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Genome-wide characterization of PhoB binding profile in Escherichia coli (ChIP-chip data)

ABSTRACT: Chromatin immunoprecipitation was combined with high-density tiling array (ChIP-chip) and gene expression microarray to reveal the adaptive responses of Escherichia coli to phosphate starvation. The first sketch of the genome-wide distribution of PhoB binding profile was unveiled and 43 regions were identified as the PhoB binding regions. The presence of a significant common motif in these binding regions allowed us to reconstruct the PhoB binding pattern. By comparing the ChIP-chip and microarray datasets, we were also able to identify genes directly or indirectly affected through PhoB regulation. Nineteen out of the 287 differentially expressed genes in the presence and absence of PhoB activity were considered as the genes directly regulated by PhoB. The adaptive responses affected through PhoB regulation are discussed and these responses involve in several important biological functions including transcriptional regulation, transportation, membrane component arrangement, sigma factor modulation and DNA replication inhibition.

ORGANISM(S): Escherichia coli Escherichia coli str. K-12 substr. MG1655

PROVIDER: GSE21856 | GEO | 2012/10/21

SECONDARY ACCESSION(S): PRJNA129323

REPOSITORIES: GEO

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Genome-wide characterization of PhoB binding profile in Escherichia coli (gene expression data)

Project description:Chromatin immunoprecipitation was combined with high-density tiling array (ChIP-chip) and gene expression microarray to reveal the adaptive responses of Escherichia coli to phosphate starvation. The first sketch of the genome-wide distribution of PhoB binding profile was unveiled and 43 regions were identified as the PhoB binding regions. The presence of a significant common motif in these binding regions allowed us to reconstruct the PhoB binding pattern. By comparing the ChIP-chip and microarray datasets, we were also able to identify genes directly or indirectly affected through PhoB regulation. Nineteen out of the 287 differentially expressed genes in the presence and absence of PhoB activity were considered as the genes directly regulated by PhoB. The adaptive responses affected through PhoB regulation are discussed and these responses involve in several important biological functions including transcriptional regulation, transportation, membrane component arrangement, sigma factor modulation and DNA replication inhibition.

2012-10-21 | GSE21820 | GEO

Genome-wide characterization of PhoB binding profile in Escherichia coli (gene expression data)

2012-10-21 | E-GEOD-21820 | biostudies-arrayexpress

Genome-wide characterization of PhoB binding profile in Escherichia coli (ChIP-chip data)

2012-10-21 | E-GEOD-21856 | biostudies-arrayexpress

Genome-wide characterization of PhoB binding profile in Escherichia coli

Project description:This SuperSeries is composed of the following subset Series: GSE21820: Genome-wide characterization of PhoB binding profile in Escherichia coli (gene expression data) GSE21856: Genome-wide characterization of PhoB binding profile in Escherichia coli (ChIP-chip data) Refer to individual Series

2012-10-21 | E-GEOD-21857 | biostudies-arrayexpress

Cross-regulation between the response regulators PhoB and TctD allows for the integration of diverse environmental signals in Pseudomonas aeruginosa

Project description:Two-component systems (TCS) serve as basic stimulus-response coupling mechanisms to allow organisms to sense and respond to a large variety of environmental conditions. In the opportunistic pathogen Pseudomonas aeruginosa, more than 100 genes encode TCS components. To avoid unwanted cross-talk between TCSs, the signaling cascades are usually very specific, with one sensor talking to its cognate response regulator. However, cross-regulation may provide effective means to integrate different environmental stimuli into a harmonized output response and thus to coordinate gene expression in response to complex and challenging habitats. Here, we applied a protein-fragment complementation assay (PCA) and identified a direct interaction of two response regulators of the OmpR/PhoB subfamily, namely PhoB and TctD in P. aeruginosa in vivo. Transcriptional profiling and ChIP-seq analysis uncovered adjacent bipartite binding motifs of the two response regulators in 8 promoter regions, of which 6 showed a common PhoB-TctD binding motif with a fixed spacing between the two motifs. We further demonstrate that phosphate limitation exhibits a PhoB-dependent activating activity on the expression of those genes, whereas the presence of a preferred carbon source inhibits gene expression in a TctD-dependent manner. Thus, the perception and the integration of two important environmental signals are achieved by a titration of the relative amounts of two phosphorylated response regulators that inversely regulate a common subset of genes. In conclusion, our results shed light on the general principles underlying two-component signal transduction pathways and the exploitation of cross-regulation to adapt bacterial behavior to complex environments. Transcriptome profiling of the UCBP-PA14 phoB and tctD mutants complemented by phoB ChIP-seq experiments.

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Cross-regulation between the response regulators PhoB and TctD allows for the integration of diverse environmental signals in Pseudomonas aeruginosa

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Identification of the PhoB regulon and role of PhoU in the phosphate-starvation response of Caulobacter crescentus (expression)

Project description:An ability to sense and respond to changes in extracellular phosphate is critical to the survival of most bacteria. For Caulobacter crescentus, which typically lives in phosphate-limited environments, this process is especially crucial. Like many bacteria, Caulobacter responds to phosphate limitation through a conserved two-component signaling pathway called PhoR-PhoB, but the direct regulon of PhoB in this organism is unknown. Here, we use ChIP-Seq to map the global binding patterns of the phosphate-responsive transcriptional regulator PhoB in both phosphate-limited and -replete conditions. Combined with genome-wide expression profiling, our work demonstrates that PhoB is induced to regulate nearly 50 genes in phosphate-starved conditions. The PhoB regulon is comprised primarily of genes known or predicted to help Caulobacter scavenge for and import inorganic phosphate, including 15 different membrane transporters. We also investigated the regulatory role of PhoU, a widely conserved protein proposed to coordinate phosphate import with expression of the PhoB regulon by directly modulating the histidine kinase PhoR. However, our studies show that it likely does not play such a role in Caulobacter as depleting PhoU has no significant effect on PhoB-dependent gene expression. Instead, cells lacking PhoU exhibit a striking accumulation of large polyphosphate granules suggesting that PhoU participates in controlling intracellular phosphate metabolism.

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Identification of the PhoB regulon and role of PhoU in the phosphate-starvation response of Caulobacter crescentus (ChIP-seq)

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Identification of the PhoB regulon and role of PhoU in the phosphate-starvation response of Caulobacter crescentus (ChIP-seq)

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Identification of the regulatory circuit of PhoB in Bacteroides fragilis strain YCH46

Project description:Comparison of transcriptional profiles of the wild-type (WT) and the phoB-mutant strain in B. fragilis strain YCH46 during phosphate (Pi) starvation. A four chip study using total RNA isolated from the WT culture and the phoB mutant culture under Pi-excess (6.6 mM) or Pi-limiting (0.0066mM) condition. Each sample contains duplicated data.

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