The vacuolar sugar transporter EARLY RESPONSE TO DEHYDRATION 6-LIKE4 regulates fructose signaling and plant growth
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE222562 | GEO | 2023/01/15
REPOSITORIES: GEO
Similar Datasets
Project description:For many organisms the ability to cold acclimate with the onset of seasonal cold has major implications for their fitness. In insects, where this ability is widespread, the physiological changes associated with increased cold tolerance have been well studied. Despite this, little work has been done to trace changes in gene expression during cold acclimation that lead to an increase in cold tolerance. We used an RNA-Seq approach to investigate this in two species of the Drosophila virilis group. We found that the majority of genes that are differentially expressed during cold acclimation differ between the two species. Despite this, the biological processes associated with the differentially expressed genes were broadly similar in the two species. These included: metabolism, cell membrane composition, and circadian rhythms, which are largely consistent with previous work on cold acclimation / cold tolerance. In addition, we also found evidence of the involvement of the rhodopsin pathway in cold acclimation, a pathway that has been recently linked to thermotaxis. Interestingly, we found no evidence of differential expression of stress genes implying that long-term cold acclimation and short-term stress response may have a different physiological basis.
2014-12-27 | GSE58925 | GEO
Project description:Intertidal zone organisms can experience transient freezing temperatures during winter low tides, but their extreme cold tolerance mechanisms are not known. Petrolisthes cinctipes is a temperate mid-high intertidal zone crab species that can experience wintertime habitat temperatures below the freezing point of seawater. We examined how cold tolerance changed during the initial phase of thermal acclimation to cold and warm temperatures, as well as the persistence of cold tolerance during long-term thermal acclimation. Thermal acclimation for as little as 6 hours at 8˚C enhanced crab tolerance during a 1h exposure to -2°C relative to crabs acclimated to 18˚C. Potential mechanisms for this enhanced tolerance were elucidated using cDNA microarrays to probe for differences in gene expression in cardiac tissue of warm and cold acclimated crabs during the first day of thermal acclimation. No changes in gene expression were detected until 12h of thermal acclimation. Genes strongly upregulated in warm acclimated crabs represented immune response and extracellular / intercellular processes, suggesting that warm acclimated crabs had a generalized stress response and may have been remodelling tissues or altering intercellular processes. Genes strongly upregulated in cold acclimated crabs included many that are involved in glucose production suggesting that cold acclimation involves increasing intracellular glucose as a cryoprotectant. Structural cytoskeletal proteins were also strongly represented among the genes upregulated in only cold acclimated crabs. There were no consistent changes in composition or the level of unsaturation of membrane phospholipid fatty acids with cold acclimation, which suggests that neither short- nor long-term changes in cold tolerance are mediated by changes in membrane fatty acid composition. Overall, our study demonstrates that initial changes in cold tolerance are likely not regulated by transcriptomic responses, but that gene expression-related changes in homeostasis begin within 12 hours – the length of a tidal cycle. all array data and raw images archived at the Porcelain Crab Array Database (http://array.sfsu.edu)
2012-03-01 | GSE35307 | GEO
Project description:Intertidal zone organisms can experience transient freezing temperatures during winter low tides, but their extreme cold tolerance mechanisms are not known. Petrolisthes cinctipes is a temperate mid-high intertidal zone crab species that can experience wintertime habitat temperatures below the freezing point of seawater. We examined how cold tolerance changed during the initial phase of thermal acclimation to cold and warm temperatures, as well as the persistence of cold tolerance during long-term thermal acclimation. Thermal acclimation for as little as 6 hours at 8˚C enhanced crab tolerance during a 1h exposure to -2°C relative to crabs acclimated to 18˚C. Potential mechanisms for this enhanced tolerance were elucidated using cDNA microarrays to probe for differences in gene expression in cardiac tissue of warm and cold acclimated crabs during the first day of thermal acclimation. No changes in gene expression were detected until 12h of thermal acclimation. Genes strongly upregulated in warm acclimated crabs represented immune response and extracellular / intercellular processes, suggesting that warm acclimated crabs had a generalized stress response and may have been remodelling tissues or altering intercellular processes. Genes strongly upregulated in cold acclimated crabs included many that are involved in glucose production suggesting that cold acclimation involves increasing intracellular glucose as a cryoprotectant. Structural cytoskeletal proteins were also strongly represented among the genes upregulated in only cold acclimated crabs. There were no consistent changes in composition or the level of unsaturation of membrane phospholipid fatty acids with cold acclimation, which suggests that neither short- nor long-term changes in cold tolerance are mediated by changes in membrane fatty acid composition. Overall, our study demonstrates that initial changes in cold tolerance are likely not regulated by transcriptomic responses, but that gene expression-related changes in homeostasis begin within 12 hours – the length of a tidal cycle. all array data and raw images archived at the Porcelain Crab Array Database (http://array.sfsu.edu) n=264 specimens were divided into warm (18°C, n=96), cold (8°C, n=96), and control (13°C, n=72) acclimation groups. Crabs were sampled from the 13°C group at 0 h (the start of the experiment) and 24 h, the termination of the experiment. Crabs were sampled from the warm and cold acclimation groups at 6, 12, 18, and 24 hours following the start of thermal acclimation. At each time point, heart tissue from n=16 crabs from each group was dissected, flash frozen and stored at −80°C. A pooled total aRNA sample was prepared for each group by mixing equal quantities of total RNA from n=5 individuals in each group in order to have the same amount of biological diversity within each pooled RNA sample. For microarray hybridizations we used n=25 slides in an incomplete loop design where each sample was hybridized n=5 times, 2-3 times labelled with each Cy dye
2012-03-01 | E-GEOD-35307 | biostudies-arrayexpress
Project description:Brassinosteroids (BRs) are growth-promoting plant hormones that play a role in abiotic stress responses, but molecular modes that enable this activity remain largely unknown. Here we show that BRs participate in the regulation of freezing tolerance. BR signaling-defective mutants of Arabidopsis thaliana were hypersensitive to freezing before and after cold acclimation. The constitutive activation of BR signaling, in contrast, enhanced freezing resistance. Evidence is provided that the BR-controlled basic helix–loop–helix transcription factor CESTA (CES) can contribute to the constitutive expression of the C-REPEAT/DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR (CBF) transcriptional regulators that control cold responsive (COR) gene expression. In addition, CBF-independent classes of BR-regulated COR genes are identified that are regulated in a BR- and CES-dependent manner during cold acclimation. A model is presented in which BRs govern different cold-responsive transcriptional cascades through the posttranslational modification of CES and redundantly acting factors. This contributes to the basal resistance against freezing stress, but also to the further improvement of this resistance through cold acclimation. We used microarray data to investigate the contribution of different pathways to cold tolerance of Arabidopsis thaliana .
2016-09-10 | GSE86605 | GEO
Project description:Mild cold acclimation increases insulin sensitivity and previous studies indicate that some level of muscle contraction is essential for provoking this effect. Here, 15 adults with overweight or obesity, the majority of which had impaired glucose tolerance (n=9), were intermittently cold exposed for 10 consecutive days to induce 1 hour of shivering per day. Cold acclimation with shivering improved oral glucose tolerance, blood pressure, fasting glucose, triglyceride, and non-esterified free-fatty acid concentrations, and may thus represent a novel lifestyle approach for the prevention and treatment of obesity-related metabolic disorders.
2024-09-24 | GSE271452 | GEO
Project description:Pre-exposure of plants to various abiotic conditions confers improved tolerance to subsequent stress. Mild drought acclimation induces acquired rapid desiccation tolerance (RDT) in the resurrection plant Boea hygrometrica, but the mechanisms underlying the priming and memory processes remain unclear. In this study, we demonstrated that drought acclimationinduced RDT can be maintained for at least four weeks but was completely erased after 18 weeks based on a combination of the phenotypic and physiological parameters. Global transcriptome analysis identified several RDT-specific rapid dehydration-responsive genes related to cytokinin and phospholipid biosynthesis, nitrogen and carbon metabolism, and epidermal morphogenesis, most of which were pre-induced by drought acclimation. Comparison of whole-genome DNA methylation revealed dehydration stress-responsive hypomethylation in the CG, CHG, and CHH contexts and acclimation-induced hypermethylation in the CHH context of the B. hygrometrica genome, consistent with the transcriptional changes in methylation pathway genes. As expected, the global promoter and gene body methylation levels were negatively correlated with gene expression levels in both acclimated and dehydrated plants but showed no association with transcriptional divergence during the procedure. Nevertheless, the promoter methylation variations in the CG and CHG contexts were significantly associated with the differential expression of genes required for fundamental genetic processes of DNA conformation, RNA splicing, translation, and post-translational protein modification during acclimation, growth, and rapid dehydration stress response. It was also associated with the dehydration stress-induced upregulation of memory genes, including pre-mRNA-splicing factor 38A, vacuolar amino acid transporter 1-like, and UDP-sugar pyrophosphorylase, which may contribute directly or indirectly to the improvement of dehydration tolerance in B. hygrometrica plants. Altogether, our findings demonstrate the potential implications of DNA methylation in dehydration stress memory and, therefore, provide a molecular basis for enhanced dehydration tolerance in plants induced by drought acclimation.
2021-06-08 | GSE158737 | GEO
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:Frost tolerance is the main component of winter-hardiness. To express this trait, plants have to sense low temperature, and respond by activating the process of cold acclimation. The molecular mechanisms of this acclimation have not been fully understood in the agronomically important group of forage grasses, including Lolium-Festuca species. Herein, the introgression forms of L. multiflorum/F. arundinacea distinct with respect to their frost tolerance, were used as models for the comprehensive, proteomic and physiological, research to recognize the crucial components of cold acclimation in forage grasses. The obtained results stressed the importance of photosynthetic performance under acclimation to low temperature. The stable level of photochemical processes after three weeks of cold acclimation in the introgression form with a higher level of frost tolerance, combined simultaneously with the stable level of CO2 assimilation after that period, despite decreased stomatal conductance, indicated the capacity for that form to acclimate its photosynthetic apparatus to low temperature. This phenomenon was driven by the Calvin cycle efficiency, associated with revealed here accumulation profiles and activities of chloroplastic aldolase. The capacity to acclimate the photosynthetic machinery to cold could be one of the most crucial components of forage grass metabolism to improve frost tolerance.
2018-04-10 | PXD007257 | Pride
Project description:Small noncoding RNA (sncRNA), including microRNAs (miRNAs) and endogenous small-interfering RNAs (endo-siRNAs) are key gene regulators in eukaryotes, playing critical roles in plant development and stress tolerance. Trans-acting siRNAs (ta-siRNAs), which are secondary siRNAs triggered by miRNAs, and siRNAs from natural antisense transcripts (nat-siRNAs) are two well-studied classes of endo-siRNAs. In order to understand sncRNAsM-bM-^@M-^Y roles in plant cold response and stress acclimation, we studied miRNAs and endo-siRNAs in Cassava (Manihot esculenta), a major source of food for the world populations in tropical regions. Combining Next-Generation sequencing and computational and experimental analyses, we profiled and characterized sncRNA species and mRNA genes from the plants that experienced severe and moderate cold stresses, that underwent further severe cold stress after cold acclimation at moderate stress, and that grew under the normal condition. We also included Castor bean (Ricinus communis) to understand conservation of sncRNAs. In addition to known miRNAs, we identified dozens of novel miRNAs as well as ta-siRNA-yielding and nat-siRNA-yielding loci in Cassava and Castor bean, respectively. Among the expressed sncRNAs, many sncRNAs were differentially expressed under cold stresses. Our study provided the results on gene regulation by sncRNAs in cold acclimation of Euphorbiaceous plants and the role of sncRNA-mediated pathways affected by cold stress and stress acclimation in Cassava. Examination of small RNA populations in Cassava cultivar SC124 under the normal condition (NC), gradual cold acclimation (CA), cold shock (CS) and stress acclimation Cold stress after cold acclimation (CCA).
2014-07-05 | E-GEOD-52177 | biostudies-arrayexpress
Project description:This dataset is associated with two publications 1. Elucidating the biochemical basis of trans-16:1 fatty acid change in leaves during cold acclimation in wheat. http://doi.org/10.1002/pei3.10044 In this study, comparative RNA-seq analyses with leaf tissues undergoing cold acclimation reveal concerted transcriptome shifts indicating a reduced chloroplast lipid pathway activity and increased cytosolic ER membrane lipid synthesis. To explore the underlying metabolic and transcriptional mechanisms responsible for the reduction of the t16:1 under cold, a detailed lipid analysis and comparative transcriptome study were conducted with four wheat cultivars during cold treatment. The RNA-seq dataset includes four wheat cultivars (Manitou, Winter Manitou, Norstar and Spring Norstar) treated with cold paired with control. The data as a whole show that leaf tissues experience a gradual decrease in chloroplast lipid pathway activity and the variation in the decline of chloroplast lipid synthesis in different cultivars manifest in the rate of decrease in t16:1decrease in leaf tissues. Future efforts are required to determine if and how the down regulation of the chloroplast lipid pathway is related to the development of winter hardiness. 2. Computational genomics insights into cold acclimation in wheat. https://doi.org/10.3389/fgene.2022.1015673 In this study, integrated computational approaches was employed to investigate the transcriptomics and lipidomics data associated with cold acclimation and vernalization in the four wheat genotypes of distinct cold tolerance. Differential expression was investigated between cold treated and control samples and between the winter-habit and spring-habit wheat genotypes. Collectively, 12,676 differentially expressed genes (DEGs) were identified. Principal component analysis of these DEGs indicated that the first, second, and third principal components (PC1, PC2, and PC3) explained the variance in cold treatment, vernalization and cold hardiness, respectively. Differential expression feature extraction (DEFE) analysis revealed that the winter-habit wheat genotype Norstar had high number of unique DEGs (1884 up and 672 down) and 63 winter-habit genes, which were clearly distinctive from the 64 spring-habit genes based on PC1, PC2 and PC3. Correlation analysis revealed 64 cold hardy genes and 39 anti-hardy genes. Cold acclimation encompasses a wide spectrum of biological processes and the involved genes work cohesively as revealed through network propagation and collective association strength of local subnetworks. Integration of transcriptome and lipidomics data revealed that the winter-habit genes, such as COR413-TM1, CIPKs and MYB20, together with the phosphatidylglycerol lipids, PG(34:3) and PG(36:6), played a pivotal role in cold acclimation and coordinated cohesively associated subnetworks to confer cold tolerance. Citations: http://doi.org/10.1002/pei3.10044 https://doi.org/10.3389/fgene.2022.1015673
2022-10-24 | GSE156300 | GEO