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Structural and functional analyses of the DNA replication machinery called replisome complex

Research Project

Project/Area Number 15310151
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Living organism molecular science
Research InstitutionKYUSHU UNIVERSITY

Principal Investigator

ISHINO Yoshizumi  Kyushu University, Faculty of Engineering, Professor, 大学院・農学研究院, 教授 (30346837)

Co-Investigator(Kenkyū-buntansha) YAMAGAMI Takeshi  Kyushu University, Faculty of Engineering, Research Associate, 大学院・農学研究院, 助手 (80243947)
KOHDA Daisuke  Kyushu University, Medical Institute of Bioregulation, Professor, 生体防御医学研究所, 教授 (80186618)
Project Period (FY) 2003 – 2005
Project Status Completed (Fiscal Year 2005)
Budget Amount *help
¥15,400,000 (Direct Cost: ¥15,400,000)
Fiscal Year 2005: ¥2,700,000 (Direct Cost: ¥2,700,000)
Fiscal Year 2004: ¥5,800,000 (Direct Cost: ¥5,800,000)
Fiscal Year 2003: ¥6,900,000 (Direct Cost: ¥6,900,000)
KeywordsDNA replication machinery / Macromolecular complex / Protein structure and function / Replication origin / DNA polymerase / DNA複製 / DNA修復 / アーキア / 複製フォーク / 耐熱性 / ヘリカーゼ / ヌクレアーゼ / 超好熱菌 / ツーハイブリッド / タンパク質相互利用 / Pyrococus
Research Abstract

DNA replication processes by a macromolecular complex called replisome, which was made of fork-structured DNA and many protein factors. The aim of this research is to understand the molecular mechanism of assembling and reorganizing of the replisome complex for the precise progress of DNA replication. The originarity of our esearch is that we use hyperthermophilic archaea, which provide very useful experimental materials especially appropriate for the structural analyses of the complexes. We characterized the Cdc6/Orc1 protein that specifically binds to the replication origin (oriC) of the chromosome DNA. Using electron microscopic analyses, we observed the structural properties of this proein, and found that this protein converts its structure depending on the nucleotide cofactors. In addition, we characterized Hef, and Hjm proteins, which were discovered from archaeal cells (Pyrococcus furiosus) by ourselves. These proteins works for the repair systems coupled with DNA replication by converting the fork-structure of replicating DNA to the appropriate form for the following recombinational repair process. Dr.Kohda, a collaborator of this research, has been elucidated that the PriA, which may be the functional homolog of Hef in Esherichia coli, has a recognizing ability of the terminus of the nascent DNA in the replication fork, and provided a structural basis of this recognition mechanism.

Report

(4 results)
  • 2005 Annual Research Report   Final Research Report Summary
  • 2004 Annual Research Report
  • 2003 Annual Research Report
  • Research Products

    (38 results)

All 2006 2005 2004 Other

All Journal Article (33 results) Publications (5 results)

  • [Journal Article] Stoichiometric complex formation by proliferating cell nuclear antigen (PCNA) and its interacting protein : purification and crystallization of the DNA polymerase and PCNA monomer mutant complex from Pyrococcus furiosus2006

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Acta Cryst F62

      Pages: 253-256

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Annual Research Report 2005 Final Research Report Summary
  • [Journal Article] Conprehensive search for DNA polymerase in the hyperthermophilic archaeon, Pyrococcus furiosus2006

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Nucleosides, Nucleotides, and Nucleic Acids (印刷中)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Structure-specific DNA nucleases : structural basis for 3D-scissors2006

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Curr. Opin. Struct. Biol 16

      Pages: 1-8

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Mechanisms of Maintaining Genetic Stability by Homologous Recombination2006

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Chem Rev 106

      Pages: 324-339

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Annual Research Report 2005 Final Research Report Summary
  • [Journal Article] Crystallization and preliminary crystallographic analysis of the N-terminal domain of PriA from Escherichia coli2006

    • Author(s)
      Kohda, D., et al.
    • Journal Title

      Biochim Biophys Acta 1764

      Pages: 157-160

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Annual Research Report 2005 Final Research Report Summary
  • [Journal Article] Structure-specific DNA nucleases : structural basis for 3D-scissors2006

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Curr.Opin.Struct.Biol 16

      Pages: 1-8

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Annual Research Report 2005 Final Research Report Summary
  • [Journal Article] Crystallization and preliminary crystallographic analysis of the N-terminal domain of PriA from Escherichia coli2006

    • Author(s)
      Khoda, D., et al.
    • Journal Title

      Biochim Biophys Acta 1764

      Pages: 157-160

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Comprehensive search for DNA polymerase in the hyperthermophilic archaeon, Pyrococcus furiosus2006

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Nucleosides, Nucleotides, and Nucleic Acids (印刷中)

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Crystal Structure and Functional Implications of Pyrococcus furiosus Hef Helicase Domain Involved in Branched DNA Processing2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Structure 13

      Pages: 143-153

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Identification of a Novel Helicase Activity Unwinding Branched DNAs from the Hyperthermophilic Archaeon, Pyrococcus furiosus2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      J. Biol. Chem 280

      Pages: 12351-12358

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Structural and Functional Analyses of an Archaeal XPF/Rad1/Mus81 Nuclease : Asymmetric DNA Binding and Cleavage Mechanisms2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Structure 13

      Pages: 1183-1192

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Identification of the critical region in Replication factor C from Pyrococcus furiosus for the stable complex formation with Proliferating cell nuclear antigen and DNA2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Genes Genet. Syst 80

      Pages: 83-93

    • NAID

      130000062161

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Expression and Molecular Characterization of Spherical Particles Derived from the Genome of the Hyperthermophilic Euryarchaeote Pyrococcus furiosus2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      J Biochem 138

      Pages: 193-199

    • NAID

      10017346692

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Overproduction, purification and crystallization of an archaeal DNA ligase from Pyrococcus furiosus2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Acta Cryst F61

      Pages: 1100-1102

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Annual Research Report 2005 Final Research Report Summary
  • [Journal Article] Open clamp structure in the clamp-loading complex visualized by electron microscopic image analysis2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Proc Natl Acad Sci USA 102

      Pages: 13795-13800

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Annual Research Report 2005 Final Research Report Summary
  • [Journal Article] The archaeal Hjm helicase has recQ-like functions, and may be involved in repair of stalled replication fork2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Genes Cells 11

      Pages: 99-110

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Annual Research Report 2005 Final Research Report Summary
  • [Journal Article] DNA複製、修復研究から遺伝子解析技術開発へ2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      DNA多型 13

      Pages: 1-13

    • NAID

      10015685088

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Annual Research Report 2005 Final Research Report Summary
  • [Journal Article] Crystal structure of a biologically functional form of PriB from Escherichia coli reveals a potential single-stranded DNA-binding site2005

    • Author(s)
      Kohda, D., et al.
    • Journal Title

      Biochem Biophys Res Commun 326

      Pages: 766-776

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2005 Annual Research Report 2005 Final Research Report Summary
  • [Journal Article] Identification of a Novel Helicase Activity Unwinding Branched DNAs from the Hyperthermophilic Archaeon, Pyrococcus furiosus2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      J.Biol.Chem 280

      Pages: 12351-12358

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Identification of the critical region in Replication factor C from Pyrococcus furiosus for the stable complex formation with Proliferating cell nuclear antigen and DNA2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Genes Genet.Syst 80

      Pages: 83-93

    • NAID

      130000062161

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Open clamp structure in the clamp-loading complex visualized by electron microscopic image analysis2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Proc Natl Acad Sci U S A 102

      Pages: 13795-13800

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] DNA replication and repair〜application of basic research to genetic engineering technology2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      DNA Polymorphism 13

      Pages: 1-13

    • NAID

      10015685088

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Journal Article] Crystal structure and functional implications of Pyrococcus furiosus Hef helicase domain involved in branched DNA processing2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Structure 13

      Pages: 143-153

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Identification of a novel helicase activity unwinding branched DNAs from the hyperthermophilic archaeon, Pyrococcus furiosus2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      J.Biol.Chem 280

      Pages: 12351-12358

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Structural and functional analyses of an archaeal XPF/Rad1/Mus81 nuclease : asymmetric DNA binding and cleavage mechanisms2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Structure 13

      Pages: 1183-1192

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Identification of the critical region in Replication factor C from Pyrococcus furiosus for the stable complex formation with proliferating cell nuclear antigen and DNA2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Genes Genet.Syst 80

      Pages: 83-93

    • NAID

      130000062161

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Expression and molecular characterization of spherical particles derived from the genome of the hyperthermophilic euryarchaeote Pyrococcus furiosus2005

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      J Biochem 138

      Pages: 193-199

    • NAID

      10017346692

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Crystal Structure and Functional Implications of Pyrococcus furiosus Hef Helicase Domain Involved in Branched DNA Processing2005

    • Author(s)
      Nishino T, Komori K, Tsuchiya D, Ishino Y, Morikawa K
    • Journal Title

      Structure 13

      Pages: 143-153

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Identification of a novel helicase activity unwinding branched DNAs from the hyperthermophilic archaeon, Pyrococcus furiosus2005

    • Author(s)
      Fujikane, R., Komori, K., Shinagawa, H., Ishino, Y.
    • Journal Title

      Journal of Biological Chemistry (in press)

    • Related Report
      2004 Annual Research Report
  • [Journal Article] The clamp-loading complex for processive DNA replication2004

    • Author(s)
      Miyata, T, Oyama, T, Mayanagi, K, Ishino, S, Ishino, Y, Morikawa, K
    • Journal Title

      Nat Struct Mol Biol. 11

      Pages: 632-636

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Role of the Escherichia coli RecQ DNA helicase in SOS signaling and genome stabilization at stalled replication forks2004

    • Author(s)
      Hishida, T, Han, YW, Shibata, T, Kubota, Y, Ishino, Y, Iwasaki, H, Shinagawa, H
    • Journal Title

      Genes and Development 18

      Pages: 1886-1897

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Cooperation of the N-terminal helicase and C-terminal endonuclease activities of archaeal Hef protein in prcessing stalled replication fork2004

    • Author(s)
      Komori K, Hidaka M, Horiuchi T, Fujikane R, Shinagawa H, Ishino Y
    • Journal Title

      Journal of Biological Chemistry 279

      Pages: 53175-53185

    • Related Report
      2004 Annual Research Report
  • [Journal Article] Conprehensive search for DNA polymerase in the hyperthermophilic archaeon, Pyrococcus furiosus

    • Author(s)
      Ishino, Y., et al.
    • Journal Title

      Nucleosides, Nucleotides, and Nucleic Acids

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2005 Final Research Report Summary
  • [Publications] Matsumiya S.et al.: "Intermolecular ion pairs maintain the toroidal structure of Pyrococcus furiosus PCNA"Protein Science. 12. 823-831 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Nishino T.et al.: "X-ray and biochemical anatomy of an archaeal XPF/Rad1?Mus81 family nuclease : similarity between its endonuclease domain and restriction enzyme"Structure. 11. 445-457 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Ishino S.et al.: "Mutational analysis of Pyrococcus furiosus replication factor C based on the three-dimensional structure"Extremophiles. 7. 169-175 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] Jolivet E.et al.: "Physiological responces of the Hyperthermophilic archaeon"Pyrococcusabyssi" to DNA damage caused by ionizing radiation"Journal of Bacteriology. 185. 3958-3961 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] 石野 良純: "アーキアは複製研究のモデルとなりうるか?"化学と生物. 41. 426-428 (2003)

    • Related Report
      2003 Annual Research Report

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Published: 2003-04-01   Modified: 2016-04-21  

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