Arabidopsis thaliana
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-71001
PROVIDER: PRJNA290083 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Soil salinity increasingly causes crop losses worldwide. Although roots are the primary targets of salt stress, the signaling networks that facilitate metabolic reprogramming to induce stress tolerance are less understood than those in leaves. Here, a combination of transcriptomic and metabolic approaches was performed in salt-treated Arabidopsis thaliana roots, which revealed that the group S1 basic leucine zipper transcription factors bZIP1 and bZIP53 reprogram primary C- and N-metabolism. In particular, gluconeogenesis and amino acid catabolism are affected by these transcription factors. Importantly, bZIP1 expression reflects cellular stress and energy status in roots. In addition to the well-described abiotic stress response pathway initiated by the hormone abscisic acid (ABA) and executed by SnRK2 (Snf1-RELATED-PROTEIN-KINASE2) and AREB-like bZIP factors, we identify a structurally related ABA-independent signaling module consisting of SnRK1s and S1 bZIPs. Crosstalk between these signaling pathways recruits particular bZIP factor combinations to establish at least four distinct gene expression patterns. Understanding this signaling network provides a framework for securing future crop productivity. RNA from roots from Control and salt treated hydroponically grown seedlings were extracted and subjected to microarray analysis
2015-09-02 | E-GEOD-71001 | biostudies-arrayexpress
Project description:Soil salinity increasingly causes crop losses worldwide. Although roots are the primary targets of salt stress, the signaling networks that facilitate metabolic reprogramming to induce stress tolerance are less understood than those in leaves. Here, a combination of transcriptomic and metabolic approaches was performed in salt-treated Arabidopsis thaliana roots, which revealed that the group S1 basic leucine zipper transcription factors bZIP1 and bZIP53 reprogram primary C- and N-metabolism. In particular, gluconeogenesis and amino acid catabolism are affected by these transcription factors. Importantly, bZIP1 expression reflects cellular stress and energy status in roots. In addition to the well-described abiotic stress response pathway initiated by the hormone abscisic acid (ABA) and executed by SnRK2 (Snf1-RELATED-PROTEIN-KINASE2) and AREB-like bZIP factors, we identify a structurally related ABA-independent signaling module consisting of SnRK1s and S1 bZIPs. Crosstalk between these signaling pathways recruits particular bZIP factor combinations to establish at least four distinct gene expression patterns. Understanding this signaling network provides a framework for securing future crop productivity.
2015-09-02 | GSE71001 | GEO
Project description:The roots of halophytes such as mangroves provide the first line of defense against the constant salt stress they experience. Such adaptation should include major reprogramming of the gene expression profiles. Using RNA-sequencing approach we identified 101,446 ‘all-unigenes’ from the seedling roots of the mangrove tree Avicennia officinalis. From the data 6618 genes were identified to be differentially regulated by salt when two-month-old greenhouse-grown seedlings without prior exposure to sea water were subjected to 24 h of 500 mM NaCl treatment. About 1,404 genes were significantly up-regulated, while 5214 genes were down-regulated. Based on Gene Ontology analysis, they could be classified under various categories, including metabolic processes, stress and defense response, signal transduction, transcription-related and transporters. Our analysis provides the baseline information towards understanding salt balance in mangroves and hence mechanism of salt tolerance in plants.
2017-09-14 | GSE73807 | GEO
Project description:Background: Rice is a staple crop for over half of the global population, but soil salinization poses a significant threat to its production. As a type of polyamine, spermidine (Spd) has been shown to reduce stress-induced damage in plants, but its specific role and mechanism in protecting rice roots under salt stress require further investigation. Results: This study suggested spermidine (Spd) mitigates salt stress on rice root growth by enhancing antioxidant enzyme activity and reducing peroxide levels. Transcriptomic analysis showed that salt stress caused 333 genes to be upregulated and 1,765 to be downregulated. However, adding Spd during salt treatment significantly altered this pattern: 2,298 genes were upregulated and 844 were downregulated, which indicated Spd reverses some transcriptional changes caused by salt stress. KEGG pathway analysis suggested that Spd influenced key signaling pathways, including MAPK signaling, plant hormone signal transduction, and phenylalanine metabolism. Additionally, the bZIP transcription factor OsbZIP73 was upregulated after Spd treatment, which is confirmed by Western blot. Further insights into the interaction between OsbZIP73 and Spd were gained through fluorescence polarization experiments, showing that Spd enhances protein OsbZIP73's affinity for RNA. Functional enrichment analyses revealed that OsPYL1, OsSPARK1, and various SAUR family genes involved in Spd-affected pathways. The presence of G/A/C-box elements in these genes suggests they are potential targets for OsbZIP73. Conclusions: Our findings suggest a strategy of using spermidine as a chemical alleviator for salt stress and provide insights into the regulatory function of OsbZIP73 in mitigating salt stress in rice roots.
2024-08-01 | GSE189665 | GEO
Project description:The molecular response to salt exposure was studied in the leaves of a S. tuberosum clone using cDNA microarray. Differentially expressed genes were classified according to their known or predicted function and their expression ratio as compared to the control. The major changes upon a 150 mM NaCl exposure in potato leaves occurred in the photosystem apparatus and Calvin cycle: many transcripts coding for proteins belonging to photosystems I and II and chlorophyll synthesis were repressed. On the other hand, we observed the induction of various kinds of transcription factors implicated in osmotic stress response via ABA-dependent or ABA-independent pathways but also in plant defense pathways. This revealed a crosstalk between abiotic and biotic stress responses during salt exposure, which activated several adaptation mechanisms including HSP, LEA, dehydrins and PR proteins. Gene expression changes related to carbohydrate and amino acid metabolism were also observed, pointing at putative modifications at the metabolic level. Gene expression has been followed at two different time-points (one and three day after salinity treatment) and conditions: salt-treatment (150 mM NaCl) and control conditions. For each time-point and conditions 3 independent biological replicates were sampled.
2010-05-05 | E-GEOD-18053 | biostudies-arrayexpress
Project description:We found that primary root (PR) is more resistant to salt stress compared with crown roots (CR) and seminal roots (SR). To understand better salt stress responses in maize roots, six RNA libraries were generated and sequenced from primary root (PR), primary roots under salt stress (PR-salt) , seminal roots (SR), seminal roots under salt stress (SR-salt), crown roots (CR), and crown roots under salt stress (CR-salt). Through integrative analysis, we identified 444 genes regulated by salt stress in maize roots, and found that the expression patterns of some genes and enzymes involved in important pathway under salt stress, such as reactive oxygen species scavenging, plant hormone signal perception and transduction, and compatible solutes synthesis differed dramatically in different maize roots. 16 of differentially expressed genes were selected for further validation with quantitative real time RT-PCR (qRT-PCR).We demonstrate that the expression patterns of differentially expressed genes are highly diversified in different maize roots. The differentially expressed genes are correlated with the differential growth responses to salt stress in maize roots. Our studies provide deeper insight into the molecular mechanisms about the differential growth responses of different root types in response to environmental stimuli in planta.
2014-03-01 | GSE53995 | GEO
Project description:Salinity tolerance is a complex trait and, despite many efforts to obtain rice plants resistant to salt, few results have been achieved since a deeper understanding of the tolerance mechanisms is still needed. We used imaging of photosynthetic parameters, ion analysis and transcriptomic approaches to unveil differences between two rice varieties differing in salt sensitivity. Moreover, we analysed H2O2 production in roots, using a fluorescent probe, and the ensuing gene regulation. Transcriptomic analyses conducted in tolerant plants supported the set-up of an adaptive program consisting of allocating sodium preferentially to roots, restricting it to the oldest leaves and activating regulatory mechanisms of photosynthesis in new leaves. As a consequence, plants resumed growth even under prolonged salt stress. By contrast, in the susceptible variety, RNA profiling unveiled a mis-targeted response, leading to senescence and cell death. In roots of tolerant plants, an increase in H2O2 was observed as early as 5 minutes after treatment. Consequently, the expression of genes involved in perception, signal transduction and response to salt were induced at earlier times when compared to susceptible plant roots. Our results demonstrate that a prompt H2O2 signalling in roots participates to a coordinated response resulting in adaptation instead of senescence in salt treated rice plants.
2018-03-14 | GSE109341 | GEO
Project description:Salt Stress response of salt-tolerant genotype FL478 compared to IR29 Rice GeneChip was used to find differential expression between two rice genotypes under control and salt stress conditions Keywords: genotype and treatment comparison Roots (tips) tissue was used for hybridization to GeneChips
2010-07-07 | E-GEOD-13735 | biostudies-arrayexpress
Project description:The goal of this study is to understand the effects of high salt diet on metabolic changes in different tissues including liver, WAT and muscle through RNA-seq. Methods: Liver, WAT and muscle mRNA profiles of control WT and 12wks high salt diet fed mice were generated by RNA deep sequencing, using Illumina Hiseq 6000. Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Hisat2. Results: We observed that several genes associated with de novo lipogenesis and cholesterol biosynthesis were significantly down-regulated in WAT and liver tissue of HSD mice group. Besides, combined with secretome datasets, our results further demonstrated that high salt diet could also down-regulate different organokines, and thus, possibly mediate crosstalk between different metabolic tissues Conclusions: Our study investigated the mechanisms of changed gene expression pattern of metabolic organs induced by high salt in terms of whole transcriptome profiling.
2022-03-08 | GSE197972 | GEO
Project description:Salt Stress response of salt-tolerant genotype Golden Promise compared to Maythorpe; Barley1 GeneChip was used to find differential expression between two barley genotypes under control and salt stress conditions at vegetative stage of growth Experiment Overall Design: Roots (tips) and shoot (crown and growing point) tissue was used for hybridization to GeneChips
2007-10-24 | E-GEOD-6325 | biostudies-arrayexpress