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The basic principles of RNA recognition mechanims of RNA modification enzymes

Research Project

Project/Area Number 16H04763
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Functional biochemistry
Research InstitutionEhime University

Principal Investigator

HORI HIROYUKI  愛媛大学, 理工学研究科(工学系), 教授 (20256960)

Co-Investigator(Kenkyū-buntansha) 竹本 千重  国立研究開発法人理化学研究所, 生命機能科学研究センター, 副チームリーダー (40306527)
Research Collaborator Hirata Akira  
Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥17,550,000 (Direct Cost: ¥13,500,000、Indirect Cost: ¥4,050,000)
Fiscal Year 2018: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2017: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2016: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000)
Keywordsタンパク質 / 酵素 / 核酸 / RNA / ゲノム / 構造
Outline of Final Research Achievements

The aim of this research is the clarifications of substrate RNA recognition mechanisms of RNA modification enzymes. The findings have been reported as follows. (1) THUMP domain, a RNA binding domain, binds to a single-stranded region of substrate RNA. In the cases of tRNA modification enzymes, it often recognizes the CCA-terminus of tRNA. (2) The C-terminal domain of thermostable TrmB, a tRNA methyltransferase, forms an S-adenosyl-L-methionine binding pocket and a part of the domain contact with the substrate tRNA. (3) In the network between modified nucleosides in tRNA and tRNA modification enzymes from extremetermophilic bacterium, TrmFO, a folate-and FAD-dependent tRNA methyltrnasfearse supports the adaptation for low-temperatures.

Academic Significance and Societal Importance of the Research Achievements

RNA修飾の基本的役割はタンパク質合成系の制御です。ヒトの場合、その制御が乱れると遺伝病や発がんに結びつくことが知られています。また、コレラ菌、チフス菌、ヒト免疫不全ウイルスなどにとって、RNA修飾は感染必須因子です。さらに、RNA修飾が環境(ストレス)応答因子であることも明らかとなりつつあります。したがって、どのようなRNA修飾酵素がどのようなRNAに作用するのか、また、いかに制御されているのかを理解することは、タンパク質合成系の基本制御の仕組みを解明し、遺伝病の病態の理解、遺伝子診断・遺伝子治療法の開発、感染性微生物対策、生物多様性の理解、環境応答の仕組みの解明などにつながります。

Report

(4 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • Research Products

    (40 results)

All 2019 2018 2017 2016 Other

All Int'l Joint Research (4 results) Journal Article (9 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 9 results,  Open Access: 7 results,  Acknowledgement Compliant: 4 results) Presentation (24 results) (of which Int'l Joint Research: 6 results,  Invited: 2 results) Book (1 results) Remarks (2 results)

  • [Int'l Joint Research] CNRS(フランス)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] New England Biolob(米国)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] CNRS(フランス)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] New England Biolab(米国)

    • Related Report
      2016 Annual Research Report
  • [Journal Article] Regulatory Factors for tRNA Modifications in Extreme- Thermophilic Bacterium Thermus thermophilus.2019

    • Author(s)
      Hori H
    • Journal Title

      Frontiers in Genetics

      Volume: 10 Pages: 204-204

    • DOI

      10.3389/fgene.2019.00204

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Consumption of N5, N10-methylenetetrahydrofolate in Thermus thermophilus under nutrient-poor condition.2018

    • Author(s)
      Yamagami R, Miyake R, Fukumoto A, Nakashima M, Hori H.
    • Journal Title

      J. Biochem.

      Volume: in press Issue: 2 Pages: 141-152

    • DOI

      10.1093/jb/mvy037

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA.2018

    • Author(s)
      Hori H, Kawamura T, Awai T, Ochi A, Yamagami R, Tomikawa C, Hirata A
    • Journal Title

      Microorganism

      Volume: 6 Issue: 4 Pages: 110-155

    • DOI

      10.3390/microorganisms6040110

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Kinetic characterization of substrate-binding sites of thermostable tRNA methyltransferase (TrmB)2017

    • Author(s)
      Tomikawa Chie、Takai Kazuyuki、Hori Hiroyuki
    • Journal Title

      The Journal of Biochemistry

      Volume: 163 Issue: 2 Pages: 133-142

    • DOI

      10.1093/jb/mvx068

    • NAID

      40021471064

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Long and branched polyamines are required for maintenance of the ribosome, tRNAHis and tRNATyr in Thermus thermophilus cells at high temperatures2017

    • Author(s)
      M. Nakashima, R. Yamagami, C. Tomikawa, Y. Ochi, T. Moriya, H. Asahara, D. Fourmy, S. Yoshizawa, *T. Oshima, and *H. Hori
    • Journal Title

      Genes to Cells

      Volume: 22 Issue: 7 Pages: 628-645

    • DOI

      10.1111/gtc.12502

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Transfer RNA methyltransferases with a SpoU-TrmD (SPOUT) fold and their modified nucleosides in tRNA2017

    • Author(s)
      H. Hori
    • Journal Title

      Biomolecules

      Volume: 7 Issue: 1 Pages: 23-23

    • DOI

      10.3390/biom7010023

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Long and branched polyamines are required for maintenance of the ribosome, tRNAHis, and tRNATyr in Thermus thermophilus cells at high temperatures2017

    • Author(s)
      M. Nakashima, R. Yamagami, C. Tomikawa, Y. Ochi, T. Moriya, H. Asahara, D. Fourmy, S. Yoshizawa, T. Oshima and H. Hori
    • Journal Title

      Genes to Cells

      Volume: 印刷中

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] The folate/FAD-dependent tRNA methyltransferase (TrmFO) from Thermus thermophilus regulates the other modifications in tRNA at low temperatures2016

    • Author(s)
      R. Yamagami, C. Tomikawa, N. Shigi, A. Kazayama, S. Asai, H. Takuma, A. Hirata, D. Fourmy, H. Asahara, K. Watanabe, S. Yoshizawa and H. Hori
    • Journal Title

      Genes to Cells

      Volume: 21 Issue: 7 Pages: 740-754

    • DOI

      10.1111/gtc.12376

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Structural and functional analyses of the archaeal tRNA m2G/m22G10 methyltransferase aTrm11 provide mechanistic insights into the site specificity of a tRNA methyltransferase that contains common RNA-binding modules.2016

    • Author(s)
      A. Hirata, S. Nishiyama, T. Tamura, A. Yamauchi, and H. Hori
    • Journal Title

      Nucleic Acids Res.

      Volume: 44 Issue: 13 Pages: 6377-6390

    • DOI

      10.1093/nar/gkw561

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] 高度好熱菌の長鎖・分岐鎖ポリアミンは、高温環境下でのリボソーム、tRNAHis、tRNATyrの維持に必要である2018

    • Author(s)
      中嶋美沙、山上龍太、冨川千恵、越智裕貴、森屋利幸、朝原治一、Dominique Fourmy、吉澤聡子、大島泰郎、堀 弘幸
    • Organizer
      第20回日本RNA学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 大腸菌tRNA (Gm18) メチル化酵素(TrmH)の基質tRNA選択システム2018

    • Author(s)
      河野 陽、伊藤亜沙子、山上龍太、平田 章、堀 弘幸
    • Organizer
      第20回日本RNA学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Long and branced polyamines are required for maintenance of 70S ribosome, tRNAHis, and tRNATyr in Thermus thermophilus2018

    • Author(s)
      Nakashima, M., Yamagami, R., Tomikawa, C., Ochi, Y., Moriya, T., Asahara, H., Fourmy, D., Yoshizawa, S., Oshima, T. and Hori, H.
    • Organizer
      27th tRNA Conference
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] アーキアtRNAメチル化酵素・Trm56の基質tRNA特異性の解明2018

    • Author(s)
      福本修平、長谷川貴洋、河村卓哉、堀 弘幸
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] hermus thermophilusの長鎖・分岐鎖ポリアミンは、高温環境下でのリボソーム、tRNAHis、tRNATyrの維持に必要である2018

    • Author(s)
      中嶋美沙、山上龍太、冨川千恵、越智裕貴、森屋利幸、朝原治一、Fourmy D, 吉澤聡子、大島泰郎、堀 弘幸
    • Organizer
      日本ポリアミン学会第9回年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] RNAメチル化酵素とメチル化ヌクレオシドの構造と機能の多様性2017

    • Author(s)
      堀 弘幸
    • Organizer
      東京大学新領域創成科学研究科メディカル情報生命専攻大学院講演会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] RNAメチル化酵素とその修飾ヌクレオシドの多様性2017

    • Author(s)
      堀 弘幸
    • Organizer
      大阪市立大学大学院工学研究科化学生物系専攻セミナー
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 好熱好酸性古細菌Thermoplasma acidophilumのアーケオシン tRNA グアニントランスグリコシラーゼは、tRNAの13位、15位のグアニンに作用するマルチサイト特異性酵素である2017

    • Author(s)
      河村卓哉、平田 章、大野 敏、能村友一朗、長野倫子、行木信一、横川隆志、堀 弘幸
    • Organizer
      第19回日本RNA学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 好熱好酸性古細菌Thermoplasma acidophilum Trm56の分析2017

    • Author(s)
      長谷川貴洋、福本修平、河村卓哉、堀 弘幸
    • Organizer
      第19回日本RNA学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 大腸菌tRNA(Gm18)メチル化酵素(TrmH)のX線結晶構造とその基質tRNA選択システム2017

    • Author(s)
      伊藤亜沙子、山上龍太、河野 陽、平田 章、堀 弘幸
    • Organizer
      第19回日本RNA学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Thermoplasma acidophilum tRNAにおける4-チオウリジンの生合成経路2017

    • Author(s)
      上田隼也、松本奈津実、河村卓哉、堀 弘幸
    • Organizer
      ConBio2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] デオキシリボザイムを用いた長鎖RNA切断法の検討2017

    • Author(s)
      上崎晃輔、荒川静花、堀 弘幸
    • Organizer
      ConBio2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] 真核生物tRNAメチル化酵素Trm7-Trm734複合体の活性発現メカニズムの構造基盤2017

    • Author(s)
      平田 章、岡田圭祐、吉井一晃、白石裕之、西條慎也、清水伸隆、堀 弘幸
    • Organizer
      ConBio2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] 古細菌Thermoplasma acidophilum tRNALeuのアンチコドン1文字目修飾に関わるタンパク質複合体調製法の検討2017

    • Author(s)
      玉井 章悟 、東口 実結、河村 卓哉、坂口 裕理子、安楽 遼 、鈴木 勉、堀 弘幸
    • Organizer
      ConBio2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] tRNA(Gm18)メチル化酵素(TrmH)のX線結晶構造とその基質tRNA認識機構2016

    • Author(s)
      伊藤亜沙子、山上龍太、平田 章、堀 弘幸
    • Organizer
      第39回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜、横浜
    • Year and Date
      2016-11-30
    • Related Report
      2016 Annual Research Report
  • [Presentation] 高度好熱菌Thermus thermophilusの長鎖・分岐鎖ポリアミンは主に高温環境下でのリボソームの維持に必要である2016

    • Author(s)
      Misa Nakashima, Ryota Yamagami, Yuki Ochi, Chie Tomikawa, Toshiyuki Moriya, Dominique Fourmy, Satoko Yoshizawa, Tairo Oshima, and Hiroyuki Hori
    • Organizer
      第39回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜、横浜
    • Year and Date
      2016-11-30
    • Related Report
      2016 Annual Research Report
  • [Presentation] 超好熱性アーキアThermococcus kodakarensis KOD1由来RNA m5C修飾酵素の構造機能解析2016

    • Author(s)
      山内綾乃、平田 章、前田雄太、堀 弘幸
    • Organizer
      極限環境生物学会2016年度(第17回)年会
    • Place of Presentation
      東京工業大学、横浜
    • Year and Date
      2016-11-25
    • Related Report
      2016 Annual Research Report
  • [Presentation] The long and branched polyamines of Thermus thermophilus, an extremely thermophilic eubacterium, are required for maintenance of ribosome at high temperatures.2016

    • Author(s)
      Misa Nakashima, Ryota Yamagami, Yuki Ochi, Chie Tomikawa, Toshiyuki Moriya, Dominique Fourmy, Satoko Yoshizawa, Tairo Oshima, and Hiroyuki Hori
    • Organizer
      Extremophiles 2016
    • Place of Presentation
      Kyoto University, Kyoto
    • Year and Date
      2016-09-12
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Structural and functional analyses reveal mechanistic insight into a site specificity of the archaeal tRNA m2G/m22G10 methyltransferase (aTrm11)2016

    • Author(s)
      Akira Hirata, Seiji Nishiyama, Toshihiro Tamura, Ayano Yamauchi and Hiroyuki Hori
    • Organizer
      Extremophiles 2016
    • Place of Presentation
      Kyoto University, Kyoto
    • Year and Date
      2016-09-12
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Multisite-specific archaeosine tRNA-guanine transglycosylase (ArcTGT) from Thermoplasma acidophilum, a thermo-acidophilic archaeon2016

    • Author(s)
      Takuya Kawamura, Akira Hirata, Satoshi Ohno, Yuichiro Nomura, Tomoko Nagano, Nobukazu Nameki, Takashi Yokogawa, and Hiroyuki Hori
    • Organizer
      tRNA 26th Conference
    • Place of Presentation
      Jeju, Korea
    • Year and Date
      2016-09-04
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] アーキアtRNA (m2G10/m22G10) メチル基転移酵素arcTrm11の基質認識機構に関する研究2016

    • Author(s)
      平田 章、西山聖示、田村俊浩、山内綾乃、堀 弘幸
    • Organizer
      第29回日本Archaea研究会
    • Place of Presentation
      東洋大学、東京
    • Year and Date
      2016-07-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] Thermoplasma acidophilum 細胞抽出液中には、tRNAの4-チオウリジン合成に関わる新たな因子が存在する2016

    • Author(s)
      上田隼也、松本奈津実、河村卓哉、堀 弘幸
    • Organizer
      第29回日本Archaea研究会
    • Place of Presentation
      東洋大学、東京
    • Year and Date
      2016-07-07
    • Related Report
      2016 Annual Research Report
  • [Presentation] Structural and functional analyses reveal mechanisitic insight into a site specifity of the archaearl tRNA methyltransferase2016

    • Author(s)
      Akira Hirata, Seiji Nishiyama, Toshihiro Tamura, Ayano Yamauchi and Hiroyuki Hori
    • Organizer
      RNA 2016
    • Place of Presentation
      Kyoto International Conference Center, Kyoto
    • Year and Date
      2016-06-28
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Substrate tRNA recognition mechanism of eubacterial tRNA (m1A58) methyltransferase (TrmI)2016

    • Author(s)
      Hiroyuki Takuma, Natsumi Ushio, Masayuki Minoji, Ai Kazayama, Naoki Shigi, Akira Hirata, Chie Tomikawa, Anna Ochi, and Hiroyuki Hori
    • Organizer
      RNA 2016
    • Place of Presentation
      Kyoto International Conference Center, Kyoto
    • Year and Date
      2016-06-28
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Book] Modified Nucleic Acids in Biology and Medicine2016

    • Author(s)
      H. Hori, R. Yamagami and C. Tomikawa
    • Total Pages
      12
    • Publisher
      Springer
    • Related Report
      2016 Annual Research Report
  • [Remarks] 応用生物化学研究室ホームページ

    • URL

      http://www.ach.ehime-u.ac.jp/bchem/

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
  • [Remarks] 応用生物化学研究室HP

    • URL

      http://www.ach.ehime-u.ac.jp/bchem/

    • Related Report
      2016 Annual Research Report

URL: 

Published: 2016-04-21   Modified: 2022-08-19  

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