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Transcriptome of E. coli during Long-Term Stationary Phase

ABSTRACT: Transcriptome of E. coli during Long-Term Stationary Phase

PROVIDER: PRJNA639834 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12026234.fastq.gz	Fastqsanger.gz
	SRR12026235.fastq.gz	Fastqsanger.gz
	SRR12026236.fastq.gz	Fastqsanger.gz
	SRR12026237.fastq.gz	Fastqsanger.gz
	SRR12026238.fastq.gz	Fastqsanger.gz

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Transcriptome of E. coli during Long-Term Stationary Phase

Project description:Microbes live in complex and constantly changing environments, but it is difficult to replicate this in the laboratory. Escherichia coli has been used as a model organism in experimental evolution studies for years; specifically, we and others have used it to study evolution in complex environments by incubating the cells into long-term stationary phase (LTSP) in rich media. In LTSP, cells experience a variety of stresses and changing conditions. While we have hypothesized that this experimental system is more similar to natural environments than some other lab conditions, we do not yet know how cells respond to this environment biochemically or physiologically. In this study, we begin to unravel the cells’ responses to this environment by characterizing the transcriptome of cells during LTSP. We found that cells in LTSP have a unique transcriptional program, and that several genes are uniquely upregulated or downregulated in this phase. Further, we identified two genes, cspB and cspI, which are most highly expressed in LTSP, even though these genes are primarily known to respond to cold-shock. By competing cells missing these genes with wild-type cells, we show that these genes are also important for survival during LTSP. These data can help identify gene products that may play a role in survival in this complex environment, and lead to identification of novel functions of proteins.

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Project description:Transcriptional profiling of A. oleivorans DR1 cells comparing wild type stationary phase cells with aqsR mutant stationary phase cells.

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Project description:To determine where Tup1 binds to chromatin during log phase, diauxic shift and stationary phase, we performed ChIP-seq.

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Transcriptome of a malO deletion mutant of Clostridium perfringens during stationary phase growth.

Project description:The MalNO is a putative two-component signal transduction system, previously known as the VirJI sytem. MalO is the putative cognate response regulator of the MalN sensor histidine kinase. Based on previous evidence that suggested the plc gene, encoding α-toxin, was upregulated during stationary phase in the malO mutant, microarrays were used to analyse the transcriptome of a malO mutant during stationary phase growth.

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Stationary phase stimulon and CspC regulon

Project description:The cold shock proteins belong to a family of RNA binding proteins presenting a highly conserved domain, called cold shock domain (CSD). They are involved in various cellular processes, including adaptation to low temperature, nutritional stress, cell growth and stationary phase. Here we investigate the role of CspC in C. crescentus stationary phase and the molecular mechanisms underlying gene regulation by this protein. A global transcriptional profiling experiment comparing cspC and the wild type strain both at exponential and stationary phases was carried out. The results showed that the absence of cspC affected the transcription of 20 genes at exponential phase and 65 genes at stationary phase. Genes encoding enzymes of the glyoxylate cycle were severely downregulated in the mutant at stationary phase. The stationary phase-induced RNA binding protein CspC has an important role in gene expression at this phase. It is required for the expression of the essential gene sciP, the ECF sigma factor sigU, as well as of the genes for the glyoxylate cycle enzymes and for oxidative stress response.

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Acinetobacter oleivorans DR1 : WT stationary phase vs. aqsR mutant stationary phase

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E. coli MG1655 pJV300 stationary phase

Project description:E. coli MG1655 pJV300 stationary phase

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Transcriptome of a malO deletion mutant of Clostridium perfringens during stationary phase growth.

Project description:The MalNO is a putative two-component signal transduction system, previously known as the VirJI sytem. MalO is the putative cognate response regulator of the MalN sensor histidine kinase. Based on previous evidence that suggested the plc gene, encoding ?-toxin, was upregulated during stationary phase in the malO mutant, microarrays were used to analyse the transcriptome of a malO mutant during stationary phase growth. Total RNA was isolated from stationary phase cells of the malO mutant and the wild-type control. Gene expression levels were compared between the malO mutant and wild-type strain 13

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