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

研究成果: 雜誌貢獻文章同行評審

29 引文 斯高帕斯(Scopus)

摘要

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.

原文英語
文章編號e47314
期刊PLoS One
7
發行號10
DOIs
出版狀態已發佈 - 十月 5 2012
對外發佈

ASJC Scopus subject areas

  • 農業與生物科學 (全部)
  • 生物化學、遺傳與分子生物學 (全部)
  • 醫藥 (全部)

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