E-MTAB-8073
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-8073 | ExpressionAtlas | 2019-08-08
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-MTAB-8073-analysis-methods.tsv | Tabular | |||
| E-MTAB-8073-analytics.tsv | Tabular | |||
| E-MTAB-8073-atlasExperimentSummary.Rdata | Rdata | |||
| E-MTAB-8073-configuration.xml | Xml | |||
| E-MTAB-8073-g1_g5-mvaPlot.png | Other |
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Project description:Transcriptional variation, also called expression level polymorphism (ELP), contributes to intra-specific phenotypic variation in many organisms. Differentially expressed transcripts are typically enriched for stress-related genes, suggesting that differences in response to the environment are a particularly common point of divergence among gentoypes. Analysis of ELPs also has been suggested as a way to assess unintended consequences of transgene introduction; however, it is important that interpretation of transcriptional changes be performed within the context of potential fitness effects. In these studies we sought to examine differential gene expression in response to salinity for two widely used Arabidopsis thaliana ecotypes, Wassilewskija (Ws) and Columbia (Col), and a single gene mutation (glabrous, gl1-1) in the Col background (Col(gl)), in relation to genetic, phenotypic, and fitness differences. Growth analyses were performed with seedlings germinated on culture media and growth chamber-grown plants carried through the full life cycle. Transcriptome analyses were performed with salt treated and control growth-chamber grown plants six days post initiation of salt stress. Ws plants had the least salt injury and highest dry matter accumulation and seed production in salt stressed conditions. ELPs among genoytypes and in response to 100 mM NaCl were enriched for genes associated with response to stress, including stress-associated transcription factors, heat shock and redox metabolism genes, and R genes. Application of salt resulted in many more transcripts up- or down-regulated in Col and Ws than in Col(gl). Many of the transcripts influenced by salt in Col were already altered in gl1-1 plants in the absence of salt, although Col(gl) plants did not show any detectable signs of stress, or effects on fecundity in the absence of salt treatment. The majority of salt-induced transcriptional changes that occurred in Ws also occurred in Col, suggesting common salt stress responses in these two ecotypes. Many more genes were affected by salt in Col than Ws, however, possibly reflecting the greater salt injury observed for Col. There was minimal overlap between the transcripts that differed for Ws and Col prior to salt treatment and those that were subsequently affected by salt stress. Thus, many genes conferring comparative salt stress tolerance in Ws likely differ from those whose expression levels are modified in response to salt stress. These studies demonstrate transcriptional variation among Arabidopsis genotypes in response to salt stress. Greater transcriptome differences did not necessarily correspond with greater genetic difference or phenotypic differences in morphology, fecundity, and resistance to salt stress. These results suggest that depending on circumstance, transcriptional changes can reflect response to injury, facilitate adaptive expression of fitness-associated traits, or allow for phenotypic buffering to minimize the impact of genetic changes.
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Project description:Bacteria are able to cope with the challenges of sudden increase of salinity by activating adaptation mechanisms. In this study, exponentially growing cells of the food-borne pathogen Bacillus cereus ATCC 14579 were exposed to both mild (2.5% NaCl w/v) and severe (5% NaCl w/v) salt stress conditions. B. cereus continued growth at a reduced rate when shifted to mild salt stress. Exposure to severe salt stress resulted in a lag period, and after 60 min cellular growth was resumed filamentously. Whole-genome expression analyses of cells exposed to 2.5% salt stress revealed an overlap with that of cells exposed to 5% salt stress, suggesting that the corresponding genes (n = 147) were involved in a general salt stress response. Up-regulation of osmolyte, Na+/H+ and di-/tripeptide transporters and activation of an oxidative stress response were important aspects of this general salt stress response. Activation of this response may confer cross-protection towards other stresses, and increased resistance to heat and H2O2 was indeed observed. Notably, a temporal shift was observed between the observed transcriptome and phenotype responses of severely salt-stressed cells including cellular filamentation, reduced chemotaxis performance, catalase activity and optimal oxidative stress resistance. The linkage of transcriptomes and phenotypic characteristics can contribute to a better understanding of cellular stress adaptation strategies and possible cross protection mechanisms. ATCC 14579 was grown to an OD600 of ~0.5, after that 2.5% or 5% NaCl (w/v) was added. Before addition of NaCl and after 10, 30 and 60 minutes of NaCl-exposure a sample was taken for RNA isolation. Comparisons (untreated versus salt-treated) performed were in duplicate with dye swap.
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