Structural analysis of the poly A polymerase activated by oxidative stress

• Project/Area Number: 16K18510
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Structural biochemistry
• Research Institution: The University of Tokyo
• Principal Investigator: Yamashita Seisuke 東京大学, 大学院新領域創成科学研究科, 特任助教 (30769576)
• Project Period (FY): 2016-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2018: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2017: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2016: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
• Keywords: ヌクレオチド転移酵素 / X線結晶構造解析 / TUTase / ヌクレオチド付加 / RNA修飾 / Star-PAP / TUT1 / U6 snRNA / Ｘ線結晶構造解析 / 生体分子

Outline of Final Research Achievements

In this project, we aimed to reveal the molecular mechanisms of the specific nucleotidyl transfer by non-canonical nucleotidyl transferases. In particular, we focused on the structural and biochemical analyses of human Star-PAP and TUT4, which are the members of human non-canonical nucleotidyl transferases. We clarified the molecular basis for the U6 snRNA specific uridilylation by Star-PAP. We also clarified the molecular basis for the complex formation which is necessary for the inhibition of let-7 miRNA.

Academic Significance and Societal Importance of the Research Achievements

生命の設計図と呼ばれるDNAはそれ自身が部品として働くのではなく、RNAに転写されたのちにさらにタンパクに翻訳されて、あるいはRNAそのものとして機能的な役割を果たす。RNAは転写された後にさらに様々なプロセシングを受けていることが近年明らかになり、プロセシングが適切な機能発現や活性制御に不可欠であることがわかってきた。本研究では転写後プロセシングの一つであるヌクレオチド転移反応を担う酵素を標的とし、その立体構造を明らかにすることで高次生命現象の制御機構の解明につなげることができた。

Research Products

• [Journal Article] Crystal structure of the enterohemorrhagic Escherichia coli AtaT-AtaR toxin-antitoxin complex. (2019)
  • Author(s): Yashiro Y, Yamashita S, Tomita K.
  • Journal Title: Structure Volume: 27 Issue: 3 Pages: 476-484
  • DOI: 10.1016/j.str.2018.11.005
  • Peer Reviewed
• [Journal Article] Crystal structure of the Lin28-interacting module of human terminal uridylyltransferase that regulates let-7 expression (2019)
  • Author(s): Yamashita Seisuke、Nagaike Takashi、Tomita Kozo
  • Journal Title: Nature Communications Volume: 10 Issue: 1 Pages: 1960-1960
  • DOI: 10.1038/s41467-019-09966-5
  • Peer Reviewed / Open Access
• [Journal Article] Acetate-dependent tRNA acetylation required for decoding fidelity in protein synthesis (2018)
  • Author(s): Taniguchi T, Miyauchi K, Sakaguchi Y, Yamashita S, Soma A, Tomita K, Suzuki T
  • Journal Title: Nature Chemical Biology Volume: 14 Issue: 11 Pages: 1010-1020
  • DOI: 10.1038/s41589-018-0119-z
  • Peer Reviewed
• [Journal Article] Crystal structures of U6 snRNA-specific terminal uridylyltransferase (2017)
  • Author(s): Yamashita Seisuke、Takagi Yuko、Nagaike Takashi、Tomita Kozo
  • Journal Title: Nature Communications Volume: 8 Issue: 1 Pages: 15788-15788
  • DOI: 10.1038/ncomms15788
• [Journal Article] Human BCDIN3D Monomethylates Cytoplasmic Histidine Transfer RNA. (2017)
  • Author(s): Martinez A, Yamashita S, Nagaike T, Sakaguchi Y, Suzuki T, Tomita K
  • Journal Title: Nucleic Acids Res Volume: - Pages: 5423-5436
  • DOI: 10.1093/nar/gkx051
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] Crystal structures of U6 snRNA-specific terminal uridylyltransferase (2017)
  • Author(s): Seisuke Yamashita, Kozo Tomita
  • Organizer: 第43回内藤コンファレンス
• [Presentation] Mechanism of 3'-matured tRNA discrimination from 3'-immature tRNA by class-II CCA-adding enzyme (2016)
  • Author(s): Seisuke Yamashita
  • Organizer: The 26th tRNA conference
  • Place of Presentation: 韓国、済州
  • Year and Date: 2016-09-04
  • Int'l Joint Research