DNA Research Advance Access originally published online on October 17, 2006
DNA Research 2006 13(4):141-153; doi:10.1093/dnares/dsl009
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Escherichia coli Histone-Like Protein H-NS Preferentially Binds to Horizontally Acquired DNA in Association with RNA Polymerase
1 Graduate School of Information Science, Nara Institute of Science and Technology 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
2 Graduate School of Bioagricultural Sciences, Nagoya University Nagoya, Aichi 464-8601, Japan
Heat-stable nucleoid-structuring protein (H-NS) is one of the main nucleoid proteins expressed in exponentially growing Escherichia coli cells. In addition to a role in nucleoid organization, H-NS functions as a pleiotropic regulator of gene expression. The genome-wide distribution of H-NS, compared with the distribution of RNA polymerase and transcriptionally active genes, was investigated using a high-density oligonucleotide chip. The new approach utilized in this study revealed that H-NS binds specifically to approximately 250 loci, covering >1000 genes, to maintain transcriptional inactivation. RNA polymerase was detected in >65% of H-NS binding sites with low or no transcriptional activity, indicating that the association of RNA polymerase to promoter regions is a general mode of transcription repression by H-NS. This study also revealed that most H-NS bound DNA have been horizontally acquired, which indicates that repression of inappropriate gene expression by H-NS plays an important role in the diversification of the E. coli genome. This study presents a comprehensive assessment of the distribution of H-NS within the E. coli genome, sheds light on the mechanism underlying the transcriptional regulation by H-NS, and provides new insight into bacterial genome evolution.
Key words: histone-like protein H-NS; RNA polymerase; horizontal genes; high-density tiling chip; ChIP-chip analysis
*To whom correspondence should be addressed. Tel. +81-743-72-5430, Fax. +81-743-72-5439, E-mail: nogasawa{at}bs.naist.jp
These authors contributed equally to this work.
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