Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S Escherichia coli O157:H7 str. EDL933 Escherichia coli str. K-12 substr. MG1655 Escherichia coli CFT073 Escherichia coli O157:H7 str. Sakai

PROVIDER: GSE106630 | GEO | 2017/11/08

SECONDARY ACCESSION(S): PRJNA417471

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

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

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

| PRJNA417483 | ENA

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

Project description:To compare the transcriptome of ompR null strains with wild-type strain of E. coli and S. Typhimurium during stress

| PRJNA417471 | ENA

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

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

| PRJNA417484 | ENA

Bacillus subtilis wild type and codY-null strain

Project description:This project is about the proteomes of wild type B. subtilis and its codY-null strain (The organism at right side was mislabeled as "E. coli")

2025-11-10 | PXD052459 | Pride

Bacillus subtilis wild type and codY-null strain

Project description:This project is about the proteomes of wild type B. subtilis and its codY-null strain (The organism at right side was mislabeled as "E. coli")

2025-11-10 | PXD055309 | Pride

Bacterial regulon evolution: distinct responses and roles for the identical OmpR proteins of Salmonella Typhimurium and Escherichia coli in the acid stress response.

Project description:The evolution of new gene networks is a primary source of genetic innovation that allows bacteria to explore and exploit new niches, including pathogenic interactions with host organisms. For example, the archetypal DNA binding protein, OmpR, is identical between Salmonella Typhimurium serovar Typhimurium and Escherichia coli, but regulatory specialization has resulted in different environmental triggers of OmpR expression and largely divergent OmpR regulons. Specifically, ompR mRNA and OmpR protein levels are elevated by acid pH in S. Typhimurium but not in E. coli. This differential expression pattern is due to differences in the promoter regions of the ompR genes and the E. coli ompR orthologue can be made acid-inducible by introduction of the appropriate sequences from S. Typhimurium. The OmpR regulon in S. Typhimurium overlaps that of E. coli at only 15 genes and includes many horizontally acquired genes (including virulence genes) that E. coli does not have. We found that OmpR binds to its genomic targets in higher abundance when the DNA is relaxed, something that occurs in S. Typhimurium as a result of acid stress and which is a requirement for optimal expression of its virulence genes. The genomic targets of OmpR do not share a strong nucleotide sequence consensus: we propose that the ability of OmpR to recruit additional genes to its regulon arises from its modest requirements for specificity in its DNA targets with its preference for relaxed DNA allowing it to cooperate with DNA-topology-based allostery to modulate transcription in response to acid stress.

| S-EPMC3945435 | biostudies-literature

Adaptation of sucrose metabolism in the Escherichia coli wild-type strain EC3132.

Project description:Although Escherichia coli strain EC3132 possesses a chromosomally encoded sucrose metabolic pathway, its growth on low sucrose concentrations (5 mM) is unusually slow, with a doubling time of 20 h. In this report we describe the subcloning and further characterization of the corresponding csc genes and adjacent genes. The csc regulon comprises three genes for a sucrose permease, a fructokinase, and a sucrose hydrolase (genes cscB, cscK, and cscA, respectively). The genes are arranged in two operons and are negatively controlled at the transcriptional level by the repressor CscR. Furthermore, csc gene expression was found to be cyclic AMP-CrpA dependent. A comparison of the genomic sequences of the E. coli strains EC3132, K-12, and O157:H7 in addition to Salmonella enterica serovar Typhimurium LT2 revealed that the csc genes are located in a hot spot region for chromosomal rearrangements in enteric bacteria. The comparison further indicated that the csc genes might have been transferred relatively recently to the E. coli wild-type EC3132 at around the time when the different strains of the enteric bacteria diverged. We found evidence that a mobile genetic element, which used the gene argW for site-specific integration into the chromosome, was probably involved in this horizontal gene transfer and that the csc genes are still in the process of optimal adaptation to the new host. Selection for such adaptational mutants growing faster on low sucrose concentrations gave three different classes of mutants. One class comprised cscR(Con) mutations that expressed all csc genes constitutively. The second class constituted a cscKo operator mutation, which became inducible for csc gene expression at low sucrose concentrations. The third class was found to be a mutation in the sucrose permease that caused an increase in transport activity.

| S-EPMC135337 | biostudies-literature