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Controlling evolutionary dynamics by feedback regulation to selection environments

Research Project

Project/Area Number 17H03622
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field System genome science
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Furusawa Chikara  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, チームリーダー (00372631)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥17,030,000 (Direct Cost: ¥13,100,000、Indirect Cost: ¥3,930,000)
Fiscal Year 2019: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2018: ¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2017: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Keywords進化実験 / 大腸菌 / フィードバック制御 / 実験自動化
Outline of Final Research Achievements

The purpose of this study is to elucidate the interaction network between stress tolerance in bacteria and to develop a method to control the evolutionary dynamics. We performed laboratory evolution of E. coli cells under 95 stress environments and obtained stress-resistant strains. Then, we quantified gene expression profiles, genome mutations, and resistance profiles to various stress environments. Based on the data, we developed a method to control evolutionary dynamics by adding feedback regulations to selection environments. As a result, we successfully observed evolutionary dynamics toward target phenotypes, which cannot be obtained by the selection using single drugs.

Academic Significance and Societal Importance of the Research Achievements

本研究では、系統的な進化実験のデータに基づき、ターゲットとした表現型への進化ダイナミクスを構成可能であることが示された。この手法を用いて様々なターゲット表現型への進化実験を行うことにより、どのような進化ダイナミクスが容易であるか、あるいは困難であるかを定量的に評価でき、進化過程がどのように拘束されているか、新たな理解をもたらすと期待できる。また、自然界で見られた進化過程を実験室で模倣することのより、そこで生じ得る表現型と遺伝子型の変化を詳細に解析することが可能となる。さらに、目的の表現型を持つ微生物をデザインする進化実験が実現すれば、医学的・生物工学的な応用を十分に期待することができる。

Report

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

    (52 results)

All 2020 2019 2018 2017

All Journal Article (9 results) (of which Peer Reviewed: 9 results,  Open Access: 7 results) Presentation (41 results) (of which Int'l Joint Research: 13 results,  Invited: 21 results) Book (2 results)

  • [Journal Article] Suppression of antibiotic resistance evolution by single-gene deletion2020

    • Author(s)
      Horinouchi Takaaki、Maeda Tomoya、Kotani Hazuki、Furusawa Chikara
    • Journal Title

      Scientific Reports

      Volume: 10 Issue: 1 Pages: 4178-4178

    • DOI

      10.1038/s41598-020-60663-6

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Understanding metabolic adaptation by using bacterial laboratory evolution and trans-omics analysis2020

    • Author(s)
      Horinouchi Takaaki、Furusawa Chikara
    • Journal Title

      Biophysical Reviews

      Volume: - Issue: 3 Pages: 677-682

    • DOI

      10.1007/s12551-020-00695-4

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Universal Laws in Phenotypic Changes through Adaptation and Evolution2019

    • Author(s)
      金子邦彦,古澤力
    • Journal Title

      Butsuri

      Volume: 74 Issue: 3 Pages: 137-145

    • DOI

      10.11316/butsuri.74.3_137

    • NAID

      130007690582

    • ISSN
      0029-0181, 2423-8872
    • Year and Date
      2019-03-05
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Analysis of Bacterial Laboratory Evolution toward Prediction, Control, and Macroscopic State Theory of Evolution2019

    • Author(s)
      FURUSAWA Chikara、HORINOUCHI Takaaki
    • Journal Title

      Seibutsu Butsuri

      Volume: 59 Issue: 5 Pages: 262-265

    • DOI

      10.2142/biophys.59.262

    • NAID

      130007718911

    • ISSN
      0582-4052, 1347-4219
    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] High-throughput identification of the sensitivities of an Escherichia coli ΔrecA mutant strain to various chemical compounds2019

    • Author(s)
      Maeda Tomoya、Horinouchi Takaaki、Sakata Natsue、Sakai Aki、Furusawa Chikara
    • Journal Title

      The Journal of Antibiotics

      Volume: - Issue: 7 Pages: 1-8

    • DOI

      10.1038/s41429-019-0160-5

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Toward prediction and control of antibiotic-resistance evolution2018

    • Author(s)
      Furusawa Chikara、Horinouchi Takaaki、Maeda Tomoya
    • Journal Title

      Current Opinion in Biotechnology

      Volume: 54 Pages: 45-49

    • DOI

      10.1016/j.copbio.2018.01.026

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Formation of dominant mode by evolution in biological systems2018

    • Author(s)
      Furusawa Chikara、Kaneko Kunihiko
    • Journal Title

      Physical Review E

      Volume: 97 Issue: 4 Pages: 1-24

    • DOI

      10.1103/physreve.97.042410

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Improvement of isopropanol tolerance of Escherichia coli using adaptive laboratory evolution and omics technologies2017

    • Author(s)
      Horinouchi Takaaki、Sakai Aki、Kotani Hazuki、Tanabe Kumi、Furusawa Chikara
    • Journal Title

      Journal of Biotechnology

      Volume: 255 Pages: 47-56

    • DOI

      10.1016/j.jbiotec.2017.06.408

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Prediction of Cross-resistance and Collateral Sensitivity by Gene Expression profiles and Genomic Mutations2017

    • Author(s)
      Horinouchi Takaaki、Suzuki Shingo、Kotani Hazuki、Tanabe Kumi、Sakata Natsue、Shimizu Hiroshi、Furusawa Chikara
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 1-11

    • DOI

      10.1038/s41598-017-14335-7

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] High-dimensional data acquisition for analysis of microbial evolution and ecology2020

    • Author(s)
      C. Furusawa
    • Organizer
      The 29th Hot Spring Harbor International Symposium
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 実験室進化手法を応用した大腸菌のストレス耐性機構の解明とその制御2020

    • Author(s)
      古澤 力
    • Organizer
      日本農芸化学会大会2020
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 機械学習と大腸菌実験室進化データを用いた進化拘束の解析2020

    • Author(s)
      岩澤諄一郎, 前田智也, 堀之内貴明, 古澤力
    • Organizer
      第14回日本ゲノム微生物学会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Analysis of Evolutionary Constraints and Plasticity by Microbial Laboratory Evolution and Computational Models2019

    • Author(s)
      C. Furusawa
    • Organizer
      2nd Joint Symposium between MBI and UBI
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] High-dimensional data acquisition for analysis of microbial evolution and ecology2019

    • Author(s)
      C. Furusawa
    • Organizer
      The 1st Symposium of China-Japan Joint Laboratory for Natural Products and Chemical Biology--Trends in Gut Microbiome Research
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Analysis of Evolutionary Constraints and Plasticity by Microbial Laboratory Evolution and Computational Models2019

    • Author(s)
      C. Furusawa
    • Organizer
      From Molecular Basis to Predictability and Control of Evolution
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Analysis of Phenotypic Constraints and Plasticity by Microbial Laboratory Evolution, The 20th International Conference on Systems Biology2019

    • Author(s)
      C. Furusawa
    • Organizer
      The 20th International Conference on Systems Biology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Combining interpretable machine learning with high dimensional multi-omics data from laboratory evolution2019

    • Author(s)
      J. Iwasawa, T. Maeda, T. Horinouchi, C. Furusawa
    • Organizer
      The 20th International Conference on Systems Biology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Identification of mutations conferring resistance to anti-tuberculosis drugs by laboratory evolution of non-pathogenic Mycobacterium on agar plate2019

    • Author(s)
      T. Maeda, C. Furusawa
    • Organizer
      The 20th International Conference on Systems Biology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Feedback control of evolutionary trajectory of bacterial cells on fitness landscape2019

    • Author(s)
      A. Shibai, C. Furusawa
    • Organizer
      The 20th International Conference on Systems Biology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 自動化システムを用いた大腸菌進化実験:進化の予測と制御へ向けて2019

    • Author(s)
      古澤 力
    • Organizer
      第92回日本生化学会大会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Analysis of Phenotypic Constraints and Plasticity by Microbial Laboratory Evolution2019

    • Author(s)
      C. Furusawa
    • Organizer
      第57回日本生物物理学会年会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 生物システムの安定性と可塑性の理解へ向けて:実験室進化と理論解析2019

    • Author(s)
      古澤 力
    • Organizer
      CBI学会2019年大会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Toward prediction and control of microbial evolution: Analysis of phenotypic constraints in laboratory evolution2019

    • Author(s)
      古澤 力
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 適応度地形の動的変化を通した細菌進化のフィードバック制御の試み2019

    • Author(s)
      芝井厚,古澤力
    • Organizer
      日本進化学会第21回大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Laboratory evolution of Escherichia coli reveals constrained evolutionary states for antibiotic resistance2019

    • Author(s)
      岩澤諄一郎, 前田智也, 堀之内貴明, 古澤力
    • Organizer
      第57回日本生物物理学会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 自動培養系を用いた細菌実験進化のフィードバック制御の試み2019

    • Author(s)
      芝井厚,古澤力
    • Organizer
      第11回生命情報科学若手の会
    • Related Report
      2019 Annual Research Report
  • [Presentation] ストレス条件と耐性獲得との関係に基づく細菌進化のフィードバック制御2019

    • Author(s)
      芝井厚,古澤力
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 全自動培養システムを用いた多種ストレス環境下における大腸菌の大規模実験室進化2019

    • Author(s)
      1前田智也、岩澤諄一郎、堀之内貴明、阪田奈津枝、川田正子、小谷葉月、酒井亜希、田邊久美、古澤力
    • Organizer
      第13回日本ゲノム微生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 細菌の薬剤耐性進化における変異率と進化速度の関係2019

    • Author(s)
      芝井厚, 井筒弥那子, 古澤力
    • Organizer
      第13回日本ゲノム微生物学会年会
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 細菌の抗生物質耐性進化における最適変異率モデルと実験検証2018

    • Author(s)
      芝井厚, 井筒弥那子, 古澤力
    • Organizer
      第41回日本分子生物学会年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 全自動培養システムを用いた多種ストレス環境下における大腸菌の大規模実験室進化2018

    • Author(s)
      1前田智也、堀之内貴明、阪田奈津枝、川田正子、小谷葉月、酒井亜希、田邊久美、古澤力
    • Organizer
      生命科学系フロンティアミーティング2018
    • Related Report
      2018 Annual Research Report
  • [Presentation] 大規模実験室進化を用いた転写因子の破壊による大腸菌の薬剤耐性化の制御2018

    • Author(s)
      堀之内貴明, 前田智也 小谷葉月, 酒井亜希, 古澤力
    • Organizer
      日本生物工学会第70回大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] High-throughput Laboratory Evolution of E. coli to Unveil Phenotypic Plasticity and Constraint2018

    • Author(s)
      Chikara Furusawa, Takaaki Horinouchi, Tomoya Maeda
    • Organizer
      第56回日本生物物理学会年会
    • 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] 「細胞状態の記述・予測・制御へ向けて:構成的実験と理論解析」2018

    • Author(s)
      古澤力
    • Organizer
      JST-CRDS 多次元生命システム研究開発戦略 科学技術未来ワークショップ
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 「生物の状態変化をどのように記述すべきか:実験室進化と理論解析」2018

    • Author(s)
      古澤力
    • Organizer
      第6回MACSコロキウム
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 「生物システムの記述と制御に向けて:大腸菌進化実験と理論解析」2018

    • Author(s)
      古澤力
    • Organizer
      第15回 生物数学の理論とその応用 -次世代の数理科学への展開-
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 「表現型進化はどのように拘束されているか:進化実験を用いた定量解析」2018

    • Author(s)
      古澤力
    • Organizer
      進化学会第20会大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] High-throughput Laboratory Evolution of E. coli to Unveil Phenotypic Plasticity and Constraint2018

    • Author(s)
      Chikara Furusawa
    • Organizer
      46th Naito Conference, Sapporo
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] High-throughput laboratory evolution of E. coli: toward understanding of phenotypic plasticity and constraint2018

    • Author(s)
      Chikara Furusawa
    • Organizer
      Euro EvoDevo2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] High-throughput Laboratory Evolution of E. coli to Unveil Phenotypic Plasticity and Constraint2018

    • Author(s)
      Chikara Furusawa
    • Organizer
      1st Asia Evo.
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Phenotypic diversity and constraints in microbial adaptive evolution2018

    • Author(s)
      Chikara Furusawa
    • Organizer
      Les Houches School“Evolution of Diversity ”
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 全自動培養システムを用いた多種ストレス環境下における大腸菌の大規模実験室 進化2018

    • Author(s)
      前田智也, 堀之内貴明, 阪田奈津枝, 小谷葉月, 酒井亜希, 田邊久美, 古澤力
    • Organizer
      第12 回日本ゲノム微生物学会年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 大腸菌進化実験を用いた進化的拘束の解析2018

    • Author(s)
      古澤力
    • Organizer
      生命の起源および進化学会第43 回学術講演会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 実験室進化・オミックス解析・破壊株スクリーニングに基づく表現型メモリー機構の理解への試み2017

    • Author(s)
      堀之内貴明, 前田智也, 古澤力
    • Organizer
      生命情報科学若手の会第9 回研究会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 実験室進化により得られたメチルグリオキサール耐性大腸菌のマルチオミクス解析2017

    • Author(s)
      堀之内貴明, 徳山健斗, 前田智也, 松田史生, 清水浩, 古澤力
    • Organizer
      第11 回メ タボロームシンポジウム
    • Related Report
      2017 Annual Research Report
  • [Presentation] 全自動培養システムを用いた多種ストレス環境化における大腸菌進化ダイナミクスの解析2017

    • Author(s)
      前田智也, 堀之内貴明, 阪田奈津枝, 小谷葉月, 酒井亜希, 田邊久美, 古澤力
    • Organizer
      第16 回微生物研究会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 大腸菌実験室進化とオミックス解析を用いて大腸菌の適応進化過程を解析する2017

    • Author(s)
      堀之内貴明, 前田智也, 古澤力
    • Organizer
      第五回NGS 現場の会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 大規模実験室進化とオミックス解析による大腸菌のストレス耐性機構の解析2017

    • Author(s)
      堀之内貴明, 前田智也, 古澤力
    • Organizer
      第69 回生物工学会大会シンポジウム
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 大腸菌の人工進化実験における表現型・遺伝子型の網羅的解析2017

    • Author(s)
      古澤力
    • Organizer
      第16 回微生物研究会-微生物の多様な生き様にせまる
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Book] 定量生物学2018

    • Author(s)
      古澤力
    • Total Pages
      290
    • Publisher
      化学同人
    • ISBN
      9784759817300
    • Related Report
      2018 Annual Research Report
  • [Book] 実験医学別冊「あなたのラボにAI×ロボットがやってくる」2017

    • Author(s)
      古澤力, 前田智也, 堀之内貴明
    • Total Pages
      144
    • Publisher
      羊土社
    • ISBN
      9784758122368
    • Related Report
      2017 Annual Research Report

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

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