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Molecular mechanisms of co-evolution of mitochondrial genetic codes and tRNA in the evolution of animals

Research Project

Project/Area Number 21570242
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field Evolutionary biology
Research InstitutionThe University of Tokyo (2010-2011)
National Institute of Advanced Industrial Science and Technology (2009)

Principal Investigator

WATANABE Kimitsuna  東京大学, 大学院・農学生命科学研究科, 名誉教授 (00134502)

Co-Investigator(Kenkyū-buntansha) YOKOBORI Shin-ichi  東京薬科大学, 生命科学部, 講師 (40291702)
SHIGI Naoki  (独)産業技術総合研究所, バイオメディシナル情報研究センター, 研究員 (20392623)
Project Period (FY) 2009 – 2011
Project Status Completed (Fiscal Year 2011)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2011: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2010: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2009: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Keywords遺伝暗号 / ミトコンドリア / tRNA / 修飾塩基 / 分子進化 / マボヤ / ヤリイカ / 非普遍暗号 / ゲノム解析
Research Abstract

In animal mitochondria, distribution of the non-universal codons(relationship between codon and amino acid) has been clarified in all animal phyla. However, relationship between codon and anticodon has not clarified except for Vertebrata and Nematoda. In order to elucidate a whole image for the decoding mechanism of genetic code, we isolated the relevant tRNAs from a tunicate(ascidian) and a mollusc(squid) and analysed them by using LC/MS. By doing so, we clarified the relationship. We found 5-taurinomethyluridine(. m5U) in the first position of ascidian tRNATrp, tRNAMet and tRNAGly, and squid tRNATrp and concluded that. m5U-bearing anticodons decode A-and G-ending codons.

Report

(4 results)
  • 2011 Annual Research Report   Final Research Report ( PDF )
  • 2010 Annual Research Report
  • 2009 Annual Research Report
  • Research Products

    (53 results)

All 2012 2011 2010 2009

All Journal Article (17 results) (of which Peer Reviewed: 17 results) Presentation (33 results) Book (3 results)

  • [Journal Article] tRNA modification and genetic code variaitons in animal mitochondria. J2011

    • Author(s)
      Watanabe, K. and Yokobori, S.
    • Journal Title

      Nucleic Acids(Online J.)

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Genetic code : introduction(Version 2)2011

    • Author(s)
      Watanabe, K. & S. Yokobori
    • Journal Title

      Encyclopedia of Life Science

    • DOI

      10.1002/9780470015902.a0000809.pub2

    • Related Report
      2011 Annual Research Report 2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Taurine-containing uridine modifications in tRNA anticodons are required to decipher non-universal genetic codes in ascidian mitochondria2011

    • Author(s)
      Suzuki, T., Miyauchi, K., Suzuki, T., Yokobori, S., Shigi, N., Kondow, A., Takeuchi, N., Yamagishi, A. and Watanabe, K.
    • Journal Title

      J. Biol. Chem.

      Volume: 286 Pages: 35494-35498

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Male death resulting from hybridization between subspecies of the gypsy moth2011

    • Author(s)
      Higashiura, Y., Yamaguchi, M., Ishihara, M., Ono, N., Tsukagoshi, H., Yokobori, S., Tokishita, S., Yamagata, H. and Fukatsu, T.
    • Journal Title

      Lymantria disapr. Heredity

      Volume: 106 Pages: 603-613

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] tRNA modification and genetic code variaitons in animal mitochondria2011

    • Author(s)
      Watanabe, K., Yokobori, S.
    • Journal Title

      J.Nucleic Acids (Online J.)

      Volume: 2011

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Taurine-containing uridine modifications in tRNA anticodons are required to decipher non-universal genetic codes in ascidian mitochondria2011

    • Author(s)
      Suzuki T (第1著者), 他8名
    • Journal Title

      J. Biol. Chem

      Volume: 286 Issue: 41 Pages: 35494

    • DOI

      10.1074/jbc.m111.279810

    • URL

      https://pure.teikyo.jp/en/publications/70d6d0f7-88b7-4afe-a2b1-a2ea848a121b

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Male death resulting from hybridisation between subspecies of the gypsy moth, Lymantria dispar2011

    • Author(s)
      Higashiura, Y., H.Yamaguchi, M.Ishihara, N.Ono, H.Tsukagoshi, S.Yokobori, S.Tokishita, H.Yamagata, T.Fukatsu
    • Journal Title

      Heredity

      Volume: 106 Issue: 4 Pages: 603-613

    • DOI

      10.1038/hdy.2010.92

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Evolution of genetic code2010

    • Author(s)
      Yokobori, S., T. Ueda, & K. Watanabe
    • Journal Title

      Encyclopedia of Life Science 2010

    • DOI

      10.1002/9780470015902.a0000548.pub2

    • URL

      http://www.els.net/

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Repetitive sequences in the lamprey mitochondrial DNA control region and speciation of Lethenteron2010

    • Author(s)
      Okada, K., Yamazaki, Y., Yokobori, S., and Wada, H.
    • Journal Title

      Gene

      Volume: 465 Pages: 45-52

    • NAID

      120007137933

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] The complete mitochondrial genome of Caprella scaaura(Caprellidea) with a note on a unique gene order pattern and duplicated ncontrol region2010

    • Author(s)
      Ito, A., Aoki, M., Yokobori, S. and Wada, A.
    • Journal Title

      Mitochondrial DNA

      Volume: 21 Pages: 183-190

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Unique features of animal mitochondrial translation systems - The non-universal genetic code, unusual features of the translational apparatus and their relevance to human mitochondrial diseases -2010

    • Author(s)
      Watanabe, K.
    • Journal Title

      Proceedings of the Japan Academy, Series B

      Volume: 86 Issue: 1 Pages: 11-39

    • DOI

      10.2183/pjab.86.11

    • NAID

      130000149631

    • ISSN
      0386-2208, 1349-2896
    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] A bacterial elongation factor G homolog exclusively functions in ribosome recycling in the spirochaete Borrelia burgdorferi.2010

    • Author(s)
      Suematsu, T., S.Yokobori, H.Morita, S.Yoshinari, T.Ueda, K.Kita, N.Takeuchi, Y.Watanabe
    • Journal Title

      Mol.Microbiol.

      Volume: 75 Pages: 1445-1454

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Repetitive sequences in the lamprey mitochondrial DNA control region and speciation of Lethenteron.2010

    • Author(s)
      Okada, K., Y.Yamazaki, S.Yokobori, H.Wada
    • Journal Title

      Gene

      Volume: 465 Pages: 45-52

    • NAID

      120007137933

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The complete mitochondrial genome of Caprella scaura (Caprellidea) with a note on a unique gene order pattern and duplicated control region.2010

    • Author(s)
      Ito, A., M.Aoki, S.Yokobori, H.Wada
    • Journal Title

      Mitochondrial DNA

      Volume: 21 Pages: 183-190

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Unique features of animal mitochondrial translation systems-The non-universal genetic code, unusual features of the translational apparatus and their relevance to human mitochondrial diseases-2010

    • Author(s)
      渡辺公綱
    • Journal Title

      Proceedings of Japan Academy, Series B 86

      Pages: 11-39

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Transfer RNA synthesis and regulation2010

    • Author(s)
      Y.Toh, H.Hori, K.Tomita, T.Ueda, K.Watanabe
    • Journal Title

      Encyclopedia of Life Sciences (in press)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Evolution of the genetic code2010

    • Author(s)
      S.Yokobori, T.Ueda, K.Watanabe
    • Journal Title

      Encyclopedia od Life Sciences (in press)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Presentation] α2型グリシルtRNA合成酵素を用いた全生物の分子系統解析2012

    • Author(s)
      古川龍太郎、横堀伸一、山岸明彦
    • Organizer
      第37回生命の起源と進化学会学術講演会
    • Place of Presentation
      高槻
    • Year and Date
      2012-03-08
    • Related Report
      2011 Annual Research Report
  • [Presentation] ロウリガイ類のミトコンドリアゲノム解析2012

    • Author(s)
      小澤元希、島村繁、高木善弘、横堀伸一、前田太郎、丸山正、吉田尊雄
    • Organizer
      ブルーアース2012
    • Place of Presentation
      東京
    • Year and Date
      2012-02-22
    • Related Report
      2011 Annual Research Report
  • [Presentation] An approach to an early genetic code table inferred from decoding system of non-universal genetic codes in animal mitochondria2011

    • Author(s)
      Watanabe, K., Yokobori, S., Suzuki, T.
    • Organizer
      Symposium on behalf of Tom RhajBhandary
    • Place of Presentation
      Bangalore, India(招待講演)
    • Year and Date
      2011-12-19
    • Related Report
      2011 Annual Research Report
  • [Presentation] An approach to an early genetic code table inferred from decoding system of non-universal genetic codes in animal mitochondria2011

    • Author(s)
      Watanabe, K., Yokobori, S. and Suzuki, T.
    • Organizer
      Symposium on behalf of Tom RajBhandary(招待講演) Bangalore
    • Place of Presentation
      India
    • Year and Date
      2011-12-17
    • Related Report
      2011 Final Research Report
  • [Presentation] molecular phylogeny of urochordates and evolution of mitochondrial genetic code in urochordate mitochondria2011

    • Author(s)
      Yokobori, S., Watanabe, K. and Yamagishi, A.
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2011-12-14
    • Related Report
      2011 Final Research Report
  • [Presentation] 深海性二枚貝シロウリガイ類のミトコンドリアゲノム解析2011

    • Author(s)
      小澤元希、島村繁、高木善弘、横堀伸一、丸山正、吉田尊雄
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      横浜
    • Year and Date
      2011-12-14
    • Related Report
      2011 Final Research Report
  • [Presentation] Molecular phylogeny of urochordates and evolution of mitochondrial genetic code in urochordate mitochondria2011

    • Author(s)
      Yokobori, S., Watanabe, K., Yamagishi
    • Organizer
      第34回日本分子生物学会年回
    • Place of Presentation
      横浜
    • Year and Date
      2011-12-14
    • Related Report
      2011 Annual Research Report
  • [Presentation] マイコプラズマtRNA修飾酵素が主導する遺伝暗号解読の進化2011

    • Author(s)
      別所義隆、北村彩、Henri Grosjean、横堀伸一
    • Organizer
      第34回日本分子生物学会年回
    • Place of Presentation
      横浜
    • Year and Date
      2011-12-14
    • Related Report
      2011 Annual Research Report
  • [Presentation] 深海性二枚貝シロウリガイ類のミトコンドリアゲノム解析2011

    • Author(s)
      小澤元希、島村繁、高木善弘、横堀伸一、丸山正、吉田尊雄
    • Organizer
      第34回日本分子生物学会年回
    • Place of Presentation
      横浜
    • Year and Date
      2011-12-14
    • Related Report
      2011 Annual Research Report
  • [Presentation] tRNAから見た遺伝暗号の進化2011

    • Author(s)
      横堀伸一
    • Organizer
      第4回アストロバイオロジーネットワークワークショップ
    • Place of Presentation
      神戸
    • Year and Date
      2011-11-27
    • Related Report
      2011 Annual Research Report 2011 Final Research Report
  • [Presentation] ミトコンドリア翻訳伸長因子EF-Gの多様性:リボソームサブユニット解離活性を「再構築」した植物ミトコンドリアEF-G?2011

    • Author(s)
      末松卓真、渡邊修、横堀伸一、北潔、渡邊洋一
    • Organizer
      第84回日本生化学会年会
    • Place of Presentation
      京都
    • Year and Date
      2011-09-24
    • Related Report
      2011 Final Research Report
  • [Presentation] ミトコンドリア翻訳伸長因子EF-Gの多様性:リボソームサブユニット解離活性を「再獲得」した植物ミトコンドリアEF-G?2011

    • Author(s)
      末松卓真、渡邊修、横堀伸一、北潔、渡邊洋一
    • Organizer
      第84回日本生化学会年回
    • Place of Presentation
      京都
    • Year and Date
      2011-09-24
    • Related Report
      2011 Annual Research Report
  • [Presentation] ミトコンドリアゲノムに基づく尾索動物の分子系統解析2011

    • Author(s)
      大曾根祐、廣瀬裕一、和田洋、西川淳、倉橋敦、山岸明彦、横堀伸一
    • Organizer
      動物学会
    • Place of Presentation
      旭川、北海道
    • Year and Date
      2011-09-21
    • Related Report
      2011 Annual Research Report 2011 Final Research Report
  • [Presentation] 尾索動物ミトコンドリア遺伝暗号の進化2011

    • Author(s)
      横堀伸一、山岸明彦、渡辺公綱
    • Organizer
      日本進化学会第13回年会
    • Place of Presentation
      京都
    • Year and Date
      2011-07-31
    • Related Report
      2011 Final Research Report
  • [Presentation] 尾索動物ミトコンドリア遺伝暗号の進化2011

    • Author(s)
      横堀伸一、山岸明彦、渡辺公綱
    • Organizer
      日本進化学会第13回年回
    • Place of Presentation
      京都
    • Year and Date
      2011-07-31
    • Related Report
      2011 Annual Research Report
  • [Presentation] α2グリシルtRNA合成酵素を用いた全生物の分子系統解析2011

    • Author(s)
      古川龍太郎、横堀伸一、山岸明彦
    • Organizer
      日本進化学会第13回年回
    • Place of Presentation
      京都
    • Year and Date
      2011-07-30
    • Related Report
      2011 Annual Research Report
  • [Presentation] 翻訳伸長因子を用いた生命の初期進化の解析2011

    • Author(s)
      金武舞、横堀伸一、山岸明彦
    • Organizer
      日本進化学会第13回年回
    • Place of Presentation
      京都
    • Year and Date
      2011-07-30
    • Related Report
      2011 Annual Research Report
  • [Presentation] Unique characteristics of ascidian mitochondrial tRNAs involved in deciphering the non-universal genetic codes and an initiator tRNA corresponding to AUG codon2011

    • Author(s)
      Suzuki, T., Miyauchi, K., Suzuki, T., Yokobori, S., Shigi, N., Kondow, A., Takeuchi, N., Yamagishi, A. and Watanabe, K.
    • Organizer
      RNA2011
    • Place of Presentation
      京都
    • Year and Date
      2011-06-17
    • Related Report
      2011 Final Research Report
  • [Presentation] Tryptophanyl-tRNA synthetase for the Mycoplasma deviant genetic code2011

    • Author(s)
      Kitamura, A., H.M. Sasaki, K.Higashijima, M.Nishimoto, T.Sengoku, S.Yokobori, S.Yokoyama, Y.Bessho
    • Organizer
      RNA2011
    • Place of Presentation
      京都
    • Year and Date
      2011-06-17
    • Related Report
      2011 Annual Research Report
  • [Presentation] Decoding the four CGN codons as arginine in mycoplasmas (Mollicutes) : possible role of partial deamination of the wobble adenosine into inosine in anticodon of tRNA ^<Arg>(ACG)2011

    • Author(s)
      Yokobori S., A.Kitamura, H.Grosjean, Y.Bessho
    • Organizer
      RNA2011
    • Place of Presentation
      京都
    • Year and Date
      2011-06-17
    • Related Report
      2011 Annual Research Report
  • [Presentation] Unique characteristics of ascidian mitochondrial tRNAs : Existence of 5-taurinometylyuridine-containing tRNAs involved in deciphering the non-universal genetic codes and an initiator tRNA corresponding to AUG codon2011

    • Author(s)
      Suzuki, T., K.Miyauchi, N.Shigi, A.Kondoh, N.Takeuchi, T.Suzuki, A.Yamagishi, S.Yokobori, K.Watanabe
    • Organizer
      RNA2011
    • Place of Presentation
      京都
    • Year and Date
      2011-06-17
    • Related Report
      2011 Annual Research Report
  • [Presentation] ミトコンドリアtRNAの解析から見た遺伝暗号の進化2011

    • Author(s)
      横堀伸一、山岸明彦、渡辺公綱
    • Organizer
      第37回生命の起源と進化学会学術講演会
    • Place of Presentation
      高槻
    • Year and Date
      2011-03-08
    • Related Report
      2011 Annual Research Report 2011 Final Research Report
  • [Presentation] シロウリガイ類のミトコンドリアゲノム解析2011

    • Author(s)
      小澤元希、島村繁、高木善弘、横堀伸一、前田太郎、丸山正、吉田尊雄
    • Organizer
      ブルーアース2012
    • Place of Presentation
      東京
    • Year and Date
      2011-02-22
    • Related Report
      2011 Final Research Report
  • [Presentation] Strategy of decoding system in Mycoplasma possessing nearly minimal genomes2010

    • Author(s)
      Yokobori, S., Kitamura, A., Grosjean, H., Y.Bessho
    • Organizer
      BMB2010
    • Place of Presentation
      神戸
    • Year and Date
      2010-12-08
    • Related Report
      2010 Annual Research Report
  • [Presentation] 遺伝暗号の進化:ミトコンドリア遺伝情報系をモデルとして2010

    • Author(s)
      横堀伸一
    • Organizer
      第3回アストロバイオロジーネットワーク・ワークショップ
    • Place of Presentation
      多摩
    • Year and Date
      2010-10-31
    • Related Report
      2011 Final Research Report 2010 Annual Research Report
  • [Presentation] 尾索動物ミトコンドリア構造多様性の進化2010

    • Author(s)
      大曾根祐、倉持祐吾、和田洋、倉橋敦、廣瀬裕一、西川淳、山岸明彦、横堀伸一
    • Organizer
      第81回動物学会年会
    • Place of Presentation
      駒場
    • Year and Date
      2010-09-24
    • Related Report
      2011 Final Research Report 2010 Annual Research Report
  • [Presentation] リボソーム再生過程に特化したバクテリアのEF-Gホモログの発見2010

    • Author(s)
      末松卓真、横堀伸一、森田寛幸、吉成茂夫、上田卓也、北潔、竹内野乃、渡邊洋一
    • Organizer
      第12回RNA学会年会
    • Place of Presentation
      一ツ橋記念講堂
    • Year and Date
      2010-07-28
    • Related Report
      2010 Annual Research Report
  • [Presentation] ミトコンドリアゲノムに基づく尾索動物の分子系統解析2009

    • Author(s)
      横堀伸一、大曽根祐、倉林敦、西川淳、広瀬裕一、山岸明彦
    • Organizer
      日本動物学会年会
    • Place of Presentation
      静岡
    • Year and Date
      2009-09-22
    • Related Report
      2009 Annual Research Report
  • [Presentation] ミトコンドリアゲノムに基づく尾索動物の分子系統解析2009

    • Author(s)
      横堀伸一、大曾根祐、倉橋敦、西川淳、廣瀬裕一、山岸明彦
    • Organizer
      第80回日本動物学会年会
    • Place of Presentation
      静岡
    • Year and Date
      2009-09-19
    • Related Report
      2011 Final Research Report
  • [Presentation] Complete nucleotide sequences of mitochondrial genomes of two salps Ritteriella amboinensis and R. picteri2009

    • Author(s)
      Ohsone, Y., Wada, H., Nishikawa, J., Kurabayashi, A., Hirose, E., Yamagishi, A. and Yokobori, S.
    • Organizer
      The 5th International Tunicate Meeting
    • Place of Presentation
      Okinawa
    • Year and Date
      2009-06-22
    • Related Report
      2011 Final Research Report
  • [Presentation] Molecular phylogeny of Urochordata(Tunicata)based on complete mitochondrial genome sequences and 18S rRNA gene sequences.2009

    • Author(s)
      Yokobori, S., A.Kurabayashi, J.Nishikawa, Y.Ohsone, A.Yamagishi, E.Hirose
    • Organizer
      The 5th International Tunicate Meeting
    • Place of Presentation
      沖縄
    • Year and Date
      2009-06-22
    • Related Report
      2009 Annual Research Report
  • [Presentation] Complete nucleotide sequences of mitochondrial genomes of two salps Ritteriella amboinensis and R.picteti2009

    • Author(s)
      Ohsone, Y., H.Wada, J.Nishikawa, A.Kurabayashi, E.Hirose, A.Yamagishi, S.Yokobori
    • Organizer
      The 5th International Tunicate Meeting
    • Place of Presentation
      沖縄
    • Year and Date
      2009-06-22
    • Related Report
      2009 Annual Research Report
  • [Presentation] Molucular phylogeny of Urochordata(Tunicata) based on complete mitochondrial genome sequences and 18S rRNA gene sequences.2009

    • Author(s)
      Yokobori, S., Kurabayashi, A., Nishikawa, J., Ohsone, Y., Yamagishi, A. and Hirose, E.
    • Organizer
      The 5th International Tunicate Meeting
    • Place of Presentation
      Okinawa
    • Year and Date
      2009-06-21
    • Related Report
      2011 Final Research Report
  • [Book] 生命化学II遺伝子の働きとその応用第2版2011

    • Author(s)
      渡辺公綱・姫野俵太著
    • Total Pages
      269
    • Publisher
      丸善出版
    • Related Report
      2011 Final Research Report
  • [Book] 生命化学II遺伝子の働きとその応用2011

    • Author(s)
      渡辺公綱・姫野俵太
    • Publisher
      丸善出版(株)
    • Related Report
      2011 Annual Research Report
  • [Book] 生命化学II 改訂版2011

    • Author(s)
      渡辺公綱・姫野俵太
    • Total Pages
      269
    • Publisher
      丸善(株)出版事業部
    • Related Report
      2010 Annual Research Report

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Published: 2009-04-01   Modified: 2023-03-16  

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