Dataset Information

Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli.

ABSTRACT: The phosphate starvation response in bacteria has been studied extensively for the past few decades and the phosphate-limiting signal is known to be mediated via the PhoBR two-component system. However, the global DNA binding profile of the response regulator PhoB and the PhoB downstream responses are currently unclear. In this study, chromatin immunoprecipitation for PhoB was combined with high-density tiling array (ChIP-chip) as well as gene expression microarray to reveal the first global down-stream responses of the responding regulator, PhoB in E. coli. Based on our ChIP-chip experimental data, forty-three binding sites were identified throughout the genome and the known PhoB binding pattern was updated by identifying the conserved pattern from these sites. From the gene expression microarray data analysis, 287 differentially expressed genes were identified in the presence of PhoB activity. By comparing the results obtained from our ChIP-chip and microarray experiments, we were also able to identify genes that were directly or indirectly affected through PhoB regulation. Nineteen out of these 287 differentially expressed genes were identified as the genes directly regulated by PhoB. Seven of the 19 directly regulated genes (including phoB) are transcriptional regulators. These transcriptional regulators then further pass the signal of phosphate starvation down to the remaining differentially expressed genes. Our results unveiled the genome-wide binding profile of PhoB and the downstream responses under phosphate starvation. We also present the hierarchical structure of the phosphate sensing regulatory network. The data suggest that PhoB plays protective roles in membrane integrity and oxidative stress reduction during phosphate starvation.

SUBMITTER: Yang C

PROVIDER: S-EPMC3465305 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli.

Yang Chi C Huang Tzu-Wen TW Wen Shiau-Yi SY Chang Chun-Yang CY Tsai Shih-Feng SF Wu Whei-Fen WF Chang Chuan-Hsiung CH

PloS one 20121005 10

The phosphate starvation response in bacteria has been studied extensively for the past few decades and the phosphate-limiting signal is known to be mediated via the PhoBR two-component system. However, the global DNA binding profile of the response regulator PhoB and the PhoB downstream responses are currently unclear. In this study, chromatin immunoprecipitation for PhoB was combined with high-density tiling array (ChIP-chip) as well as gene expression microarray to reveal the first global dow ...[more]

PMID: 23071782

Similar Datasets

Project description:An ability to sense and respond to changes in extracellular phosphate is critical for 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 used chromatin immunoprecipitation-DNA sequencing (ChIP-Seq) to map the global binding patterns of the phosphate-responsive transcriptional regulator PhoB under phosphate-limited and -replete conditions. Combined with genome-wide expression profiling, our work demonstrates that PhoB is induced to regulate nearly 50 genes under 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 PhoU depletion has no significant effect on PhoB-dependent gene expression. Instead, cells lacking PhoU exhibit striking accumulation of large polyphosphate granules, suggesting that PhoU participates in controlling intracellular phosphate metabolism.The transcription factor PhoB is widely conserved throughout the bacterial kingdom, where it helps organisms respond to phosphate limitation by driving the expression of a battery of genes. Most of what is known about PhoB and its target genes is derived from studies of Escherichia coli. Our work documents the PhoB regulon in Caulobacter crescentus, and comparison to the regulon in E. coli reveals significant differences, highlighting the evolutionary plasticity of transcriptional responses driven by highly conserved transcription factors. We also demonstrated that the conserved protein PhoU, which is implicated in bacterial persistence, does not regulate PhoB activity, as previously suggested. Instead, our results favor a model in which PhoU affects intracellular phosphate accumulation, possibly through the high-affinity phosphate transporter.

Dataset Information

Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli.

Publications

Genome-wide PhoB binding and gene expression profiles reveal the hierarchical gene regulatory network of phosphate starvation in Escherichia coli.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure