Functional analysis of a codon-independent release factor YaeJ

2013 Fiscal Year Final Research Report

• Project/Area Number: 23570205
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Molecular biology
• Research Institution: Gunma University
• Principal Investigator: NAMEKI Nobukazu 群馬大学, 理工学研究院, 准教授 (80302959)
• Co-Investigator(Kenkyū-buntansha): IMENO Hyota 弘前大学, 農学生命科学部, 教授 (80208785)
• Project Period (FY): 2011 – 2013
• Keywords: 翻訳停滞解消因子 / リボソームレスキュー

Research Abstract

The YaeJ protein is a codon-independent release factor with peptidyl-tRNA hydrolysis (PTH) activity, and functions as a stalled-ribosome rescue factor in Escherichia coli. To identify residues required for YaeJ function, we performed mutational analysis for in vitro PTH activity towards rescue of ribosomes stalled on a nonstop mRNA, and for ribosome binding efficiency. We focused on residues conserved among bacterial YaeJ proteins. While no YaeJ-specific residues important for PTH activity occur in the structured GGQ domain, Arg118, Leu119, Lys122, Lys129, and Arg132 in the following C-terminal extension were required for PTH activity. All of these residues are completely conserved among bacteria. Single amino acid substitutions for each of these residues significantly decreased ribosome binding efficiency. These biochemical findings provide clues to understanding how YaeJ enters the A-site of stalled ribosomes.

Research Products

• [Journal Article] 細菌・ミトコンドリアにおけるtmRNA非依存的な翻訳停滞解消機構[総説] (2014)
  • Author(s): 行木信一
  • Journal Title: 生化学 Volume: 86 Pages: 86-91
• [Journal Article] Identification of residues required for stalled-ribosome rescue in the codon-independent release factor YaeJ (2014)
  • Author(s): Kogure, H., Handa, H., Nagata, M., Kanai, N., Güntert, P., Kubota, K., Nameki, N.
  • Journal Title: Nucleic Acids Res. Volume: 42 Pages: 3152-3163
  • DOI: 10.1093/nar/gkt1280
  • Peer Reviewed
• [Journal Article] Solution structure and siRNA-mediated knockdown analysis of the mitochondrial disease-related protein C12orf65 (2012)
  • Author(s): Kogure, H., Hikawa, Y., Hagihara, M., Tochio, N., Koshiba, S., Inoue, Y., Güntert, P., Kigawa, T., Yokoyama, S., Nameki, N.
  • Journal Title: Proteins Volume: 80 Pages: 2629-2642
  • Peer Reviewed
• [Journal Article] Inhibitory effects of choline-O-sulfate on amyloid formation of human islet amyloid polypeptide (2012)
  • Author(s): Hagihara, M., Takei, A., Ishii, T., Kubota, K., Wakamatsu, K., Nameki, N.
  • Journal Title: FEBS Open Bio. Volume: 2 Pages: 20-25
  • DOI: 10.1016/j.fob.2012.02.001
  • Peer Reviewed
• [Presentation] Functional analysis of stalled-ribosome rescue factors ICT1 and C12orf65 in mitochondria (2013)
  • Author(s): 小暮裕幸,半田佳宏,金井直人,岸本宏基,今泉友紀,永田昌弘,窪田健二,行木信一
  • Organizer: 第7回International Conference on Advanced Micro-Device Engineering
  • Place of Presentation: 桐生市市民文化会館(群馬県)
  • Year and Date: 2013-12-19
• [Presentation] Solution structure of the GGQ domain of the ICT1 protein that is essential for cell vitality and mitochondrial function (2013)
  • Author(s): 半田佳宏,小暮裕幸,樋川雄介,Peter Güntert,井上裕介,栃尾尚哉,行木信一
  • Organizer: 第7回International Conference on Advanced Micro-Device Engineering
  • Place of Presentation: 桐生市市民文化会館(群馬県)
  • Year and Date: 2013-12-19
• [Presentation] YaeJタンパク質の機能解析 (2013)
  • Author(s): 金井直人,小暮裕幸,永田昌弘,半田佳宏,行木信一
  • Place of Presentation: ろうきん研修所富士センター(静岡県)
  • Year and Date: 2013-09-19
• [Presentation] ミトコンドリアにおける翻訳停滞解消機構の解析 (2013)
  • Author(s): 小暮裕幸,半田佳宏,井上裕介,行木信一
  • Organizer: 第6回RNA Frontier Meeting
  • Place of Presentation: ラフォーレ修善寺(静岡県)
  • Year and Date: 2013-09-03
• [Presentation] ミトコンドリアにおける翻訳停滞解消因子ICT1およびC12orf65の機能解析 (2013)
  • Author(s): 小暮裕幸,半田佳宏,井上裕介,行木信一
  • Organizer: 第15回日本RNA学会年会
  • Place of Presentation: 県民文化会館・ひめぎんホール(愛媛県)
  • Year and Date: 2013-07-24
• [Presentation] 翻訳停滞解消に関わるyICT1とyICT2遺伝子欠損による酵母ミトコンドリアへの影響 (2012)
  • Author(s): 千葉麻里子,今泉友紀,行木信一
  • Organizer: 第35回日本分子生物学会年会
  • Place of Presentation: 福岡国際会議場
  • Year and Date: 2012-12-11
• [Presentation] 変異体解析によるYaeJタンパク質の機能解析 (2012)
  • Author(s): 金井直人,小暮裕幸,稲穂紀幸,半田佳宏,行木信一
  • Organizer: 平成24年度日本生化学会関東支部例会
  • Place of Presentation: 群馬大学昭和キャンパス
  • Year and Date: 2012-06-23
• [Presentation] 大腸菌におけるyaeJホモログ遺伝子の機能解明 (2012)
  • Author(s): 千葉麻里子,小椋義俊,行木信一
  • Organizer: 平成24年度日本生化学会関東支部例会
  • Place of Presentation: 群馬大学昭和キャンパス
  • Year and Date: 2012-06-23
• [Presentation] Transcriptional analysis of the gene encoding the mitochondrial protein C12orf65 (2011)
  • Author(s): 樋川雄介,小暮裕幸,井上裕介,行木信一
  • Organizer: 第34回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜(神奈川県)
  • Year and Date: 2011-12-13
• [Presentation] 細菌・ミトコンドリアにおける翻訳停滞解消(ribosome rescue)機構の新展開 (2011)
  • Author(s): 行木信一
  • Organizer: 東京理科大学総合研究機構RNA科学総合研究センター公開セミナー
  • Place of Presentation: 東京理科大学野田キャンパス
  • Year and Date: 2011-10-13
  • Invited
• [Presentation] 翻訳の滞りを解消するYaeJタンパク質の機能解析 (2011)
  • Author(s): 稲穂紀幸,半田佳宏,金井直人,小暮裕幸,行木信一
  • Organizer: 第5回日本ゲノム微生物学会若手の会研究会
  • Place of Presentation: ろうきん研修所富士センター(静岡県)
  • Year and Date: 2011-09-29
• [Presentation] Transcriptional Analysis of the Gene Encoding the Mitochondrial Protein ICT1 (2011)
  • Author(s): Hiroyuki Kogure, Yoshihiro Handa, Yusuke Hikawa, Yusuke Inoue, Nobukazu Nameki.
  • Organizer: The 16th Annual Meeting of the RNA Society and The 13^<th> Annual Meeting of the RNA Society of Japan
  • Place of Presentation: 国立京都国際会館(京都府)
  • Year and Date: 2011-06-14
• [Book] Encyclopedia of Systems Biology (2013)
  • Author(s): Nameki, N., Someya, T., Kawai, G.
  • Total Pages: 2289-92
  • Publisher: Springer New York (著書, 分担) Translational control with small RNAs. In : Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H. (editors)
• [Remarks] 行木研ホームページ
  • URL: http://molbio.chem-bio.st.gunma-u.ac.jp