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Toward manual control of the initiation of homologous recombination for genome diversification

Research Project

Project/Area Number 22247002
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Genetics/Genome dynamics
Research InstitutionThe Institute of Physical and Chemical Research

Principal Investigator

SHIBATA Takehiko  独立行政法人理化学研究所, その他部局等, 研究員 (70087550)

Co-Investigator(Kenkyū-buntansha) MIKAWA Tsutomu  理化学研究所, 生命システム研究センター, 専任研究員 (20321820)
KUSANO Kohji  明治大学, 研究知財戦略機構, 研究推進員(客員研究員) (70336098)
ARAI Naoto  日本大学, 生物資源科学部, 講師 (70297795)
Project Period (FY) 2010-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥42,770,000 (Direct Cost: ¥32,900,000、Indirect Cost: ¥9,870,000)
Fiscal Year 2014: ¥8,320,000 (Direct Cost: ¥6,400,000、Indirect Cost: ¥1,920,000)
Fiscal Year 2013: ¥8,320,000 (Direct Cost: ¥6,400,000、Indirect Cost: ¥1,920,000)
Fiscal Year 2012: ¥8,320,000 (Direct Cost: ¥6,400,000、Indirect Cost: ¥1,920,000)
Fiscal Year 2011: ¥8,320,000 (Direct Cost: ¥6,400,000、Indirect Cost: ¥1,920,000)
Fiscal Year 2010: ¥9,490,000 (Direct Cost: ¥7,300,000、Indirect Cost: ¥2,190,000)
Keywordsゲノム構築 / ゲノム再編 / ゲノム維持 / 遺伝的多様化 / 二本鎖切断修復 / 経路選択 / RecA/Rad51 / ゲノム / 遺伝子 / 蛋白質 / 酵素 / バイオテクノロジー / 相同DNA組換え / 二本鎖切断 / 減数分裂期組換え / 体細胞組換え / 植物 / 酵母 / DNA二本鎖切断 / ゲノム構築・再編 / 遺伝子多様性 / 減数分裂 / 相同組換え / 蛋白質創出
Outline of Final Research Achievements

Homologous DNA recombination (HR) is regulated by double-strand DNA-break (DSB) formation and recombination-pathway choice among two types of HR (non-crossing-over and crossing-over) and non-homologous end-joining (NHEJ). (1) Using new bio-assays, we identified rice and Arabidopsis SPO11s (meiotic recombination-initiating proteins) and their intrinsic DSB-forming activity for the first time. (2) We identified using a newly devised genetic assay, DSB-repair pathway-choice functions of Srs2 helicase, which forms an active complex with Rad51 (a eukaryotic RecA-family recombinase). (3) We unexpectedly found that Rad51 functions in end-joining fidelity of the canonical NHEJ. (4) We revealed by structural and biochemical studies, roles of an acidic residue on a flexible loop of RecA in selecting ssDNA in its various in vitro functions, and in activation and inactivation of its recombinase activity. These results suggest new roles of RecA/Rad51 in all the three major DSB-repair pathways.

Report

(6 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (45 results)

All 2015 2014 2013 2012 2011 2010 Other

All Journal Article (11 results) (of which Peer Reviewed: 11 results,  Open Access: 1 results,  Acknowledgement Compliant: 1 results) Presentation (29 results) Remarks (3 results) Patent(Industrial Property Rights) (2 results)

  • [Journal Article] Loop L1 governs the DNA-binding specificity and order for RecA-catalyzed reactions in homologous recombination and DNA repair2015

    • Author(s)
      Shinohara, T., Ikawa, S., Iwasaki, W., Hiraki, T., Hikima, T., Mikawa, T., Arai, N., Kamiya, N. and Shibata, T.
    • Journal Title

      Nucleic acids research

      Volume: 43 Issue: 2 Pages: 973-986

    • DOI

      10.1093/nar/gku1364

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Functional analyses of the C terminal half of the Saccharomyces cerevisiae Rad52 protein2014

    • Author(s)
      Kagawa, W., Arai, N., Ichikawa, Y., Saito, K., Sugiyama, S., Saotome, M., Shibata, T. and Kurumizaka, H.
    • Journal Title

      Nucleic Acids Res

      Volume: 42 Issue: 2 Pages: 941-951

    • DOI

      10.1093/nar/gkt986

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A visible assay for meiotic homologous recombination in pollens of rice2014

    • Author(s)
      Shingu, Y., Kanno, Y., Tokai, T., Shibata, T. and Wakasa, K.
    • Journal Title

      Plant Biotechnology

      Volume: 31 Issue: 1 Pages: 55-59

    • DOI

      10.5511/plantbiotechnology.13.1121a

    • NAID

      130003382509

    • ISSN
      1342-4580, 1347-6114
    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Homologous pairing activities of two rice RAD51 proteins, RAD51A1 and RAD51A22013

    • Author(s)
      Morozumi, Y., Ino, R., Ikawa, S., Mimida, N., Shimizu, T., Toki, S., Ichikawa, H., Shibata, T. and Kurumizaka, H.
    • Journal Title

      PLoS ONE

      Volume: 8 Issue: 10 Pages: e75451-e75451

    • DOI

      10.1371/journal.pone.0075451

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Putative antirecombinase Srs2 DNA helicase promotes noncrossover homologous recombination avoiding loss of heterozygosity2013

    • Author(s)
      Miura, T., Shibata, T. and Kusano, K.
    • Journal Title

      Proc Natl Acad Sci USA

      Volume: 110 Issue: 40 Pages: 16067-16072

    • DOI

      10.1073/pnas.1303111110

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Use of Native Gels to Measure Protein Binding to SSB2012

    • Author(s)
      Inoue, J.
    • Journal Title

      Methods Mol Biol

      Volume: 922 Pages: 175-182

    • DOI

      10.1007/978-1-62703-032-8_13

    • ISBN
      9781627030311, 9781627030328
    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] RecQ5 interacts with Rad51 and is involved in resistance of Drosophila to cisplatin treatment2012

    • Author(s)
      Maruyama, S
    • Journal Title

      Biol. Pharm. Bull.

      Volume: 35 Pages: 2017-2022

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The double-stranded break-forming activity of plant SPO11s and a novel rice SPO11 revealed by a Drosophila bioassay2012

    • Author(s)
      Yoshinori Shingu
    • Journal Title

      BMC molecular biology

      Volume: 13 Issue: 1 Pages: 1-1

    • Total Pages
      16
    • DOI

      10.1186/1471-2199-13-1

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Enlightenment of yeast mitochondrial homoplasmy : diversified roles of gene conversion2011

    • Author(s)
      Ling, Feng
    • Journal Title

      Genes

      Volume: 2 Pages: 169-190

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A DNA-binding surface of SPO11-1, an Arabidopsis SPO11 orthologue required for normal meiosis2010

    • Author(s)
      Shingu, Yoshinori
    • Journal Title

      FEBS Journal

      Volume: 277 Pages: 2360-2374

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 相同DNA組換えの機構理解から新規蛋白質創出へ2010

    • Author(s)
      柴田武彦
    • Journal Title

      酸素工学ニュース

      Volume: 63 Pages: 16-22

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] RecAのLI-loop領域でのDNA結合選択が、相同組換えやDNA修復を制御する2014

    • Author(s)
      篠原 赳, 井川 しゅく子, 岩崎 わかな, 美川 務, 新井 直人, 柴田 武彦
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2014-11-26
    • Related Report
      2014 Annual Research Report
  • [Presentation] 重合体形成を欠損したrad51-F144AのDNA結合について2014

    • Author(s)
      鎮目 恭平, 新井 直人, 新宮 良宣, 美川 務, 柴田 武彦
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2014-11-26
    • Related Report
      2014 Annual Research Report
  • [Presentation] 組換え活性を向上させたRecA変異体を利用した高精度なPCR2014

    • Author(s)
      篠原 赳、飯倉 ゆかり、重森 康司、柴田 武彦、美川 務
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2014-11-26
    • Related Report
      2014 Annual Research Report
  • [Presentation] Dimer of a C-terminal deletion mutant of RecA conserves recombinase-activity, and the recombinase activity is enhanced by dATP2014

    • Author(s)
      飯倉ゆかり, 篠原赳, 笠置原央, 山口祐樹, 岩崎わかな, 柴田武彦, 美川務
    • Organizer
      第37回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2014-11-25
    • Related Report
      2014 Annual Research Report
  • [Presentation] Selection of DNA in binding to RecA by its Li-loop resion regulates homologous recombination and DNA repair2014

    • Author(s)
      Shinohara, T., Ikawa, S., Iwasaki, W., Mikawa, T., Arai, N. and Shibata, T.
    • Organizer
      The 9th 3R Symposium
    • Place of Presentation
      Gotenba, Shizuoka, Japan
    • Year and Date
      2014-11-17 – 2014-11-21
    • Related Report
      2014 Annual Research Report
  • [Presentation] RecAはE.coli/T4リガーゼのDNA末端結合活性をATP依存的に促進する2014

    • Author(s)
      此村 直人, 新井 直人, 井川 粛子, 柴田 武彦
    • Organizer
      第87回日本生化学会大会
    • Place of Presentation
      京都
    • Year and Date
      2014-11-16
    • Related Report
      2014 Annual Research Report
  • [Presentation] Purification and characterization of Thermus thermophilus UvrD2013

    • Author(s)
      飯倉 ゆかり, 柴田 武彦, 美川 務
    • Organizer
      第3回モデル生物丸ごと一匹学会, 第12回丸ごと一匹プロジェクト連携研究会
    • Place of Presentation
      豊中市
    • Related Report
      2013 Annual Research Report
  • [Presentation] 栄養増殖細胞での制御されたDNA二重鎖切断による相同組換え開始の可能性2012

    • Author(s)
      新宮 良宣
    • Organizer
      第29回染色体ワークショップ
    • Place of Presentation
      仙台
    • Year and Date
      2012-01-25
    • Related Report
      2011 Annual Research Report
  • [Presentation] イネSPO11の新規共役因子の探索2012

    • Author(s)
      大岩 利和
    • Organizer
      第30回植物細胞分子生物学会 (生駒) 大会
    • Place of Presentation
      生駒市
    • Related Report
      2012 Annual Research Report
  • [Presentation] T. thermophilus由来組換えメディエーターの機能比較2012

    • Author(s)
      篠原 赳
    • Organizer
      第2回モデル生物丸ごと一匹学会/第11回丸ごと一匹プロジェクト連携研究会
    • Place of Presentation
      播磨
    • Related Report
      2012 Annual Research Report
  • [Presentation] Thermus thermophilus由来組換えメディエーターの分子機能解析2012

    • Author(s)
      篠原 赳
    • Organizer
      第35回分子生物学会年会
    • Place of Presentation
      福岡
    • Related Report
      2012 Annual Research Report
  • [Presentation] RecQ5 interacts with Rad51 and is involved in resistance of Drosophila against cisplatin treatment2012

    • Author(s)
      川崎 勝己
    • Organizer
      第35回分子生物学会年会
    • Place of Presentation
      福岡
    • Related Report
      2012 Annual Research Report
  • [Presentation] RecA組換え酵素のL1ループの制御機能2012

    • Author(s)
      柴田 武彦
    • Organizer
      第30回染色体ワークショップ/第11回核ダイナミクス研究会
    • Place of Presentation
      淡路市
    • Related Report
      2012 Annual Research Report
  • [Presentation] バクテリアにおけるDNA組換え修復の制御機構2012

    • Author(s)
      井上 仁
    • Organizer
      第30回染色体ワークショップ/第11回核ダイナミクス研究会
    • Place of Presentation
      淡路市
    • Related Report
      2012 Annual Research Report
  • [Presentation] Functional analysis of Arabidopsis thaliana homologues of the Saccharomyces cerevisiae DNA repair enzyme Ntg12011

    • Author(s)
      此村 直人
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2011-12-13
    • Related Report
      2011 Annual Research Report
  • [Presentation] REC8遺伝子欠損時の相同組換え開始反応複合体形成の解析2011

    • Author(s)
      久郷 和人
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2011-12-13
    • Related Report
      2011 Annual Research Report
  • [Presentation] Mitochondrial DNA homoplasmy as gene homogenization of repeated sequences by rolling circle replication2010

    • Author(s)
      Takehiko Shibata
    • Organizer
      7th Conference of Asian Society for Mitochondrial Research and Medicine and 10th Conference of Japanese Society of Mitochondrial Research and Medicine
    • Place of Presentation
      福岡県福岡市
    • Year and Date
      2010-12-16
    • Related Report
      2010 Annual Research Report
  • [Presentation] RecA/Rad51ファミリーのフィラメント形成は相同DNA対合反応には必要ない2010

    • Author(s)
      増田ときは
    • Organizer
      第33回日本分子生物学会年会・第83回日本生化学会大会(BMB2010)
    • Place of Presentation
      兵庫県神戸市
    • Year and Date
      2010-12-07
    • Related Report
      2010 Annual Research Report
  • [Presentation] A mechanism of DNA homology search, based on the structure of DNA bound to proteins that promote homologous recombination2010

    • Author(s)
      Tokiha Masuda
    • Organizer
      The 12th IUBMB (OzBio 2010) The Molecules of Life from Discovery to Biotechnology
    • Place of Presentation
      Melbourne, Australia
    • Year and Date
      2010-09-27
    • Related Report
      2010 Annual Research Report
  • [Presentation] イネの相同組換え開始酵素SPO11ホモログの解析2010

    • Author(s)
      新宮良宣
    • Organizer
      第28回日本植物細胞分子生物学会大会・シンポジウム
    • Place of Presentation
      宮城県仙台市
    • Year and Date
      2010-09-02
    • Related Report
      2010 Annual Research Report
  • [Presentation] The universal DNA structure in homologous recombination2010

    • Author(s)
      Tsutomu Mikawa
    • Organizer
      The 24th Annual Symposium of The Protien Society
    • Place of Presentation
      San Diego, CA, USA
    • Year and Date
      2010-08-03
    • Related Report
      2010 Annual Research Report
  • [Presentation] RecAはなぜフィラメントを形成する必要があるのか?-単量体及び二量体の活性をもとに-2010

    • Author(s)
      笠置原央
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      北海道札幌市
    • Year and Date
      2010-06-17
    • Related Report
      2010 Annual Research Report
  • [Presentation] A novel rice SPO11 homologue, SPO11D, induces meiotic chromosme aberration and DNA double-stranded breaks in the fruit-fly2010

    • Author(s)
      Yoshinori Shingu
    • Organizer
      EMBO Conference Series on Recombination & Connections to SUMO and Ubiquitin Modifications
    • Place of Presentation
      Lucca, Italy
    • Year and Date
      2010-05-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] Bases of break-induced replication in mitochondrial genome dynamics2010

    • Author(s)
      Takehiko Shibata
    • Organizer
      57th NIBB Conference : The Dynamic Genome
    • Place of Presentation
      愛知県岡崎市
    • Related Report
      2010 Annual Research Report
  • [Presentation] 抗組換え酵素Srs2の新たな機能:非交差型の相同組換えを促進してヘテロ接合性の喪失を防ぐ

    • Author(s)
      草野 好司, 三浦 徹, 柴田 武彦
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸市
    • Related Report
      2013 Annual Research Report
  • [Presentation] RecA二量体蛋白質のNMRによる構造機能解析

    • Author(s)
      山口 祐樹, 飯倉 ゆかり, 井上 仁, 伊藤 隆, 柴田 武彦, 美川 務
    • Organizer
      第36回日本分子生物学会年会
    • Place of Presentation
      神戸市
    • Related Report
      2013 Annual Research Report
  • [Presentation] ゲノム不安定化防止に寄与するRecA組換え酵素のDNA結合順序決定機構

    • Author(s)
      柴田 武彦, 篠原 赳, 岩崎 わかな, 井川 粛子, 美川 務, 新井 直人
    • Organizer
      第31回染色体ワークショップ・第12回核ダイナミクス研究会
    • Place of Presentation
      神戸市
    • Related Report
      2013 Annual Research Report
  • [Presentation] Arabidopsis thalianaのScNtg1ホモログであるAtNth1, AtNth2の持つN-グリコシラーゼ、APリアーゼ活性の機能について

    • Author(s)
      此村 直人, 新宮 良宣, 柴田 武彦
    • Organizer
      第86回日本生化学会大会
    • Place of Presentation
      横浜
    • Related Report
      2013 Annual Research Report
  • [Presentation] C-terminal acidic region of Thermus thermophilus RecA play a role in dissociataion

    • Author(s)
      篠原 赳, 柴田 武彦, 美川 務
    • Organizer
      第3回モデル生物丸ごと一匹学会, 第12回丸ごと一匹プロジェクト連携研究会
    • Place of Presentation
      豊中市
    • Related Report
      2013 Annual Research Report
  • [Remarks]

    • URL

      http://www.riken.jp/r-world/research/lab/wako/shibata/index.html

    • Related Report
      2011 Annual Research Report
  • [Remarks] 理研

    • URL

      http://www.riken.jp/r-world/research/lab/wako/shibata/index.html

    • Related Report
      2010 Annual Research Report
  • [Remarks] 市大

    • URL

      http://www.tsurumi.yokohama-cu.ac.jp/mcp/index.html

    • Related Report
      2010 Annual Research Report
  • [Patent(Industrial Property Rights)] Re c A組換え酵素および組換え活性をもっ蛋白質を用いた亘鎖二重鎖DN A多量体形成技術2014

    • Inventor(s)
      柴田武彦、此村直人、新井直人
    • Industrial Property Rights Holder
      柴田武彦、此村直人、新井直人
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2014-209498
    • Filing Date
      2014-10-10
    • Related Report
      2014 Annual Research Report
  • [Patent(Industrial Property Rights)] 変型の耐熱性RecA蛋白質、該タンパク質をコードする核酸分子、該タンパク質を用いた核酸の増幅方法、及び核酸増幅用キット2014

    • Inventor(s)
      重森康司、柴田武彦、美川 務、篠原 赳、飯倉ゆかり
    • Industrial Property Rights Holder
      重森康司、柴田武彦、美川 務、篠原 赳、飯倉ゆかり
    • Industrial Property Rights Type
      特許
    • Filing Date
      2014-07-24
    • Related Report
      2014 Annual Research Report

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Published: 2010-08-23   Modified: 2019-07-29  

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