Functions and mechanisms of functional nascent chains

• Project Area: Nascent-chain Biology
• Project/Area Number: 26116008
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Kyoto Sangyo University
• Principal Investigator: Chiba Shinobu 京都産業大学, 総合生命科学部, 准教授 (20523517)
• Co-Investigator(Kenkyū-buntansha): 伊藤 維昭 京都産業大学, 研究機構, シニアリサーチフェロー (90027334)
• Project Period (FY): 2014-07-10 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥90,220,000 (Direct Cost: ¥69,400,000、Indirect Cost: ¥20,820,000); Fiscal Year 2018: ¥15,210,000 (Direct Cost: ¥11,700,000、Indirect Cost: ¥3,510,000); Fiscal Year 2017: ¥15,210,000 (Direct Cost: ¥11,700,000、Indirect Cost: ¥3,510,000); Fiscal Year 2016: ¥15,210,000 (Direct Cost: ¥11,700,000、Indirect Cost: ¥3,510,000); Fiscal Year 2015: ¥15,080,000 (Direct Cost: ¥11,600,000、Indirect Cost: ¥3,480,000); Fiscal Year 2014: ¥29,510,000 (Direct Cost: ¥22,700,000、Indirect Cost: ¥6,810,000)
• Keywords: 翻訳アレスト / リボソーム / 機能性新生鎖 / タンパク質局在化 / 新生鎖 / 蛋白質局在化

Outline of Final Research Achievements

We have studied regulatory nascent chains such as B. subtilis MifM and E. coli SecM. We collaborated with structural biologists to determine the structure of the MifM-ribosome complexes. Our genetic analysis revealed that MifM interacts with the ribosome, extensively, including the ribosomal surface to arrest translation. We also found that the release of the elongation arrest of MifM depends on the hydrophilic cavity of the membrane protein insertion factor YidC.

Academic Significance and Societal Importance of the Research Achievements

タンパク質は合成が完了した後に生理機能を発揮するのが一般的であるが、合成の途上でのみ生理機能を発揮する風変わりなタンパク質が近年見出された。本研究で対象とした枯草菌MifMや大腸菌SecMもそのような因子である。これらの因子は、自身の合成を途中で一時停止することで生理機能を発揮する。本研究では、構造学、生化学、遺伝学的手法を駆使してその分子機構の解明を目指した。その結果、これらの因子とタンパク質合成装置リボソームとの相互作用様式の詳細が明らかとなった。これらの因子がどうやって合成途上で機能を発揮するのかという基本的な問題を理解する上で意義深いものとなった。

Research Products

• [Int'l Joint Research] University of Hambrug/University of Munich(ドイツ)
• [Int'l Joint Research] ミュンヘン大学(ドイツ)
• [Journal Article] Heat shock transcription factor σ³² defective in membrane transport can be suppressed by transposon insertion into genes encoding a restriction enzyme subunit or a putative autotransporter in <i>Escherichia coli</i> (2018)
  • Author(s): Yura Takashi、Miyazaki Ryoji、Fujiwara Keigo、Ito Koreaki、Chiba Shinobu、Mori Hiroyuki、Akiyama Yoshinori
  • Journal Title: Genes & Genetic Systems Volume: 93 Issue: 6 Pages: 229-235
  • DOI: 10.1266/ggs.18-00040
  • NAID: 130007582071
  • ISSN: 1341-7568, 1880-5779
  • Year and Date: 2018-12-01
  • Peer Reviewed
• [Journal Article] Regulation of cellular functions by regulatory arrest peptides (2018)
  • Author(s): 千葉 志信
  • Journal Title: 生化学 Volume: 90 Issue: 2 Pages: 147-157
  • DOI: 10.14952/SEIKAGAKU.2018.900147
  • NAID: 40021617371
  • ISSN: 0037-1017
  • Year and Date: 2018-04-25
• [Journal Article] MifM-instructed translation arrest involves nascent chain interactions with the exterior as well as the interior of the ribosome (2018)
  • Author(s): Fujiwara Keigo、Ito Koreaki、Chiba Shinobu
  • Journal Title: Scientific Reports Volume: 8 Issue: 1 Pages: 1-12
  • DOI: 10.1038/s41598-018-28628-y
  • Peer Reviewed / Open Access
• [Journal Article] Monitoring substrate enables real-time regulation of a protein localization pathway (2018)
  • Author(s): Ito Koreaki、Mori Hiroyuki、Chiba Shinobu
  • Journal Title: FEMS Microbiology Letters Volume: 365 Issue: 11 Pages: 1-11
  • DOI: 10.1093/femsle/fny109
  • Peer Reviewed
• [Journal Article] 終止コドンに依らず翻訳を途中終了させる酸性アミノ酸の連続配列 (2018)
  • Author(s): 田口英樹、茶谷悠平、千葉志信、伊藤維昭
  • Journal Title: B&I Volume: 76 Pages: 239-241
  • NAID: 40021578678
• [Journal Article] 翻訳途上の新生ポリペプチド鎖が引き起こすリボソームの不安定化とその生理的意義 (2018)
  • Author(s): 茶谷悠平、千葉志信、伊藤維昭、田口英樹
  • Journal Title: 実験医学 Volume: 36 Pages: 1364-1367
• [Journal Article] Intrinsic Ribosome Destabilization Underlies Translation and Provides an Organism with a Strategy of Environmental Sensing (2017)
  • Author(s): Chadani Yuhei、Niwa Tatsuya、Izumi Takashi、Sugata Nobuyuki、Nagao Asuteka、Suzuki Tsutomu、Chiba Shinobu、Ito Koreaki、Taguchi Hideki
  • Journal Title: Molecular Cell Volume: 68 Issue: 3 Pages: 528-539
  • DOI: 10.1016/j.molcel.2017.10.020
  • Peer Reviewed
• [Journal Article] Integrated in vivo and in vitro nascent chain profiling reveals widespread translational pausing. (2016)
  • Author(s): Chadani Y, Niwa T, Chiba S, Taguchi, H., Ito K.
  • Journal Title: Proc Natl Acad Sci USA. Volume: 113 Issue: 7
  • DOI: 10.1073/pnas.1520560113
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Hydrophilic microenvironment required for the channel-independent insertase function of YidC protein. (2015)
  • Author(s): Shimokawa-Chiba, N., Kumazaki, K., Tsukazaki, T., Nureki, O., Ito, K. and Chiba, S.
  • Journal Title: Proc. Natl. Acad. Sci. USA. Volume: 112 Issue: 16 Pages: 5063-5068
  • DOI: 10.1073/pnas.1423817112
  • NAID: 120005716850
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling. (2015)
  • Author(s): Sohmen, D., Chiba, S., Shimokawa-Chiba, N., Innis, A., Berninghausen, O., Beckmann, R., Ito, K. and Wilson, D.
  • Journal Title: Nat. Commun. Volume: 6 Issue: 1 Pages: 6941-6941
  • DOI: 10.1038/ncomms7941
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Nascent chain-monitored remodeling of the Sec machinery for salinity adaptation of marine bacteria (2015)
  • Author(s): Ishii, E., Chiba, S., Hashimoto, N., Kojima, S., Homma, M., Ito, K., Akiyama, Y. and Mori, H.
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 112 Issue: 40
  • DOI: 10.1073/pnas.1513001112
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] MifM monitors total YidC activities of Bacillus subtilis including that of YidC2, the target of regulation. (2015)
  • Author(s): Chiba, S. and Ito, K
  • Journal Title: J Bacteriol Volume: 197 Issue: 1 Pages: 99-107
  • DOI: 10.1128/jb.02074-14
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Identification of a SecM segment required for export-coupled release from elongation arrest. (2014)
  • Author(s): Nakamori, K., Chiba, S. and Ito, K.
  • Journal Title: FEBS Lett. Volume: 588 Issue: 17 Pages: 3098-3103
  • DOI: 10.1016/j.febslet.2014.06.038
  • Peer Reviewed / Acknowledgement Compliant
• [Presentation] Identification and characterization of novel translation-arrest peptides in bacteria (2018)
  • Author(s): 千葉志信
  • Organizer: International symposium Proteins; from the cradle to the grave
  • Int'l Joint Research
• [Presentation] Things that I am proud of, ...or rather trivial? (2018)
  • Author(s): 伊藤維昭
  • Organizer: International symposium Proteins; from the cradle to the grave
  • Int'l Joint Research / Invited
• [Presentation] 新規翻訳アレスト因子の探索 (2018)
  • Author(s): 千葉志信
  • Organizer: ２０１８年度グラム陽性菌ゲノム機能会議
• [Presentation] Characterization of novel translation-arrest peptides encoded upstream of genes for protein localization machinery (2018)
  • Author(s): 千葉志信
  • Organizer: CSHL meeting: Translational control
  • Int'l Joint Research
• [Presentation] Monitoring substrate enables real-time regulation of a protein localization pathway (2018)
  • Author(s): 伊藤維昭
  • Organizer: "BACTERIAL PROTEIN EXPORT 2018"
  • Int'l Joint Research
• [Presentation] Translation-arrest peptides encoded upstream of genes for protein localization machinery (2018)
  • Author(s): 千葉志信
  • Organizer: "BACTERIAL PROTEIN EXPORT 2018"
  • Int'l Joint Research
• [Presentation] 新規調節性アレストペプチドの探索 (2018)
  • Author(s): 千葉志信
  • Organizer: 第41回日本分子生物学会年会
• [Presentation] Studying co-translational protein dynamics using force-sensing arrest peptides (2018)
  • Author(s): 伊藤維昭
  • Organizer: RIBOSOME 2019 meeting
  • Int'l Joint Research
• [Presentation] Nascent polypeptide handling of the translating ribosome (2017)
  • Author(s): 伊藤維昭
  • Organizer: Microbial Genetics and Genomics VII
  • Int'l Joint Research
• [Presentation] Screening of translation arrest-releasable elements (2017)
  • Author(s): 千葉志信
  • Organizer: 新学術領域「新生鎖の生物学」主催・国際シンポジウム「Protein Quality Control」
  • Int'l Joint Research
• [Presentation] トランスロコンから翻訳に立ち返って（Revisiting translation after the translocon） (2017)
  • Author(s): 伊藤維昭
  • Organizer: 第１７回日本蛋白質科学会年会
  • Invited
• [Presentation] MifMの翻訳アレストを解除できる因子のスクリーニング (2017)
  • Author(s): 藤原圭吾、樫祐太朗、伊藤維昭、千葉志信
  • Organizer: 2017年度グラム陽性菌ゲノム機能会議
• [Presentation] Screening of Translation Arrest-Releasable Elements (2017)
  • Author(s): 藤原圭吾、樫祐太朗、伊藤維昭、千葉志信
  • Organizer: 新学術領域「新生鎖の生物学」若手ワークショップ2017
• [Presentation] 生命を支える動的翻訳とタンパク質の一生 (2017)
  • Author(s): 伊藤維昭
  • Organizer: アイエム翻訳サービス株式会社主催 第３回医薬翻訳セミナー
  • Invited
• [Presentation] Nascent polypeptide handling of the translating ribosome (2017)
  • Author(s): 伊藤維昭
  • Organizer: THE INs-and-OUTs OF MEMBRANE BIOLOGY
  • Int'l Joint Research / Invited
• [Presentation] タンパク質誕生の秘密 (2017)
  • Author(s): 伊藤維昭
  • Organizer: 大隅良典氏ノーベル賞受賞記念「七人の侍」講演会
  • Invited
• [Presentation] 遺伝情報の翻訳に携わる分子の自律性 (2016)
  • Author(s): 伊藤維昭
  • Organizer: 第39回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2016-11-30
  • Invited
• [Presentation] チャネル非依存的タンパク質膜挿入装置YidCの分子機構解明に向けて (2016)
  • Author(s): 千葉志信、下川（千葉）直美、美濃部隼、伊藤維昭
  • Organizer: 第89回日本生化学会大会
  • Place of Presentation: 東北大学
  • Year and Date: 2016-09-25
  • Invited
• [Presentation] 自身の翻訳伸長を制御する枯草菌MifMの分子機構と生理機能 (2016)
  • Author(s): 千葉志信、Daniel Sohmen、Daniel Wilson、藤原圭吾、下川（千葉）直美、伊藤維昭
  • Organizer: 第4回リボソームミーティング
  • Place of Presentation: 大阪医大
  • Year and Date: 2016-09-17
• [Presentation] 上流ORFによる翻訳アレストを介したタンパク質膜組込装置のモニタリングと発現調節 (2016)
  • Author(s): 千葉志信
  • Organizer: 日本遺伝学会第88回大会
  • Place of Presentation: 三島
  • Year and Date: 2016-09-07
  • Invited
• [Presentation] A nascent chain-based reporter to study the mechanism of membrane protein insertion (2016)
  • Author(s): Naomi Shimokawa-Chiba, Shun Minobe, Koreaki Ito, Shinobu Chiba
  • Organizer: Nascent Chain Biology Meeting 2016
  • Place of Presentation: 河口湖
  • Year and Date: 2016-09-01
  • Int'l Joint Research
• [Presentation] Dynamic translation entails nascent polypeptides as active players in gene regulation and protein biogenesis. (2016)
  • Author(s): Koreaki Ito
  • Organizer: Nascent Chain Biology Meeting 2016.
  • Place of Presentation: 河口湖
  • Year and Date: 2016-09-01
  • Int'l Joint Research / Invited
• [Presentation] Nascent chain-mediated monitoring of protein localization machineries. (2016)
  • Author(s): Shinobu Chiba, Eiji Ishii, Yoshinori Akiyama, Koreaki Ito, Hiroyuki Mori
  • Organizer: EMBO Ribosome Structure and Function 2016
  • Place of Presentation: Strasbourg, France
  • Year and Date: 2016-07-06
  • Int'l Joint Research
• [Presentation] Nascent chain-mediated monitoring of the membrane protein biogenesis factor. (2016)
  • Author(s): Shinobu Chiba
  • Organizer: Nascent Biology and Ribosome Functions
  • Place of Presentation: 京都大学
  • Year and Date: 2016-06-27
  • Int'l Joint Research / Invited
• [Presentation] Use of Bacillus subtilis MifM to dissect the YidC functions to facilitate membrane protein insertion (2016)
  • Author(s): Shinobu Chiba, Naomi Shimokawa-Chiba, Koreaki, Ito
  • Organizer: Gordon Research Conference
  • Place of Presentation: Galveston, TX, USA
  • Year and Date: 2016-03-06
  • Int'l Joint Research
• [Presentation] Nascent chain-mediated monitoring of a protein localization machinery (2016)
  • Author(s): 千葉志信
  • Organizer: 第18回Tokyo RNA Club
  • Place of Presentation: 東京大学
  • Year and Date: 2016-01-14
  • Int'l Joint Research / Invited
• [Presentation] Nascent chain-mediated monitoring of the membrane protein biogenesis pathway (2015)
  • Author(s): 千葉志信
  • Organizer: Nascent Chain Biology Meeting 2015 in Tokyo
  • Place of Presentation: 東京大学
  • Year and Date: 2015-10-01
  • Int'l Joint Research / Invited
• [Presentation] 枯草菌MifM翻訳途上鎖とリボソームとの相互作用様式の解明 (2015)
  • Author(s): 千葉志信、Daniel Sohmen、千葉（下川）直美、伊藤維昭、Daniel Wilson
  • Organizer: 2015年度グラム陽性菌ゲノム機能会議
  • Place of Presentation: 滋賀県大津市
  • Year and Date: 2015-08-27
• [Presentation] YidCによるタンパク質膜組込機構の解明 (2014)
  • Author(s): 千葉志信、熊崎薫、塚崎智也、濡木理、伊藤維昭
  • Organizer: 第37回日本分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2014-11-25 – 2014-11-27
• [Presentation] YidCによるチャネルに依存しない蛋白質膜組込機構 (2014)
  • Author(s): 千葉志信、熊崎薫、塚崎智也、濡木理、伊藤維昭
  • Organizer: 第87回日本生化学会大会
  • Place of Presentation: 京都
  • Year and Date: 2014-10-15 – 2014-10-18
  • Invited
• [Presentation] チャネルに依存しない蛋白質膜組込機構：アレスト因子MifMを利用したYidCの機能解析 (2014)
  • Author(s): 千葉志信、熊崎薫、塚崎智也、濡木理、伊藤維昭
  • Organizer: 2014年度グラム陽性菌ゲノム機能会議
  • Place of Presentation: 鶴岡
  • Year and Date: 2014-09-03 – 2014-09-05
• [Remarks] 千葉研HP
  • URL: http://www.cc.kyoto-su.ac.jp/~k4563/index-j.html
• [Remarks] 新生鎖の生物学HP
  • URL: http://www.pharm.tohoku.ac.jp/nascentbiology/index.html
• [Remarks] 「リボソームがタンパク質を作る時に、自身（リボソーム）の構造不安定化のリスクを負うこと」を発見！
  • URL: http://www.kyoto-su.ac.jp/news/20171107_850_tanpaku.html
• [Remarks] 千葉研究室HP
  • URL: http://www.cc.kyoto-su.ac.jp/~k4563/index-j.html