Expression data from TabZIP6-overexpressed Arabidopsis before/after cold treatment
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE106635 | GEO | 2018/01/01
SECONDARY ACCESSION(S): PRJNA417485
REPOSITORIES: GEO
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Project description:In the field, abiotic stresses are rarely applied individually. Crops are often subjected to a combination of stresses. To date, no study has been performed on the proteomic investigation of the response of common wheat to a combination of drought and cold stresses. In this study, wheat seedlings exposed to drought-cold stress for 24 h showed inhibited growth, increased lipid peroxidation, relative electrolyte leakage, and soluble sugar contents. To determine the wheat protein response to drought-cold stress, iTRAQ-based quantitative proteomic and liquid chromatography tandem mass spectrometry (LC-MS/MS) methods were employed to determine the proteomic profiles of the roots and leaves of wheat seedlings exposed to drought-cold stress conditions. We identified 250 and 258 proteins with significantly altered abundance in the roots and leaves, respectively. These proteins were classified into several main groups, as follows: protein metabolism, stress/defense, carbohydrate metabolism, lipid metabolism, transcription-related processes, energy production, cell-wall and cytoskeleton metabolism, membrane and transportation, signal transduction, other metabolic processes, and unknown biological processes. Nine proteins were simultaneously presented in both roots and leaves exposed to drought-cold stress, and the majority of proteins identified differed from one another and displayed differently altered abundance. These findings uncovered organ-specific differences in adaptation to drought-cold stress. Exogenous abscisic acid (ABA) application conferred the plant with protection against drought-cold stress and significantly increased catalase and peroxidase enzyme activities, as well as the transcription of glutathione S-transferase and other 11 sample genes in the roots or leaves, respectively. These results suggested that ABA is a potentially vital factor that contributes to the drought-cold signaling pathway and a promising target for growth recovery. Furthermore, VIGS (virus-induced gene silencing)-treated plants generated for three candidate protein genes TaGRP2, CDCP and WCOR410c were subjected to drought-cold limitation, they showed more serious droop and wilt, increased rate of relative electrolyte leakage, and reduced relative water content (RWC) compared to viral control plants. These results may indicate that TaGRP2, CDCP and WCOR410c play important roles in conferring drought-cold tolerance in wheat. These findings can provide useful insights into the molecular mechanisms of drought-cold responses in higher plants.
2018-05-17 | PXD004396 | Pride
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
Project description:Abstract Lysine crotonylation (Kcr) is a recently identified post-translational modification (PTM) in the prokaryotic and eukaryotic organisms. However, the function of lysine-crotonylated proteins in response to abiotic stress in plants remains largely unknown. Here, we report the first global profiling of the Kcr proteome in common wheat, identifying 4,696 Kcr sites on 1,726 substrate proteins, participating in a wide variety of biological and metabolic pathways. Combination of transcriptome and proteome in a RIL (recombinant inbred line) population, Kcr proteome, and genome-wide association study, a candidate gene phosphoglycerate kinase (TaPGK) was identified to potentially affect on cold tolerance in common wheat. Using EMS-mutants, overexpressed transgenic wheat plants and CRISPR/Cas9-mediated know-out mutants, we demonstrated that TaPGK played a positively key role in regulation of plant cold tolerance. Moreover, TaPGK protein strongly interacted with sirtuin-like (TaSRT1). EMS-mutant tetraploid and overexpressed transgenic wheat experiments confirmed that TaSRT1 gene negatively regulated wheat cold tolerance. Immunoprecipitation demonstrated that TaSRT1 promoted the degradation of TaPGK by erasing Kcr. Additionally, RNA-sequencing results showed that overexpressed TaPGK significantly improved expression of peroxidase genes. It concluded that a large number of Kcr sites were present in wheat important proteins and TaPGK crotonylated by TaSRT1 played a key role in wheat response to cold stress through scavenging the accumulation of ROS.
2023-07-20 | PXD030768 | Pride
Project description:Jojoba (Simmondsia chinensis) is a new semi- arid, oil- producing industrial crop that has attracted much attention in recent years. Low temperature is one of the major environmental stress that impairs plant growth and development. To better understand the molecular mechanisms of cold stress adaptation and acclimation of jojoba plants, a quantitative proteomic analysis using iTRAQ technology was conducted to detect the effects of cold stress on protein expression profiles in jojoba seedlings. Our work provided useful infomation for understanding the cold stress response and cold acclimation in jojoba.
2019-11-11 | PXD007063 | Pride
Project description:Agilent 44k barley microarray was used to screen calcium dependent cold induced genes. Calcium chelator (EGTA) or calcium channel blocker (lanthanum) or phospholipase C activator (mastoparan) pretreatments were performed to block/enhance calcium response in barley seedlings. Calcium depleted and control plants were cold treated and the difference in the gene expression was investigated.
2014-12-31 | GSE47432 | GEO
Project description:adt06-03-mkk2 - mkk2_mkk2_and_wrky19_cold_time_course - early response targets of MKK2 upon cold stress treatment and its role in adaptation. - seedlings were put to 4 ° comparing wild type ColO versus mkk2 knockouts, MKK2 overexpressors and wrky19 knockouts. Keywords: time course,wt vs mutant comparison
2008-07-01 | GSE10763 | GEO
Project description:Expression data from TabZIP6-overexpressed Arabidopsis before/after cold treatment
| PRJNA417485 | ENA
Project description:RNA-Seq was performed to study the change of gene expression before and after cold treatment in Brachypodium. Different change patterns were identified. We have provided a complete view of transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants. The mRNA profiles of 12-day-old Brachypodium seedlings with and without cold treatment (4 M-BM-0C for 24 h) were generated by deep sequencing using Illumina HiSeqM-bM-^DM-" 2000.
2013-07-15 | E-GEOD-48040 | biostudies-arrayexpress
Project description:To reveal the involvement of OsERF096 in response to cold stress, this study performed transcriptome sequencing of WT, OsERF096-OX and OsERF096-RNAi rice before and after cold stress.Based on transcriptome sequencing, this study found that OsERF096 is involved in the regulation of hormone signal transduction.
2022-02-01 | GSE195853 | GEO
Project description:Different wheat cultivars may be classified as either winter or spring varieties depending on whether they require exposure to an extended period of cold in order to become competent to flower. Using a growth regime that mimics the conditions that occur during a typical winter in Britain, we wished to survey the genes that are involved in phase transition as well as those involved in cold-acclimation. Keywords: Time course
2008-10-01 | GSE11774 | GEO