Thermal adaptation in closely related virbios
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ABSTRACT:
PROVIDER: PRJNA325804 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Here, we investigate the genetic mechanisms that underlie thermal specialization of closely-related vibrios isolated from coastal water at the Beaufort Inlet (Beaufort, NC, USA). This location experiences large seasonal temperature fluctuations (annual range of ~20°C), and a clear seasonal shift in vibrio diversity has been observed (Yung et al. 2015). This previous study suggested that the mechanisms of thermal adaptation apparently differ based on evolutionary timescale: shifts in the temperature of maximal growth occur between deeply branching clades but the shape of the thermal performance curve changes on shorter time scales (Yung et al. 2015). The observed thermal specialization in vibrio populations over relatively short evolutionary time scales indicates that few genes or cellular processes may contribute to the differences in thermal performance between populations. In order to understand the molecular mechanisms that underlie adaptation to local thermal regimes in environmental vibrio populations, we employ genomic and transcriptomic approaches to examine transcriptomic changes that occur within strains grown at their thermal optima and under heat and cold stress. Moreover, we compare two closely-related strains with different laboratory thermal preferences to identify in situ evolutionary responses to different thermal environments in genome content and alleles as well as gene expression.
2018-07-31 | GSE83396 | GEO
Project description:Microbiome mediated plasticity promotes thermal adaptation in Nematostella vectensis
| PRJNA714634 | ENA
Project description:Several microorganisms have wide temperature growth range and versatility to tolerate large thermal fluctuations in diverse environments. To better understand thermal adaptation of psychrotrophs, Exiguobacterium sibiricum strain 255-15 was used, a psychrotrophic bacterium that grows from -5°C to 39°C. Its genome is approximately 3 Mb in size, has a GC content of 47.7% and includes 2,978 putative protein-encoding genes (CDS). The genome and transcriptome analysis along with the organism's known physiology was used to better understand its thermal adaptation. A total of about 27%, 3.2% and 5.2% of E. sibiricum strain 255-15 CDS spotted on the DNA microarray yielded differentially expressed genes in cells grown at -2.5°C, 10°C and 39°C, respectively, when compared to cells grown at 28°C. The hypothetical and unknown genes represented 10.6%, 0.89% and 2.3% of the CDS differentially expressed when grown at -2.5°C, 10°C and 39°C versus 28°C. The transcriptome analyses showed that E. sibiricum is constitutively adapted to cold temperatures since little differential gene expression was observed at growth temperatures of 10°C and 28°C, but at the extremities of its Arrhenius growth profile, namely -2.5°C and 39°C, much more differential gene expression occurred. The genes that responded were more typically associated with stress response. Keywords: stress response to cold and hot temperatures
2008-02-11 | GSE10133 | GEO
Project description:[original title] Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. We demonstrate extensive quantitative changes in binding of six factors that control early embryonic patterning between two closely related Drosophila species ChIP-Seq based binding measurements of six transcription factors in embryos of two Drosophila species, D.melanogaster and D.yakuba.
2010-02-18 | E-GEOD-20369 | biostudies-arrayexpress
Project description:Several microorganisms have wide temperature growth range and versatility to tolerate large thermal fluctuations in diverse environments. To better understand thermal adaptation of psychrotrophs, Exiguobacterium sibiricum strain 255-15 was used, a psychrotrophic bacterium that grows from -5°C to 39°C. Its genome is approximately 3 Mb in size, has a GC content of 47.7% and includes 2,978 putative protein-encoding genes (CDS). The genome and transcriptome analysis along with the organism's known physiology was used to better understand its thermal adaptation. A total of about 27%, 3.2% and 5.2% of E. sibiricum strain 255-15 CDS spotted on the DNA microarray yielded differentially expressed genes in cells grown at -2.5°C, 10°C and 39°C, respectively, when compared to cells grown at 28°C. The hypothetical and unknown genes represented 10.6%, 0.89% and 2.3% of the CDS differentially expressed when grown at -2.5°C, 10°C and 39°C versus 28°C. The transcriptome analyses showed that E. sibiricum is constitutively adapted to cold temperatures since little differential gene expression was observed at growth temperatures of 10°C and 28°C, but at the extremities of its Arrhenius growth profile, namely -2.5°C and 39°C, much more differential gene expression occurred. The genes that responded were more typically associated with stress response. Keywords: stress response to cold and hot temperatures Six-condition experiment: -2.5°C vs10°C, -2.5°C vs 28°C, -2.5°C vs 39°C, 28°C vs10°C, 28°C vs 39°C, 10°C vs 39°C. Biological replicates: 6 replicates grown and harvested independently for each different temperature (-2.5°C, 10°C, 28°C and 39°C). One replicate per array.
2010-05-26 | E-GEOD-10133 | biostudies-arrayexpress
Project description:[original title] Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. We demonstrate extensive quantitative changes in binding of six factors that control early embryonic patterning between two closely related Drosophila species
2010-02-18 | GSE20369 | GEO
Project description:Thermal exposure of sessile marine animals inhabiting estuarine intertidal regions is a matter of serious concern. The Hong Kong oyster, Crassostrea hongkongensis is one of the dominant sessile inhabitants of marine intertidal region which undergoes large seasonal temperature fluctuations every year. The oyster has developed several adaptation mechanisms to cope with acute thermal stress. However, the genetic basis of these mechanisms remain largely unclear. To better understand how acute thermal exposure affects the biology of the oyster, two cDNA libraries obtained from the gill of oysters exposed to thermal stress and ambient temperature were sequenced using the Digital Gene Expression (DGE) tag profiling strategy. In total, 5.9 and 6.2 million reads were obtained for thermal stress and control libraries respectively, with approximately 74.25% and 75.02 % of the reads mapping to the C. hongkongensis reference sequence. A total of 605 differentially expressed transcripts could be detected in the thermal stress group as compared to the control group, of which 378 are up-regulated and 227 are down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these Differentially Expressed Genes (DEGs) were enriched with a broad spectrum of biological processes and pathways, including those associated with chaperones, antioxidants, immunity, apoptosis and cytoskeletal reorganization. Among these significantly enriched pathways, protein processing in the endoplasmic reticulum was the most affected metabolic pathway, which plays an important role in the unfolded protein response (UPR) and ER-associated degradation (ERAD) processes. Our results demonstrate the complex multi-modal cellular response to thermal stress in C. hongkongensis.
2016-10-11 | GSE85707 | GEO
Project description:Microbial communities respond to temperature with physiological adaptation and compositional turnover. Whether thermal selection of enzymes explains marine microbiome plasticity in response to temperature remains unresolved. By quantifying the thermal behaviour of seven functionally-independent enzyme classes (esterase, extradiol dioxygenase, phosphatase, beta-galactosidase, nuclease, transaminase, and aldo-keto reductase) in native proteomes of marine sediment microbiomes from the Irish Sea to the southern Red Sea, we record a significant effect of the mean annual temperature (MAT) on enzyme’s response (R2, 0.51–0.80, p < 0.01 in all cases). Activity and stability profiles of 228 esterases and 5 extradiol dioxygenases from sediment and seawater across 70 locations worldwide (latitude 62.2°S–16°N, MAT –1.4ºC–29.5ºC) validate this thermal pattern. Modelling the esterase phase transition temperature as a measure of structural flexibility, confirm the observed relationship with MAT. Furthermore, when considering temperature variability in sites with non-significantly different MATs, the broadest range of enzyme thermal behaviour and the highest growth plasticity of the enriched heterotrophic bacteria occur in samples with the widest annual thermal variability. These results indicate that temperature-driven enzyme selection shapes microbiome thermal plasticity and that thermal variability finely tunes such processes and should be considered alongside MAT in forecasting microbial community thermal response
2023-02-07 | PXD039714 | Pride
Project description:This SuperSeries is composed of the following subset Series: GSE15626: Using high-density exon arrays to profile gene expression in closely related species (Exon 1.0 ST) GSE15665: Using high-density exon arrays to profile gene expression in closely related species (HJAY) Refer to individual Series
2009-05-04 | E-GEOD-15666 | biostudies-arrayexpress