Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli

Chi Yang, Tzu Wen Huang, Shiau Yi Wen, Chun Yang Chang, Shih Feng Tsai, Whei Fen Wu, Chuan Hsiung Chang

Research output: Contribution to journalArticle

21 Citations (Scopus)

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.

Original languageEnglish
Article numbere47314
JournalPLoS One
Volume7
Issue number10
DOIs
Publication statusPublished - Oct 5 2012
Externally publishedYes

Fingerprint

Gene Regulatory Networks
Starvation
Transcriptome
Gene expression
Escherichia coli
starvation
Genes
Phosphates
Genome
phosphates
gene expression
genome
genes
Microarrays
transcription factors
Gene Expression
Chromatin Immunoprecipitation
Microarray Analysis
Oxidative stress
chromatin

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli. / Yang, Chi; Huang, Tzu Wen; Wen, Shiau Yi; Chang, Chun Yang; Tsai, Shih Feng; Wu, Whei Fen; Chang, Chuan Hsiung.

In: PLoS One, Vol. 7, No. 10, e47314, 05.10.2012.

Research output: Contribution to journalArticle

Yang, Chi ; Huang, Tzu Wen ; Wen, Shiau Yi ; Chang, Chun Yang ; Tsai, Shih Feng ; Wu, Whei Fen ; Chang, Chuan Hsiung. / Genome-Wide PhoB Binding and Gene Expression Profiles Reveal the Hierarchical Gene Regulatory Network of Phosphate Starvation in Escherichia coli. In: PLoS One. 2012 ; Vol. 7, No. 10.
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