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ChIP-on-chip of OmpR binding in Salmonella enterica serovar Typhimurium strain SL1344 and E.scherichia coli strain CSH50 at pH 7 and pH 4.5 including analysis of OmpR binding in SL1344 in the absence and presence of novobiocin (25 μg/ml)

ABSTRACT: ChIP-on-chip of OmpR binding in Salmonella enterica serovar Typhimurium strain SL1344 and E.scherichia coli strain CSH50 at pH 7 and pH 4.5 including analysis of OmpR binding in SL1344 in the absence and presence of novobiocin (25 μg/ml)

PROVIDER: PRJNA215321 | ENA |

REPOSITORIES: ENA

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ChIP-on-chip of OmpR binding in Salmonella enterica serovar Typhimurium strain SL1344 and E.scherichia coli strain CSH50 at pH 7 and pH 4.5 including analysis of OmpR binding in SL1344 in the absence and presence of novobiocin (25 M-NM-<g/ml)

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.

2014-03-27 | E-GEOD-49914 | biostudies-arrayexpress

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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.

2012-12-01 | GSE35938 | GEO

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.

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To compare the transcriptome of ompR null strains with wild-type strain of S. Typhimurium during osmotic stress

Project description:In bacteria, one paradigm for signal transduction is the two-component regulatory system, consisting of a sensor kinase (usually a membrane protein) and a response regulator (usually a membrane protein) and a response regulator (usually a DNA binding protein). The EnvZ/OmpR two-component system in S. Typhimurium responds to osmotic stress and regulates expression of outer membrane proteins. Furthermore, bacteria were believed to regulate pH by acidifying after external acid stress, then immediately recovering. Using a pH-sensor in single living cells, we show that S. Typhimurium maintain an acidic cytoplasm under sucrose-driven osmotic stress which requires OmpR. Thus, we set out to identify the OmpR targets of S. Typhimurium under osmotic stress.

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To compare the transcriptome of ompR null strains with wild-type strain of E. coli during acid or osmotic stress

Project description:In bacteria, one paradigm for signal transduction is the two-component regulatory system, consisting of a sensor kinase (usually a membrane protein) and a response regulator (usually a membrane protein) and a response regulator (usually a DNA binding protein). The EnvZ/OmpR two-component system in E. coli responds to osmotic stress and regulates expression of outer membrane proteins. Furthermore, bacteria were believed to regulate pH by acidifying after external acid stress, then immediately recovering. Using a pH-sensor in single living cells, we show that E. coli maintain an acidic cytoplasm. The osmotic stress transcription factor OmpR, was required. Thus, we set out to identify the OmpR targets under acid and osmotic stress.

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Project description:In order to explore the transcriptional reprogramming in EvgSc, ompR and EvgSc/ompR mutants we have used whole genome microarray profiling. EvgSc, ompR and EvgSc/ompR mutants were developed. Each mutant was profiled in duplicate.

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Expression profiling of EvgSc and ompR mutants

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