Nascent chain biology

2012 Fiscal Year Final Research Report

• Project/Area Number: 20247020
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Molecular biology
• Research Institution: Kyoto Sangyo University (2009-2012); Kyoto University (2008)
• Principal Investigator: ITO Koreaki 京都産業大学, 総合生命科学部, 教授 (90027334)
• Co-Investigator(Kenkyū-buntansha): CHIBA Shinobu 京都産業大学, 総合生命科学部, 助教 (20523517)
• Co-Investigator(Renkei-kenkyūsha): AKIYAMA Yoshinori 京都大学, ウイルス研究所, 教授 (10192460) ; MORI Hiroyuki 京都大学, ウイルス研究所, 准教授 (10243271)
• Project Period (FY): 2008 – 2012
• Keywords: 翻訳

Research Abstract

We develop a new area of research, which might be called“nascent chain biology” by addressing a concept that translation elongation speed isfine-tuned by the amino acid sequences of the nascent polypeptide as well as bydynamic behaviors of the extra-ribosomal portion of the same nascent chain. Weidentified regulatory nascent polypeptides such as SecM and MifM that function inaccordance with this principle and studied molecular mechanisms and physiologicaloutcomes of the regulation. Also, we have developed an experimental method thatenables us to display cellular polypeptidyl-tRNAs, obligatory but poorly studiedintermediates in translation, which we have proposed to call "nascentome".

Research Products

• [Journal Article] Arrest peptides:cis-acting modulators of translation (2013)
  • Author(s): Ito, K., and Chiba, S
  • Journal Title: Annu. Rev. Biochem Volume: (in press) Pages: 82
  • Peer Reviewed
• [Journal Article] Multisite ribosomalstalling: a unique mode of regulatorynascent chain action revealed for MifM (2012)
  • Author(s): Chiba, S. and Ito, K.
  • Journal Title: Mol. Cell Volume: 47 Pages: 863-872
  • DOI: DOI:10.1016/j.molcel.2012.06.034
  • Peer Reviewed
• [Journal Article] ArfA recruits release factor 2 to rescuestalled ribosomes by peptidyl-tRNAhydrolysis in Escherichia coli (2012)
  • Author(s): Chadani, Y., Ito, K., Kutsukake, K. and Abo T
  • Journal Title: Mol. Microbiol. Volume: 86 Pages: 37-50
  • DOI: DOI:10.1111/j.1365-2958.2012.08190.x
  • Peer Reviewed
• [Journal Article] Nascentomea nalysis uncovers futile protein synthesis inEscherichia 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
  • DOI: DOI:10.1371/journal.pone.0028413
  • Peer Reviewed
• [Journal Article] Post-liberation cleavage ofsignal peptides is catalyzed by the site-2protease (S2P) in bacteria (2011)
  • Author(s): Saito, A., Hizukuri, Y., Matsuo, E., Chiba,S., Mori, H., Nishimura, O., Ito, K. andAkiyama, Y.
  • Journal Title: Proc.Natl. Acad. Sci. USA Volume: 108 Pages: 13740-13745
  • DOI: DOI:10.1073/pnas.1108376108
  • Peer Reviewed
• [Journal Article] Structure andfunction of a membrane component SecDF that enhances protein export (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
  • DOI: DOI:10.1038/nature09980
  • Peer Reviewed
• [Journal Article] Recruitment of a species-specific translational arrest moduleto 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
  • DOI: DOI:10.1016/j.molcel.2012.06.034
  • Peer Reviewed
• [Journal Article] A translational pause tolocalize (2011)
  • Author(s): Ron, D. and Ito, K.
  • Journal Title: Science Volume: 331 Pages: 543-544
  • DOI: DOI:10.1126/science.1202075
• [Journal Article] Divergent stalling sequences sense andcontrol cellular physiology (2010)
  • Author(s): Ito, K., Chiba, S. and Pogliano, K.
  • Journal Title: Biochem. Biophys. Res. Commun. Volume: 393 Pages: 1-5
  • DOI: DOI:10.1016/j.bbrc.2010.01.073
  • Peer Reviewed
• [Journal Article] Aribosome-nascent chain sensor of membrane protein biogenesis in Bacillus subtilis (2009)
  • Author(s): Chiba, S., Lamsa, A. and Pogliano, K.
  • Journal Title: EMBO J Volume: 28 Pages: 3461-3475
  • DOI: DOI:10.1038/emboj.2009.280
  • Peer Reviewed
• [Journal Article] Dynamic nature of disulphide bondformation catalysts revealed by crystalstructures of DsbB (2009)
  • Author(s): Inaba, K., Murakami, S., Nakagawa, A., Iida,H. Kinjo, M., Ito, K. and Suzuki, M.
  • Journal Title: EMBO J. Volume: 28 Pages: 779-791
  • DOI: DOI:10.1038/emboj.2009.21
  • Peer Reviewed
• [Journal Article] Editing disulphide bonds: errorcorrection using redox currencies (2009)
  • Author(s): Ito, K.
  • Journal Title: Mol Microbiol Volume: 75 Pages: 1-5
  • DOI: DOI:10.1111/j.1365-2958.2009.06953.x
  • 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
  • DOI: DOI:10.1038/nature07421
  • Peer Reviewed
• [Journal Article] Peptidyl-prolyl-tRNA at the ribosomal P site reacts poorly withpuromycin (2008)
  • Author(s): Muto, H. and Ito, K.
  • Journal Title: Biochem. Biophys.Res. Commun. Volume: 366 Pages: 1043-1047
  • DOI: DOI:10.1016/j.bbrc.2007.12.072
  • Peer Reviewed
• [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
  • DOI: DOI:10.1074/jbc.M709984200
  • Peer Reviewed
• [Journal Article] Structure andmechanisms of the DsbB-DsbA disulfide generation machine (2008)
  • Author(s): Inaba, K. and Ito, K.
  • Journal Title: Biochim.Biophys. Acta. Volume: 1783 Pages: 520-529
  • DOI: DOI:10.1016/j.bbamcr.2007.11.006
  • Peer Reviewed
• [Journal Article] The disulfide bondformation (Dsb) system. (2008)
  • Author(s): Ito, K. and Inaba, K.
  • Journal Title: Curr.Opinion Struct. Biol. Volume: 18 Pages: 450-458
  • DOI: DOI:10.1016/j.sbi.2008.02.002
  • Peer Reviewed
• [Journal Article] Apair of circularly permutated PDZ domainscontrol RseP, the S2P family intramembraneprotease of Escherichia 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
  • DOI: DOI:10.1074/jbc.M806603200
  • Peer Reviewed
• [Presentation] Analysis of cellularpolypeptidyl-tRNAs (2012)
  • Author(s): Ito, K.
  • Organizer: SFB594-3rdInternational Symposium "MolecularMachines in Protein Folding andTranslocation"
  • Place of Presentation: Bavarian Academy of Sciences, Munich, Germany
  • Year and Date: 20120723-25
• [Presentation] 合成途上鎖の働きと運命 (2012)
  • Author(s): 千葉志信、伊藤維昭
  • Organizer: 12回蛋白質科学会年会
  • Place of Presentation: 名古屋
  • Year and Date: 20120620-22
• [Presentation] Analysis of "nascentome", cellularpolypeptidyl-tRNAs (2012)
  • Author(s): Ito, K.
  • Organizer: CECAM Workshop"Ribosome-associated protein folding:Translation, auxiliary factors, andtranslocation"
  • Place of Presentation: Lausanne,Switzerland.
  • Year and Date: 20120529-31
• [Presentation] 翻訳のスピード制御について.独創的発想に富む科学者育成プログラム「出る杭を伸ばすヘリックスプロジェクト」採択事業 (2012)
  • Author(s): 伊藤維昭
  • Organizer: 七人の侍による記念講演会
  • Place of Presentation: 秋田
  • Year and Date: 2012-10-24
• [Presentation] 合成途上鎖のバイオロジー (2012)
  • Author(s): 伊藤維昭
  • Organizer: 九州大学グローバルCOEプログラム理医連携特別講演会
  • Place of Presentation: 福岡市
  • Year and Date: 2012-02-29
• [Presentation] In vitro study oftranslation arrest of MifM, a regulatorynascent chain that monitors membrane proteinbiogenesis in Bacillus subtilis (2011)
  • Author(s): Chiba, S., Kanomori, T., Ueda, T., Akiyama,Y., Pogliano, K. and Ito, K.
  • Organizer: 第34回日本分子生物学会年会 Symposium "RegulatorySystems Mediated by ProgrammedRibosomal Stalling"
  • Place of Presentation: 横浜
  • Year and Date: 20111213-16
• [Presentation] Vsualization ofcellular polypeptidyl-tRNAs uncovers futileprotein synthesis in E. coli (2011)
  • Author(s): Ito, K., Chadani, Y., Nakamori, K., Chiba, S.,Akiyma, Y. and Abo, T.
  • Organizer: Cold SpringHarbor Asia Conference Protein Homeostasisin Health and Disease
  • Place of Presentation: Suzhou, China
  • Year and Date: 20110926-30
• [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] Structure, function and regulation ofbacterial Sec machinery (2011)
  • Author(s): Ito, K., Tsukazaki, T., Mori, H. and Nureki,O
  • Organizer: International Unionof Microbiological Societies 2011 Congress.Symposium Bacterial Protein Transport
  • Place of Presentation: Sapporo
  • Year and Date: 20110906-10
• [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:Invitro再構成系によるアプローチ」
  • Place of Presentation: 大阪
  • Year and Date: 20110607-09
• [Presentation] Controlling epigenetic connectivity inproteins (2011)
  • Author(s): Ito, K.
  • Organizer: Microbial Genetics and GenomicsIV
  • Place of Presentation: Harvard MedicalSchool, Boston, U.S.A.
  • Year and Date: 20110429-0501
• [Presentation] タンパク質誕生の初期における出来事 (2011)
  • Author(s): 伊藤維昭
  • Organizer: 京都産業大学総合生命科学部開設記念シンポジウム
  • Place of Presentation: 京都市
  • Year and Date: 2011-03-10
• [Presentation] From SecY to nascent chain biology (2010)
  • Author(s): Ito, K.
  • Organizer: International Symposium on Protein Community
  • Place of Presentation: Nara(Japan)
  • Year and Date: 20100913-16
• [Presentation] Visualizing dynamic nascentome of the cell (2010)
  • Author(s): Ito, K., Chiba, S., Akiyama, Y. and Abo, T.
  • Organizer: FASEB Summer Research Conference Protein Folding in the Cell
  • Place of Presentation: Saxtons River, Vermont (USA)
  • Year and Date: 20100725-30
• [Presentation] Structure, function and regulation of the Sec translocation system (2010)
  • Author(s): Ito, K.
  • Organizer: International Symposium "Life of Proteins" in Honor of the 1st Retirement of Professor Kazuhiro Nagata
  • Place of Presentation: Kyoto (Japan).
  • Year and Date: 2010-03-18
• [Presentation] Sec膜透過装置の構造 (2009)
  • Author(s): 伊藤維昭、森博幸、塚崎智也、濡木理
  • Organizer: 機能および制御九州大学P&P合同公開シンポジウム「生命活動を制御する高次複合体の構造と機能」
  • Place of Presentation: 福岡
  • Year and Date: 20091222-23
• [Presentation] Structure of bacterial SecY transloconand its interaction with SecA (2008)
  • Author(s): Ito, K.
  • Organizer: Beckwith Reunion Meeting "Microbial Genetics andGenomics"
  • Place of Presentation: Cassis, France
  • Year and Date: 20080516-19
• [Presentation] Quality control pathways used tomonitor membrane protein abnormalities androles of translocon in the correct biogenesis ofmembrane proteins (2008)
  • Author(s): Ito, K.
  • Organizer: Symposium "Insertion,Folding, Assembly and Quality Control",108th ASM General Meeting
  • Place of Presentation: Boston,U.S.A.
  • Year and Date: 2008-06-05
• [Book] Handbook of Proteolytic Enzymes 3rd ed(ed. Rawlings, N. D. and Salvesen, G.) (2013)
  • Author(s): Akiyama, Y., and Ito, K. HtpX.
  • Total Pages: 683-685
  • Publisher: Academic Press
• [Book] Handbook ofProteolytic Enzymes 3rd ed. (ed. Rawlings,N. D. and Salvesen, G.) (2013)
  • Author(s): Hizukuri, Y., Ito, K., and Akiyama, Y.RseP.
  • Total Pages: 1545-1550
  • Publisher: Academic Press
• [Book] in Bacterial Secreted Proteins, Ed. K. Wooldridge,Caister Academic Press, Norfolk, UK (2009)
  • Author(s): Ito, K. and Mori, H.
  • Total Pages: 3-22
  • Publisher: The Sec proteinsecretion system.
• [Remarks]
  • URL: http://www.cc.kyoto-su.ac.jp/~k4563/index-j.html