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The effect of stpA deletion on S. Typhimurium gene expression during growth in rich medium

ABSTRACT: StpA is a paralogue of the nucleoid associated protein H-NS that is conserved in a range of enteric bacteria and had no known function in Salmonella enterica serovar Typhimurium. Here, we show that 5% of the Salmonella genome is regulated by StpA, which contrasts with the situation in Escherichia coli where deletion of stpA only had minor effects on gene expression. The StpA-dependent genes of S. Typhimurium are a specific subset of the H-NS regulon that are predominantly under the positive control of sigma38 (RpoS), CRP-cAMP and PhoP. The regulatory role of StpA varied at different growth phases; StpA only controlled sigma38 levels at mid-exponential phase when it prevented inappropriate activation of sigma38 during rapid bacterial growth. In contrast, StpA only activated the CRP-cAMP regulon during late exponential phase.

ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344 Salmonella enterica

PROVIDER: GSE18424 | GEO | 2009/10/28

SECONDARY ACCESSION(S): PRJNA123333

REPOSITORIES: GEO

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StpA prevents RpoS-dependent transcription during mid-exponential growth in S. Typhimurium

2009-10-28 | GSE18428 | GEO

StpA prevents RpoS-dependent transcription during mid-exponential growth in S. Typhimurium

Project description:StpA is a paralogue of the nucleoid associated protein H-NS that is conserved in a range of enteric bacteria and had no known function in Salmonella enterica serovar Typhimurium. Here, we show that 5% of the Salmonella genome is regulated by StpA, which contrasts with the situation in Escherichia coli where deletion of stpA only had minor effects on gene expression. The StpA-dependent genes of S. Typhimurium are a specific subset of the H-NS regulon that are predominantly under the positive control of sigma38 (RpoS), CRP-cAMP and PhoP. The regulatory role of StpA varied at different growth phases; StpA only controlled sigma38 levels at mid-exponential phase when it prevented inappropriate activation of sigma38 during rapid bacterial growth. In contrast, StpA only activated the CRP-cAMP regulon during late exponential phase. To test the hypothesis that stpA prevents Sigma38-dependent transcription during mid-exponential growth in S. Typhimurium, we analysed the effect of the stpA deletion on transcription in the presence and absence of rpoS. Three biological replicates were performed for each strain. For this study, we used Salmonella genomic DNA as the comparator which also acted as the control for spot quality.

2010-06-20 | E-GEOD-18428 | biostudies-arrayexpress

The effect of stpA deletion on S. Typhimurium gene expression during growth in rich medium

Project description:StpA is a paralogue of the nucleoid associated protein H-NS that is conserved in a range of enteric bacteria and had no known function in Salmonella enterica serovar Typhimurium. Here, we show that 5% of the Salmonella genome is regulated by StpA, which contrasts with the situation in Escherichia coli where deletion of stpA only had minor effects on gene expression. The StpA-dependent genes of S. Typhimurium are a specific subset of the H-NS regulon that are predominantly under the positive control of sigma38 (RpoS), CRP-cAMP and PhoP. The regulatory role of StpA varied at different growth phases; StpA only controlled sigma38 levels at mid-exponential phase when it prevented inappropriate activation of sigma38 during rapid bacterial growth. In contrast, StpA only activated the CRP-cAMP regulon during late exponential phase. The effect of stpA deletion on S. Typhimurium gene expression during growth in LB was analysed at 4 different time points (early-log, mid-log, late-log, and stationary phase) where the gene expression profile of the stpA-deletion strain was compared to that of the parental strain. Between two and three biological replicates were performed for each strain and time point. For this study, we used Salmonella genomic DNA as the comparator which also acted as the control for spot quality.

2009-10-27 | E-GEOD-18424 | biostudies-arrayexpress

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Role of stpA in Salmonella typhimurium

Project description:This SuperSeries is composed of the following subset Series: GSE18424: The effect of stpA deletion on S. Typhimurium gene expression during growth in rich medium GSE18428: StpA prevents RpoS-dependent transcription during mid-exponential growth in S. Typhimurium GSE18450: Identification of StpA-binding sites on the Salmonella genome Refer to individual Series

2010-06-21 | E-GEOD-18452 | biostudies-arrayexpress

Identification of StpA-binding sites on the Salmonella genome

Project description:We used ChIP-chip analysis to identify where the nucleoid associated protein StpA binds on the Salmonella Typhimurium genome. We identified 285 chromosomal regions bound by StpA, ranging in size from 400 to 3500 base pairs and containing 572 genes. Comparison of the ChIP data revealed that StpA displayed an identical binding profile to H-NS; all genomic regions associated with StpA were also bound by H-NS. Of the 88 StpA-dependent genes that are de-repressed in the absence of StpA, only 25 were bound by StpA, suggesting that StpA generally regulates gene expression indirectly. To identify the direct StpA targets, we co-immunoprecipitated DNA from a strain expressing a 3xFLAG-tagged StpA-protein using an anti-3xFLAG antibody. As a negative control, we used the same antibody (anti-3xFLAG) to co-immunoprecipitate DNA from an isogenic strain expressing the non-tagged StpA-protein. Three independent biological replicates were generated. For comparative purposes we also performed the co-immunoprecipitation on wild type Salmonella using a monoclonal anti-H-NS antibody. In that case, the negative control was obtained by performing the co-immunoprecipitation protocol on wild type Salmonella without adding antibody.

2009-10-28 | E-GEOD-18450 | biostudies-arrayexpress

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ChIP-chip analysis of RNAP and Sigma factor binding to the Salmonella enterica serovar Typhimurium chromosome

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