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Transcriptome analysis of the Salmonella enterica OmpR regulon

ABSTRACT: Transcriptional profiling of Salmonella Typhimurium SL1344 wild type and ompR mutant grown to mil-exponential phase in LB. The goal was to define the ompR-regulated genes.

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

PROVIDER: GSE35938 | GEO | 2012/12/01

SECONDARY ACCESSION(S): PRJNA152083

REPOSITORIES: GEO

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Transcriptome analysis of the Salmonella enterica OmpR regulon

Project description:Transcriptional profiling of Salmonella Typhimurium SL1344 wild type and ompR mutant grown to mil-exponential phase in LB. The goal was to define the ompR-regulated genes. Two strains (wild type, ompR mutant), 4 biological replicates of each. Each sample was hybridised in a two-channel hybridization against Salmonella genomic DNA as the comparator/reference, which also acted as a control for spot quality.

2012-12-01 | E-GEOD-35938 | biostudies-arrayexpress

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Project description:OmpR is a DNA binding protein belonging to the OmpR/EnvZ two component system. This system is known to sense changes in osmolarity in Escherichia coli. Recently, OmpR in Salmonella enterica serovar Typhimurium was found to be activated by acidic pH and DNA relaxation. In this study, ChIP-on-chip was employed to ascertain the genome-wide distribution of OmpR in Salmonella Typhimurium and Escherichia coli in acidic and neutral pH. In addition we investigated the affect of DNA relaxation on OmpR binding in Salmonella Typhimurium. Analysis of OmpR binding at pH 7 and pH 4.5 in E-minimal medium in both SL1344 and CSH50. Three independent biological replicates at each pH 7 and pH 4.5 was performed. This was done in each strain background. DNA was immunopreciptated using an anti-FLAG anitbody which binds to flag-tagged OmpR in both strains. Two control M-bM-^@M-^XmockM-bM-^@M-^Y experiments were performed under the same culture condtions in each strain background; DNA was immunopreciptated using normal mouse IgG antibody. To analyse the effect of DNA relaxation onOmpR binding SL1344 was maintained in the exponential growth phase in LB broth with and without treatment with the drug novobiocin (25 M-NM-<g/ml) for 40 min. This was peformed on two independent occasions. In all cases the experimental immunoprecipitated DNA was hybridised against the input DNA.

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