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RNA binding partners of the post-transcriptional regulator CsrA

ABSTRACT: Analysis of RNA binding partners of the post-transcriptional regulator CsrA to translation during exponential growth in Escherichia coli

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

PROVIDER: GSE102380 | GEO | 2017/12/06

SECONDARY ACCESSION(S): PRJNA397601

REPOSITORIES: GEO

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The contribution of the post-transcriptional regulator CsrA to translation

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Proteomics identification of CsrA-regulated proteins in Legionella pneumophila

Project description:The carbon storage regulator protein CsrA regulates cellular processes post-transcriptionally by binding to target-RNAs altering translation efficiency and/or their stability. In this dataset we identified proteins regulated by CsrA in the human bacterial pathogen Legionella pneumophila by labelfree shotgun proteomics. WT and ∆csrA bacteria were grown to exponential phase in three biological replicates. Bacteria were lysed by sonication and extracted proteins were reducted, alkylated and digested with trypsin. The resulting peptide mixtures were analyzed by LC-MS/MS and proteins were identified by the MaxQuant software. In total of 1,448 proteins were quantified by the MaxLFQ algorithm in a labelfree approach. Cluster analysis showed that expression of almost all proteins was affected by the mutation of CsrA as about half of the identified proteins were up and half were down regulated. About 15% of the proteome (238 proteins) was strongly affected with 132 proteins significantly up and 109 significantly down regulated dependent on CsrA.

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Analysis of the contribution of CsrA, CsrB/C, and CsrD to gene expression in E. coli

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Metabolome and transcriptome-wide effects of the carbon storage regulator A in enteropathogenic Escherichia coli.

Project description:The carbon storage regulator A (CsrA) is a conserved swivel of a global regulatory system known to regulate central carbon pathways, biofilm formation, motility, and pathogenicity. The aim of this study was to characterize changes in major metabolic pathways induced by CsrA in the human enteropathogenic Escherichia coli (EPEC) strain E2348/69. The EPEC strain E2348/69 and a csrA deletion mutant were grown under virulence factor inducing conditions and characterized by a combined analysis of their metabolomes and transcriptomes. Of the 159 metabolites identified from untargeted GC/MS and LC/MS data, 70 were significantly (fold change ≥ 1.5; p-value ≤ 0.05) regulated between the knockout and the wildtype strain. A lack of csrA led to an upregulation of upper glycolysis and glycogen synthesis pathways, whereas lower glycolysis and the citric acid cycle were downregulated. Associated pathways from the citric acid cycle like aromatic amino acid and siderophore biosynthesis were also negatively influenced. The nucleoside salvage pathways were featured by an accumulation of nucleosides and nucleobases, and a downregulation of nucleotides. In addition, a pronounced downregulation of lyso-lipid metabolites was observed. A drastic change in the morphology in the form of vesicle-like structures of the csrA knockout strain was visible by electron microscopy, which is supposed to be a consequence of a strong upregulation of colanic acid synthesis. The findings expand the scope of pathways affected by the csrA regulon and emphasize its importance as a global regulator.

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