Dataset Information

RNA-seq of wild type Mycobacterium smegmatis mc2 155 (exponential and stationary phase) and Ms1 deletion strain (exponential and stationary phase)

ABSTRACT: Ms1 RNA is ~300 nt sRNA that is highly expressed in stationary phase of growth and binds to the RNA polymerase (RNAP) core. We assume that by binding to RNAP, Ms1 could regulate transcription. Our aim was to reveal the most prominent changes in the transcriptome upon entry into stationary phase that might be dependent on Ms1. We performed RNA-seq data to characterize exponential (Ms_WT_exp) and stationary phase (Ms_WT_stat) transcriptome in M. smegmatis in wild type cells. In addition, we compared the transcriptome of the Ms1 knockout cells (Ms_KO_stat) with wild type cells in stationary phase and in exponential phase (Ms_KO_exp).

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mycolicibacterium Smegmatis

SUBMITTER: Martin Prevorovsky Michaela Sikova Jarmila Hnilicova Libor Krasny

PROVIDER: E-MTAB-7004 | ArrayExpress | 2018-11-12

SECONDARY ACCESSION(S): ERP109850

REPOSITORIES: ArrayExpress, ENA

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			Action	DRS
	E-MTAB-7004.idf.txt	Idf
	E-MTAB-7004.idf.txt_original	Idf
	E-MTAB-7004.sdrf.txt	Txt

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Project description:Campylobacter jejuni has been reported as a major cause of bacterial food-borne enteritides in developed countries during the last decade. Despite its fastidious growth requirements, including low level of oxygen and high level of CO2, this pathogen is able to persist in the environment without permanent loss of its viability and virulence. As C. jejuni is not able to multiply outside a host, the cells spend significant amount of time in stationary phase of growth. The entry into the stationary phase is often correlated to resistance to various stresses in bacteria. The switching between exponential and stationary phases is frequently mediated by the regulator sigma S (RpoS). However, this factor is absent in C. jejuni and molecular mechanisms responsible for transition of cells to the stationary phase remain elusive. In this work, proteomic profiles of cells from exponential and stationary phases were compared using 2-D electrophoresis (2DE) fingerprinting combined with mass spectrometry analysis and qRT-PCR. The identified proteins, whose expression differed between the two phases, are mostly involved in protein biosynthesis, carbon metabolism, stress response and motility. Altered expression was observed also in the pleiotropic regulator CosR that was over-expressed during stationary phase. A shift between transcript and protein level evolution of CosR throughout the growth of C. jejuni was observed using qRT-PCR and (2DE). From these data, we hypothesized that CosR could undergo a negative autoregulation in stationary phase. A consensus sequence resulting from promoter sequence alignment of genes potentially regulated by CosR, including its own upstream region, among C. jejuni strains is proposed. To verify experimentally the potential autoregulation of CosR at the DNA level, electrophoretic mobility shift assay was performed with DNA fragments of CosR promoter region and rCosR. Different migration pattern of the promoter fragments indicates the binding capacity of CosR, suggesting its auto-regulation potential.

Dataset Information

RNA-seq of wild type Mycobacterium smegmatis mc2 155 (exponential and stationary phase) and Ms1 deletion strain (exponential and stationary phase)

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