Quality control of E. coli membrane proteins

2011 Fiscal Year Final Research Report

• Project Area: Protein community: organization and maintenance of protein functions
• Project/Area Number: 19058007
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Kyoto University
• Principal Investigator: AKIYAMA Yoshinori 京都大学, ウイルス研究所, 教授 (10192460)
• Co-Investigator(Kenkyū-buntansha): MORI Hiroyuki 京都大学, ウイルス研究所, 准教授 (10243271)
• Project Period (FY): 2007 – 2011
• Keywords: 膜タンパク質 / 品質管理 / 膜プロテアーゼ / ストレス応答 / タンパク質膜透過

Research Abstract

We studied the structures and functions of cellular factors participating in quality control of E. coli membrane proteins. We revealed the cellular functions and substrate recognition mechanisms of intramembrane cleaving proteases, RseP (S2P family) and GlpG (Rhomboid family). We also elucidated the structures of SecYE (translocon) and SecDF, membrane complexes involved in protein translocation, and proposed the mechanism of their actions. In addition, we identified proteins whose functions would be related to ‘membrane stress responses'.

Research Products

• [Journal Article] Nascentome analysis uncovers futile protein synthesis in Escherichia coli (2011)
  • Author(s): Ito, K., Chadani, Y., Nakamori, K., Chiba, S., Akiyama, Y., and Abo, T.
  • Journal Title: PLoS ONE Volume: 6 Pages: e28413
  • Peer Reviewed
• [Journal Article] Post liberation cleavage of signal peptides is catalyzed by the S2P protease in bacteria (2011)
  • Author(s): Saito, A., Hizukuri, Y., Matsuo, E.-i., Chiba, S., Mori, H., Nishimura, O., Ito, K., and Akiyama, Y.
  • Journal Title: Proc. Natl. Acad. Sci, USA Volume: 108 Pages: 13740-13745
  • Peer Reviewed
• [Journal Article] Structure and function of SecDF, a protein export-enhancing membrane component (2011)
  • Author(s): Tsukazaki, T., Mori, H. , Echizen, Y., Ishitani, R., Fukai, S., Tanaka, T, Perederina, A., Vassylyev, D. G., Kohno, T., Maturana, A. D., Ito, K. and Nureki, O.
  • Journal Title: Nature Volume: 474 Pages: 235-238
  • Peer Reviewed
• [Journal Article] Recruitment of a species-specific arrest module to monitor different cellular processes (2011)
  • Author(s): Chiba. S., Kanamori, T., Ueda, T., Akiyama, Y., Pogliano, K. and Ito, K.
  • Journal Title: Proc. Natl. Acad. Sci, USA Volume: 108 Pages: 6073-6078
  • Peer Reviewed
• [Journal Article] Quality control of cytoplasmic membrane proteins in Escherichia coli. (2009)
  • Author(s): Akiyama, Y.
  • Journal Title: J. Biochem. Volume: 46 Pages: 449-454
  • Peer Reviewed
• [Journal Article] The Sec protein secretion system (2009)
  • Author(s): Ito, K. and Mori, H.
  • Journal Title: Bacterial Secreted Proteins, Ed. K. Wooldridge Pages: 3-22
• [Journal Article] Substrate recognition and binding by RseP, an Escherichia coli intramembrane protease (2008)
  • Author(s): Koide, K., Ito. K., and Akiyama, Y.
  • Journal Title: J. Biol. Chem. Volume: 283 Pages: 9562-9570
  • Peer Reviewed
• [Journal Article] Conformational transition of Sec machinery inferred from bacterial SecYE structures (2008)
  • Author(s): Tsukazaki, T., Mori, H., Fukai, S., Ishitani, R., Mori, T., Dohmae, N., Perederina, A., Sugita, Y., Vassylyev, D. G., Ito, K. and Nureki, O.
  • Journal Title: Nature Volume: 455 Pages: 988-991
  • Peer Reviewed
• [Journal Article] A pair of circularly permutated PDZ domains control RseP, the S2P family intramembrane protease of E. coli. (2008)
  • Author(s): Inaba, K., Suzuki, M., Maegawa, K., Akiyama, S., Ito, K., and Akiyama, Y.
  • Journal Title: J. Biol. Chem. Volume: 283 Pages: 35042-35052
  • Peer Reviewed
• [Journal Article] The role of L1 loop in the mechanism of rhomboid intramembrane protease GlpG. (2007)
  • Author(s): Wang, Y., Maegawa, S., Akiyama, Y. and Ha, Y.
  • Journal Title: J. Mol. Biol. Volume: 374 Pages: 1104-1113
  • Peer Reviewed
• [Journal Article] Sequence features of substrates required for cleavage by GlpG, an Escherichia coli rhomboid protease. (2007)
  • Author(s): Akiyama, Y. and Maegawa, S.
  • Journal Title: Mol. Microbiol. Volume: 64 Pages: 1028-1037
  • Peer Reviewed
• [Journal Article] The intramembrane active site of GlpG, an Escherichia coli rhomboid protease, is accessible to water and hydrolyzes an extramembrane peptide-bond of substrates (2007)
  • Author(s): Maegawa, S., Koide, K., Ito, K., and Akiyama, Y.
  • Journal Title: Mol. Microbiol. Volume: 64 Pages: 435-447
  • Peer Reviewed
• [Journal Article] Environments of the active site region of RseP, an Escherichia coli RIP protease, assessed by site-directed cysteine alkylation (2007)
  • Author(s): Koide, K., Maegawa, S., Ito, K., and Akiyama, Y.
  • Journal Title: J. Biol. Chem. Volume: 282 Pages: 4553-4560
  • Peer Reviewed
• [Journal Article] SecY alterations that impair membrane protein folding and generate a membrane stress (2007)
  • Author(s): Shimohata, N., Nagamori, S., Akiyama, Y., Kaback, H.R., and Ito, K.
  • Journal Title: J. Cell Biol. Volume: 176 Pages: 307-317
  • Peer Reviewed
• [Presentation] Post-liberation cleavage of signal peptides is catalyzed by the site-2 protease (S2P) in bacteria (2011)
  • Author(s): Akiyama, Y.
  • Organizer: The 18th East Asia Joint Symposium on Biomedical Research
  • Place of Presentation: Shanghai, China
  • Year and Date: 20111207-09
• [Presentation] 細菌の蛋白質膜透過装置の構造・機能・病原性との関わり (2011)
  • Author(s): 森博幸
  • Organizer: 第48回細菌学会中部支部会
  • Place of Presentation: 名古屋
  • Year and Date: 20111021-22
• [Presentation] 蛋白質膜透過を促進する膜内在性因子SecDFの構造と機能 (2011)
  • Author(s): 森博幸、塚崎智也、越前友香、秋山芳展、濡木理、伊藤維昭
  • Organizer: 第84回日本生化学会大会シンポジウム「生体膜エネルギー変換装置の超分子科学」
  • Place of Presentation: 京都
  • Year and Date: 20110921-24
• [Presentation] Function and regulation of RseP, the S2P family intramembrane protease of E. coli (2011)
  • Author(s): Akiyama, Y. and Hizukuri, Y.
  • Organizer: International Union of Microbiological Societies 2011 Congress
  • Place of Presentation: Sapporo, Japan
  • Year and Date: 20110905-10
• [Presentation] プロトン駆動力を用いたSecDFによる蛋白質膜透過の昂進機構 (2011)
  • Author(s): 森博幸、塚崎智也、越前友香、濡木理、伊藤維昭
  • Organizer: 第11回日本蛋白質科学会年会ワークショップ「細胞膜ダイナミクス : In vitro再構成系によるアプローチ」
  • Place of Presentation: 大阪
  • Year and Date: 20110607-09
• [Presentation] バクテリアの蛋白質膜透過チャネルSecYEGと相互作用する因子の解析 (2011)
  • Author(s): 森博幸
  • Organizer: 理研シンポジウム「第3回生体分子の分離・解析法の進展-膜タンパク質への応用-」
  • Place of Presentation: 和光
  • Year and Date: 2011-10-28
• [Presentation] Structure, function and evolution of bacterial protein translocation machinery (2010)
  • Author(s): Mori, H., Tsukazaki, T., Akiyama, Y., Nureki, O. and Ito, K.
  • 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合同大会ワークショップ「進化からみたタンパク質社会」
  • Place of Presentation: 神戸
  • Year and Date: 20101207-10
• [Presentation] Fate of signal peptides in bacteria: post liberation cleavage by S2P protease. (2010)
  • Author(s): 斎藤啓、千葉志信、松尾英一、西村紀、伊藤維昭、秋山芳展
  • Organizer: 第33回日本分子生物学会大会・第83会日本生化学会大会合同大会ワークショップ「膜タンパク質の構造・機能から見るオルガネラの進化」
  • Place of Presentation: 神戸
  • Year and Date: 20101207-10
• [Presentation] Roles of the two PDZ domains of RseP, the S2P family intramembrane protease of Escherichia coli, in regulation of its protease function (2010)
  • Author(s): Hizukuri, Y. and Akiyama, Y.
  • Organizer: The 3^<rd> International Symposium on Protein Community
  • Place of Presentation: Nara, Japan
  • Year and Date: 20100913-16
• [Presentation] A functionally important intramolecular interaction in SecA : involvement of hydrophobic amino acids in motif IV and anti-parallel beta sheet in translocase activation (2010)
  • Author(s): Mori, H., Tsukazaki, T., Nureki, O., Ito, K. and Akiyama, Y.
  • Organizer: The 3^<rd> International Symposium on Protein Community
  • Place of Presentation: Nara
  • Year and Date: 20100913-16
• [Presentation] 細菌のタンパク質膜透過装置の構造と機能 (2010)
  • Author(s): 森博幸
  • Organizer: 第4階細菌学若手コロッセウム
  • Place of Presentation: 修善寺
  • Year and Date: 20100826-28
• [Presentation] New function of RseP, the E. coli S2P family protease (2010)
  • Author(s): Akiyama, Y.
  • Organizer: Gordon Research Conference on Proteolytic enzymes & their inhibitors
  • Place of Presentation: Lucca, Italy
  • Year and Date: 20100502-07
• [Presentation] Molecular mechanisms of SecA mediated protein translocation (2009)
  • Author(s): 森博幸、塚崎智也、濡木理、伊藤維昭
  • Organizer: 第47回日本生物物理学会年会シンポジウム「タンパク質の膜透過輸送の最前線」
  • Place of Presentation: 徳島
  • Year and Date: 20091030-1101
• [Presentation] バクテリアのタンパク質膜透過装置の構造と機能 (2009)
  • Author(s): 森博幸、塚崎智也、越前友香、濡木理、伊藤維昭
  • Organizer: 第82回日本生化学会大会シンポジウム「タンパク質膜透過装置の構造とダイナミックな機能」
  • Place of Presentation: 神戸
  • Year and Date: 20091021-24
• [Presentation] Functional dissection of bacterial Sec translocation machinery (2009)
  • Author(s): Mori H., Tsukazaki T., Echizen, Y., Ishitani, R., Nureki, O. and Ito, K.
  • Organizer: Innovative Nanoscience of Supermolecular Motor Proteins Working in Biomembranes
  • Place of Presentation: Kyoto, Japan
  • Year and Date: 20090908-10
• [Presentation] 大腸菌RIPプ「直接性、不可逆性を特徴とする新しいシグナル伝達のメカニズム」 (2008)
  • Author(s): 秋山芳展
  • Organizer: 第31回日本神経科学大会
  • Place of Presentation: 東京
  • Year and Date: 20080709-11
• [Presentation] How does SecA ATPase interact with translocon and drive protein translocation? (2008)
  • Author(s): Mori, H.
  • Organizer: G-COE in Chemistry "Frontier of Organelle Dynamics and Protein Functions"
  • Place of Presentation: Nagoya, Japan
  • Year and Date: 20080311-13
• [Presentation] Function and regulation of E. coli membrane metalloproteases (2007)
  • Author(s): Akiyama, Y.
  • Organizer: Gordon Research Conference on Matrix metalloproteinases
  • Place of Presentation: Lucca, Italy
  • Year and Date: 20070603-08
• [Presentation] How does SecA ATPase drive protein translocation? (2007)
  • Author(s): Mori, H. and Ito, K.
  • Organizer: The 14th East Asia Joint Symposium on Biomedical Research
  • Place of Presentation: Tokyo, Japan
  • Year and Date: 2007-11-14
• [Remarks]
  • URL: http://www.virus.kyoto-u.ac.jp/Lab/akiyama/index.html