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Evolutionary improvement of mutational robustness at the genomic scale

Research Project

Project/Area Number 15KT0078
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeMulti-year Fund
Section特設分野
Research Field Constructive Systems Biology
Research InstitutionThe University of Tokyo (2017-2018)
Osaka University (2015-2016)

Principal Investigator

tsuru saburo  東京大学, 大学院理学系研究科(理学部), 特任助教 (80594506)

Project Period (FY) 2015-07-10 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥17,940,000 (Direct Cost: ¥13,800,000、Indirect Cost: ¥4,140,000)
Fiscal Year 2017: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Fiscal Year 2016: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Fiscal Year 2015: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
Keywordsゲノム / 変異 / 遺伝子 / 遺伝子発現 / ゆらぎ / 大腸菌 / 変異率 / 進化 / ゲノム進化 / 進化生物学
Outline of Final Research Achievements

Using Escherichia coli, a model bacterium, an evolution experiment was performed under highly mutagenic environment for several years. Analyzing genomic mutations revealed that mutations tends were enriched in genes related to stress response. In addition, growth reduction under highly mutagenic environment was derived not only by deleterious load of the accumulated mutations, but also by another harmful effect associated with mutagenic physiology. Moreover, mutations were likely to be accumulated at a specific sequence motif which consists of few nucleotide at least. These evidence would help us identify specific genes responsible for growth robustness against deleterious mutations at the genomic scale and design mutationally stable genome.

Academic Significance and Societal Importance of the Research Achievements

変異は、遺伝情報に生じるエラーであり、病気の原因となるだけでなく、有用物質の生産性を低下させる原因になるなど、私たちの日常社会と深い関わりがあります。そのため、変異や変異の影響を抑制する原理の発見や技術開発が多くの学術分野で望まれています。本研究で得られた成果は、変異が細胞の増殖に与える悪影響に注目し、どのような遺伝子群が変異の有害作用の抑制に関わっており、どのような塩基配列であれば変異そのものが生じにくくなるかについて、示唆に富む情報を提供しています。本研究で得られた情報を基礎として発展させれば、変異に頑強でより安定な人工ゲノムを開発するなどの応用が可能になると期待されます。

Report

(5 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • 2016 Research-status Report
  • 2015 Research-status Report
  • Research Products

    (26 results)

All 2019 2018 2017 2016 2015 Other

All Int'l Joint Research (2 results) Journal Article (8 results) (of which Int'l Joint Research: 2 results,  Peer Reviewed: 8 results,  Open Access: 8 results,  Acknowledgement Compliant: 2 results) Presentation (16 results) (of which Int'l Joint Research: 6 results)

  • [Int'l Joint Research] University of Exeter/Newcastle university(United Kingdom)

    • Related Report
      2017 Research-status Report
  • [Int'l Joint Research] University of Exeter(英国)

    • Related Report
      2016 Research-status Report
  • [Journal Article] Development of an Automated UV Irradiation Device for Microbial Cell Culture2018

    • Author(s)
      Shibai Atsushi、Tsuru Saburo、Yomo Tetsuya
    • Journal Title

      SLAS TECHNOLOGY: Translating Life Sciences Innovation

      Volume: 2472630318800283 Issue: 3 Pages: 1-7

    • DOI

      10.1177/2472630318800283

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Enhancement of K-strategy evolution in histidine utilization using a container with compartments2018

    • Author(s)
      Komori Takahiro、Shibai Atsushi、Saito Hiromi、Akeno Yuya、Germond Arno、Horinouchi Takaaki、Furusawa Chikara、Tsuru Saburo
    • Journal Title

      Genes to Cells

      Volume: 23 Issue: 10 Pages: 893-903

    • DOI

      10.1111/gtc.12640

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Mutation accumulation under UV radiation in Escherichia coli2017

    • Author(s)
      Atsushi Shibai, Yusuke Takahashi, Yuka Ishizawa, Daisuke Motooka, Shota Nakamura, Bei-Wen Ying, Saburo Tsuru
    • Journal Title

      Scientific Reports

      Volume: 7(14531) Issue: 1 Pages: 1-12

    • DOI

      10.1038/s41598-017-15008-1

    • NAID

      120007128813

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Density-Dependent Recycling Promotes the Long-Term Survival of Bacterial Populations during Periods of Starvation2017

    • Author(s)
      Sotaro Takano, Bogna J. Pawlowsk, Ivana Gudelj, Tetsuya Yomo, Saburo Tsuru
    • Journal Title

      mBio

      Volume: 8 Issue: 1 Pages: 1-14

    • DOI

      10.1128/mbio.02336-16

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Molecular Clock of Neutral Mutations in a Fitness-Increasing Evolutionary Process2015

    • Author(s)
      Kishimoto T, Ying BW, Tsuru S, Iijima L, Suzuki S, Hashimoto T, Oyake A, Kobayashi H, Someya Y, Narisawa D, Yomo T
    • Journal Title

      PLOS Genetics

      Volume: 11(7) Issue: 7 Pages: 1-18

    • DOI

      10.1371/journal.pgen.1005392

    • NAID

      120007136182

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Evolutionary Consequence of a Trade-Off between Growth and Maintenance along with Ribosomal Damages2015

    • Author(s)
      Ying BW, Honda T, Tsuru S, Seno S, Matsuda H, Kazuta Y, Yomo T
    • Journal Title

      PLOS ONE

      Volume: 10(8) Issue: 8 Pages: e0135639-e0135639

    • DOI

      10.1371/journal.pone.0135639

    • NAID

      120007136183

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genomic confirmation of nutrient-dependent mutability of mutators in Escherichia coli2015

    • Author(s)
      Tsuru S, Ishizawa Y, Shibai A, Takahashi Y, Motooka D, Nakamura S, Yomo T
    • Journal Title

      Genes to Cells

      Volume: 20(12) Issue: 12 Pages: 972-981

    • DOI

      10.1111/gtc.12300

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] The propagation of perturbations in rewired bacterial gene networks2015

    • Author(s)
      Rebecca Baumstark, Sonja H?nzelmann, Saburo Tsuru, Yolanda Schaerli, Mirko Francesconi, Francesco M. Mancuso, Robert Castelo & Mark Isalan
    • Journal Title

      Nature Communications

      Volume: 6(10105) Issue: 1

    • DOI

      10.1038/ncomms10105

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] トランスポゾーム発現大腸菌によるゲノム縮小の進化実験2019

    • Author(s)
      金井雄樹, 津留三良, 古澤力
    • Organizer
      定量生物学の会第九回年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 高変異率条件における細菌の長期実験進化2018

    • Author(s)
      芝井厚, 堀之内貴明, 古澤力, 津留三良
    • Organizer
      日本進化学会第20回大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 分子進化速度の発現量依存性2018

    • Author(s)
      分子進化速度の発現量依存性
    • Organizer
      新学術領域:進化制約方向性理論情報交換会
    • Related Report
      2018 Annual Research Report
  • [Presentation] A persisting constraint on the rate of protein sequence evolution2018

    • Author(s)
      Saburo Tsuru
    • Organizer
      46th Naito Conference
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] タンパク質の進化速度における進化的制約の持続性2018

    • Author(s)
      津留三良, 芝井厚, 堀之内貴明, 古澤力
    • Organizer
      第12回日本ゲノム微生物学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] 細菌ゲノムへの遺伝子不活化変異の蓄積2018

    • Author(s)
      芝井厚, 津留三良, 堀之内貴明, 古澤力
    • Organizer
      12回日本ゲノム微生物学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] タンパク質の進化速度における進化的制約の持続性2018

    • Author(s)
      津留三良
    • Organizer
      第43回生命の起源および進化学会学術講演会
    • Related Report
      2017 Research-status Report
  • [Presentation] 細胞の増殖能力は変異に対してどれほど頑強か2017

    • Author(s)
      芝井厚, 石澤裕佳, 高橋祐輔, 元岡大祐, 中村昇太, 津留三良
    • Organizer
      日本進化学会第19回大会
    • Related Report
      2017 Research-status Report
  • [Presentation] バクテリアの長期定常期における密度依存的なリサイクリング活動2017

    • Author(s)
      高野壮太朗, Pawlowska Bogna J., Gudelj Ivana, 四方哲也, 津留三良
    • Organizer
      第55回日本生物物理学会年会
    • Related Report
      2017 Research-status Report
  • [Presentation] Maintenance of bacterial population survival during starvation realised by interactions between dead and viable cells2016

    • Author(s)
      Sotaro Takano, Saburo Tsuru
    • Organizer
      International Conference on Systems Biology 2016 (ICSB 16)
    • Place of Presentation
      Barcelona, Spain
    • Year and Date
      2016-09-16
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Prediction and experimental verification of experimental evolution of Escherichia coli2016

    • Author(s)
      Atsushi Shibai, Shigeto Seno, Daisuke Motooka, Shota Nakamura, Yoshihiro Sakatani, Mari Otokura, Hiromi Saito, Taro Furubayashi, Chikara Furusawa, Norikazu Ichihashi, Saburo Tsuru
    • Organizer
      16th International Symposium on Microbial Ecology (ISME 16)
    • Place of Presentation
      Montreal, Canada
    • Year and Date
      2016-08-21
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Modeling of bacterial persistence by population density-dependent recycling during long-term starvation2016

    • Author(s)
      Sotaro Takano, Bogna J. Pawlowska, Ivana Gudelj, Saburo Tsuru
    • Organizer
      16th International Symposium on Microbial Ecology (ISME 16)
    • Place of Presentation
      Montreal, Canada
    • Year and Date
      2016-08-21
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] Reductive evolution towards primitive life: What will we see?2016

    • Author(s)
      Atsushi Shibai, Daisuke Motooka, Shota Nakamura and Saburo Tsuru
    • Organizer
      The 15th International Conference on the Synthesis and Simulation of Living Systems
    • Place of Presentation
      Cancun, Mexico
    • Year and Date
      2016-07-04
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Presentation] 栄養依存的な変異率のゲノムワイドな実証2016

    • Author(s)
      津留 三良、石澤 裕佳、芝井 厚、高橋 佑輔、元岡 大祐、中村 昇太
    • Organizer
      第10回日本ゲノム微生物学会年会
    • Place of Presentation
      東京工業大学 大岡山キャンパス(東京)
    • Year and Date
      2016-03-04
    • Related Report
      2015 Research-status Report
  • [Presentation] Mutation accumulation of bacterial genome toward genomic inactivation2015

    • Author(s)
      Saburo Tsuru, Atsushi Shibai
    • Organizer
       第53回日本生物物理学会
    • Place of Presentation
      金沢大学角間キャンパス(金沢)
    • Year and Date
      2015-09-13
    • Related Report
      2015 Research-status Report
  • [Presentation] Bacterial genome reduction through experimental evolution2015

    • Author(s)
      Atsushi Shibai, Saburo Tsuru,Tetsuya Yomo
    • Organizer
      QBiC Symposium 2015
    • Place of Presentation
      RIKEN Quantitative Biology Center (QBiC)(大阪)
    • Year and Date
      2015-08-24
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research

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Published: 2015-07-14   Modified: 2020-03-30  

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