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Nucleoid architecture related to RNA molecules

Research Project

Project/Area Number 19770145
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Molecular biology
Research InstitutionUniversity of Tsukuba

Principal Investigator

OHNIWA Ryosuke  University of Tsukuba, 大学院・人間総合科学研究科, 助教 (30447883)

Project Period (FY) 2007 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥600,000)
Fiscal Year 2009: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2008: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2007: ¥1,300,000 (Direct Cost: ¥1,300,000)
Keywords染色体構築 / 機能 / 分配 / 大腸菌 / 核様体 / 転写 / 原子間力顕微鏡 / 黄色ブドウ球菌 / 動態制御機構 / ゲノム / 核様体タンパク質
Research Abstract

The genomic DNA in bacteria is packed into cells as nucleoid, which is composed of genomic DNA, RNAs and proteins. I focused on the regulatory mechanism of the nucleoid structure because its dynamics is closely related to the essential biological processes such as transcription, translation, replication etc. In the present study, I found i) nucleoid structures are sustained by nascent single stranded RNA, ii) the proteins involved in the nucleoid is highly varied in species-specific and environmental-specific manners.

Report

(4 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • Research Products

    (36 results)

All 2010 2009 2008 2007 Other

All Journal Article (12 results) (of which Peer Reviewed: 12 results) Presentation (16 results) Book (4 results) Remarks (4 results)

  • [Journal Article] C. elegans sym-1 is a downstream target of the Hunchback-like-1 developmental timing transcription factor.2009

    • Author(s)
      Niwa R, Hada K, Moliyama K, Ohniwa RL, Tan Y, Cather KO, Chi W, Reinke W, Slack FJ
    • Journal Title

      Cell Cycle 15;8(24)

      Pages: 4147-54

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] C.elegans sym-1 is a downstream target of the Hunchback-like-1 developmental timing transcription factor2009

    • Author(s)
      Ryusuke Niwa, et al.
    • Journal Title

      Cell Cycle 15

      Pages: 4147-54

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The sigH gene sequence can subspeciate staphylococci.2008

    • Author(s)
      Morikawa K, Ohniwa RL, Kumano M, Okamura H, Saito S, Ohta T
    • Journal Title

      Diagnostic Microbiology and Infectious Disease 61

      Pages: 373-380

    • NAID

      120007138668

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] In situ analysis of the higher-order genome structure in a single Escherichia coli cell.2008

    • Author(s)
      Shindo E, Kubo K, Ohniwa RL, Takeyasu K, Yoshikawa K
    • Journal Title

      J Biotech 133

      Pages: 172-176

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Role of HPF (Hibernation promoting factor) on translational activity in Escherichia coli2008

    • Author(s)
      Ueta M, Ohniwa RL, Yoshida H, Maki Y, Wada C, Wada A
    • Journal Title

      J Biochem 143

      Pages: 425-433

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] The sigH gene sequence can subspeciate staphylococci2008

    • Author(s)
      Morikawa K
    • Journal Title

      Diagnostic Microbiology and Infectious Disease 61

      Pages: 373-380

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Role of HPF (Hibernation promoting factor) on translational acivity in Escherichia coli2008

    • Author(s)
      Ueta M, et. al.
    • Journal Title

      J Biochem 143

      Pages: 425-433

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] In situ analysis of the higher-order genome structure in a single Escherichia coli cell.2008

    • Author(s)
      Shindo E, et. al.
    • Journal Title

      J Biochem 133

      Pages: 172-176

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Transcription-coupled Nucleoid Architecture in Bacteria.2007

    • Author(s)
      Ohniwa RL, Morikawa K, Takeshita SL, Kim J, Ohta T, Wada C, Takeyasu K
    • Journal Title

      Genes Cells 12

      Pages: 1141-52

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Perspective Factor; Past, Present and Future of Life Sciences.2007

    • Author(s)
      Ohniwa RL, Hibino A, Takeyasu K
    • Journal Title

      PROCEEDINGS OF International Society for Scientometrics and Infometrics 2007 II

      Pages: 908-909

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Transcription-coupled Nucleoid Architecture in Bacteria2007

    • Author(s)
      Ohniwa RL, et. al.
    • Journal Title

      Genes Cells 12

      Pages: 1141-52

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Perspective Factor; Past, Present and Future of Life Sciences.2007

    • Author(s)
      Ohniwa RL, et. al.
    • Journal Title

      PROCEEDINGS OF International Society for Scie ntometrics and Infometrics 2007 II

      Pages: 908-909

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Presentation] 核様体タンパク質の多様性;核様体タンパク質の比較プロテオミクス解析2009

    • Author(s)
      大庭良介、牛島由理、森川一也、斉藤慎二
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      神奈川県横浜市
    • Year and Date
      2009-12-09
    • Related Report
      2009 Final Research Report
  • [Presentation] 核様体タンパク質の多様性;核様体タンパク質の比較プロテオミクス解析2009

    • Author(s)
      大庭良介, 他
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      神奈川県
    • Year and Date
      2009-12-09
    • Related Report
      2009 Annual Research Report
  • [Presentation] Diversification of nucleoid associated proteins in bacteria revealed by comparative proteomic analysis.2009

    • Author(s)
      Ohniwa RL, Ushijima Y, Morikawa K, Saito S
    • Organizer
      BioMicroWorld
    • Place of Presentation
      ポルトガル、リスボン
    • Year and Date
      2009-12-04
    • Related Report
      2009 Final Research Report
  • [Presentation] The genome of a hyperthermophilic archaeaon Thermococcus kodakaraens is consists of distinct structural domains enriched with histone or TK04712009

    • Author(s)
      Ryosuke Ohniwa, et al.
    • Organizer
      BioMicroWorld
    • Place of Presentation
      スペイン リスボン大学
    • Year and Date
      2009-12-04
    • Related Report
      2009 Annual Research Report
  • [Presentation] The genome of a hyperthermophilic archaeaon Thermococcus kodakaraens is consists of distinct structural domains enriched with histone or TK04712009

    • Author(s)
      H.Maruyama el al.
    • Organizer
      Gordon Research Conference
    • Place of Presentation
      米国 Waterville Valley Resort
    • Year and Date
      2009-07-27
    • Related Report
      2009 Annual Research Report
  • [Presentation] Escherichia coli mutants deficient in nucleoid proteins exhibit distinct genome folding.2008

    • Author(s)
      Ohniwa RL, Muchaku H, Morikawa K, Ohta T, Satio S, Wada C, Takeyasu K
    • Organizer
      48th American Society of Cell Biology Annual Meeting
    • Place of Presentation
      米国、サンフランシスコ
    • Year and Date
      2008-12-06
    • Related Report
      2009 Final Research Report
  • [Presentation] Escherichia coli mutants deficient in nucleoid proteins exhibit distinct genome folding2008

    • Author(s)
      Ohniwa RL, et.al.
    • Organizer
      48th American Society of Cell Biology Annual Meeting
    • Place of Presentation
      米国、サンフランシスコ
    • Related Report
      2008 Annual Research Report
  • [Presentation] ヒストン様タシパク質Huが核様体構造に与える影響の解析2008

    • Author(s)
      無着弘喜, 他
    • Organizer
      第31回日本分子生物学会年会
    • Place of Presentation
      兵庫県神戸市
    • Related Report
      2008 Annual Research Report
  • [Presentation] Analysis of chromatin structure of the hyperthermophilic archaeaon Thermococcus kodakaraensis2008

    • Author(s)
      Hugo Maruyama 他
    • Organizer
      第31回日本分子生物学会年会
    • Place of Presentation
      兵庫県神戸市
    • Related Report
      2008 Annual Research Report
  • [Presentation] 細菌核様体の階層構造と動態制御機構2008

    • Author(s)
      大庭良介, 他
    • Organizer
      日本顕微鏡学会第64回学術講演会
    • Place of Presentation
      京都府京都市
    • Related Report
      2008 Annual Research Report
  • [Presentation] Ebb and flow of life science researches in past 30 years2007

    • Author(s)
      Ohniwa, RL, et. al.
    • Organizer
      BMB
    • Place of Presentation
      神奈川県
    • Year and Date
      2007-12-11
    • Related Report
      2007 Annual Research Report
  • [Presentation] Thermococcus kodakaraensis KOD1の染色体構造の解析2007

    • Author(s)
      円山由郷, 他
    • Organizer
      極限微生物学会年会
    • Place of Presentation
      福岡県
    • Year and Date
      2007-11-29
    • Related Report
      2007 Annual Research Report
  • [Presentation] 黄色ブドウ球菌核様体の動態制御機構;大腸菌との類似点・相違点2007

    • Author(s)
      大庭良介, 他
    • Organizer
      第52回黄色ブドウ球菌学会
    • Place of Presentation
      徳島県
    • Year and Date
      2007-09-15
    • Related Report
      2007 Annual Research Report
  • [Presentation] Involvement of Topoisomerase I and nascent single-stranded RNA in the bacterial chromosome architecture and dynamics.2007

    • Author(s)
      Ohniwa, RL, et. al.
    • Organizer
      16th International Chromosome Conference
    • Place of Presentation
      オランダ・アムステルダム
    • Year and Date
      2007-08-26
    • Related Report
      2007 Annual Research Report
  • [Presentation] Involvement of Topoisomerase I and nascent single-stranded RNA in the bacterial chromosome architecture and dynamics.2007

    • Author(s)
      Ohniwa RL, Morikawa K, Kim J, Ohta T Ishihama A, Wada C, Takeyasu K
    • Organizer
      16th International Chromosome Conference
    • Place of Presentation
      オランダ、アムステルダム
    • Year and Date
      2007-08-08
    • Related Report
      2009 Final Research Report
  • [Presentation] Perspective Factor;Past,Present and Future of Life Sciences.2007

    • Author(s)
      Ohniwa, RL, et. al.
    • Organizer
      11th International Conference of the International Society for Scientometrics and Informetrics
    • Place of Presentation
      スペイン・マドリッド
    • Year and Date
      2007-06-26
    • Related Report
      2007 Annual Research Report
  • [Book] "Nucleoid Architecture and Dynamics in bacteria" Bacterial DNA, DNA Polymerase and DNA Helicases2010

    • Author(s)
      Ohniwa RL, Morikawa K, Wada C, Ohta T, Takeyasu T
    • Total Pages
      456
    • Publisher
      Nova Science Publishers, Inc.
    • Related Report
      2009 Final Research Report
  • [Book] Bacterial DNA, DNA Polymerase and DNA Helicases(Nucleoid Architecture and Dynamics in bacteria)2010

    • Author(s)
      Ryosuke Ohniwa, et al.
    • Publisher
      Nova Science Publishers(印刷中)
    • Related Report
      2009 Annual Research Report
  • [Book] 萌芽する科学技術(第四章データマイニングからの接近―「抽出する」―)2009

    • Author(s)
      大庭良介, 他
    • Publisher
      京都大学出版会
    • Related Report
      2009 Annual Research Report
  • [Book] "Biochemical and Biophysical Basis of Genome Folding Mechanisms" Progress in Biopolymer Research2008

    • Author(s)
      Kobori T, Hizume K, Ohniwa RL, Yoshimura SH, Takeyasu K
    • Publisher
      Nova Science Publishers, Inc.
    • Related Report
      2009 Final Research Report
  • [Remarks]

    • URL

      http://www.md.tsukuba.ac.jp/basic-med/infectionbiology/microbiology/

    • Related Report
      2009 Final Research Report
  • [Remarks]

    • URL

      http://www.md.tsukuba.ac.jp/basic-med/infectionbiology/microbiology/

    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

      http://www.md.tsukuba.ac.jp/basic-med/infectionbiology/microbiology/

    • Related Report
      2008 Annual Research Report
  • [Remarks]

    • URL

      http://www.md.tsukuba.ac.jp/basic-med/infectionbiology/microbiology/

    • Related Report
      2007 Annual Research Report

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Published: 2007-04-01   Modified: 2016-04-21  

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