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Identification of Limiting Step and Optimization of Metabolism based on Analysis of Dynamic Behaviors of Multilayers Omics Data

Research Project

Project/Area Number 16H04576
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Biofunction/Bioprocess
Research InstitutionOsaka University

Principal Investigator

SHIMIZU Hiroshi  大阪大学, 情報科学研究科, 教授 (00226250)

Co-Investigator(Kenkyū-buntansha) 松田 史生  大阪大学, 情報科学研究科, 教授 (50462734)
戸谷 吉博  大阪大学, 情報科学研究科, 准教授 (70582162)
Project Period (FY) 2016-04-01 – 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 2018: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000)
Fiscal Year 2017: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2016: ¥7,150,000 (Direct Cost: ¥5,500,000、Indirect Cost: ¥1,650,000)
Keywords反応速度論 / 物質生産 / インシリコデザイン / 代謝フラックス / 生物情報工学
Outline of Final Research Achievements

In microbial production system, it is important to rationally improve microbial metabolism and optimize production yield and production rate. In this study, we mainly focused on the improvement of production rate. We tried to develop a systematic method to extract limiting steps in the metabolic pathway. Precise analytical methods of metabolism, 13C-metabolic flux analysis, quantitation of proteins related to metabolism, and absolute quantitation of metabolite concentrations were conducted. These analytical data was used for thermodynamics analysis and kinetic modeling. Limiting steps in the central carbon metabolism of Escherichia coli was successfully identified and target production improvement was realized by designed genetic modification of the cells.

Academic Significance and Societal Importance of the Research Achievements

微生物細胞の代謝は多段階の化学反応であり、微生物生体触媒として用いることで、一つのプロセスによって原料を目的物質に変換することが可能である。しかし、多段階の反応が関与するため、どこにその律速点が存在するのかを知ることは容易ではない。微生物の代謝フラックス解析、酵素タンパク質定量、代謝物質絶対値を解析し、熱力学的手法の導入や代謝反応速度論モデルの利用によって代謝の律速点をシステマティックに抽出し効率的に遺伝子操作の戦略を提案できるシステムを開発したところに大きな意義がある。大腸菌のメバロン酸生産に適用することで、その有効性への道筋を示している。

Report

(4 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • Research Products

    (33 results)

All 2019 2018 2017 2016 Other

All Journal Article (10 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 9 results,  Acknowledgement Compliant: 1 results) Presentation (19 results) (of which Int'l Joint Research: 4 results,  Invited: 5 results) Book (3 results) Remarks (1 results)

  • [Journal Article] Magnesium starvation improves production of malonyl-CoA-derived metabolites in Escherichia coli2019

    • Author(s)
      Tokuyama Kento、Toya Yoshihiro、Matsuda Fumio、Cress Brady F.、Koffas Mattheos A.G.、Shimizu Hiroshi
    • Journal Title

      Metabolic Engineering

      Volume: 52 Pages: 215-223

    • DOI

      10.1016/j.ymben.2018.12.002

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] 計算機工学に基づく代謝設計とその有効性の実証に関する研究2019

    • Author(s)
      清水 浩
    • Journal Title

      生物工学誌

      Volume: 97 Pages: 13-20

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Metabolic engineering of mevalonate-producing Escherichia coli strains based on thermodynamic analysis2018

    • Author(s)
      Nagai Hikaru、Masuda Ami、Toya Yoshihiro、Matsuda Fumio、Shimizu Hiroshi
    • Journal Title

      Metabolic Engineering

      Volume: 47 Pages: 1-9

    • DOI

      10.1016/j.ymben.2018.02.012

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Application of adaptive laboratory evolution to overcome a flux limitation in an Escherichia coli production strain2018

    • Author(s)
      Tokuyama Kento、Toya Yoshihiro、Horinouchi Takaaki、Furusawa Chikara、Matsuda Fumio、Shimizu Hiroshi
    • Journal Title

      Biotechnology and Bioengineering

      Volume: 115 Issue: 6 Pages: 1542-1551

    • DOI

      10.1002/bit.26568

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Optimal 13 C-labeling of glycerol carbon source for precise flux estimation in Escherichia coli2018

    • Author(s)
      Toya Yoshihiro、Ohashi Shugo、Shimizu Hiroshi
    • Journal Title

      Journal of Bioscience and Bioengineering

      Volume: 125 Issue: 3 Pages: 301-305

    • DOI

      10.1016/j.jbiosc.2017.09.009

    • NAID

      210000005652

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Metabolic engineering of isopropyl alcohol-producing Escherichia coli strains with 13C-metabolic flux analysis2017

    • Author(s)
      Okahashi Nobuyuki、Matsuda Fumio、Yoshikawa Katsunori、Shirai Tomokazu、Matsumoto Yoshiko、Wada Mitsufumi、Shimizu Hiroshi
    • Journal Title

      Biotechnolgy and Bioengineering

      Volume: 114 Issue: 12 Pages: 2782-2793

    • DOI

      10.1002/bit.26390

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Learning from quantitative data to understand central carbon metabolism2017

    • Author(s)
      Matsuda Fumio、Toya Yoshihiro、Shimizu Hiroshi
    • Journal Title

      Biotechnology Advances

      Volume: 35 Issue: 8 Pages: 971-980

    • DOI

      10.1016/j.biotechadv.2017.09.006

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 第4章-13 細胞内中心代謝フラックスの解析」できる・わかる生命科学の数理モデルとシミュレーション2017

    • Author(s)
      松田史生
    • Journal Title

      実験医学2017年3月増刊号

      Volume: 35 Pages: 207-210

    • Related Report
      2016 Annual Research Report
  • [Journal Article] 13C-metabolic flux analysis for mevalonate producing Escherichia coli2016

    • Author(s)
      Keisuke Wada, Yoshihiro Toya, Satomi Banno, Katsunori Yoshikawa, Fumio Matsuda, Hiroshi Shimizu
    • Journal Title

      Journal of Bioscience and Bioengineering

      Volume: 123 Issue: 2 Pages: 177-182

    • DOI

      10.1016/j.jbiosc.2016.08.001

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Recent advances in amino acid production by microbial cells2016

    • Author(s)
      Takashi Hirasawa and Hiroshi Shimizu
    • Journal Title

      Current Opinion in Biotechnology

      Volume: 42 Pages: 133-146

    • DOI

      10.1016/j.copbio.2016.04.017

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Presentation] Expanding the space of actual metabolic network in Escherichia coli by adaptive laboratory evolution2018

    • Author(s)
      Tokuyama Kento、Toya Yoshihiro、 Horinouchi Takaaki,、Furusawa Chikara、Matsuda Fumio、Shimizu Hiroshi
    • Organizer
      Metabolic Engineering 12
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 微生物バイオプロセスにおける計測と育種・プロセス開発への展開2018

    • Author(s)
      清水浩
    • Organizer
      日本生物工学会バイオ計測サイエンス研究部会第一回シンポジウム
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 増殖連動型物質生産のin silico解析における反応律速点の同定法の開発と実験検証2018

    • Author(s)
      清水浩、徳山健斗、戸谷吉博、松田史生
    • Organizer
      化学工学会第50回秋季大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 計算機工学に基づく代謝設計とその有効性の実証に関する研究2018

    • Author(s)
      清水浩
    • Organizer
      第70回日本生物工学会大会 生物工学功績賞受賞講演
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] フェノールが大腸菌の中枢代謝に及ぼす影響の解析2018

    • Author(s)
      北村さや香、戸谷吉博、清水浩
    • Organizer
      第70回日本生物工学会大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 代謝工学に基づく大腸菌フェノール生産株の育種2018

    • Author(s)
      北村さや香, 戸谷吉博, 清水浩
    • Organizer
      化学工学会第83年会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 定常期における大腸菌メバロン酸生産株の13C代謝フラックス解析2017

    • Author(s)
      増田亜美、徳山健斗、戸谷吉博、清水浩
    • Organizer
      化学工学会 第82年会
    • Place of Presentation
      芝浦工業大学豊洲キャンパス(東京都江東区)
    • Year and Date
      2017-03-06
    • Related Report
      2016 Annual Research Report
  • [Presentation] 実験室進化実験に基づく大腸菌の高コハク酸生産に有効な変異同定2017

    • Author(s)
      徳山 健斗, 戸谷 吉博, 堀之内 貴明, 古澤 力, 清水 浩,
    • Organizer
      化学工学会 第82年会
    • Place of Presentation
      芝浦工業大学豊洲キャンパス(東京都江東区)
    • Year and Date
      2017-03-06
    • Related Report
      2016 Annual Research Report
  • [Presentation] 13C代謝フラックス解析による細胞の生理状態の理解と工学応用2017

    • Author(s)
      清水浩, 松田史生, 戸谷吉博, 岡橋伸幸, 前田昂亮
    • Organizer
      化学工学会第49回秋季大会
    • Related Report
      2017 Annual Research Report
  • [Presentation] Metabolic flux measurement for efficient mevalonate production in Escherichia coli2016

    • Author(s)
      Yoshihiro Toya, Keisuke Wada, Ami Masuda, Kento Tokuyama, Satomi Banno, Katsunori Yoshikawa, Fumio Matsuda, Hiroshi Shimizu
    • Organizer
      i-BioP2016
    • Place of Presentation
      Haeundae Grand Hotel , Busan, South Korea
    • Year and Date
      2016-12-16
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Integration of in silico design and experimental evaluation of metabolic pathways for creation of microbial cell factories,2016

    • Author(s)
      Hiroshi Shimizu
    • Organizer
      International Conference on the Metabolic Science,
    • Place of Presentation
      Nanjiao Hotel, Shanghai China,
    • Year and Date
      2016-10-20
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 13C-metabolic flux analysis for rational design of metabolic pathway modification of the industrially useful microorganisms2016

    • Author(s)
      Hiroshi Shimizu
    • Organizer
      The 13th International Symposium on the Genetics of Industrial Microorganisms
    • Place of Presentation
      East Lake Hotel, Wuhan, China
    • Year and Date
      2016-10-16
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] メバロン酸生産大腸菌の細胞内代謝状態の定量的な評価2016

    • Author(s)
      永井 暉, 戸谷 吉博, 松田 史生, 清水 浩
    • Organizer
      第68回日本生物工学会大会(2016)
    • Place of Presentation
      冨山国際会議場 ANAクラウンプラザホテル富山(富山県富山市)
    • Year and Date
      2016-09-28
    • Related Report
      2016 Annual Research Report
  • [Presentation] メバロン酸生産大腸菌株の定常期における代謝状態の解明2016

    • Author(s)
      増田亜美,戸谷 吉博、徳山 健斗、坂野 聡美、吉川 勝徳、清水 浩
    • Organizer
      第68回日本生物工学会大会(2016)
    • Place of Presentation
      冨山国際会議場 ANAクラウンプラザホテル富山(富山県富山市)
    • Year and Date
      2016-09-28
    • Related Report
      2016 Annual Research Report
  • [Presentation] #in silico#代謝設計と実験室進化実験の統合によるコハク酸高生産大腸菌の構築2016

    • Author(s)
      徳山 健斗、戸谷 吉博、清水 浩
    • Organizer
      化学工学会第48回秋季大会
    • Place of Presentation
      徳島大学 常三島キャンパス(徳島県徳島市)
    • Year and Date
      2016-09-06
    • Related Report
      2016 Annual Research Report
  • [Presentation] 大腸菌による効率的なメバロン酸生産のための代謝解析2016

    • Author(s)
      戸谷吉博、和田圭介、増田亜美、徳山健斗、坂野聡美、吉川勝徳、松田史生、清水浩
    • Organizer
      化学工学会第48回秋季大会
    • Place of Presentation
      徳島大学 常三島キャンパス(徳島県徳島市)
    • Year and Date
      2016-09-06
    • Related Report
      2016 Annual Research Report
  • [Presentation] グリセロールからのコハク酸生産に向けたin silico代謝設計と実験評価2016

    • Author(s)
      徳山健斗、戸谷吉博、清水浩
    • Organizer
      2016年度生物工学若手研究者の集い(若手会)夏のセミナー
    • Place of Presentation
      ホテルコンチネンタル府中(東京都府中市)
    • Year and Date
      2016-07-16
    • Related Report
      2016 Annual Research Report
  • [Presentation] 13C-Metabolic Flux Analysis for Mevalonate-Producing Strain of Escherichia coli.2016

    • Author(s)
      Wada, K., Toya, Y., Matsuda, F. and Shimizu, H.
    • Organizer
      Metabolic Engineering 11
    • Place of Presentation
      Awaji Yumebutai(兵庫県淡路市)
    • Year and Date
      2016-06-26
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] In silico代謝デザインと13C代謝フラックス解析による微生物細胞工場の創製2016

    • Author(s)
      清水浩
    • Organizer
      第6回合成生物工学シンポジウム
    • Place of Presentation
      神戸大学百年記念館六甲ホール(兵庫県神戸市灘区)
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Book] BIOTECHNOLOGY, Wiley-VCH book series, Weinheim, Vol 5: Applied Bioengineering: Innovations and Future Directions, Chapter 7, Omics integrations for the state analysis of microbial processes2017

    • Author(s)
      Hiroshi Shimizu, Chikara Fursawa, Takashi Hirasawa, KatsunoriYoshikawa, Yoshihiro Toya, Tomokazu Shirai, and Fumio Matsuda
    • Total Pages
      36
    • Publisher
      Wiley-VCH
    • Related Report
      2016 Annual Research Report
  • [Book] BIOTECHNOLOGY, Wiley-VCH book series, Weinheim, Vol 5: Applied Bioengineering: Innovations and Future Directions, Chapter 8, Control of Microbial Processes2017

    • Author(s)
      Kazuyuki Shimizu, Hiroshi Shimizu, Toshiomi Yoshida,
    • Total Pages
      22
    • Publisher
      Wiley-VCH
    • Related Report
      2016 Annual Research Report
  • [Book] BIOTECHNOLOGY, Wiley-VCH book series, Weinheim, Vol 4: Indsutrial Biotechnology Products and Processes, Chapter 11. Glutamic acid fermentation: Discovery of glutamic acid-producing microorganisms, analysis of the production mechanism, metabolic engineering and industrial production process2017

    • Author(s)
      Takashi Hirasawa and Hiroshi Shimizu
    • Total Pages
      22
    • Publisher
      Wiley-VCH
    • Related Report
      2016 Annual Research Report
  • [Remarks] 清水浩研究室

    • URL

      http://www-shimizu.ist.osaka-u.ac.jp/hp/index.html

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report 2016 Annual Research Report

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Published: 2016-04-21   Modified: 2020-03-30  

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