Systematic Study on the Three-Dimensional Genome of Escherichia Coli and Its Thermal Adaptation Mechanism (RNA-Seq)
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ABSTRACT:
PROVIDER: PRJNA872175 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21226531_1.fastq.gz | Fastqsanger.gz | |||
| SRR21226531_2.fastq.gz | Fastqsanger.gz | |||
| SRR21226532_1.fastq.gz | Fastqsanger.gz | |||
| SRR21226532_2.fastq.gz | Fastqsanger.gz | |||
| SRR21226533_1.fastq.gz | Fastqsanger.gz |
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Project description:Systematic Study on the Three-Dimensional Genome of Escherichia Coli and Its Thermal Adaptation Mechanism (3C-Seq)
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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
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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.
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