Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344
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ABSTRACT:
PROVIDER: PRJNA123337 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
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
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.
2009-10-28 | GSE18428 | GEO
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.
2009-10-28 | GSE18424 | GEO
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
Project description:We performed transcriptome abundance analysis of Salmonella Typhimurium strain SL1344 swap which has been genetically engineered to express the hns open-reading frame from the stpA promoter and the stpA open reading frame from the hns promoter. This strain is designated SL1344(swap). Transcript abundance was compared with that of wild-type SL1344. This comparison was performed to determine the effect of chromosome location of the expression of two related global regulators and how alterations to their expression patterns would impact on their regulons.
2013-11-09 | GSE52235 | GEO
Project description:We performed transcriptome abundance analysis of Salmonella Typhimurium strain SL1344 swap which has been genetically engineered to express the hns open-reading frame from the stpA promoter and the stpA open reading frame from the hns promoter. This strain is designated SL1344(swap). Transcript abundance was compared with that of wild-type SL1344. This comparison was performed to determine the effect of chromosome location of the expression of two related global regulators and how alterations to their expression patterns would impact on their regulons. Three independent RNA samples were harvested from wild-type SL1344 and SL1344(swap) grown to exponential phase (OD600nm = 0.3) and hybridized to a microarray containing multiple probes for each of the SL1344 open reading frames. Please note that the original raw data file for the 'SL1344_wildtype_BR2' sample is unavailable, however, the 'wildtype SL1344 BR2.gpr' contains the raw data missing only the header information.
2013-11-09 | E-GEOD-52235 | biostudies-arrayexpress
Project description:The effect of stpA deletion on S. Typhimurium gene expression during growth in rich medium
| PRJNA123333 | ENA
Project description:FabR ChIP-chip on Salmonella enterica subsp. enterica serovar Typhimurium SL1344 using anti-Myc antibody against strain with chromosomally 9Myc-tagged FabR (IP samples) and wildtype strain (mock IP samples)
2014-12-31 | GSE52877 | GEO
Project description:The regulatory role of the Fis protein in fis and in the transcription of several gene regions during mid-exponential and late-stationary phase, and during different growth aeration regimes, has been investigated. Studies were done during those two growth phases and in aerated and non-aerated (microaerobic) conditions, to measure Fis enrichment and binding peaks in strategic gene regions by genome-wide microarray analysis ChIP-chip. This research investigation points to central roles for SPI-1, SPI-2, DNA gyrase and topoisomerase I, the elements of the stringent response, and the regulatory function of Fis-binding patterns, in setting and re-setting the activity of the fis gene and other involved promoters as a function of the growth conditions and aeration regimes experienced by Salmonella.
2013-05-01 | GSE38661 | GEO