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The role of nucleoid structure in bacterial transcriptional regulation

Research Project

Project/Area Number 26450090
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Applied microbiology
Research InstitutionNara Institute of Science and Technology

Principal Investigator

Oshima Taku  奈良先端科学技術大学院大学, バイオサイエンス研究科, 助教 (50346318)

Co-Investigator(Renkei-kenkyūsha) YAMAMOTO Kaneyoshi  法政大学, 生命科学部, 教授 (40351580)
ISHIKAWA Shu  奈良先端科学技術大学院大学, バイオサイエンス研究科, 助教 (30359872)
Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2015: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2014: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
KeywordsChIP-seq / GeF-seq / 大腸菌 / 核様体 / H-NS / HU / Fis / IHF / AFM
Outline of Final Research Achievements

We performed the modified high resolution ChIP-seq analysis of E. coli nucleoid proteins to identify the binding regions of nucleoid proteins in base pair resolution. The results indicated that some nucleoid proteins recognize specific sequences at over 3000 regions in E. coli genome, while we could not find the specific recognition sequences of H-NS and HU. Our results also suggested that each nucleoid protein may independently interact with genomic DNA. However, because the independent interaction of each nucleoid protein affects to the functions of other nucleoid proteins, there is the inter-relation of nucleoid proteins to form functional nucleoid structure in E. coli cells.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (16 results)

All 2016 2015 2014

All Journal Article (7 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 7 results,  Open Access: 7 results,  Acknowledgement Compliant: 6 results) Presentation (8 results) (of which Invited: 2 results) Book (1 results)

  • [Journal Article] Replication fork progression is paused in two large chromosomal zones flanking the DNA replication origin in Escherichia coli2016

    • Author(s)
      Masahiro Tatsumi Akiyama, Taku Oshima, Onuma Chumsakul, Shu Ishikawa and Hisaji Mak
    • Journal Title

      Genes to Cells

      Volume: 21 Issue: 8 Pages: 907-914

    • DOI

      10.1111/gtc.12388

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Chromosomal location of the DnaA-reactivating sequence DARS2 is important to regulate timely initiation of DNA replication in Escherichia coli2016

    • Author(s)
      Yukie Inoue, Hiroyuki Tanaka, Kazutoshi Kasho, Kazuyuki Fujimitsu, Taku Oshima, Tsutomu Katayama
    • Journal Title

      Genes Cells

      Volume: 21 Issue: 9 Pages: 1015-1023

    • DOI

      10.1111/gtc.12395

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Gene Activation through the Modulation of Nucleoid Structures by a Horizontally Transferred Regulator, Pch, in Enterohemorrhagic Escherichia coli2016

    • Author(s)
      Fukui N, Oshima T, Ueda T, Ogasawara N, Tobe T.
    • Journal Title

      PLoS One

      Volume: 11 Issue: 2 Pages: e0149718-e0149718

    • DOI

      10.1371/journal.pone.0149718

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes2016

    • Author(s)
      Higashi K., Tobe T., Kanai A., Uyar E., Ishikawa S., Suzuki Y., Ogasawara N., Kurokawa K., and Oshima T
    • Journal Title

      PLoS genetics

      Volume: 12 Issue: 1 Pages: e1005796-e1005796

    • DOI

      10.1371/journal.pgen.1005796

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo2015

    • Author(s)
      Imashimizu M., Takahashi H., Oshima T., McIntosh C., Bubunenko M., Court DL., and Kashlev M.
    • Journal Title

      Genome Biology

      Volume: 16 Issue: 1 Pages: 98-98

    • DOI

      10.1186/s13059-015-0666-5

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] The Role of YdeO regulator for Escherichia coli response to acidic and anaerobic stresses.2014

    • Author(s)
      Yamanaka, Y., Oshima, T., Ishihama, A. and Yamamoto, K.
    • Journal Title

      PLoS ONE

      Volume: 9 Issue: 11 Pages: e111962-e111962

    • DOI

      10.1371/journal.pone.0111962

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Timely binding of IHF and Fis to DARS2 regulates ATP-DnaA production and replication initiation2014

    • Author(s)
      Kazutoshi Kasho, Fujimitsu Kazuyuki, Toshihiro Matoba, Taku Oshima, Tsutomu Katayama
    • Journal Title

      Nucleic Acids Research

      Volume: 42 Issue: 21 Pages: 13134-13149

    • DOI

      10.1093/nar/gku1051

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] H-NSが促す外来DNAの塩基配列の多様化2016

    • Author(s)
      大島 拓
    • Organizer
      第88回日本遺伝学会
    • Place of Presentation
      日本大学国際関係学部(静岡県三島市)
    • Year and Date
      2016-09-07
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 大腸菌は、H-NSタンパク質の働きにより水平伝搬遺伝子の変異を許容する2016

    • Author(s)
      大島 拓
    • Organizer
      第13回21世紀大腸菌研究会
    • Place of Presentation
      ホテルグリーンピア南阿蘇(熊本県阿蘇群南阿蘇村)
    • Year and Date
      2016-06-02
    • Related Report
      2016 Annual Research Report
  • [Presentation] RNAポリメラーゼの動きをゲノムワイドに解析する、(ワークショップ:バクテリア細胞増殖プロセス研究の最前線)2016

    • Author(s)
      大島 拓
    • Organizer
      第89回日本細菌学会総会
    • Place of Presentation
      大阪国際交流センター (大阪府大阪市)
    • Year and Date
      2016-03-23
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] H-NS による転写抑制を介した大腸菌ゲノムの多様性獲得機構2016

    • Author(s)
      東 光一、戸邉 亨、石川 周、鈴木 穣、小笠原 直毅、黒川 顕、大島 拓
    • Organizer
      第10回日本ゲノム微生物学会年会
    • Place of Presentation
      東京工業大学 (東京都目黒区)
    • Year and Date
      2016-03-04
    • Related Report
      2015 Research-status Report
  • [Presentation] Genome Footprinting (GeF-seq)により明らかにされたIhfAおよびIhaB特異的認識配列2015

    • Author(s)
      Onuma Chumsakul、中村 健介、石川 周、大島 拓
    • Organizer
      第12回 21世紀大腸菌研究会
    • Place of Presentation
      琵琶湖グランドホテル (滋賀県大津市)
    • Year and Date
      2015-06-04
    • Related Report
      2015 Research-status Report
  • [Presentation] 細菌ヒストン様タンパク質H-NSによるゲノム転写制御の機能解析2014

    • Author(s)
      山本 兼良、山中 幸、大島 拓、石浜 明
    • Organizer
      第37回日本分子生物学会年回
    • Place of Presentation
      パシフィコ横浜 (神奈川県横浜市)
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Research-status Report
  • [Presentation] High resolution mapping of nucleoid protein binding sites on E. coli chromosome using DNaseI footprinting followed by high-throughput sequencing2014

    • Author(s)
      Taku Oshima, Onuma Chumsakul, Shu Ishikawa
    • Organizer
      The 9th Symposium
    • Place of Presentation
      御殿場高原ホテル (静岡県御殿場市)
    • Year and Date
      2014-11-17 – 2014-11-21
    • Related Report
      2014 Research-status Report
  • [Presentation] GeF-seqによる大腸菌核様体タンパク質の結合配列のゲノムワイド解析2014

    • Author(s)
      大島 拓
    • Organizer
      第11回 21世紀大腸菌研究会
    • Place of Presentation
      ホテル大観 (岩手県盛岡市)
    • Year and Date
      2014-06-05 – 2014-06-06
    • Related Report
      2014 Research-status Report
  • [Book] 高精度で結合領域を決定するGeF-seq、高精度で結合領域を決定するGeF-seq, 次世代シークエンス解析スタンダード:NGSのポテンシャルを活かしきるWET&DRY2014

    • Author(s)
      大島 拓、石川 周、Chumsakul Onuma、中村 健介
    • Total Pages
      401
    • Publisher
      羊土社
    • Related Report
      2014 Research-status Report

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Published: 2014-04-04   Modified: 2018-03-22  

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