Quantitative modeling and systemic understanding of the regulatory mechanisms of the E. coli ammonium assimilation

• Project/Area Number: 26870432
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: System genome science; Life / Health / Medical informatics
• Research Institution: Kyushu Institute of Technology
• Principal Investigator: Maeda Kazuhiro 九州工業大学, 若手研究者フロンティア研究アカデミー, 特任助教 (50631230)
• Project Period (FY): 2014-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000); Fiscal Year 2016: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2015: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2014: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: 大腸菌 / 窒素代謝 / 生化学パラメータ推定 / シミュレーション / システム生物学 / パラメータ推定 / システムバイオロジー / アンモニア / ダイナミックモデル / 微分方程式 / 最適化

Outline of Final Research Achievements

For E. coli, glutamate and glutamine are important as precursors for amino acids and nucleotides, and ammonium is necessary for the synthesis of glutamate and glutamine. Construction of a mathematical model is indispensable for understanding the complex control mechanism of ammonium assimilation. In this study, we constructed a quantitative dynamic model of the E. coli ammonium assimilation network. We pointed out that AmtB, which was considered to be an ammonia channel so far, is an active ammonium transporter. In addition, we developed a novel kinetic parameter estimation method to accelerate the kinetic modeling and developed a C language library to support it.

Research Products

• [Int'l Joint Research] アムステルダム自由大学(オランダ)
• [Int'l Joint Research] アムステルダム自由大学(オランダ)
• [Journal Article] Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli. (2016)
  • Author(s): Nusrat Jahan, Kazuhiro Maeda, Yu Matsuoka, Yurie Sugimoto, Hiroyuki Kurata.
  • Journal Title: Microbial Cell Factories Volume: 15 Issue: 1 Pages: 112-112
  • DOI: 10.1186/s12934-016-0511-x
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Web application for Genetic Modification Flux with database to estimate metabolic fluxes of genetic mutants (2016)
  • Author(s): Noorlin Mohd Ali, Ryo Tsuboi, Yuta Matsumoto, Daisuke Koishi, Kentaro Inoue, Kazuhiro Maeda, and Hiroyuki Kurata
  • Journal Title: Journal of Bioscience and Bioengineering Volume: 印刷中 Issue: 1 Pages: 111-116
  • DOI: 10.1016/j.jbiosc.2015.12.001
  • NAID: 40020886002
  • Peer Reviewed / Open Access
• [Presentation] Developing a kinetic model of the E. coli ammonium assimilation network for the metabolic engineering of efficient glutamate fermentation (2015)
  • Author(s): Kazuhiro Maeda, Fred C. Boogerd, Hans V. Westerhoff, and Hiroyuki Kurata
  • Organizer: The International Conference on Systems Biology 2015
  • Place of Presentation: Biopolis, Singapore
  • Year and Date: 2015-11-23
  • Int'l Joint Research
• [Presentation] A Modeling Approach for Analysis of Regulation of Glutamine Synthetase and Ammonium Transporter in E. coli (2015)
  • Author(s): Kazuhiro Maeda, Fred C. Boogerd, Hans V. Westerhoff, and Hiroyuki Kurata
  • Organizer: Asian Congress on Biotechnology 2015
  • Place of Presentation: Istana Hotel, Kuala Lumpur, Malaysia
  • Year and Date: 2015-11-15
  • Int'l Joint Research
• [Presentation] 大腸菌アンモニア同化制御の解析：ダイナミックモデリングによるアプローチ (2015)
  • Author(s): 前田和勲, Fred C. Boogerd, Hans V. Westerhoff, 倉田博之
  • Organizer: 生命情報科学若手の会 第7回研究会
  • Place of Presentation: 慶應義塾大学鶴岡タウンキャンパス TTCK レクチャーホール（山形県鶴岡市）
  • Year and Date: 2015-10-01
• [Presentation] Multiparameter Sensitivity Analysis of Simple Oscillator Models (2015)
  • Author(s): Kazuhiro Maeda and Hiroyuki Kurata
  • Organizer: International Symposium on Synthetic Systems Biology (BST 2015)
  • Place of Presentation: Fukuoka, Japan
  • Year and Date: 2015-09-17
  • Int'l Joint Research
• [Presentation] Dynamic Modeling of the E. coli Ammonium Assimilation Network (2015)
  • Author(s): Kazuhiro Maeda, Fred C. Boogerd, Hans V. Westerhoff, and Hiroyuki Kurata
  • Organizer: GIW/InCoB 2015
  • Place of Presentation: MIRAIKAN, Odaiba, Tokyo, Japan
  • Year and Date: 2015-09-09
  • Int'l Joint Research
• [Presentation] Systems Biology of Body Clocks: Toward a Cancer Therapy Based on a Systems Understanding of Circadian Rhythms (2015)
  • Author(s): Kazuhiro Maeda and Hiroyuki Kurata
  • Organizer: 計測自動制御学会 ライフエンジニアリング部門シンポジウム 2015
  • Place of Presentation: 九州工業大学飯塚キャンパス
  • Year and Date: 2015-09-02
• [Presentation] Toward a quantitative in silico model for the E. coli ammonium assimilation system (2015)
  • Author(s): Kazuhiro Maeda, Fred C. Boogerd, Hans V. Westerhoff, and Hiroyuki Kurata
  • Organizer: BMIRC Symposium 2015
  • Place of Presentation: 福岡県飯塚市 野上プレジデントホテル
  • Year and Date: 2015-03-06
• [Presentation] 大腸菌アンモニア同化システムのダイナミックモデル構築 (2015)
  • Author(s): Kazuhiro Maeda, Fred C. Boogerd, Frank J. Bruggeman, Hans V. Westerhoff, and Hiroyuki Kurata
  • Organizer: 定量生物学の会 第七回年会
  • Place of Presentation: 福岡県春日市 九州大学筑紫キャンパス 筑紫ホール・C-cube
  • Year and Date: 2015-01-11 – 2015-01-12
• [Presentation] BioFNet Database for Rational Design of Biological Systems (2014)
  • Author(s): Hiroyuki Kurata, Yurie Sugimoto and Kazuhiro Maeda
  • Organizer: GIW/ISCB-Asia 2014
  • Place of Presentation: 東京お台場 東京国際交流館
  • Year and Date: 2014-12-15 – 2014-12-17
• [Presentation] Analytical study of robustness of a negative feedback oscillator by multiparameter sensitivity (2014)
  • Author(s): Kazuhiro Maeda and Hiroyuki Kurata
  • Organizer: GIW/ISCB-Asia 2014
  • Place of Presentation: 東京お台場 東京国際交流館
  • Year and Date: 2014-12-15
• [Presentation] マルチパラメータ感度を用いたネガティブフィードバック振動子のロバストネス解析 (2014)
  • Author(s): 前田和勲、倉田博之
  • Organizer: 生命情報科学若手の会 第6回研究会
  • Place of Presentation: 兵庫県神戸市 理化学研究所 発生・再生科学総合研究センター
  • Year and Date: 2014-10-30
• [Presentation] BioFNet: Biological Function Network Database (2014)
  • Author(s): Hiroyuki Kurata and Kazuhiro Maeda
  • Organizer: IIBMP2014
  • Place of Presentation: 宮城県仙台市
  • Year and Date: 2014-10-02 – 2014-10-03
• [Presentation] ネガティブフィードバック振動子のマルチパラメータ感度解析 (2014)
  • Author(s): Kazuhiro Maeda and Hiroyuki Kurata,
  • Organizer: IIBMP2014
  • Place of Presentation: 宮城県仙台市
  • Year and Date: 2014-10-02 – 2014-10-03
• [Presentation] BioFNet database supports analysis and synthesis of biochemical networks (2014)
  • Author(s): Hiroyuki Kurata and Kazuhiro Maeda
  • Organizer: ICSB 2014 (The International Conference on Systems Biology)
  • Place of Presentation: Melbourne, Australia
  • Year and Date: 2014-09-14 – 2014-09-18
• [Presentation] Robustness analysis of a negative feedback oscillator (2014)
  • Author(s): Kazuhiro Maeda and Hiroyuki Kurata
  • Organizer: ICSB 2014 (The International Conference on Systems Biology)
  • Place of Presentation: Melbourne, Australia
  • Year and Date: 2014-09-14 – 2014-09-18
• [Remarks] 研究者が作成したWebページ
  • URL: http://kurata21.bio.kyutech.ac.jp/maeda/
• [Remarks] 所属研究機関が作成したWebページ
  • URL: http://www.ccr.kyutech.ac.jp/professors/iizuka/i-12/i12-3/entry-2636.html