Molecular architecture and regulation mechanism of replication fork complex revealed by single partic le analysis

2011 Fiscal Year Final Research Report

• Project/Area Number: 21570114
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Kyushu University
• Principal Investigator: MAYANAGI Kouta 九州大学, 生体防御医学研究所 (50418571)
• Co-Investigator(Renkei-kenkyūsha): ISHINOYO Shizumi 九州大学, 大学院・農学研究院, 教授 (30346837)
• Project Period (FY): 2009 – 2011
• Keywords: 可視化 / 生物物理 / 電子顕微鏡 / ナノバイオ / 生体分子

Research Abstract

We investigated the three-dimensional structure of the DNA polymerase B(PolB)-PCNA-DNA complex, which is the core components of the replisome, by single particle electron microscopy. Notably, besides the authentic interaction through a PCNA-interacting protein box(PIP-box), a novel contact was found between PolB and PCNA. The obtained molecular architecture of the complex, including the new contacts found in this work, provides clearer insights into the mechanism of switching between the two distinct modes of the complex.

Research Products

• [Journal Article] Mechanistic insights into the activation of the Radsl-mediated strand exchange from the structure of a recombination activator, Swis-Sfrl complex (2012)
  • Author(s): Naoyuki Kuwabara, Yasuto Murayama, Hiroshi Hashimoto, Yuuichi Kokabu, Mitsunori Ikeguchi, Mamoru Sate, Kouta Mayanagi, Hiroshi Iwasaki and Toshiyuki Shimizu.
  • Journal Title: Structure Volume: 20(3) Pages: 440-449
  • Peer Reviewed
• [Journal Article] The GINS complex from the thermophilic archaeon, Thermoplasma acidophilum may function as a homotetramer in DNA replication (2011)
  • Author(s): Hiromi Ogino, Sonoko Ishino, Kouta Mayanagi, Gyri Teien Haugland, Nils Kare Birkeland, Akihiko Yamagishi, Yoshizumi Ishino.
  • Journal Title: Extremophiles Volume: 15(4) Pages: 529-539
  • Peer Reviewed
• [Journal Article] Architectures of archaeal GINS complexes, essential DNA replication initiation factors (2011)
  • Author(s): Takuji Oyama, Sonoko Ishino, Seiji Fu j ine, Hiromi Ogino, Tsuyoshi Shirai, Kouta Mayanagi, Mihoko Saito, Naoko Nagasawa, Yoshizumi Ishino, Kosuke Morikawa.
  • Journal Title: BMC Biol Volume: 9 Pages: 28
  • Peer Reviewed
• [Journal Article] Relationship between heat-induced fibrillogenicity and hemolytic activity of thermostable direct hemolysin and a related hemolysin of Vibrio parahaemolyticus FEMS (2011)
  • Author(s): Kiyouhira Ohnishi, Kumiko Nakahira, Satoru Unzai, Kouta Mayanagi, Horoshi Hashimoto, Kentaro Shiraki, Takeshi Honda, Itaru Yanagihara
  • Journal Title: MicroBiol Left Volume: 381(1) Pages: 10-17
  • Peer Reviewed
• [Journal Article] Architecture of the DNA polymerase B-proliferating cell nuclear antigen(PCNA)-DNA ternary complex (2011)
  • Author(s): Kouta Mayanagi, Shinichi Kiyonari, Hirokazu Nishida, Mihoko Saito, Daisuke Kohda, Yoshizumi Ishino, Tsuyoshi Shirai, Kosuke Morikawa
  • Journal Title: PNAS Volume: 108 Pages: 1845-1849
  • Peer Reviewed
• [Journal Article] characterization of Vibrio parahaemolyticus thermostable direct hemolysin(TDH) (2010)
  • Author(s): Itaru Yanagihara, Kumiko Nakahira, Tsutomu Yamane, Shuji Kaieda, Kouta Mayanagi, Daizo Hamada, Takashi Fukui, Kiyouhisa Ohnishi, Shin' ichiro Kajiyama, Toshiyuki Shimizu, Mamoru Sato, Takahisa Ikegami, Mitsunori Ikeguchi, Takeshi Honda, Hiroshi Hashimoto.
  • Journal Title: J Biel Chem Volume: 285(20) Pages: 16267-74
  • Peer Reviewed
• [Journal Article] DNAクランプ/複製DNAポリメラーゼ複合体におけるDNA合成・修正スイッチング機構 (2010)
  • Author(s): 西田洋一, 真柳浩太, 五里避屯, 森川取助
  • Journal Title: 日本結晶学会誌 Volume: 52 Pages: 201-207
  • Peer Reviewed
• [Journal Article] Effects of antibody affinity and antigen valence on molecular forms of immune complexes (2009)
  • Author(s): Masayuki Oda, Susumu Uchiyama, Masanori Noda, Yoshinori Nishi, Maiko Koga, Kouta Mayanagi, Carol V. Robinson, Kiichi Fukui, Yuji Kobayashi, Kosuke Morikawa, and Takachika Azuma.
  • Journal Title: Molecular Immunology Volume: 47 Pages: 357-364
  • Peer Reviewed
• [Journal Article] Structural determinant for switching between the polymerase and exonuclease modes in the PCNA-replicative DNA polymerase complex (2009)
  • Author(s): Hirokazu Nishida, Kouta Mayanagi, Shinich Kiyonari, Yuichi Sato, Takuji Oyama, Yoshizumi Ishino, Kosuke. Morikawa.
  • Journal Title: PNAS Volume: 106 Pages: 20693-20698
  • Peer Reviewed
• [Journal Article] Mechanism of replication machinery assembly as revealed by the DNA ligase-PCNA-DNA complex architecture (2009)
  • Author(s): Kouta Mayanagi, Shinichi Kiyonari, Mihoko Saito, Tsuyoshi Shirai, Yoshizumi Ishino, Kosuke Morikawa￥
  • Journal Title: PNAS Volume: 106 Pages: 4647-4652
  • Peer Reviewed
• [Journal Article] implications of the archaeal RecQ-like helicase Hjm (2009)
  • Author(s): Takuji Oyama, Hayato Oka, Kouta Mayanagi, Tsuyoshi Shirai, Kyoko Matoba, Ryosuke Fujikane, Yoshizumi Ishino, Kosuke Morikawa, Atomic structures and functional
  • Journal Title: BMC Structural Biology Volume: 9 Pages: 2
  • Peer Reviewed
• [Presentation] 3D ultrastructure within intact cells explored by electron cryo-tomography in TEM and STEM (2012)
  • Author(s): Shinji Aramaki, Kazuaki Aoyama, Kouta Mayanagi, Takuo Yasunaga
  • Organizer: The 10th Asia-Pacific Microscopy Conference(APMC10)
  • Place of Presentation: Perth, Australia
  • Year and Date: 20120205-09
• [Presentation] 電子顕微鏡単粒子解析による複製因子の切換機構の研究 (2011)
  • Author(s): 真柳浩太,清成信一,西田洋一,齊藤美保子,神田大輔,石野良純,白井剛,森川取右
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 20111213-16
• [Presentation] The GINS complex from the thermoacidophilic archaeon, Thermoplasma acidophilum may (2011)
  • Author(s): Hiromi Ogino, Sonoko Ishino, Kouta Mayanagi, Gyri Teien Haugland, Nils-Kare Birkeland, Akihiko Yamagishi and Yoshizumi Ishino
  • Organizer: function as a homotetramer in DNA replication
  • Place of Presentation: 横浜
  • Year and Date: 20111213-16
• [Presentation] 超好熱性アーキアThermococcuskodakaraensisの複製フォーク複合体解明に向けてのMCM, GINS複合体解析,第33回日本分子生物学会年会 (2011)
  • Author(s): 藤野誠司,石野園子,井田梨沙,尾木野弘実,冨田宏矢,金井保,跡見晴幸,真拠L造太,大山拓次,森川取右,石野良麺
  • Organizer: 第83回日本生化学会大会
  • Place of Presentation: 神戸
  • Year and Date: 20111207-10
• [Presentation] Molecular architecture and switching mechanism of DNA replication fork (2011)
  • Author(s): Kouta Mayanagi
  • Organizer: Structural Biology & DNA Repair
  • Place of Presentation: Amsterdam, The Netherlands
  • Year and Date: 20111016-18
• [Presentation] クライオ電子線トモグラフィーによる遺伝的な重金属でラベルしたLC4の検出 (2011)
  • Author(s): 金明月,柳澤春明,小屋迫光太郎,神谷律,真柳浩太,安永卓生
  • Organizer: 第49回日本生物物理学会年会
  • Place of Presentation: 姫路
  • Year and Date: 20110916-18
• [Presentation] 電子線クライオトモグラフィー法による神経細胞NG108-15の超微細構造観察 (2011)
  • Author(s): 荒牧慎二,青山一弘,真柳浩太,安永卓生
  • Organizer: 第49回日本生物物理学会年会
  • Place of Presentation: 姫路
  • Year and Date: 20110916-18
• [Presentation] 単粒子解析によるDNA複製の制御機構の研究 (2011)
  • Author(s): 真柳浩太,清成信一,西田洋一,齊藤美保子,神田大輔,互野良純,白井剛,森川取右
  • Organizer: 第ll回日本蛋白質科学会年会
  • Place of Presentation: 大阪
  • Year and Date: 20110607-09
• [Presentation] 相同組換えに関わるSwi5-Sfr1複合体の構造機i能解析 (2011)
  • Author(s): 桑原直之,橋本博,小甲裕一,池口満徳,佐藤衛,真柳浩太,村山泰人,岩崎博史,清水敏之
  • Organizer: 第11回日本蛋白質科学会年会
  • Place of Presentation: 大阪
  • Year and Date: 20110607-09
• [Presentation] TEM及びSTEMを用いたクライオ電子線トモグラフィーによる神経細胞の超微細構造観察 (2011)
  • Author(s): 荒牧慎二,青山一弘,真ロ浩太,安永卓生
  • Organizer: 2011年日本生物物理学会九州支部例会
  • Place of Presentation: 飯塚
  • Year and Date: 2011-12-04
• [Presentation] 超好熱古細菌リボヌクレアーゼPの高次構造解析を目指した再構成酵素の精製 (2010)
  • Author(s): 中尾祐士,服部淳子,原唯史,山口浩輝,郷田秀一郎,真ロ浩太,神田大輔,角田佳充,木村誠
  • 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
  • Place of Presentation: 神戸
  • Year and Date: 20101207-10
• [Presentation] 相同組換えに関わるSwi5-Sfr1複合体の構造機i能解析 (2010)
  • Author(s): 桑原直之,橋本博,小甲裕一,池口満徳,佐藤衛,真柳浩太,村山泰斗,岩崎博史,清水敏之
  • 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
  • Place of Presentation: 神戸
  • Year and Date: 20101207-10
• [Presentation] 電子顕微鏡単粒子解析による複製関連複合体の反応制御機構の研究 (2010)
  • Author(s): 14.真柳浩太、西田洋一、清成信一、斉藤美保子、神田大輔、石塁随、白井剛、森川取右
  • 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
  • Place of Presentation: 神戸
  • Year and Date: 20101207-10
• [Presentation] Modelingof3Rcomplexesfromstructuredatabase (2010)
  • Author(s): MayanagiK, SaitoM, OyamaT, IshinoY, ShiraiT
  • Organizer: 日本生物物理学会第48回年会
  • Place of Presentation: 仙台
  • Year and Date: 20100920-22
• [Presentation] 大腸菌膜に発現させたAsn結合型糖鎖修飾を決定するオリゴ糖転移酵素の精製と結晶化 (2010)
  • Author(s): 井倉真由美、真柳浩太、神田大輔
  • Organizer: 第10回日本蛋白質科学会年会
  • Place of Presentation: 札幌
  • Year and Date: 20100616-18
• [Presentation] DNAPol-PCNA-DNA複合体の電子顕微鏡単粒子解析 (2010)
  • Author(s): 真柳浩太,西田洋一,清成信一,神田大輔,白井剛,石野良純,森川取右
  • Organizer: 第10回日本蛋白質科学会年会
  • Place of Presentation: 札幌
  • Year and Date: 20100616-18
• [Presentation] HomotetramericGINSfromthethermoacidophilicarchaeon, Thermoplasmaacidophilum (2010)
  • Author(s): 尾木野弘実,石野園子,真柳浩太, Nils-KareBirkeland,山岸明彦,石野良純
  • 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
  • Place of Presentation: 神戸
  • Year and Date: 2010-07-10
• [Presentation] DNAligase-PCNA-DNA複合体の単粒子解析 (2009)
  • Author(s): 真柳浩太,清成信一,斉藤美保子,白井剛,石野良純,森川取右
  • Organizer: 第9回日本蛋白質科学会年会
  • Place of Presentation: 貢員本
  • Year and Date: 20090520-22
• [Presentation] RecQに関連する古細菌由来Hjmヘリカーゼの結晶構造とその機能 (2009)
  • Author(s): 大山託次,真ロ浩太,白井剛,藤兼亮輔,石里塵,森川取
  • Organizer: 第9回日本蛋白質科学会年会
  • Place of Presentation: 熊本
  • Year and Date: 20090520-22
• [Presentation] DNA複製ポリメラーゼの複製⇔校正モード変換の分子基盤 (2009)
  • Author(s): 西田洋一,真ロ浩太,清成信一,石野良麺,森川取右
  • Organizer: 第9回日本蛋白質科学会年会
  • Place of Presentation: 貢員本
  • Year and Date: 20090520-22
• [Presentation] 大腸菌膜に発現させたオリゴ糖転移酵素の精製と結晶化 (2009)
  • Author(s): 井倉真由美,真柳浩太,ニレンダジエイムス,神田大輔
  • Organizer: 第9回日本蛋白質科学会年会
  • Place of Presentation: 熊本
  • Year and Date: 20090520-22
• [Presentation] 高速AFMによる蛋白質天然変性領域の観察 (2009)
  • Author(s): 宮城篤,津中康央,内橋貴之,真拠造太,広瀬進,西野達哉,安藤敏夫,森川取右
  • Organizer: 第9回日本蛋白質科学会年会
  • Place of Presentation: 熊本
  • Year and Date: 20090520-22
• [Presentation] TheswitchingmechanismofreplicationfactorsasrevealedbythemoleculararchitectureoftheDNAligase-PCNA-DNAcomplex (2009)
  • Author(s): 真柳浩太、清成信一、斉藤美保子、白井剛、五塁壁、森川取右
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 北九州
  • Year and Date: 2009-12-05
• [Presentation] 単粒子解析によるDNA複製関連複合体の構造研究 (2009)
  • Author(s): 真柳浩太
  • Organizer: 第51回日本顕微鏡学会九州支部総会・学術講演会
  • Place of Presentation: 北九州
  • Year and Date: 2009-12-05
• [Presentation] 複製関連超分子複合体の電子顕微鏡単粒子解析 (2009)
  • Author(s): 真柳浩太
  • Organizer: 第19回WSフォーラムータンパク質・ペプチド研究の現状と展望
  • Place of Presentation: 福岡
  • Year and Date: 2009-11-27
• [Presentation] Mechanism of replication machinery assembly as revealed by the single particle analysis of DNA ligase猶CNA優NA complex (2009)
  • Author(s): Kouta Mayanagi, Hirokazu Nishida, Yoshizumi Ishino, and Kosuke Morikawa
  • Organizer: ordon Research Conferences on Three Dimensional Electron microscopy
  • Place of Presentation: Colby祐awyer College
  • Year and Date: 2009-06-28
• [Book] タンパク質の立体構造 7章構造決定法 (2010)
  • Author(s): 真柳浩太, 廣明秀一, 白井剛
  • Publisher: 講談社