissue types
2016-07-01 | GSE10958 | GEO
Project description:Experiment was designed to identify transcriptome changes during cold acclimation of Drosophila melanogaster male flies. Resistance to cold is often measured by recovery times from chill coma, which is induced almost immediately upon exposure to low but non-freezing temperatures (~0C), with flies becoming immobilised and losing motor activity. This paralysis is also ostensibly reversible upon return to normal temperatures, although again there can be longer term effects. Acclimation for increased cold resistance requires exposure periods ranging from hours or days to several weeks at low temperatures between 0C to 12C, and samples were taken during the cold acclimation period (1 hr, 2 hr, 3 hr, 6 hr, 12 hr, 24 hr, 36 hr and 48 hr).
2014-05-01 | E-MTAB-1607 | biostudies-arrayexpress
Project description:To understand physiological mechanisms of cold acclimation in pea, we performed a transcriptomique analysis in order to compare the response to LT treatment in two varieties, one being cold tolerant (Champagne) and the other cold sensitive (Terese).
2010-04-01 | GSE19209 | 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
2014-03-12 | GSE55835 | GEO
Project description:Adult male fish were exposed to the various temperature acclimation conditions as outlined in the published manuscript and RNA was extracted from fish at each time point as listed in the experiment set description. Abstract: Eurythermal ectotherms commonly thrive in environments that expose them to large variations in temperature on daily and seasonal bases. The roles played by alterations in gene expression in enabling eurytherms to adjust to these two temporally distinct patterns of thermal stress are poorly understood. We used cDNA microarray analysis to examine changes in gene expression in a eurythermal fish, Austrofundulus limnaeus, subjected to long-term acclimation to constant temperatures of 20, 26 and 37 degrees C and to environmentally realistic daily fluctuations in temperature between 20 degrees C and 37 degrees C. Our data reveal major differences between the transcriptional responses in the liver made during acclimation to constant temperatures and in response to daily temperature fluctuations. Control of cell growth and proliferation appears to be an important part of the response to change in temperature, based on large-scale changes in mRNA transcript levels for several key regulators of these pathways. However, cell growth and proliferation appear to be regulated by different genes in constant versus fluctuating temperature regimes. The gene expression response of molecular chaperones is also different between constant and fluctuating temperatures. Small heat shock proteins appear to play an important role in response to fluctuating temperatures whereas larger molecular mass chaperones such as Hsp70 and Hsp90 respond more strongly to chronic high temperatures. A number of transcripts that encode for enzymes involved in the biosynthesis of nitrogen-containing organic osmolytes have gene expression patterns that indicate a possible role for these 'chemical chaperones' during acclimation to chronic high temperatures and daily temperature cycling. Genes important for the maintenance of membrane integrity are highly responsive to temperature change. Changes in fatty acid saturation may be important in long-term acclimation and in response to fluctuating temperatures; however cholesterol metabolism may be most critical for short-term acclimation to fluctuating temperatures. The variable effect of temperature on the expression of genes with daily rhythms of expression indicates that there is a complex interaction between the temperature cycle and daily rhythmicity in gene expression. A number of new hypotheses concerning temperature acclimation in fish have been generated as a result of this study. The most notable of these hypotheses is the possibility that the high mobility group b1 (HMGB1) protein, which plays key roles in the assembly of transcription initiation and enhanceosome complexes, may act as a compensatory modulator of transcription in response to temperature, and thus as a global gene expression temperature sensor. This study illustrates the utility of cDNA microarray approaches in both hypothesis-driven and 'discovery-based' investigations of environmental effects on organisms. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Keywords: all_pairs
2006-01-06 | GSE3981 | GEO