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Study on the evolution of amino acid usage in early translation system

Research Project

Project/Area Number 17H03716
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Evolutionary biology
Research InstitutionWaseda University

Principal Investigator

Akanuma Satoshi  早稲田大学, 人間科学学術院, 准教授 (10321720)

Co-Investigator(Kenkyū-buntansha) 横堀 伸一  東京薬科大学, 生命科学部, 講師 (40291702)
Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥18,070,000 (Direct Cost: ¥13,900,000、Indirect Cost: ¥4,170,000)
Fiscal Year 2019: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Fiscal Year 2018: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000)
Fiscal Year 2017: ¥11,310,000 (Direct Cost: ¥8,700,000、Indirect Cost: ¥2,610,000)
Keywords生命の起源 / アミノ酸組成 / 初期進化 / 原始タンパク質 / 翻訳系 / 祖先復元型タンパク質 / 祖先型再構成 / 進化系統解析 / 翻訳 / アミノ酸
Outline of Final Research Achievements

By comprehensively simplifying the amino acid composition of a reconstructed ancestral nucleoside diphosphate kinase, we found that 13 amino acid types are enough to reconstitute a catalytically active protein. In addition, we showed that 10 amino acid types can produce a sequence that folds into a stable tertiary structure. Moreover, not all but many of the 10 amino acid types required for the formation of the stable structure are consistent with the prebiotic amino acids that may have been relatively abundant in primitive Earth.
Phylogenetic analyses and ancestral reconstruction of aminoacyl-tRNA synthetases (ARSs) belonging to class Ia showed that the ancestral form of IleRS, that of ValRS, and the common ancestor of IleRS and ValRS catalyzed respective amino acid-dependent reactions. We also analyzed the evolution of class IIa ARSs.

Academic Significance and Societal Importance of the Research Achievements

本研究から、生命誕生初期の原始タンパク質のアミノ酸組成に関する重要な知見が得られた。特に、初期地球環境で容易に合成されるアミノ酸、隕石中から見つかっているアミノ酸など、初期地球上に比較的多く存在したと推測されるアミノ酸種が、タンパク質の安定な立体構造形成に重要であることを明らかにした。加えて、本研究成果から、宇宙における生命起源の場として、タンパク質、あるいは、タンパク質に代わる生命機能を司る生体高分子の安定な立体構造形成に必須な10種類程度のアミノ酸、あるいは、アミノ酸に代わるビルディングブロックが利用可能な地域・天体が有力であると予想できる。

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • Research Products

    (28 results)

All 2020 2019 2018 2017

All Journal Article (8 results) (of which Peer Reviewed: 6 results,  Open Access: 4 results) Presentation (20 results) (of which Int'l Joint Research: 4 results,  Invited: 4 results)

  • [Journal Article] Reconstruction and characterization of thermally stable and catalytically active proteins comprising an alphabet of ~13 amino acids2020

    • Author(s)
      Kimura M, Akanuma S.
    • Journal Title

      J. Mol. Evol.

      Volume: - Issue: 4 Pages: 372-381

    • DOI

      10.1007/s00239-020-09938-0

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Planktonic adaptive evolution to the sea surface temperature in the Neoproterozoic inferred from ancestral NDK of marine cyanobacteria2019

    • Author(s)
      Harada M, Nagano A, Yagi S, Furukawa R, Yokobori S, Yamagishi A.
    • Journal Title

      Earth and Planetary Science Letters

      Volume: 522 Pages: 98-106

    • DOI

      10.1016/j.epsl.2019.06.014

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Exploring the Amino Acid Composition in Primitive Proteins Using a Reconstructed Ancestral Protein2019

    • Author(s)
      AKANUMA Satoshi
    • Journal Title

      Seibutsu Butsuri

      Volume: 59 Issue: 1 Pages: 023-025

    • DOI

      10.2142/biophys.59.023

    • NAID

      130007557828

    • ISSN
      0582-4052, 1347-4219
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The Common Ancestor of All Modern Life2019

    • Author(s)
      Akanuma Satoshi
    • Journal Title

      Astrobiology:From the Origins of Life to the Search for Extraterrestrial Intelligence (eds. Yamagishi A, Kakegawa T, Usui T) Springer

      Volume: - Pages: 91-103

    • DOI

      10.1007/978-981-13-3639-3_7

    • ISBN
      9789811336386, 9789811336393
    • Related Report
      2018 Annual Research Report
  • [Journal Article] Reduced amino acid set proteins suggest a role of prebiotic amino acids in primitive protein synthesis2018

    • Author(s)
      Shibue Rei, Akanuma Satoshi
    • Journal Title

      Viva Origino

      Volume: 46 Pages: 4-4

    • NAID

      130008116896

    • Related Report
      2018 Annual Research Report
    • Open Access
  • [Journal Article] 人類への進化のはじまり:生命の起源と全生物の最後の共通祖先2018

    • Author(s)
      赤沼哲史、渋江怜
    • Journal Title

      人間科学研究

      Volume: 31 Pages: 139-145

    • NAID

      120006734701

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Comprehensive reduction of amino acid set in a protein suggests the importance of prebiotic amino acids for stable proteins2018

    • Author(s)
      Shibue Rei、Sasamoto Takahiro、Shimada Masami、Zhang Bowen、Yamagishi Akihiko、Akanuma Satoshi
    • Journal Title

      Scientific Reports

      Volume: 8 Issue: 1 Pages: 1227-1227

    • DOI

      10.1038/s41598-018-19561-1

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Characterization of Reconstructed Ancestral Proteins Suggests a Change in Temperature of the Ancient Biosphere2017

    • Author(s)
      Akanuma Satoshi
    • Journal Title

      Life

      Volume: 7 Issue: 3 Pages: 33-33

    • DOI

      10.3390/life7030033

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] 祖先アミノアシル tRNA 合成酵素の復元に基づく遺伝暗号の進化の解析2019

    • Author(s)
      横堀伸一,馬場柾,笹本峻弘,松田直樹,橋本ちひろ,村松あやか,佐藤陸, 遠藤有紀,宮下奈津実,丸山真歩,横川隆志,古川龍太郎,山岸明彦
    • Organizer
      第21回日本進化学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 遺伝暗号は進化する2019

    • Author(s)
      横堀伸一
    • Organizer
      2019年度生命の起原・アストロバイオロジー夏の学校
    • Related Report
      2019 Annual Research Report
  • [Presentation] ほぼ10アミノ酸種で再構成した酵素の解析2019

    • Author(s)
      赤沼哲史
    • Organizer
      2019年度アストロバイオロジーワークショップ
    • Related Report
      2019 Annual Research Report
  • [Presentation] 祖先配列復元とその解析に基づくClass IaアミノアシルtRNA合成酵素の進化2019

    • Author(s)
      横堀伸一、古川龍太郎、松田直樹、笹本峻弘、横川隆志、山岸明彦
    • Organizer
      2019年度アストロバイオロジーワークショップ
    • Related Report
      2019 Annual Research Report
  • [Presentation] 祖先配列の再構成とタンパク質単純化による原始アミノ酸組成の探索2019

    • Author(s)
      赤沼哲史、古川龍太郎
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 祖先Class IaアミノアシルtRNA合成酵素の基質特異性に基づく初期翻訳系の進化2019

    • Author(s)
      古川龍太郎、馬場柾、松田直樹、笹本峻弘、横川隆志、横堀伸一、山岸明彦
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 11アミノ酸種だけを用いた活性を持つ酵素の再構成2019

    • Author(s)
      赤沼哲史
    • Organizer
      第44回生命の起原および進化学会学術講演会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Class IIaアミノアシルtRNA合成酵素の分子系統解析に基づく初期翻訳系の進化2019

    • Author(s)
      古川龍太郎、横堀伸一、山岸明彦
    • Organizer
      第44回生命の起原および進化学会学術講演会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Protein engineering experiments to explore the evolution of early life2019

    • Author(s)
      Akanuma S
    • Organizer
      New Frontier in Protein Design & Engineering
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Evolution of life revealed from genetic information2018

    • Author(s)
      Yamagishi, A., Yokobori S., Akanuma S.
    • Organizer
      Puzzles and Solutions in Astrobiology
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Quest for ancestors of eukaryotic cell; Implications from evolution of aminoacyl tRNA synthethases2018

    • Author(s)
      Yokobori S
    • Organizer
      Puzzles and Solutions in Astrobiology
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 生命の初期進化を探る蛋白質工学研究2018

    • Author(s)
      赤沼哲史
    • Organizer
      第18回日本蛋白質科学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 少数種アミノ酸で再構成されたタンパク質が示唆する前生物的アミノ酸の役割2018

    • Author(s)
      渋江 怜、笹本 峻弘、山岸 明彦、赤沼 哲史
    • Organizer
      第18回日本蛋白質科学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 原始地球上に比較的多く存在したと推定されるアミノ酸種のタンパク質合成における役割2018

    • Author(s)
      赤沼哲史
    • Organizer
      日本進化学会第20回大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Protein engineering studies to explore primordial proteins’ characteristics2018

    • Author(s)
      Akanuma S
    • Organizer
      Extremophiles 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Contribution of a hydrophobic amino acid letter(s) to the stability and activity of a reconstructed ancestral nucleoside diphosphate kinase2018

    • Author(s)
      Shibue R., Akanuma S.
    • Organizer
      Extremophiles 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] アミノアシルtRNA合成酵素の分子系統解析と祖先酵素復元に基づく翻訳系の進化の解析2018

    • Author(s)
      横堀伸一
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 共通祖先2018

    • Author(s)
      赤沼哲史
    • Organizer
      アストロバイオロジーセンター(ABC)シンポジウム2018
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 網羅的アミノ酸欠損実験によって示唆された前生物的アミノ酸のタンパク質安定性への寄与2018

    • Author(s)
      渋江怜、赤沼哲史
    • Organizer
      生命の起原および進化学会第43回学術講演会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 20種未満のアミノ酸によるタンパク質の再構成2017

    • Author(s)
      赤沼哲史
    • Organizer
      2017年度日本アストロバイオロジーネットワークワークショップ
    • Related Report
      2017 Annual Research Report

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Published: 2017-04-28   Modified: 2021-02-19  

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