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Genome wide analysis of translation efficiency by local structure of mRNA and nascent peptide

Research Project

Project/Area Number 24310148
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field System genome science
Research InstitutionKeio University

Principal Investigator

NAKAHIGASHI Kenji  慶應義塾大学, 政策・メディア研究科, 特任准教授 (70322740)

Co-Investigator(Kenkyū-buntansha) MORI Hirotada  奈良先端科学技術大学院大学, バイオサイエンス研究科, 教授 (90182203)
KANAI Akio  慶應義塾大学, 環境情報学部, 教授 (60260329)
Project Period (FY) 2012-04-01 – 2015-03-31
Project Status Completed (Fiscal Year 2014)
Budget Amount *help
¥20,410,000 (Direct Cost: ¥15,700,000、Indirect Cost: ¥4,710,000)
Fiscal Year 2014: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2013: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2012: ¥8,320,000 (Direct Cost: ¥6,400,000、Indirect Cost: ¥1,920,000)
Keywordsリボソームプロファイリング / ゲノム解析技術 / リボソーム / 翻訳 / 翻訳制御 / コドン / 抗生物質
Outline of Final Research Achievements

We performed genome wide analysis of efficiency in mRNA translation to protein, employing new method. We experimentally showed that rate of initiation largely affected the overall efficiency of a gene, while difference in elongation efficiency by codon usage did exist but the effect was much smaller.
We also found new insights in the nature of translation apparatus and factors, such as efficiency of non-canonical codon-anticodon recognition at 3rd letter and translational regulation by sRNA/Hfq, as well as effect of nascent-peptide sequence on specificity of various antibiotics.

Report

(4 results)
  • 2014 Annual Research Report   Final Research Report ( PDF )
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • Research Products

    (12 results)

All 2015 2014 2013 2012

All Journal Article (5 results) (of which Peer Reviewed: 5 results,  Open Access: 2 results,  Acknowledgement Compliant: 1 results) Presentation (7 results) (of which Invited: 1 results)

  • [Journal Article] GenoBase: comprehensive resource database of Escherichia coli K-122015

    • Author(s)
      Otsuka Y, Muto A, Takeuchi R, Okada C, Ishikawa M, Nakamura K, Yamamoto N, Dose H, Nakahigashi K, Tanishima S, Suharnan S, Nomura W, Nakayashiki T, Aref WG, Bochner BR, Conway T, Gribskov M, Kihara D, Rudd KE, Tohsato Y, Wanner BL & Mori H
    • Journal Title

      Nucleic Acids Research

      Volume: 43 Issue: D1 Pages: 606-617

    • DOI

      10.1093/nar/gku1164

    • NAID

      120005830851

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo2014

    • Author(s)
      Nakahigashi K, Takai Y, Shiwa Y, Wada M, Honma M, Yoshikawa H, Tomita M, Kanai A, and Mori H
    • Journal Title

      BMC Genomics

      Volume: 15 Issue: 1 Pages: 1115-1115

    • DOI

      10.1186/1471-2164-15-1115

    • NAID

      120005830843

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] The tRNA Thiolation Pathway Modulates the Intracellular Redox State in Escherichia coli.2013

    • Author(s)
      NakayashikiT., Saito N., Takeuchi R., Kadokura H., Nakahigashi K., Wanner B. L., & Mori H.
    • Journal Title

      J Bacteriol

      Volume: 195 Issue: 9 Pages: 2039-2049

    • DOI

      10.1128/jb.02180-12

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Metabolomic study of Chilean biomining bacteria Acidithiobacillus ferrooxidans strain Wenelen and Acidithiobacillus thiooxidans strain Licanantay2013

    • Author(s)
      Martinez P
    • Journal Title

      Metabolomics

      Volume: 9 Pages: 247-257

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Glycogen is the primary source of glucose during the lag phase of E. coli proliferation2012

    • Author(s)
      Yamamotoya T., Dose H., Tian Z., Faure A., Toya Y., Honma M., Igarashi K., Nakahigashi K., Soga T., Mori H., & Matsuno H
    • Journal Title

      Biochim Biophys Acta

      Volume: 1824 Issue: 12 Pages: 1442-1448

    • DOI

      10.1016/j.bbapap.2012.06.010

    • NAID

      120005615684

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Presentation] 大腸菌の増殖停止・再開と RNA-seq 解析2015

    • Author(s)
      牧 泰史、大塚悠太、上田雅美、和田 明、古池 晶、吉田秀司、中東憲治、森 浩禎
    • Organizer
      第九回ゲノム微生物学会
    • Place of Presentation
      神戸大学(神戸)
    • Year and Date
      2015-03-06 – 2015-03-08
    • Related Report
      2014 Annual Research Report
  • [Presentation] Hfqとデグラドソーム変異によるsRNAとmRNA翻訳への影響2014

    • Author(s)
      松井 求、池田 幸樹、牧野 岳都、志波 優、兼崎 友、吉川 博文、冨田 勝、金井 昭夫、中東 憲治
    • Organizer
      第37回日本分子学会年会
    • Place of Presentation
      パシフィコ横浜(横浜)
    • Year and Date
      2014-11-25 – 2014-11-27
    • Related Report
      2014 Annual Research Report
  • [Presentation] 遺伝子レベル、コドンレベルでの翻訳効率解析2014

    • Author(s)
      中東憲治、高井幸、志波優、兼崎友、吉川博文、森浩禎、冨田勝
    • Organizer
      第8回ゲノム微生物学会年会
    • Place of Presentation
      東京都世田谷区
    • Related Report
      2013 Annual Research Report
  • [Presentation] Ribosome profilingによる翻訳開始部位の精密マッピング2013

    • Author(s)
      中東憲治
    • Organizer
      第7回日本ゲノム微生物学会年会
    • Place of Presentation
      長浜バイオ大学
    • Year and Date
      2013-03-10
    • Related Report
      2012 Annual Research Report
  • [Presentation] Deep Sequence Analysis of the relationship between sRNA- related factors and Dynamic Changes of sRNA Expression in Escherichia coli2013

    • Author(s)
      Motomu Matsui, Yoshiki Ikeda, Gakuto Makino, Masaru Tomita, Akio Kanai, Kenji Nakahigashi
    • Organizer
      JSBi2013
    • Place of Presentation
      東京都江戸川区
    • Related Report
      2013 Annual Research Report
  • [Presentation] Precise mapping of Translational initiation sites by Ribosome profiling2013

    • Author(s)
      Kenji Nakahigashi
    • Organizer
      UK-Japan Systems Microbiology Workshop
    • Place of Presentation
      京都府京都市
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Ribosome profilingと抗生物質の特性を利用した大腸菌翻訳開始部位の再アノテーション2012

    • Author(s)
      中東憲治
    • Organizer
      第35回日本分子生物学会年会
    • Place of Presentation
      福岡国際会議場・マリンメッセ福岡
    • Year and Date
      2012-12-11
    • Related Report
      2012 Annual Research Report

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Published: 2012-04-24   Modified: 2019-07-29  

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