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

PLoS One. 2012;7(10):e47314. doi: 10.1371/journal.pone.0047314. Epub 2012 Oct 5.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Bacterial Proteins / physiology
  • Biological Transport
  • Chromatin Immunoprecipitation
  • Escherichia coli / genetics*
  • Gene Expression Profiling
  • Gene Expression Regulation, Bacterial
  • Gene Regulatory Networks
  • Genome, Bacterial*
  • Lipid A / metabolism
  • Oligonucleotide Array Sequence Analysis
  • Oxidative Stress
  • Peptidoglycan / metabolism
  • Phosphates / metabolism*
  • Polysaccharides / metabolism
  • Putrescine / metabolism


  • Bacterial Proteins
  • Lipid A
  • Peptidoglycan
  • Phosphates
  • Polysaccharides
  • PhoB protein, Bacteria
  • colanic acid
  • Putrescine

Grant support

This work was supported by a grant from the National Science Council, Taiwan (NSC 100-2319-B-010-002), and the Aim for the Top University Plan grant from the Ministry of Education, Taiwan. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.