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2011 Fiscal Year Final Research Report

Selfish DNases at a diverging point to survival, death and evolution

Research Project

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Project/Area Number 21370001
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Genetics/Genome dynamics
Research InstitutionThe University of Tokyo

Principal Investigator

KOBAYASHI Ichizo  東京大学, 大学院・新領域創成科学研究科, 教授 (30126057)

Co-Investigator(Renkei-kenkyūsha) HANDA Naofumi  東京大学, 大学院・新領域創成科学研究科, 特任助教 (00396855)
TAKAHASHI Noriko  東京大学, 大学院・新領域創成科学研究科, 特任助教 (70466829)
MIKIHIKO Kawai  東京大学, 大学院・新領域創成科学研究科, 特任研究員 (80451904)
FURUTA Yoshikazu  東京大学, 大学院・新領域創成科学研究科, 特任助教 (40613667)
Research Collaborator UCHIYAMA Ikuo  基礎生物学研究所, ゲノム情報研究室, 助教 (90243089)
JANUSZ Bujnicki  IIMCB, Poland
KOJI Yahara  学振, 特別研究員(PD)
MASAKI Fukuyo  学振, 特別研究員(PD)
Project Period (FY) 2009 – 2011
Keywordsゲノム構築 / ゲノム再編 / ゲノム維持 / ゲノム進化
Research Abstract

Our experimental analyses and genome comparisons revealed how DNAases distinguishing self and non-self genome acted on genomes and drove their evolution.1. We revealed role of antisense RNA in their gene regulation and life cycle.2. We showed several restriction enzymes cleave a DNA replication fork.3. With restriction enzyme attacking the chromosome, we demonstrated success of suicidal defense strategy against infection.4. Genome comparison of H. pylori revealed novel mechanisms of genome rearrangements and suggested that restriction modification systems frequently switch their recognition sequence.

  • Research Products

    (48 results)

All 2013 2012 2011 2010 2009

All Journal Article (23 results) (of which Peer Reviewed: 23 results) Presentation (21 results) Book (4 results)

  • [Journal Article] Chromosome painting in silico in a bacterial species reveals fine population structure2013

    • Author(s)
      K Yahara, et al., I Kobayashi
    • Journal Title

      Molecular Biology and Evolution

      Volume: 30 Pages: 1454-1464

    • DOI

      DOI:10.1093/molbev/mst055

    • Peer Reviewed
  • [Journal Article] Movement of DNAsequence recognition domains between non-orthologous proteins2012

    • Author(s)
      Y Furuta, I Kobayashi
    • Journal Title

      Nucleic AcidsRes

      Volume: 40(18) Pages: 9218-9232

    • DOI

      doi:10.1093/nar/gks681

    • Peer Reviewed
  • [Journal Article] Molecular determinants responsible for recognition of the single-stranded DNA regulatory sequence, χ, by RecBCD enzyme2012

    • Author(s)
      N Handa, et al., I Kobayashi, S C Kowalczykowski
    • Journal Title

      Proc. Nat.Acad. Sci. USA

      Volume: 109(23) Pages: 8901-8906

    • DOI

      doi:10.1073/pnas.1206076109

    • Peer Reviewed
  • [Journal Article] Genome-wide survey of mutual homologous recombination in a highly sexual bacterial species2012

    • Author(s)
      K Yahara, et al., I Kobayashi
    • Journal Title

      Genome Biol. Evol

      Volume: 4(5) Pages: 628-640

    • DOI

      doi:10.1093/gbe/evs043

    • Peer Reviewed
  • [Journal Article] Large variations in bacterial ribosomal RNA genes.2012

    • Author(s)
      K Lim, Y Furuta, I Kobayashi
    • Journal Title

      Mol. Biol. Evol

      Volume: 29(10) Pages: 2937-2948

    • DOI

      doi:10.1093/molbev/mss101

    • Peer Reviewed
  • [Journal Article] Success of a suicidal defense strategy against infection in a structured habitat2012

    • Author(s)
      M Fukuyo, A Sasaki, I Kobayashi
    • Journal Title

      Scientific Reports

      Volume: 2 Pages: 238

    • DOI

      doi:10.1038/srep00238

    • Peer Reviewed
  • [Journal Article] Evolution of cagA oncogene of Helicobacter pylori through recombination2011

    • Author(s)
      Y Furuta, K Yahara, M Hatakeyama, I Kobayashi
    • Journal Title

      PLoS ONE

      Volume: 6(8) Pages: e23499

    • DOI

      doi:10.1371/journal.pone.0023499

    • Peer Reviewed
  • [Journal Article] Evolutionary Genome Engineering using a Restriction-modification System2011

    • Author(s)
      Y Asakura, H Kojima, I Kobayashi
    • Journal Title

      Nucleic Acids Research

      Volume: 39(20) Pages: 9034-9046

    • DOI

      doi:10.1093/nar/gkr585

    • Peer Reviewed
  • [Journal Article] Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes2011

    • Author(s)
      M Kawai, et al., I Kobayashi
    • Journal Title

      BMC Microbiology

      Volume: 11 Pages: 104

    • DOI

      doi:10.1186/1471-2180-11-104

    • Peer Reviewed
  • [Journal Article] Domain movement within a gene: a novel evolutionary mechanism for protein diversification2011

    • Author(s)
      Y Furuta, M Kawai, I Uchiyama, I Kobayashi
    • Journal Title

      PLoS ONE

      Volume: 6(4) Pages: e18819

    • DOI

      doi:10.1371/journal.pone.0018819

    • Peer Reviewed
  • [Journal Article] Antisense RNA associated with biological regulation of a restriction-modification system2011

    • Author(s)
      I Mruk*, Y Liu*, L Ge, I Kobayashi (*: Equal contribution)
    • Journal Title

      Nucleic Acids Research

      Volume: 39(13) Pages: 5622-5632

    • DOI

      doi:10.1093/nar/gkr166

    • Peer Reviewed
  • [Journal Article] Cleavage of a model DNA replication fork by a methyl-specific endonuclease2011

    • Author(s)
      K Ishikawa, et al., I Kobayashi
    • Journal Title

      Nucleic Acids Research

      Volume: 39(13) Pages: 5489-5498

    • DOI

      doi:10.1093/nar/gkr153

    • Peer Reviewed
  • [Journal Article] IS-linked Movement of a Restriction-modification System2011

    • Author(s)
      N Takahashi, et al., I Kobayashi
    • Journal Title

      PLoS ONE

      Volume: 6 Pages: e16554

    • DOI

      doi:10.1371/journal.pone.0016554

    • Peer Reviewed
  • [Journal Article] Birth and death of genes linked to chromosomal inversion2011

    • Author(s)
      Y Furuta*, M Kawai*, et al., I Kobayashi (*: Equal contribution)
    • Journal Title

      Proc. Nat. Acad. Sci. USA

      Volume: 108 no. 4 Pages: 1501-1506

    • DOI

      doi:10.1073/pnas.1012579108

    • Peer Reviewed
  • [Journal Article] Conflicts targeting epigenetic systems and their resolution by cell death: new biology of methyl-specific and other restriction systems2010

    • Author(s)
      Ken Ishikawa, Eri Fukuda, Ichizo Kobayashi
    • Journal Title

      DNA Research

      Volume: 17 Pages: 325-342

    • DOI

      doi:10.1093/dnares/dsq027

    • Peer Reviewed
  • [Journal Article] MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity2010

    • Author(s)
      Uchiyama, I., Higuchi, T., and Kawai, M.
    • Journal Title

      Nucleic Acids Res

      Volume: 38 Pages: D361-D365.

    • DOI

      doi:10.1093/nar/gkp948

    • Peer Reviewed
  • [Journal Article] A putative mobile genetic element carrying a novel Type IIF restriction-modification system (PluTI)2010

    • Author(s)
      F Khan, et al., I Kobayashi
    • Journal Title

      Nucleic Acids Res

      Volume: 38 Pages: 3019-3030

    • DOI

      doi:10.1093/nar/gkp1221

    • Peer Reviewed
  • [Journal Article] Genome comparison and context analysis reveals putative mobile forms ofrestriction-modification systems and related rearrangements2010

    • Author(s)
      Y Furuta, K Abe, I Kobayashi
    • Journal Title

      Nucleic Acids Res

      Volume: 38 Pages: 2428-2443

    • DOI

      doi:10.1093/nar/gkp1226

    • Peer Reviewed
  • [Journal Article] Evolutionary maintenance of selfish homing endonuclease genes in the absence of horizontal transfer2009

    • Author(s)
      K Yahara, M Fukuyo, A Sasaki and I Kobayashi
    • Journal Title

      Proc. Nat. Acad. Sci. USA

      Volume: 106 Pages: 18861-18866

    • DOI

      doi:10.1073/pnas.0908404106

    • Peer Reviewed
  • [Journal Article] DNA Double- strand Breaks and their Consequences in Bacteria2009

    • Author(s)
      I Kobayashi and N Handa
    • Journal Title

      Encyclopedia of Life Sciences

      Pages: A21652

    • DOI

      DOI:10.1002/9780470015902.a0000576.pub2

    • Peer Reviewed
  • [Journal Article] Single-molecule analysis of a red fluorescent RecA protein reveals a defect in nucleoprotein filament nucleation that relates to its reduced biological functions2009

    • Author(s)
      N Handa, et al., S C Kowalczykowski
    • Journal Title

      Journal of Biological Chemistry

      Volume: 284 Pages: 18664-18673

    • DOI

      doi:10.1074/jbc.M109.004895

    • Peer Reviewed
  • [Journal Article] Contribution of RecFOR machinery of homologous recombination to cell survival after loss of a restriction-modification gene complex2009

    • Author(s)
      N Handa, A Ichige, and I Kobayashi
    • Journal Title

      Microbiology

      Volume: 155 Pages: 2320-2332

    • DOI

      doi:10.1099/mic.0.026401-0

    • Peer Reviewed
  • [Journal Article] Reconstitution of Initial Steps of Double-strand DNA Break Repair by the RecF pathway of E. coli2009

    • Author(s)
      N Handa, K Morimatsu, S T Lovett, and S C Kowalczykowski
    • Journal Title

      Genes and Development

      Volume: 23 Pages: 1234-1245

    • DOI

      doi:10.1101/gad.1780709

    • Peer Reviewed
  • [Presentation] Genome-wide survey of mutual homologous recombination in H. pylori2012

    • Author(s)
      K Yahara, et al. I Kobayashi
    • Organizer
      10th International Workshop on Pathogenesis and Host Response in Helicobacter Infections
    • Place of Presentation
      Helsingor, Denmark
    • Year and Date
      2012-07-06
  • [Presentation] Evolutionary genome dynamics revealed by microbial genome comparison2012

    • Author(s)
      小林 一三
    • Organizer
      東京農業大学国際シンポジウム" Genome Research: Current Challenges and Future Directions"(招待講演)
    • Place of Presentation
      東京
    • Year and Date
      2012-01-21
  • [Presentation] Evolutionary genome dynamics revealed through close genome comparison2011

    • Author(s)
      I Kobayashi
    • Organizer
      Max Planck Institute for Evolutionary Anthropology
    • Place of Presentation
      Leipzig, Germany.
    • Year and Date
      2011-11-21
  • [Presentation] Genome comparison of Helicobacter pylori strains from the West and the Far East2011

    • Author(s)
      I Kobayashi
    • Organizer
      XXIVth International Workshop of the European Helicobacter Study Group(招待講演)
    • Place of Presentation
      Dublin, Ireland
    • Year and Date
      2011-09-13
  • [Presentation] Evolution of cagA Oncogene of Helicobacter pylori through Recombination2011

    • Author(s)
      Y Furuta, K Yahara, M Hatakeyama, I Kobayashi
    • Organizer
      XXIVth International Workshop of the European Helicobacter Study Group
    • Place of Presentation
      Dublin, Ireland
    • Year and Date
      2011-09-13
  • [Presentation] Novel genome rearrangement mechanisms detected by Helicobacter pylori genome comparison2011

    • Author(s)
      Y Furuta, et al., I Kobayashi
    • Organizer
      International Union of Microbiological Societies 2011 Congress (IUMS2011)
    • Place of Presentation
      Sapporo
    • Year and Date
      2011-09-09
  • [Presentation] Evolutionary genome dynamics revealed by comparison of Japanese and other Helicobacter pylori complete genomes2011

    • Author(s)
      I Kobayashi
    • Organizer
      International Union of Microbiological Societies 2011 Congress (IUMS2011)(招待講演)
    • Place of Presentation
      Sapporo
    • Year and Date
      2011-09-06
  • [Presentation] Novel evolutionary dynamics revealed through comparison of East Asian and other H. pylori complete genomes2011

    • Author(s)
      I Kobayashi
    • Organizer
      the 16th International Workshop on Campylobacter, Helicobacter, and Related Organisms (CHRO 2011)
    • Place of Presentation
      Vancouver, Canada
    • Year and Date
      2011-08-30
  • [Presentation] DNA duplication associated with inversion (DDAI) and domain movement (DoMo): two novel genome rearrangement mechanisms discovered through genome comparison2011

    • Author(s)
      I Kobayashi
    • Organizer
      SMBE2011 (Annual Conference of Society for Molecular Biology and Evolution)
    • Place of Presentation
      Kyoto
    • Year and Date
      2011-07-11
  • [Presentation] Biology of restriction-modification systems2011

    • Author(s)
      I Kobayashi
    • Organizer
      Nucleic Acid Enzymes & Enzymes in Human Disease(招待講演)
    • Place of Presentation
      Tianjin, China
    • Year and Date
      2011-06-21
  • [Presentation] Genome dynamics and evolution2011

    • Author(s)
      I Kobayashi
    • Organizer
      OIST Summer School on Quantitative Evolutionary and Comparative Genomics (招待講演)
    • Place of Presentation
      Okinawa
    • Year and Date
      2011-05-28
  • [Presentation] Genome rearrangements revealed through comparison of four complete genomes of Japanese Helicobacter pylori2010

    • Author(s)
      Y Furuta, et al., I Kobayashi
    • Organizer
      XXIIIrd International Workshop on Helicobacter and related bacteria in chronic digestive inflammation and gastric cancer, W7
    • Place of Presentation
      Rotterdam, The Netherlands
    • Year and Date
      2010-09-02
  • [Presentation] Selfish restriction systems switching on bacterial death program2010

    • Author(s)
      I Kobayashi
    • Organizer
      International Institute of Molecular and Cellular Biology
    • Place of Presentation
      Warsaw, Poland
    • Year and Date
      2010-08-30
  • [Presentation] H. pylori evolution: clues from Japanese isolates' genomes2010

    • Author(s)
      M Kawai, et al., I Kobayashi
    • Organizer
      Hannover Medical School
    • Place of Presentation
      Hannover, Germany
    • Year and Date
      2010-08-06
  • [Presentation] Selfish restriction systems switching on bacterial death program2010

    • Author(s)
      I Kobayashi
    • Organizer
      6^<th> New England Biolabs Meeting on DNA Restriction and Modification
    • Place of Presentation
      Bremen, Germany
    • Year and Date
      2010-08-04
  • [Presentation] East Asian Helicobacter pylori Genomes: Co-evolution with their Human Host2009

    • Author(s)
      M Kawai, et al., I Kobayashi
    • Organizer
      Global COE Workshop on Bioinformatics in the Era of "Genome Information Big Bang"(招待講演)
    • Place of Presentation
      Shenzhen,China
    • Year and Date
      20091105-08
  • [Presentation] Complete genome sequences of multiple Japanese Helicobacter pylori strains: a progress report2009

    • Author(s)
      I Kobayashi, et al., I Uchiyama
    • Organizer
      CHRO 2009 15th International Workshop on Campylobacter, Helicobacter and Related Organisms(招待講演)
    • Place of Presentation
      Toki Messe,Niigata.
    • Year and Date
      20090902-05
  • [Presentation] Selfish genes into a genome society2009

    • Author(s)
      I Kobayashi
    • Organizer
      NIMBioS Workgroup on Intragenomic conflicts
    • Place of Presentation
      Knoxville, USA
    • Year and Date
      20090420-22
  • [Presentation] Selfish genes vs. genome: Roles of selfish DNase genes programming deaths2009

    • Author(s)
      I Kobayashi
    • Organizer
      17th Annual Microbial Genomics Conference
    • Place of Presentation
      Rocky Gap State Park, MD, USA.
    • Year and Date
      2009-10-14
  • [Presentation] Selfish genes vs. genome: Roles of selfish DNase genes programming deaths2009

    • Author(s)
      I Kobayashi
    • Organizer
      17th Annual Microbial Genomics Conference
    • Place of Presentation
      Rocky Gap State Park, MD, USA
    • Year and Date
      2009-10-14
  • [Presentation] Selfish DNases programming bacterial deaths2009

    • Author(s)
      I Kobayashi
    • Organizer
      National Cancer Institute
    • Place of Presentation
      NIH, Bethesda, USA
    • Year and Date
      2009-04-23
  • [Book] 遺伝子にハマって進化する. Carl Zimmer (カール・ジンマー)著、長谷 川真理子監訳: 進化2012

    • Author(s)
      小林一三
    • Total Pages
      111-113
    • Publisher
      岩波書店
  • [Book] I Kobayashi. Bacterial Integrative Mobile Genetic Elements ("Restriction-modification systems as mobile epigenetic elements.")2012

    • Author(s)
      Y Furuta
    • Publisher
      Landes Bioscience
  • [Book] Random-Walk Mechanism in the Genetic Recombination2011

    • Author(s)
      Y Fujitani, J Kawai, I Kobayashi
    • Total Pages
      275-282
    • Publisher
      In Advances in Computational Biology (series: Advances in Experimental Medicine and Biology)
  • [Book] Cell-free protein synthesis for structure determination by X-ray crystallography2010

    • Author(s)
      M Watanabe-Matsui, et al., I Kobayashi
    • Total Pages
      149-160
    • Publisher
      In Cell-free Expression Systems (Series: Methods in Molecular Biology) Editors: Yaeta Endo, Kazuyuki Takai, Takuya Ueda. Humana Press

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Published: 2014-08-29  

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