Comparative analysis of H-NS binding profiles of three E.coli strains suggests H-NS binding contributes to sequence diversification of E.coli genome

• Project/Area Number: 23310131
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Genome biology
• Research Institution: Tokyo Institute of Technology
• Principal Investigator: KUROKAWA Ken 東京工業大学, 地球生命研究所, 教授 (20343246)
• Co-Investigator(Kenkyū-buntansha): MARUYAMA Fumito 東京医科歯科大学, 医歯(薬)学総合研究科, 准教授 (30423122)
• Project Period (FY): 2011-04-01 – 2014-03-31
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥9,880,000 (Direct Cost: ¥7,600,000、Indirect Cost: ¥2,280,000); Fiscal Year 2013: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000); Fiscal Year 2012: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
• Keywords: 微生物ゲノム / ゲノム構造多様性 / 核様体

Research Abstract

The nucleoid protein, H-NS, binds hundreds of regions on the E. coli genome and consequently silences the expression of many genes. Interestingly, many of the genes silenced by H-NS are horizontally acquired, some that are integrated into host transcriptional regulatory networks contribute to stress response, virulence and pathogenicity of the host E. coli strains. Here, we report a comparative evaluation of H-NS binding profiles, determined using the ChAP-seq method, to conserved common segments in the genome sequences of three E.coli strains, K-12, SE11, and SE15. We observed that the H-NS binding profiles are highly conserved in common segments among the strains, and sequence diversity within these regions in the different strains does not affect H-NS interactions. Rather, sequence-diverse regions of the common segments in the E. coli genome tend to bind H-NS, and the encoded genes in these regions seem to play important roles in growth during intestinal environment.

Research Products

• [Journal Article] Analysis of the complete plastid genome of the unicellular red alga Porphyridium purpureum (2014)
  • Author(s): Tajima N, Sato S,Maruyama F,Kurokawa K,Ohta H, Tabata S, Sekine K, Moriyama T, Sato N
  • Journal Title: J Plant Res Volume: 127 Issue: 3 Pages: 389-397
  • DOI: 10.1007/s10265-014-0627-1
  • NAID: 40020051727
  • Peer Reviewed
• [Journal Article] A novel small regulatory RNA enhances cell motility in enterohemorrhagic <i>Escherichia coli</i> (2014)
  • Author(s): Sudo N, Soma A, Muto A, Iyoda S, Suh M, Kurihara N, Abe H, Tobe T, Ogura Y, Hayashi T, Kurokawa K,Ohinishi M, Sekine Y
  • Journal Title: The Journal of General and Applied Microbiology Volume: 60 Issue: 1 Pages: 44-50
  • DOI: 10.2323/jgam.60.44
  • NAID: 130004802264
  • ISSN: 0022-1260, 1349-8037
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• [Journal Article] Updating the Vibrio clades defined by multilocus sequence phylogeny : Proposal of eight new clades, and the description of Vibrio tritonius sp. Nov. (2013)
  • Author(s): Sawabe T, Ogura Y, Matsumura Y, Gao F, Amin A, Mino S, Nakagawa S, Sawabe T, Kumar R, Fukui Y, Satomi M, Matsushima R,Thompson F, Gomez -Gil B, Christen R,Maruyama F,Kurokawa K, Hayashi T
  • Journal Title: Frontiers in Aquatic Microbiol Volume: 4 Pages: 1-14
  • Peer Reviewed
• [Journal Article] Design and experimental application of a novel non-degenerate universal primer set that amplifies prokaryotic 16S rRNA genes with a low possibility to amplify eukaryotic rRNA genes (2013)
  • Author(s): Mori H, Maruyama F, Kato H, Toyoda A, Dozono A, Ohtsubo Y, Nagata Y, Fujiyama A, Tsuda M Kurokawa K
  • Journal Title: DNA Res Volume: 21 Issue: 2 Pages: 217-227
  • DOI: 10.1093/dnares/dst052
  • Peer Reviewed / Open Access
• [Journal Article] Whole-genome sequence of the purple photosynthetic bacterium Rhodovulum sulfidophilum strainW4 (2013)
  • Author(s): Masuda M, Hori K, Maruyama F, Ren S, Sugimoto S, Yamamoto N, Mori H, Yamada T, Sato S, Tabata S, Ohta H, Kurokawa K
  • Journal Title: Genome Announc Volume: 1(4) Issue: 4
  • DOI: 10.1128/genomea.00577-13
  • Peer Reviewed
• [Journal Article] Complete genome sequence of a Propionibacterium acnes isolate from a sarcoidosis patient. (2013)
  • Author(s): Minegishi K, Aikawa C, Furukawa A, Watanabe T, Nakano T, Ogura Y, Ohtsubo Y, Kurokawa K, Hayashi T, Maruyama F, Nakagawa I, Eishi Y
  • Journal Title: Genome Announcement Volume: 1 Issue: 1 Pages: 16-12
  • DOI: 10.1128/genomea.00016-12
  • Peer Reviewed
• [Journal Article] Updating the vibrio phylogeny defined by multilocus sequence phylogeny (2013)
  • Author(s): T. Sawabe, Y. Ogura, Y. Matsumura et al.
  • Journal Title: Front. Microbiol. Volume: 4 Pages: 414-414
  • DOI: 10.3389/fmicb.2013.00414
  • Peer Reviewed
• [Journal Article] GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics (2012)
  • Author(s): Suzuki S, Ishida T, Kurokawa K, Akiyama Y
  • Journal Title: PLoS ONE Volume: 7 Issue: 5 Pages: 1-8
  • DOI: 10.1371/journal.pone.0036060
  • Peer Reviewed
• [Journal Article] Transcription factor GreA contributes to resolve promoter proximal pausing of RNA polymerase in B.subtilis cells (2011)
  • Author(s): Kusuya Y, et al
  • Journal Title: J.Bacteriol. Volume: 193 Pages: 3090-3099
  • Peer Reviewed
• [Journal Article] CRISPR inhibition of prophage acquisition in Streptococcus pyogenes (2011)
  • Author(s): Nozawa T, et al
  • Journal Title: PLoS one Volume: 6
  • Peer Reviewed
• [Journal Article] Complete genome sequence of the periodontogenic bacterium Porphyromonas gingivalis TDC60 (2011)
  • Author(s): Watanabe T, et al
  • Journal Title: J.Bacteriol Volume: 193 Pages: 4259-60
  • Peer Reviewed
• [Presentation] Comparative analysis of H-NS binding profiles of three E.coli strains suggests H-NS binding contributes to sequence diversification of E.coli genome (2012)
  • Author(s): Higashi K, Oshima T, Kurokawa K.
  • Organizer: ASM the 112th General Meeting, San Francisco
  • Place of Presentation: California (USA)
  • Year and Date: 2012-06-16
• [Presentation] Comparative analysis of H-NS binding profiles of three E.coli strains suggests H-NS binding contributes to sequence diversification of E.coli genome (2012)
  • Author(s): Koichi Higashi
  • Organizer: American Society for Microbiology: 112th General Meeting
  • Place of Presentation: San Francisco, California (USA)
• [Presentation] 生態系の理解に向けたゲノム情報の解析と活用 (2011)
  • Author(s): 黒川顕
  • Organizer: 農業環境技術研究所公開セミナー
  • Place of Presentation: つくば(招待講演)
  • Year and Date: 2011-12-06