Analysis on regulatory factors and functional mechanisms for the initiator protein of the chromosomal replication

2009 Fiscal Year Final Research Report

• Project/Area Number: 17080005
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Kyushu University
• Principal Investigator: TSUTOMU Katayama Kyushu University, 大学院・薬学研究院, 教授 (70264059)
• Project Period (FY): 2005 – 2009
• Keywords: DNA複製 / 複製開始 / DnaA / DiaA / ヘリカーゼ / DARS / 試験管内再構成 / タンパク質複合体

Research Abstract

Initiation of the chromosomal DNA replication is a crucial reaction that regulates the cell proliferation. The active form of Escherichia coli DnaA protein initiates the chromosomal replication, whereas the inactive form does not. This study revealed for the first time that specific DNA sequences (termed DARS) on the chromosome directly activate DnaA. Moreover, it revealed molecular mechanisms in stimulation for the initiation reaction by the DnaA-binding protein DiaA and in post-initiational inactivation of DnaA by Hda protein.

Research Products

• [Journal Article] Novel essential residues of Hda for interaction with DnaA in the regulatory inactivation of DnaA: Unique roles for Hda AAA+ Box VI and VII motifs (2010)
  • Author(s): Nakamura, K., Katayama, T.
  • Journal Title: Mol. Microbiol. 76 Pages: 302-317
• [Journal Article] Regulation of the replication cycle: Conserved and diverse regulatory systems for DnaA and oriC (2010)
  • Author(s): Katayama, T., Ozaki, S., Keyamura, K., Fujimitsu, K.
  • Journal Title: Nature Rev. Microbiol. 8 Pages: 163-170
• [Journal Article] DnaA, ORC, and Cdc6: Similarity beyond the domains of life and diversity. Biochem (2010)
  • Author(s): Kawakami, H., Katayama, T.
  • Journal Title: Cell Biol. 88 Pages: 49-62
• [Journal Article] Specific genomic sequences of E. coli promote replicational initiation by directly reactivating ADP-DnaA (2009)
  • Author(s): Fujimitsu, K., Senriuchi, T., Katayama, T.
  • Journal Title: Genes Dev. 23 Pages: 221-1233
• [Journal Article] DiaA dynamics are coupled with changes in initial origin complexes leading to helicase loading. (2009)
  • Author(s): Keyamura, K., Abe, Y., Higashi, M., Ueda, T., Katayama, T.
  • Journal Title: J. Biol. Chem. 284 Pages: 25038-25050
• [Journal Article] A. Loss of Hda activity stimulates replication initiation from I-box, but not R4 mutant origins in Escherichia coli (2009)
  • Author(s): Riber, L., Fujimitsu, K., Katayama, T., Lobner-Olesen
  • Journal Title: Mol. Microbiol. 71 Pages: 107-22
• [Journal Article] DnaA structure, function, and dynamics in the initiation at the chromosomal origin (2009)
  • Author(s): Ozaki, S., Katayama, T.
  • Journal Title: Plasmid 62 Pages: 71-82
• [Journal Article] A common mechanism for the ATP-DnaA-dependent formation of open complexes at the replication origin. (2008)
  • Author(s): Ozaki, S., Kawakami, H., Nakamura, K., Fujikawa, N., Kagawa, W., Park, S. -Y., Yokoyama, S., Kurumizaka, H., Katayama, T.
  • Journal Title: J. Biol. Chem. 283 Pages: 8351-8362
• [Journal Article] Hda monomerization by ADP binding promotes replicase clamp-mediated DnaA-ATP hydrolysis (2008)
  • Author(s): Su'etsugu, M., Nakamura, K., Keyamura, K., Kudo, Y., Katayama, T.
  • Journal Title: J. Biol. Chem. 283 Pages: 36118-36131
• [Journal Article] Modes of over-initiation, dnaA gene expression and the inhibition of cell division in a novel cold-sensitive hda mutant in Escherichia coli J. (2008)
  • Author(s): Fujimitsu, K., Su'etsugu, M., Yamaguchi, Y., Mazda, K., Fu, N., Kawakami, H., Katayama, T.
  • Journal Title: Bacteriol. 190 Pages: 5368-5381
• [Journal Article] Roles for the AAA+ motifs of DnaA in the initiation of DNA replication (2008)
  • Author(s): Katayama, T.
  • Journal Title: Biochem. Soc. Trans. 36 Pages: 78-82
• [Journal Article] The interaction of DiaA and DnaA regulates the replication cycle in E. coli by directly promoting ATP-DnaA-specific initiation complexes (2007)
  • Author(s): Keyamura, K., Fujikawa, N,, Ishida, T., Ozaki, S., Su'etsugu, M., Fujimitsu, K., Kagawa, W., Yokoyama, S., Kurumizaka, H., Katayama, T.
  • Journal Title: Genes Dev. 21 Pages: 2083-2099
• [Journal Article] Structure and function of DnaA N-terminal domains: Specific sites and mechanisms in inter-DnaA interaction and in DnaB helicase loading on oriC (2007)
  • Author(s): Abe, Y., Jo, T., Matsuda, Y., Matsunaga, C., Katayama, T., Ueda, T.
  • Journal Title: J. Biol. Chem. 282 Pages: 17816-17827
• [Journal Article] Assignment of 1H, 13C and 15N resonances of N-terminal domains of DnaA protein (2007)
  • Author(s): Abe, Y., Watanabe, N., Yoshida, Y., Ebata, F., Katayama, T., Ueda, T.
  • Journal Title: Biomol. NMR Assign. 1 Pages: 57-59
• [Journal Article] The exceptionally tight affinity of DnaA for ATP/ADP requires a unique aspartic acid residue in the AAA+ sensor 1 motif (2006)
  • Author(s): Kawakami, H., Ozaki, S., Suzuki, S., Nakamura, K., Senriuchi, T., Su'etsugu, M., Fujimitsu, K., Katayama, T.
  • Journal Title: Mol. Microbiol. 62 Pages: 1310-1324
• [Journal Article] The DnaA homolog of the hyperthermophilic eubacterium Thermotoga maritima forms an open complex with a minimal 149-bp origin region in an ATP-dependent manner (2006)
  • Author(s): Ozaki, S., Fujimitsu, K., Kurumizaka, H., Katayama, T.
  • Journal Title: Genes Cells 11 Pages: 425-438
• [Journal Article] An isolated Hda-clamp complex is functional in the regulatory inactivation of DnaA and DNA replication (2006)
  • Author(s): Kawakami, H., Su'etsugu, M., Katayama, T.
  • Journal Title: J. Struct. Biol. 156 Pages: 220-229
• [Journal Article] Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation (2006)
  • Author(s): Ote, T., Hashimoto, M., Ikeuchi, Y., Su'etsugu, M., Suzuki, T., Katayama, T., Kato, J.
  • Journal Title: Mol. Microbiol. 59 Pages: 265-274
• [Journal Article] Formation of an ATP-DnaA-specific initiation complex requires DnaA arginine-285, a conserved motif in the AAA+ protein family (2005)
  • Author(s): Kawakami, H., Keyamura, K., Katayama, T.
  • Journal Title: J. Biol. Chem. 280 Pages: 27420-27430
• [Journal Article] Protein associations in DnaA-ATP hydrolysis mediated by the Hda-replicase clamp complex. (2005)
  • Author(s): Su'etsugu, M., Shimuta, T., Ishida, T., Kawakami, H., Katayama, T.
  • Journal Title: J. Biol. Chem. 280 Pages: 6528-6536
• [Journal Article] Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. (2005)
  • Author(s): Hishimoto, M., Ichimura, Y., Mizoguchi, H., Tanaka, K., Fujimitsu, K., Keyamura, K., Ote, T., Yamakawa, T., Yamazaki, Y., Mori, H., Katayama, T., Kato, J.
  • Journal Title: Mol. Microbiol. 55 Pages: 137-149
• [Journal Article] Crystal structure of a biologically functional form of PriB from Escherichia coli reveals a potential single-stranded DNA-binding site. Biochem (2005)
  • Author(s): Shioi, S., Ose, T., Maenaka, K., Shiroishi, M., Abe, Y., Kohda, D., Katayama, T., Ueda, T.
  • Journal Title: Biophys. Res. Commun. 326 Pages: 766-776
• [Presentation] 染色体複製開始タンパク質の機能制御因子とその作動メカニズムの解析:まとめと展望 (2010)
  • Author(s): 片山勉
  • Organizer: 最終回「染色体サイクル」特定領域会議
  • Place of Presentation: 霧島
  • Year and Date: 20100301-20100303
• [Presentation] Novel fundamental mechanism regulating the replicational initiation in E. coli (2009)
  • Author(s): Katayama, T., Keyamura, K., Fujimitsu, K., Ozaki, S., Shinozuka, S., Hatano, T., Niki, H.
  • Organizer: 第32回日本分子生物学会ワークショップ「Frontier of Bacterial Cell Duplication」
  • Place of Presentation: 横浜
  • Year and Date: 20091209-20091212
• [Presentation] DnaAと複製クランプに依存したDnaA不活性化因子Hdaの活性制御 (2009)
  • Author(s): 中村賢太、末次正幸、片山勉
  • Organizer: 第20回DNA複製・組換え・修復ワークショップ
  • Place of Presentation: 彦根市
  • Year and Date: 20091101-20091103
• [Presentation] Functional mechanism and regulation for the E. coli chromosomal replication initiator DnaA (2009)
  • Author(s): Katayama, T.
  • Organizer: 12th Asia-Pacific International Molecular Biology Network Conference
  • Place of Presentation: Penang, Malaysia
  • Year and Date: 20091027-20091028
• [Presentation] 大腸菌染色体複製イニシエーターDnaAは特異的なDNA配列上で高次複合体を形成し活性化される (2009)
  • Author(s): 藤光和之、片山勉
  • Organizer: 第82回日本生化学会大会シンポジウム「高次タンパク質複合体構造の変遷によるDNA複製の進行制御」
  • Place of Presentation: 神戸
  • Year and Date: 20091021-20091024
• [Presentation] 大腸菌の複製開始因子DnaAの構造、機能、および制御 (2009)
  • Author(s): 片山勉
  • Organizer: 日本遺伝学会第81回大会シンポジウム「日本のDNA複製研究の過去、現在、未来」
  • Place of Presentation: 信州大学
  • Year and Date: 20090916-20090918
• [Presentation] 大腸菌の複製開始複合体形成におけるDiaA-DnaA相互作用メカニズムの解析 (2009)
  • Author(s): 毛谷村賢司、東雅裕、片山勉
  • Organizer: 日本遺伝学会第81回大会
  • Place of Presentation: 信州大学
  • Year and Date: 20090916-20090918
• [Presentation] The replication initiator DnaA is reactivated in a specific nucleoprotein complex (2009)
  • Author(s): Fujimitsu, K., Senriuchi, T., Katayama, T.
  • Organizer: 8th International Conference on AAA Proteins
  • Place of Presentation: Tronto, Canada
  • Year and Date: 20090712-20090716
• [Presentation] AAA+ domain-specific interaction of Hda with DnaA in the replicase clamp-mediated DnaA-ATP hydrolysis (2009)
  • Author(s): Nakamura, K., Katayama, T.
  • Organizer: 8th International Conference on AAA Proteins
  • Place of Presentation: Tronto, Canada
  • Year and Date: 20090712-20090716
• [Presentation] DARS:大腸菌DnaAを活性化する新規染色体DNA因子 (2009)
  • Author(s): 片山勉
  • Organizer: 第5回「染色体サイクル」特定領域会議
  • Place of Presentation: 伊豆市
  • Year and Date: 20090615-20090617
• [Presentation] Functional regulation of Hda, a replicase clamp-binding protein that promotes the regulatory inactivation of DnaA in E. coli (2008)
  • Author(s): Su'etsugu, M., Nakamura, K., Keyamura, K., Katayama, T.
  • 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シンポジウム「染色体サイクルの制御機構」
  • Place of Presentation: 神戸
  • Year and Date: 20081209-20081212
• [Presentation] Mechanism and Regulation for ATP-DnaA Assembly and Duplex DNA Unwinding on the E. coli Chromosomal Origin oriC (2008)
  • Author(s): Katayama, T.
  • Organizer: 6th 3R (Replication, Recombination, Repair) Symposium
  • Place of Presentation: Kakegawa, Japan
  • Year and Date: 20081027-20081030
• [Presentation] Mechanisms of ATP-DnaA Assembly and Duplex DNA Unwinding for the Initiation of DNA Replication in Reconstituted Systems (2008)
  • Author(s): Katayama, T.
  • Organizer: The 17th RIKEN CDB Meeting "Towards Synthesis of Cells"
  • Place of Presentation: Kobe, Japan
  • Year and Date: 20081014-20081015
• [Presentation] DnaAによる2重鎖開裂における複製起点の最小機能構造 (2008)
  • Author(s): 尾崎省吾, 片山勉
  • Organizer: 第80回日本遺伝学会大会ワークショップ「染色体機能とDNAトランスアクション」
  • Place of Presentation: 名古屋大学
  • Year and Date: 20080903-20080905
• [Presentation] Analysis on Mechanisms of ATP-DnaA Assembly on oriC and Duplex Unwinding (2008)
  • Author(s): Katayama, T., Ozaki, S., Keyamura, K., Kawakami, H., Fujikawa, N., Kagawa, W., Nakamura, K., Fujimitsu, K., Su'etsugu, M., Yokoyama, S., Kurumizaka, H.
  • Organizer: EMBO Workshop on Replication & Segregation of Chromosomes
  • Place of Presentation: Geilo, Norway
  • Year and Date: 20080616-20080620
• [Presentation] 新規因子DiaA蛋白質を含む, 複製開始複合体の構造とメカニズム (2008)
  • Author(s): 片山勉, 毛谷村賢司, 尾崎省吾, 藤川乃り映, 香川亘, 川上広宣, 中村賢太, 石田琢磨, 末次正幸, 藤光和之, 横山茂之, 胡桃坂仁志
  • Organizer: 第8回蛋白質科学会年会ワークショップ「構造から理解するDNA結合タンパク質の機能」
  • Place of Presentation: 東京都江戸川区
  • Year and Date: 20080610-20080612
• [Presentation] A novel initiation-stimulator DiaA directly promotes ATP-DnaA-specific initiation complexes in E. coli (2008)
  • Author(s): Keyamura, K., Fujikawa, N., Ishida, T., Ozaki, S., Su'etsugu, M., Fujimitsu, K., Kagawa, W., Yokoyama, S., Kurumizaka, H., Katayama, T.
  • Organizer: Keysone Symposia in Molecular and Cellular Biology: DNA Replication and Recombination
  • Place of Presentation: Santa Fe, NM, USA
  • Year and Date: 20080210-20080215
• [Presentation] DnaAによる複製開始複合体の形成と2重鎖開裂機構モデル (2007)
  • Author(s): 片山勉、尾崎省吾、川上広宣、中村賢太、藤川乃り映、香川亘、横山茂之、胡桃坂仁志
  • 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合同大会ワークショップ「複製開始複合体形成のダイナミクスと分子制御」(オーガナイザー:片山勉、西谷秀男)
  • Place of Presentation: 横浜
  • Year and Date: 20071211-20071215
• [Presentation] DnaA結合因子DiaA蛋白質による複製開始の制御機構 (2007)
  • Author(s): 片山勉、毛谷村賢司、藤川乃り映、石田琢磨、尾崎省吾、末次正幸、藤光和之、香川亘、横山茂之、胡桃坂仁志
  • Organizer: 日本遺伝学会第79回大会、ミニシンポジウム「染色体の複製機構とゲノム安定性」
  • Place of Presentation: 岡山大学
  • Year and Date: 20070919-20070921
• [Presentation] Role for specific residues of DnaA AAA+ domain in duplex DNA unwinding during the initiation of chromosomal replication (2007)
  • Author(s): Ozaki, S., Kawakami, H., Nakamura, N., Fujikawa, N., Kagawa, W., Yokoyama, S., Kurumizaka, H., Katayama, T.
  • Organizer: 7th International Meeting on AAA Proteins
  • Place of Presentation: Royal Agricultural College, Cirencester, UK
  • Year and Date: 20070909-20090913
• [Presentation] Biochemical analysis of DnaA AAA+ domain on the ATP-dependent regulation for the initiation of chromosomal replication (2007)
  • Author(s): Katayama, T., Ozaki, S., Kawakami, H., Nakamura, N., Keyamura, K., Fujikawa, N., Kagawa, W., Yokoyama, S., Kurumizaka, H.
  • Organizer: 7th International Meeting on AAA Proteins
  • Place of Presentation: Royal Agricultural College, Cirencester, UK
  • Year and Date: 20070909-20070913
• [Presentation] DnaA蛋白質の特異的AAA+領域を介した複製開始点開裂のメカニズム、日本分子生物学会2006フォーラム (2006)
  • Author(s): 尾崎省吾、川上広宣、中村賢太、胡桃坂仁志、片山勉
  • Organizer: シンポジウム「染色体複製開始サイクルの分子機構と制御スイッチ」(世話人:片山勉、西谷秀男)
  • Place of Presentation: 名古屋
  • Year and Date: 20061206-20061208
• [Presentation] 特異的なDNA配列による大腸菌染色体複製イニシエーターDnaAの再活性化 (2006)
  • Author(s): 藤光和之、千里内啓行、片山勉
  • Organizer: 第18回DNA複製ワークショップ
  • Place of Presentation: 熱海
  • Year and Date: 20061030-20061101
• [Presentation] 大腸菌スライディングクランプ新規相互作用因子の同定とその機能解析 (2006)
  • Author(s): 松田雄作、片山勉
  • Organizer: 第18回DNA複製ワークショップ
  • Place of Presentation: 熱海
  • Year and Date: 20061030-20061101
• [Presentation] Analysis on molecular mechanism of the clamp/Hda-dependent DnaA-ATP hydrolysis and on a novel role for the clamp EMBO Workshop (2006)
  • Author(s): Katayama, T., Matsuda, Y., Kawakami, H., Su'etsugu, M.
  • Organizer: Cell Cycle and Cytoskeletal Elements in Bacteria
  • Place of Presentation: Copenhagen, Denmark
  • Year and Date: 20060823-20060827
• [Presentation] The nucleotide-dependent activation of Hda in the replicase clamp-mediated DnaA-ATP hydrolysis in Escherichia coli, EMBO Workshop (2006)
  • Author(s): Su'etsugu, M., Keyamura, K., Kudo, Y., Nakamura, K., Katayama, T.
  • Organizer: Cell Cycle and Cytoskeletal Elements in Bacteria
  • Place of Presentation: Copenhagen, Denmark
  • Year and Date: 20060823-20060827
• [Presentation] Mechanism in the ATP-specific Conformational Activation of the Initiation Complex by DnaA initiator, The First International Symposium on the MEXT Priority Research Project (2006)
  • Author(s): Katayama, T., Ozaki, S., Kawakami, H., Kurumizaka, H.
  • Organizer: he Chromosome Cycle (A Satellite Meeting of 20th IUBMB International Congress of Biochemistry and Molecular Biology & 11th FAOBMB Congress)
  • Place of Presentation: Sanjo Conference Hall (Tokyo University Hongo Campus)
  • Year and Date: 20060626-20060627
• [Presentation] Analysis on Structure and Regulation of a Bacterial Initiation Complex (2005)
  • Author(s): Katayama, T., Kawakami, H., Ozaki, S., Kurumizaka, H.
  • Organizer: 第28回日本分子生物学会年会、シンポジウム「複製装置の集合と維持」
  • Place of Presentation: 福岡
  • Year and Date: 20051207-20051210
• [Presentation] クランプ依存性DnaA不活化機構におけるHdaの機能構造とヌクレオチド依存性 (2005)
  • Author(s): 末次正幸、工藤由佳、毛谷村賢司、松永千佳、紫牟田透、石田琢磨、川上広宣、片山勉
  • Organizer: 第28回日本分子生物学会年会、ワークショップ「タンパク質構造から展開するDNA複製システムのダイナミクス」(世話人:石野良純、片山勉)
  • Place of Presentation: 福岡
  • Year and Date: 20051207-20051210
• [Presentation] DnaA結合性ATPの複製開始複合体形成における役割 (2005)
  • Author(s): 川上広宣、尾崎省吾、鈴木滋夫、中村賢太、千里内啓行、毛谷村賢司、末次正幸、藤光和之、片山勉
  • Organizer: 第28回日本分子生物学会年会、ワークショップ「細胞機能のキープレイヤーAAA+タンパク質の世界」
  • Place of Presentation: 福岡
  • Year and Date: 20051207-20051210
• [Presentation] 毛谷村賢治染色体複製開始におけるATP依存的高次複合体形成の分子機構 (2005)
  • Author(s): 片山勉、川上広宣、尾崎省吾、藤光和之
  • Organizer: 日本遺伝学会第77回大会ミニシンポジウム「大腸菌の染色体ダイナミクス」(世話人:堀内嵩、片山勉)
  • Place of Presentation: 東京
  • Year and Date: 20050927-20050929
• [Presentation] DARS: the chromosomal locus for reactivation of the replication initiator DnaA in E. coli
  • Author(s): Fujimitsu, K., Kasho, K., Senriuchi, T., Ohyama, H., Katayama, T.
  • Organizer: International Symposium on Chromosomal Cycle and Genome Dynamics
  • Place of Presentation: Nasu, Tochigi, Japan
• [Book] 染色体サイクル(正井久雄、升方久夫、釣本敏樹、仁木宏典、篠原彰編集, 大腸菌の染色体複製開始制御機構) (2009)
  • Author(s): 片山勉
  • Total Pages: 343-349
  • Publisher: 共立出版
• [Book] 細胞工学(複製再開始抑制の分子機構実験医) (2008)
  • Author(s): 片山勉
  • Total Pages: 974-979
  • Publisher: 秀潤社
• [Book] 染色体サイクル(正井久雄, 渡邊嘉典編集, 複製再開始抑制の分子機構実験医) (2007)
  • Author(s): 片山勉
  • Total Pages: 49-55
  • Publisher: 羊土社
• [Book] タンパク質実験マニュアル(胡桃坂仁志編集, 大腸菌DnaA) (2006)
  • Author(s): 毛谷村賢司、尾崎省吾、片山勉
  • Total Pages: 7-14
  • Publisher: 朝倉書店
• [Remarks]
  • URL: http://bunsei.phar.kyushu-u.ac.jp/