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E. coli cells growing under starvation

Research Project

Project/Area Number 26506003
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field 宇宙生命学
Research InstitutionUniversity of Tsukuba

Principal Investigator

YING BEIWEN  筑波大学, 生命環境系, 准教授 (90422401)

Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2016: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2015: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2014: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Keywords増殖 / 実験進化 / 適応 / 栄養枯渇 / 大腸菌 / 翻訳 / 飢餓 / 増殖速度
Outline of Final Research Achievements

Expreimental evolution with the E. coli cells in a repeated starvation and resuscitation manner was performed. As a common evolutionary consequence in multiple lines, the evovled cells showed a significant decrease in growth fitness under rich conditions but an improved competence with enhanced affinity to resource under poor conditions. This evolutionary change was accompanied by the fixation of repressed translation and improved transport, owing to the genetic disturbance in regulator and ribosome. Our study provides an experimental evidence of an evolutionary transition in growth economics from time-saving to resource-saving strategies, in adaptation to the slowly and irregularly oscillated environments. It indicated that the resource-saving nature of the evolved cells compensated the deficiency in growth fitness.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (22 results)

All 2017 2016 2015 2014 Other

All Journal Article (11 results) (of which Peer Reviewed: 11 results,  Open Access: 10 results,  Acknowledgement Compliant: 4 results) Presentation (8 results) (of which Int'l Joint Research: 1 results,  Invited: 2 results) Remarks (3 results)

  • [Journal Article] Precise analysis of bacterial growth in a high-throughput manner2017

    • Author(s)
      M Kurokawa, BW Ying
    • Journal Title

      JoVE

      Volume: in press

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Correlation between genome reduction and bacterial growth.2016

    • Author(s)
      M Kurokawa, S Seno, H Matsuda, BW Ying
    • Journal Title

      DNA Res

      Volume: 23 Issue: 6 Pages: 517-525

    • DOI

      10.1093/dnares/dsw035

    • NAID

      120007135048

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] The Escherichia coli transcriptome linked to growth fitness2016

    • Author(s)
      BW Ying, K Yama, K Kitahara, T Yomo
    • Journal Title

      Genomics Data

      Volume: 7 Pages: 1-3

    • DOI

      10.1016/j.gdata.2015.11.011

    • NAID

      120007135353

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Functional specialization in regulation and quality control in thermal adaptive evolution2015

    • Author(s)
      K Yama, Y Matsumoto, Y Murakami, S Seno, H Matsuda, K Gotoh, D Motooka, S Nakamura, BW Ying, T Yomo
    • Journal Title

      Genes Cells

      Volume: 20 Issue: 11 Pages: 943-955

    • DOI

      10.1111/gtc.12298

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Bacterial transcriptome reorganization in thermal adaptive evolution2015

    • Author(s)
      B-W. Ying, Y. Matsumoto, K. Kitahara, S. Suzuki, N. Ono, C. Furusawa, T. Kishimoto, T. Yomo
    • Journal Title

      BMC Genomics

      Volume: 16 Issue: 1 Pages: 1-11

    • DOI

      10.1186/s12864-015-1999-x

    • NAID

      120007136181

    • 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] 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] Global coordination in adaptation to gene rewiring.2015

    • Author(s)
      Y Murakami, Y Matsumoto, S Tsuru, BW Ying & T Yomo
    • Journal Title

      Nucleic Acids Res

      Volume: 43 Issue: 2 Pages: 1304-1316

    • DOI

      10.1093/nar/gku1366

    • NAID

      120007130352

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Nutrient-dependent growth defects and mutability of mutators in Escherichia coli.2015

    • Author(s)
      Y Ishizawa, BW Ying, S Tsuru & T Yomo
    • Journal Title

      Genes Cells

      Volume: 20 Issue: 1 Pages: 68-76

    • DOI

      10.1111/gtc.12199

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Directed evolution of cell size in Escherichia coli.2014

    • Author(s)
      Yoshida M, Tsuru S, Hirata N, Seno S, Matsuda H, Ying BW, Yomo T.
    • Journal Title

      BMC Evol Biol

      Volume: 14

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A reduced genome decreases the host carrying capacity for foreign DNA.2014

    • Author(s)
      Y Akeno, BW Ying, S Tsuru & T Yomo
    • Journal Title

      Microbiol Cell Factories

      Volume: 13 Issue: 1

    • DOI

      10.1186/1475-2859-13-49

    • NAID

      120007136730

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] 大腸菌ゲノム縮小株の増殖に対する研究2017

    • Author(s)
      黒川真臣、瀬尾茂人、松田秀雄、應ベイ文
    • Organizer
      第11回日本ゲノム微生物学会年会
    • Place of Presentation
      慶応義塾大学、神奈川県藤沢市
    • Year and Date
      2017-03-02
    • Related Report
      2016 Annual Research Report
  • [Presentation] ヒスチジン枯渇を長期間経験したヒスチジン要求性大腸菌株に対する解析2017

    • Author(s)
      日原奨希、瀬尾茂人、松田秀雄、小椋義俊、林哲也、應ベイ文
    • Organizer
      第11回日本ゲノム微生物学会年会
    • Place of Presentation
      慶応義塾大学、神奈川県藤沢市
    • Year and Date
      2017-03-02
    • Related Report
      2016 Annual Research Report
  • [Presentation] 大腸菌ゲノム縮小における増殖速度と変異率の相関2017

    • Author(s)
      西村一成、黒川真臣、應ベイ文
    • Organizer
      第11回日本ゲノム微生物学会年会
    • Place of Presentation
      慶応義塾大学、神奈川県藤沢市
    • Year and Date
      2017-03-02
    • Related Report
      2016 Annual Research Report
  • [Presentation] Connecting bacterial growth with genome and transcriptome2016

    • Author(s)
      BW Ying
    • Organizer
      International Workshop on Synthetic Biology and Systems Biology of Microbes
    • Place of Presentation
      奈良先端技術大学院大学(奈良県生駒市)
    • Year and Date
      2016-03-17
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] An evolutionary trade-off between growth and sustainability accompanied by ribosomal damages2016

    • Author(s)
      BW Ying, T Honda, S Tsuru, S Seno, H Matsuda, Y Kazuta, T Yomo
    • Organizer
      日本ゲノム微生物学会第10回大会
    • Place of Presentation
      東京工業大学(東京都目黒区)
    • Year and Date
      2016-03-04
    • Related Report
      2015 Research-status Report
  • [Presentation] 大腸菌広域欠失株の増殖に対する数理的評価2016

    • Author(s)
      黒川真臣、瀬尾茂人、松田秀雄、イン ベイウェン
    • Organizer
      日本ゲノム微生物学会第10回大会
    • Place of Presentation
      東京工業大学(東京都目黒区)
    • Year and Date
      2016-03-04
    • Related Report
      2015 Research-status Report
  • [Presentation] Survival strategies learned from bacterial cells in laboratory2015

    • Author(s)
      BW Ying
    • Organizer
      2015 JSBi SIG Bio-Systems Theory Workshop
    • Place of Presentation
      東京医科歯科大学(東京都文京区)
    • Year and Date
      2015-11-27
    • Related Report
      2015 Research-status Report
    • Invited
  • [Presentation] 実験進化による極少栄養下で生きる大腸菌の創出2015

    • Author(s)
      イン ベイウェン、本田朋也、四方哲也
    • Organizer
      日本宇宙生物科学会第29回大会
    • Place of Presentation
      帝京大学(東京都板橋区)
    • Year and Date
      2015-09-26
    • Related Report
      2015 Research-status Report
  • [Remarks] 筑波大学研究者総覧

    • URL

      http://www.trios.tsukuba.ac.jp/researcher/0000003489

    • Related Report
      2016 Annual Research Report
  • [Remarks] 研究室HP

    • URL

      http://www.agbi.tsukuba.ac.jp/~ying/index.html

    • Related Report
      2016 Annual Research Report
  • [Remarks] 論文HP

    • URL

      https://academic.oup.com/dnaresearch/article-lookup/doi/10.1093/dnares/dsw035

    • Related Report
      2016 Annual Research Report

URL: 

Published: 2014-04-04   Modified: 2019-03-07  

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