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Molecular mechanism for the accurate recognition of homologous sequences

Research Project

Project/Area Number 19370004
Research Category

Grant-in-Aid for Scientific Research (B)

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

Principal Investigator

SHIBATA Takehiko  The Institute of Physical and Chemical Research, 柴田遺伝制御科学研究室, 上席研究員 (70087550)

Co-Investigator(Kenkyū-buntansha) MIKAWA Tsutomu  独立行政法人理化学研究所, 城生体金属科学研究室, 専任研究員 (20321820)
INOUE Jin  独立行政法人理化学研究所, 柴田遺伝制御科学研究室, 協力研究員 (10469893)
Research Collaborator LING Feng  独立行政法人理化学研究所, 吉田化学遺伝学研究室, 専任研究員
KURUMIZAKA Hitoshi  早稲田大学, 理工学術院, 教授
KAGAWA Wataru  早稲田大学, 理工学術院, 講師
ARAI Naoto  日本大学, 生物資源科学部, 講師
MASUDA Tokiha  横浜市立大学, 大学院・生体超分子科学専攻・博士後期課程, 学生
Project Period (FY) 2007 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥18,070,000 (Direct Cost: ¥13,900,000、Indirect Cost: ¥4,170,000)
Fiscal Year 2009: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2008: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2007: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000)
Keywordsゲノム構築・機能・再編・発現・維持 / 相同DNA組換え / RecA / Rad51型相同対合蛋白質 / ATP非依存型相同DNA対合蛋白質 / 組換えメディエーター / ヘテロ二重鎖形成 / 並行三重鎖DNA / DNAトポロジー / Rad51型相同的対合蛋白質 / 相同DNA組換え酵素 / Recombinase
Research Abstract

Homologous DNA recombination plays roles in the maintenance of genome integrity and in genetic diversification. While RecA/Rad51 homologous pairing proteins pairs DNA molecules with an exact sequence matching by an ATP-hydrolysis-dependent reaction, ATP-independent pairing proteins is unlikely to have such a function. To understand the molecular bases of the recombination functions, we compared RecA/Rad51 and ATP-independent homologous pairing proteins in their reactions. NMR analyses indicate that basic mechanisms of homologous pairing are common independent of the proteins. On the other hand, biochemical and topological studies suggest that an ATP-independent protein generates triplexes, instead of D-loops which RecA/Rad51 produces. These results suggest roles of the two groups of the proteins in homologous recombination.

Report

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

    (63 results)

All 2010 2009 2008 2007

All Journal Article (18 results) (of which Peer Reviewed: 18 results) Presentation (43 results) Book (2 results)

  • [Journal Article] Analysis of DNA-binding sites on Mhr1, a yeast mitochondrial ATP-independent homologous pairing protein2010

    • Author(s)
      asuda, T., Ling, F., Shibata, T., Mikawa, T.
    • Journal Title

      FEBS J. 277

      Pages: 1440-1452

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of DNA-binding sites on Mhr1, a yeast mitochondrial ATP-independent homologous pairing protein2010

    • Author(s)
      Masuda, T.
    • Journal Title

      FEBS J. 277

      Pages: 1440-1452

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A non-canonical DNA structure enables homologous recombination in various genetic sys-tems2009

    • Author(s)
      Masuda, T., Ito, Y., Terada, T., Shibata, T., Mikawa, T.
    • Journal Title

      J. Biol. Chem. 284

      Pages: 30230-30239

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Heteroduplex joint formation free of net topological change by Mhr1, a mi-tochondrial recombinase2009

    • Author(s)
      Ling, F., Yoshida, M., Shibata, T.
    • Journal Title

      J. Biol. Chem. 284

      Pages: 9341-9353

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] i-ochemical analysis of the human DMC1-I37N polymorphism2009

    • Author(s)
      Hikiba, J., Takizawa, Y., Ikawa, S., Shibata, T., Kurumizaka, H.
    • Journal Title

      FEBS J. 276

      Pages: 457-465

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] A non-canonical DNA structure enables homologous recombination in various genetic systems2009

    • Author(s)
      Masuda, T.
    • Journal Title

      J.Biol.Chem. 284

      Pages: 30230-30239

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Heteroduplex joint formation free of net topological change by Mhr1, a mitochondrial recombinase2009

    • Author(s)
      Ling, F.
    • Journal Title

      J.Biol.Chem. 284

      Pages: 9341-9353

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Biochemical analysis of the human DMC1-I37N polymorphism2009

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

      FEBS J. 276

      Pages: 457-465

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identification of a second DNA binding site in the human Rad52 protein2008

    • Author(s)
      Kagawa, W., Kagawa, A., Saito, K., Ikawa, S., Shibata, T., Kurumizaka, H., Yokoyama, S.
    • Journal Title

      J. Biol. Chem. 283

      Pages: 24264-24273

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Struc-tural and functional analyses of the DMC1-M200V polymorphism found in the human population2008

    • Author(s)
      Hikiba, J., Hirota, K., Kagawa, W., Ikawa, S., Kinebuchi, T., Sakane, I., Takizawa, Y., Yokoyama, S., Man-don-Pepin, B., Nicolas, A., Shibata, T., Ohta, K., Kurumizaka, H.
    • Journal Title

      Nucleic Acids Res. 36

      Pages: 4181-4190

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] RecR forms a ring-like tetramer that encircles dsDNA by forming a complex with RecF2008

    • Author(s)
      Honda, M., Fujisawa, T., Shibata, T., Mikawa, T.
    • Journal Title

      Nucleic Acids Res. 36

      Pages: 5013-5020

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Filament formation and robust strand exchange activities of the rice DMC1A and DMC1B proteins2008

    • Author(s)
      Sakane, I., Kamataki, C., Takizawa, Y., Nakashima, M., Toki, S., Ichikawa, H., Ikawa, S., Shibata, T., Kurumizaka, H.
    • Journal Title

      Nucleic Acids Res. 36

      Pages: 4266-4276

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] The process of displacing the single stranded DNA binding protein from single stranded DNA by RecO and RecR proteins2008

    • Author(s)
      Inoue, J., Honda, M., Ikawa, S., Shibata, T., Mikawa, T.
    • Journal Title

      Nucleic Acids Res. 36

      Pages: 94-109

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Identification of a second DNA binding site in the human Rad52 protein2008

    • Author(s)
      Kagawa, W.
    • Journal Title

      J.Biol.Chem. 283

      Pages: 24264-24273

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural and functional analyses of the DMC1-M200V polymorphism found in the human population2008

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

      Nucleic Acids Res. 36

      Pages: 4181-4190

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] RecR forms a ring-like tetramer that encircles dsDNA by forming a complex with RecF2008

    • Author(s)
      Honda, M.
    • Journal Title

      Nucleic Acids Res. 36

      Pages: 5013-5020

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Filament formation and robust strand exchange activities of the rice DMC1A and DMC1B proteins2008

    • Author(s)
      Sakane, I.
    • Journal Title

      Nucleic Acids Res. 36

      Pages: 4266-4276

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The process of displacing the single-stranded DNA-binding protein from single-stranded DNA by RecO and RecR proteins2008

    • Author(s)
      Jin Inoue
    • Journal Title

      Nucleic Acids Research 36

      Pages: 94-109

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Presentation] 相同DNA組換えにおける2種の相同DNA対合蛋白質の役割分担2010

    • Author(s)
      柴田武彦
    • Organizer
      第27回染色体ワークショップ
    • Place of Presentation
      静岡県御殿場市
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] Search for new functions of a recombination mediator, RAD522009

    • Author(s)
      Shibata, T.
    • Organizer
      Interna-tional Symposium on Chromosome cycle and genome dynamics
    • Place of Presentation
      Nasu, Tochigi
    • Related Report
      2009 Final Research Report
  • [Presentation] The universal structure of ssDNA in homologous recombination2009

    • Author(s)
      増田ときは
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      神奈川県横浜市
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] NMR analyses of inter-actions of RecO with SSB and ssDNA2009

    • Author(s)
      井上仁
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      神奈川県横浜市
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] Thermus thermophilus HB8のDNA相同組換え系2009

    • Author(s)
      井上仁
    • Organizer
      理研シンポジウム「高度好熱菌丸ごと一匹プロジェクト第8回連携研究会」
    • Place of Presentation
      兵庫県播磨
    • Related Report
      2009 Final Research Report
  • [Presentation] NMR解析によるRecO上のSSB結合部位の同定2009

    • Author(s)
      井上仁
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本県熊本市
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] DNAの位相幾何学的変化を伴わない組換え中間体形成2009

    • Author(s)
      柴田武彦
    • Organizer
      第26回染色体ワークショップ
    • Place of Presentation
      兵庫県姫路市
    • Related Report
      2009 Final Research Report 2008 Annual Research Report
  • [Presentation] Search for new functions of a recombination mediator, RAD522009

    • Author(s)
      柴田武彦
    • Organizer
      International Symposium on Chromosome cycle and genome dynamics
    • Place of Presentation
      Nasu, Tochigi
    • Related Report
      2009 Annual Research Report
  • [Presentation] RecAの最小機能単位-単量体及び二重体の活性-2009

    • Author(s)
      笠置原央
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      神奈川県横浜市
    • Related Report
      2009 Annual Research Report
  • [Presentation] Thermus thermophilusHB8のDNA相同組換え系2009

    • Author(s)
      井上仁
    • Organizer
      理研シンポジウム「高度好熱菌丸ごと一匹プロジェクト第8回連携研究会」
    • Place of Presentation
      兵庫県播磨
    • Related Report
      2009 Annual Research Report
  • [Presentation] 体細胞のDNA組換えに働く3種の制御2008

    • Author(s)
      柴田武彦
    • Organizer
      公開シンポジウム:進化リアクター・セルスタット30年と進化タンパク質工学の進展, (埼玉県中小企業振興公社, 埼玉大学)
    • Place of Presentation
      埼玉県さいたま市
    • Year and Date
      2008-05-17
    • Related Report
      2009 Final Research Report 2008 Annual Research Report
  • [Presentation] RecO, RecR蛋白質によるSSBのssDNAからの解離のメカニズム2008

    • Author(s)
      井上仁
    • Organizer
      2007年度組換え・染色体再編ワークショップ
    • Place of Presentation
      伊豆
    • Year and Date
      2008-03-04
    • Related Report
      2009 Final Research Report
  • [Presentation] 繰り返し塩基配列での相同DNA組換え開始の多様な機能2008

    • Author(s)
      柴田武彦
    • Organizer
      2007年度組換え・染色体再編ワークショップ
    • Place of Presentation
      伊豆
    • Year and Date
      2008-03-04
    • Related Report
      2009 Final Research Report 2007 Annual Research Report
  • [Presentation] RecO,RecR蛋自質によるSSBのssDNAからの解離のメカニズム2008

    • Author(s)
      井上 仁
    • Organizer
      2007年度組換え・染色体再編ワークショップ
    • Place of Presentation
      伊豆
    • Year and Date
      2008-03-04
    • Related Report
      2007 Annual Research Report
  • [Presentation] 出芽酵母Rad52-Rad51蛋白質複合体におけるRad52の機能2008

    • Author(s)
      新井 直人、柴田 武彦
    • Organizer
      2007年度組換え・染色体再編ワークショップ
    • Place of Presentation
      伊豆
    • Year and Date
      2008-03-04
    • Related Report
      2007 Annual Research Report
  • [Presentation] RecO, RecR蛋白質による一本鎖DNA結合蛋白質(SSB)の一本鎖DNAからの解離機構の解明2008

    • Author(s)
      井上仁
    • Organizer
      第25回染色体ワークショップ
    • Place of Presentation
      熱海
    • Year and Date
      2008-01-30
    • Related Report
      2009 Final Research Report
  • [Presentation] RecO,RecR蛋白質による一本鎖DNA結合蛋白質(SSB)の一本鎖DNAからの解離機構の解明2008

    • Author(s)
      井上 仁
    • Organizer
      第25回染色体ワークショップ
    • Place of Presentation
      熱海
    • Year and Date
      2008-01-30
    • Related Report
      2007 Annual Research Report
  • [Presentation] ミトコンドリアの相同組換え酵素反応ヘのDNAの高次構造の効果2008

    • Author(s)
      凌楓
    • Organizer
      第8回日本ミトコンドリア学会年会
    • Place of Presentation
      東京
    • Related Report
      2009 Final Research Report
  • [Presentation] 出芽酵母Rad52-Rad51複合体によるD-loop形成におけるRad52の二本鎖DNAへの結合の影響2008

    • Author(s)
      新井直人
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会合同大会(BMB2008)
    • Place of Presentation
      兵庫県神戸市
    • Related Report
      2009 Final Research Report
  • [Presentation] 相同組換えに重要なDNA特異的な構造変化2008

    • Author(s)
      増田ときは
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会合同大会(BMB2008)
    • Place of Presentation
      兵庫県神戸市
    • Related Report
      2009 Final Research Report 2008 Annual Research Report
  • [Presentation] Identification of the SSB binding site on RecO by NMR analy-sis2008

    • Author(s)
      井上仁
    • Organizer
      理研シンポジウム「高度好熱菌丸ごと一匹プロジェクト第8回連携研究会」
    • Place of Presentation
      兵庫県播磨
    • Related Report
      2009 Final Research Report
  • [Presentation] RecO, RecR蛋白質によるSSBのssDNAからの解離のメカニズム2008

    • Author(s)
      井上仁
    • Organizer
      第8回日本蛋白質科学会年会
    • Place of Presentation
      東京
    • Related Report
      2009 Final Research Report 2008 Annual Research Report
  • [Presentation] 相同的DNA組換え反応を調節する組換えメディエーター蛋白質群の構造と機能2008

    • Author(s)
      美川務
    • Organizer
      第8回日本蛋白質科学会年会
    • Place of Presentation
      東京
    • Related Report
      2009 Final Research Report 2008 Annual Research Report
  • [Presentation] ミトコンドリアの相同組換え酵素反応へのDNAの高次構造の効果2008

    • Author(s)
      凌楓
    • Organizer
      第8回日本ミトコンドリア学会年会
    • Place of Presentation
      東京
    • Related Report
      2008 Annual Research Report
  • [Presentation] 酵母ミトコンドリアDNA複製開始点での二重鎖切断修復に働く相同DNA対合酵素Mhr12008

    • Author(s)
      凌楓
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会合同大会(BMB2008)
    • Place of Presentation
      兵庫県神戸市
    • Related Report
      2008 Annual Research Report
  • [Presentation] ヒトDMC1タンパク質およびDMC1バリアントの機能・構造解析2008

    • Author(s)
      引場樹里
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会合同大会(BMB2008)
    • Place of Presentation
      兵庫県神戸市
    • Related Report
      2008 Annual Research Report
  • [Presentation] 減数分裂特異的組換えタンパク質イネDMC1の精製と生化学的機能解析2008

    • Author(s)
      鎌滝千晶
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会合同大会(BMB2008)
    • Place of Presentation
      兵庫県神戸市
    • Related Report
      2008 Annual Research Report
  • [Presentation] 高度好熱菌RecO蛋白質の高次構造解析2008

    • Author(s)
      永江峰幸
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会合同大会(BMB2008)
    • Place of Presentation
      兵庫県神戸市
    • Related Report
      2008 Annual Research Report
  • [Presentation] 出芽酵母Rad52-Rad51複合体によるD-loop 形成におけるRad52の二本鎖DNAへの結合の影響2008

    • Author(s)
      新井直人
    • Organizer
      第31回日本分子生物学会年会・第81回日本生化学会大会合同大会(BMB2008)
    • Place of Presentation
      兵庫県神戸市
    • Related Report
      2008 Annual Research Report
  • [Presentation] Identification of theSSB binding site on RecO by NMR analysis2008

    • Author(s)
      井上仁
    • Organizer
      理研シンポジウム「高度好熱菌丸ごと一匹プロジェクト第8回連携研究会」
    • Place of Presentation
      兵庫県播磨
    • Related Report
      2008 Annual Research Report
  • [Presentation] RecF, RecO, RecR蛋白質によるdsDNA-ssDNA領域の認識機構2008

    • Author(s)
      本多賢吉
    • Organizer
      理研シンポジウム「高度好熱菌丸ごと一匹プロジェクト第8回連携研究会」
    • Place of Presentation
      兵庫県播磨
    • Related Report
      2008 Annual Research Report
  • [Presentation] Rad52の立体構造に基づく相同DNA組換え反応機構の解析2008

    • Author(s)
      香川亘
    • Organizer
      第8回日本蛋白質科学会年会
    • Place of Presentation
      東京
    • Related Report
      2008 Annual Research Report
  • [Presentation] Functional analysis of Mhr1 protein involved in homologous recombination and replication of mtDNA2007

    • Author(s)
      Masuda, T.
    • Organizer
      日本ミトコンドリア学会第7回年会
    • Place of Presentation
      鹿児島
    • Year and Date
      2007-12-21
    • Related Report
      2009 Final Research Report 2007 Annual Research Report
  • [Presentation] 相同組換え蛋白質が共通して誘導する一本鎖DNA伸張構造2007

    • Author(s)
      増田ときは
    • Organizer
      第30回日本分子生物学会年会・第80回日本生化学会大会
    • Place of Presentation
      横浜
    • Year and Date
      2007-12-11
    • Related Report
      2009 Final Research Report
  • [Presentation] 相同組換え蛋白質が共通して誘導する一本鎖DNA伸張構造2007

    • Author(s)
      増田 ときは
    • Organizer
      第30回日本分子生物学会年会・第80回日本生化学会大会(BMB2007)
    • Place of Presentation
      横浜
    • Year and Date
      2007-12-11
    • Related Report
      2007 Annual Research Report
  • [Presentation] Role of RecF, RecO, RecR proteins in SSB displacement from sin-gle-stranded DNA2007

    • Author(s)
      Mikawa, T.
    • Organizer
      FASEB Summer Re-search Conferences, Genetic Recombina-tion & Genome Rearrangements
    • Place of Presentation
      Snowmass Village, CO, USA
    • Related Report
      2009 Final Research Report
  • [Presentation] The rearrangement of SSB on ssDNA by the RecF pathway proteins2007

    • Author(s)
      Mikawa, T.
    • Organizer
      FASEB Summer Research Conferences, Genetic Recombination & Genome Rear-rangements
    • Place of Presentation
      Snowmass Village, CO, USA
    • Related Report
      2009 Final Research Report
  • [Presentation] The process of displacing the single stranded DNA binding protein from single stranded DNA by the RecF pathway proteins2007

    • Author(s)
      井上仁
    • Organizer
      理研シンポジウム「高度好熱菌丸ごと一匹プロジェクト」第6回連携研究会
    • Place of Presentation
      播磨
    • Related Report
      2009 Final Research Report 2007 Annual Research Report
  • [Presentation] The rearrangement of SSB on ssDNA by the RecF pathway proteins2007

    • Author(s)
      Tsutomu Mikawa
    • Organizer
      FASEB Summer Research Conferences, Genetic Recombination & Genome Rearrangements
    • Place of Presentation
      Snowmass Village,CO,USA
    • Related Report
      2007 Annual Research Report
  • [Presentation] A Role of RecF,RecO,RecR proteins in SSB displacement from single-stranded DNA2007

    • Author(s)
      Tsutomu Mikawa
    • Organizer
      FASEB Summer Research Conferences, Genetic Recombination & Genome Rearrangements
    • Place of Presentation
      Snowmass Village,CO,USA
    • Related Report
      2007 Annual Research Report
  • [Presentation] 酵素の反応中間体を捕らえる,DNA組換え反応の中間体から何がわかるか?2007

    • Author(s)
      増田 ときは
    • Organizer
      第7回日本蛋白質科学会年会
    • Place of Presentation
      仙台
    • Related Report
      2007 Annual Research Report
  • [Presentation] 相同組換え蛋白質が誘導する共通のDNA構造変化2007

    • Author(s)
      増田 ときは
    • Organizer
      第7回日本蛋白質科学会年会
    • Place of Presentation
      仙台
    • Related Report
      2007 Annual Research Report
  • [Presentation] RecRによるRecOの機能変換がSSBのssDNAからの解離に貢献する2007

    • Author(s)
      井上 仁
    • Organizer
      第7回日本蛋白質科学会年会
    • Place of Presentation
      仙台
    • Related Report
      2007 Annual Research Report
  • [Book] Epitope mapping by region-specified pcr-mutagenesis(Reineke, U. and Schutkowski, M., eds, in Epitope mapping protocols: second edition. Methods in Mo-lecular Biology. vol. 524)2009

    • Author(s)
      Mikawa, T., lkeda, M., Shibata, T.
    • Publisher
      Humana Press Inc.
    • Related Report
      2009 Final Research Report
  • [Book] "Epitope mapping by region-specified pcr-mutagenesis" in Epitope mapping protocols : second edition. Methods in Molecular Biology. vol.524, (Reineke, U.and Schutkowski, M., eds)pp.305-3132009

    • Author(s)
      Mikawa, T.
    • Total Pages
      9
    • Publisher
      The Humana Press Inc., New York, NY, USA
    • Related Report
      2009 Annual Research Report

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

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