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RNA sequencing to identify differences between two E. coli strains that respond differently to volatiles of Streptomyces sp.

ABSTRACT: The goals of this study are to compare the transcriptomic response of a E. coli strain with a mutation in the promotor region of the outer membrane porins regulator ompR-envZ that has an increased resistance to ammonia released by a Streptomyces strain.

ORGANISM(S): Escherichia coli

PROVIDER: GSE111370 | GEO | 2019/03/02

REPOSITORIES: GEO

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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)

2014-03-27 | GSE49914 | GEO

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

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.

2017-11-08 | GSE106629 | GEO

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.

2017-11-08 | GSE106628 | GEO

Pseudomonas syringae Virulence Regulatory Network construction

Project description:Pseudomonas syringae, a Gram-negative plant pathogen, infects more than 50 crops with its type III secretion system (T3SS) and causes severe economic losses around the world. Although the mechanisms of virulence-associated regulators of P. syringae T3SS have been studied for decades, the crosstalk and network underlying these regulators are still elusive. Previously, we have individually studied a group of T3SS regulators, including AefR, HrpS, and RhpRS. In the present study, we found 4 new T3SS regulator genes (envZ, ompR, tsiS and phoQ) via transposon-mediated mutagenesis. Two-component systems EnvZ and TsiS natively regulate T3SS. In order to uncover the crosstalk between 16 virulence-associated regulators, (including AefR, AlgU, CvsR, GacA, HrpL, HrpR, HrpS, MgrA, OmpR, PhoP, PilR, PsrA, RhpR, RpoN, TsiR and Vfr) in P. syringae, we mapped an intricate network named PSVnet (Pseudomonas syringae Virulence Regulatory Network) by combining differentially expression genes in RNA-seq and binding loci in ChIP-seq of all regulators.

2021-03-29 | GSE138204 | GEO

Phenotypic and transcriptional analysis of the osmotic regulator OmpR in Yersinia pestis

Project description:Background The osmotic regulator OmpR in Escherichia coli regulates differentially the expression of major porin proteins OmpF and OmpC. In Yersinia enterocolitica and Y. pseudotuberculosis, OmpR is required for both virulence and survival within macrophages. However, the phenotypic and regulatory roles of OmpR in Y. pestis are not yet fully understood. Results Y. pestis OmpR is involved in building resistance against phagocytosis and controls the adaptation to various stressful conditions met in macrophages. The ompR mutation likely did not affect the virulence of Y. pestis strain 201 that was a human-avirulent enzootic strain. The microarray-based comparative transcriptome analysis disclosed a set of 224 genes whose expressions were affected by the ompR mutation, indicating the global regulatory role of OmpR in Y. pestis. Real-time RT-PCR or lacZ fusion reporter assay further validated 16 OmpR-dependent genes, for which OmpR consensus-like sequences were found within their upstream DNA regions. ompC, F, X, and R were up-regulated dramatically with the increase of medium osmolarity, which was mediated by OmpR occupying the target promoter regions in a tandem manner. Conclusion OmpR contributes to the resistance against phagocytosis or survival within macrophages, which is conserved in the pathogenic yersiniae. Y. pestis OmpR regulates ompC, F, X, and R directly through OmpR-promoter DNA association. There is an inducible expressions of the pore-forming proteins OmpF, C, and X at high osmolarity in Y. pestis, in contrast to the reciprocal regulation of them in E. coli. The main difference is that ompF expression is not repressed at high osmolarity in Y. pestis, which is likely due to the absence of a promoter-distal OmpR-binding site for ompF.

2011-10-24 | GSE26601 | GEO

Dual RNA-seq on Klebsiella pneumoniae infection to human epithelial cells

Project description:Klebsiella pneumoniae poses significant threat to global health. Detailed investigation to the nature of its interaction to human epithelial cells is still lacking. OmpR is an important regulator to the expression of major outer membrane protein genes, ompF and ompC. Here, we exploited the recently described dual RNA-seq to simultaneously measure genome-wide expression of host and pathogen two hours into infection. By comparing OmpR deleted strain to its wildtype parental strain, we, simultaneously, reconstructed OmpR regulon and deletion effect to host response.

2021-12-14 | GSE123964 | GEO

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Leaf Plasmodesmata Respond Differently to TMV, ToBRFV and TYLCV Infection.

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