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

• Project/Area Number: 24310148
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: System genome science
• Research Institution: Keio 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: ¥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.

Research Products

• [Journal Article] GenoBase: comprehensive resource database of Escherichia coli K-12 (2015)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo (2014)
  • 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
  • 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
  • Peer Reviewed
• [Journal Article] Metabolomic study of Chilean biomining bacteria Acidithiobacillus ferrooxidans strain Wenelen and Acidithiobacillus thiooxidans strain Licanantay (2013)
  • Author(s): Martinez P
  • Journal Title: Metabolomics Volume: 9 Pages: 247-257
  • Peer Reviewed
• [Journal Article] Glycogen is the primary source of glucose during the lag phase of E. coli proliferation (2012)
  • 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
  • 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
• [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
• [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
• [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
• [Presentation] Deep Sequence Analysis of the relationship between sRNA- related factors and Dynamic Changes of sRNA Expression in Escherichia coli (2013)
  • 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
• [Presentation] Precise mapping of Translational initiation sites by Ribosome profiling (2013)
  • Author(s): Kenji Nakahigashi
  • Organizer: UK-Japan Systems Microbiology Workshop
  • Place of Presentation: 京都府京都市
  • 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