• Search Research Projects
  • Search Researchers
  • How to Use
  1. Back to previous page

Comprehensive analysis of protein turnover

Research Project

Project/Area Number 20310117
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field 基礎ゲノム科学
Research InstitutionKeio University

Principal Investigator

NAKAHIGASHI Kenji  Keio University, 政策・メディア研究科, 准教授 (70322740)

Co-Investigator(Kenkyū-buntansha) ISHIHAMA YASUSHI  京都大学, 大学院・薬学研究科, 教授 (30439244)
Project Period (FY) 2008 – 2010
Project Status Completed (Fiscal Year 2010)
Budget Amount *help
¥18,590,000 (Direct Cost: ¥14,300,000、Indirect Cost: ¥4,290,000)
Fiscal Year 2010: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2009: ¥6,760,000 (Direct Cost: ¥5,200,000、Indirect Cost: ¥1,560,000)
Fiscal Year 2008: ¥7,540,000 (Direct Cost: ¥5,800,000、Indirect Cost: ¥1,740,000)
Keywordsゲノム発現 / タンパク質ターンオーバー / 翻訳 / タンパク質分解 / 翻訳郊率 / プロテオミクス / 大腸菌 / タンパク質代謝 / 分子遺伝学 / マルチオミクス
Research Abstract

We have developed methods to comprehensively quantify cellular protein turnover, including synthesis rate, degradation rate and translation efficiency of corresponding mRNA. Using these methods we quantified turnover of more than 1500 protein in E. coli, and found that most of the protein, excluding about 5% of unstable protein, were quite stable without any degradation. Upon transition from anaerobic to aerobic growth condition, levels of metabolic enzymes changes dramatically. However these changes are brought mostly by changes in synthesis rate but no apparent degradation of unwanted enzymes in central carbon metabolism were observed.

Report

(4 results)
  • 2010 Annual Research Report   Final Research Report ( PDF )
  • 2009 Annual Research Report
  • 2008 Annual Research Report
  • Research Products

    (28 results)

All 2010 2009 2008 Other

All Journal Article (9 results) (of which Peer Reviewed: 8 results) Presentation (16 results) Book (2 results) Remarks (1 results)

  • [Journal Article] A systematic survey of in vivo obligate chaperonin-dependent substrates.2010

    • Author(s)
      Fujiwara K, Ishihama Y, Nakahigashi K, Soga T, Taguchi H
    • Journal Title

      EMBO J 29(9)

      Pages: 1552-1564

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] 13C-metabolic flux analysis for batch culture of Escherichia coli and its Pyk and Pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites2010

    • Author(s)
      Toya Y, Ishii N, Nakahigashi K, Hirasawa T, Soga T, Tomita M, Shimizu K
    • Journal Title

      Biotechnol Prog 26(4)

      Pages: 975-992

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] 13C-metabolic flux analysis for batch culture of Escherichia coli and its Pyk and Pgi gene knockout mutants based on mass iso topomer distribution of intracellular metabolites.2010

    • Author(s)
      Toya Y
    • Journal Title

      Biotechno Prog.

      Volume: 26 Pages: 975-992

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A systematic survey of in vivo obligate chaperonin-dependent substrates2010

    • Author(s)
      Fujiwara, K.
    • Journal Title

      EMBO J. (Epub ahead of print)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism2009

    • Author(s)
      Nakahigashi K, Toya Y, Ishii N, Soga T, Hasegawa M, Watanabe H, Takai Y, Honma M, Mori H, Tomita M
    • Journal Title

      Mol Syst Biol 5

      Pages: 306-306

    • NAID

      120005830850

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Update on the Keio collection of Escherichia coli single-gene deletion mutants2009

    • Author(s)
      Yamamoto N, Nakahigashi K, Nakamichi T, Yoshino M, Takai Y, Touda Y, Furubayashi A, Kinjyo S, Dose H, Hasegawa M, Datsenko KA, Nakayashiki T, Tomita M, Wanner BL, Mori H
    • Journal Title

      Mol Syst Biol 5

      Pages: 335-335

    • NAID

      120005830849

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism2009

    • Author(s)
      中東憲治
    • Journal Title

      Molecular Systems Biology 5

      Pages: 306-306

    • NAID

      120005830850

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Update on the Keio collection of Escherichia coli single-gene deletion mutants2009

    • Author(s)
      Yamamoto, N.
    • Journal Title

      Molecular Systems Biology 5

      Pages: 335-335

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] マルチオミクス解析で見えてきた大腸菌の遺伝・環境変化に対する応答機構2009

    • Author(s)
      中東憲治
    • Journal Title

      遺伝子医学MOOK 16

      Pages: 152-158

    • Related Report
      2009 Annual Research Report
  • [Presentation] Degradation and turnover of protein in growing and non-growing E. coli cell after environmental perturbation.2010

    • Author(s)
      Kenji Nakahigashi, Yasushi Ishihama, Toya Yoshihiro, Masaru Tomita
    • Organizer
      BMB2010
    • Place of Presentation
      神戸
    • Year and Date
      2010-12-09
    • Related Report
      2010 Final Research Report
  • [Presentation] 増殖、非増殖状態におけるタンパク質ターンオーバーの環境変化に伴う変化2010

    • Author(s)
      中東憲治
    • 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
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2010-12-09
    • Related Report
      2010 Annual Research Report
  • [Presentation] 大腸菌の栄養環境応答のトランスクリプトーム2010

    • Author(s)
      牧泰史
    • 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
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2010-12-09
    • Related Report
      2010 Annual Research Report
  • [Presentation] ゲノムデザイン学:人工解糖系オペロンによるオペロン構築原理の解明2010

    • Author(s)
      柘植謙爾
    • 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
    • Place of Presentation
      神戸ポートアイランド
    • Year and Date
      2010-12-08
    • Related Report
      2010 Annual Research Report
  • [Presentation] Comprehensive analysis of protein turnover (and its effect on metabolic simulation).2010

    • Author(s)
      Kenji Nakahigashi
    • Organizer
      UK-Japan Symposium of Systems and Synthetic Biology
    • Place of Presentation
      Guildford UK
    • Year and Date
      2010-09-14
    • Related Report
      2010 Final Research Report
  • [Presentation] Comprehensive analysis of protein turnover2010

    • Author(s)
      Nakahigashi, K
    • Organizer
      UK-Japan Systems & Synthetic Biology workshop
    • Place of Presentation
      Surrey大学(英国)(招待講演)
    • Year and Date
      2010-09-14
    • Related Report
      2010 Annual Research Report
  • [Presentation] Comprehensive analysis of protein turnover in aerobic and anaerobic continuous culture of E. coli2009

    • Author(s)
      中東憲治, 石濱泰, 本間雅之, 高井幸, 冨田勝
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2009-12-11
    • Related Report
      2010 Final Research Report
  • [Presentation] Comprehensive analysis of protein turnover in aerobic and an aerobic continuous culture of E.coli2009

    • Author(s)
      中東憲治
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜
    • Year and Date
      2009-12-11
    • Related Report
      2009 Annual Research Report
  • [Presentation] Systematic phenome analysis of E. coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism2009

    • Author(s)
      Kenji Nakahigashi
    • Organizer
      UK-Japan Symposium of Systems Biology
    • Place of Presentation
      Osaka
    • Year and Date
      2009-09-23
    • Related Report
      2010 Final Research Report
  • [Presentation] Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism2009

    • Author(s)
      中東憲治
    • Organizer
      UK-Japan Workshop on Systems Biology
    • Place of Presentation
      コスモスクエア国際交流センター大阪
    • Year and Date
      2009-09-23
    • Related Report
      2009 Annual Research Report
  • [Presentation] Robustness of bacterial metabolic network. Views from multi-omics analysis2008

    • Author(s)
      Kenji Nakahigashi
    • Organizer
      Seminar at Center for Mathematical Modeling, University of Chile
    • Place of Presentation
      サンチアゴ, チリ国
    • Year and Date
      2008-12-27
    • Related Report
      2008 Annual Research Report
  • [Presentation] Robustness of bacterial metabolic network. Views from Multi-Omics analysis.2008

    • Author(s)
      Kenji Nakahigashi
    • Organizer
      Design and Engineering of Microbial Genomes Academia Sinica Workshop
    • Place of Presentation
      Taipei, Taiwan
    • Year and Date
      2008-11-26
    • Related Report
      2010 Final Research Report
  • [Presentation] Robustness of bacterial metabolic network. Views from Multi-Omics analysis.2008

    • Author(s)
      Kenji Nakahigashi
    • Organizer
      Design and Engineering of Microbial Genomes
    • Place of Presentation
      中央研究院, 台北, 台湾
    • Year and Date
      2008-11-26
    • Related Report
      2008 Annual Research Report
  • [Presentation] Multi-Omics解析からてくるバクテリア代謝の頑強性2008

    • Author(s)
      中東憲治
    • Organizer
      第18回玉川微生物資源ワークショップ
    • Place of Presentation
      三島
    • Year and Date
      2008-10-31
    • Related Report
      2010 Final Research Report
  • [Presentation] Protein-turnoveromics ; global analyses of protein turnover in E. coli2008

    • Author(s)
      Kenji Nakahigashi, Yasushi Ishihama, Nobuyuki Ishii, Masaru Tomita
    • Organizer
      IECA2008
    • Place of Presentation
      Hixton UK
    • Year and Date
      2008-09-26
    • Related Report
      2010 Final Research Report
  • [Presentation] Protein turnover-omics : Comprehensive analysis of protein turnover in E. coli.2008

    • Author(s)
      Kenji Nakahigashi
    • Organizer
      International E. coli Alliance for Systerns Biology
    • Place of Presentation
      イギリス・ケンブリッジ
    • Year and Date
      2008-09-25
    • Related Report
      2008 Annual Research Report
  • [Book] In Systems biology and biotechnology of Escherichia coli.(Yup LS ed)(Resources for Escherichia coli Systems Biology)2009

    • Author(s)
      Mori H, Yamamoto N, Dose H, Nakahigashi K, Datsenko KA, Wanner BL
    • Publisher
      Springer
    • Related Report
      2010 Final Research Report
  • [Book] 遺伝子医学MOOK(マルチオミクス(multi-omics)解析で見えてきた大腸菌の遺伝・環境変化に対する応答機構, 16)

    • Author(s)
      中東憲治、冨田勝
    • Publisher
      株式会社メディカルドウ
    • Related Report
      2010 Final Research Report
  • [Remarks] 現在、ecoli multiomics-database上に、可視化したデータを公開する準備中である

    • URL

      http://ecoli.iab.keio.ac.jp/

    • Related Report
      2010 Final Research Report

URL: 

Published: 2008-04-01   Modified: 2016-04-21  

Information User Guide FAQ News Terms of Use Attribution of KAKENHI

Powered by NII kakenhi