Metabolic design of higher plants for useful material production by metabolic engineering

• Project/Area Number: 25660084
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Applied biochemistry
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: Hirai Masami 国立研究開発法人理化学研究所, 環境資源科学研究センター, チームリーダー (90415274)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000); Fiscal Year 2014: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2013: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: 数理モデル / 代謝 / 高等植物 / メタボローム

Outline of Final Research Achievements

Aiming at designing metabolism of higher plants for metabolic engineering and generating crops with enhanced useful material production, I established a method for genome-scale mathematical modeling of metabolism in Arabidopsis thaliana. Differential equations in a model were symbolically established based only on a metabolic map. Then parameters in the model were estimated by using time-series metabolome data which were obtained from metabolically perturbed A. thaliana. The established model were successfully used for system analyses.

Research Products

• [Journal Article] Mathematical modeling and dynamic simulation of metabolic reaction systems using metabolome time series data. (2016)
  • Author(s): Sriyudthsak K, Shiraishi F, Hirai MY
  • Journal Title: Front. Mol. Biosci. Volume: 3 Pages: 1-3
  • DOI: 10.3389/fmolb.2016.00015
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] PENDISC: A Simple Method for Constructing a Mathematical Model from Time-Series Data of Metabolite Concentrations. (2014)
  • Author(s): Sriyudthsak, K., Iwata, M., Hirai, M.Y. and Shiraishi, F.
  • Journal Title: Bulletin of Mathematical Biology Volume: 76 Issue: 6 Pages: 1333-1351
  • DOI: 10.1007/s11538-014-9960-8
  • Peer Reviewed / Open Access
• [Journal Article] A U-system approach for predicting metabolic behaviors and responses based on an alleged metabolic reaction network. (2014)
  • Author(s): Sriyudthsak K, Sawada Y, Chiba Y, Yamashita Y, Kanaya S, Onouchi H, Fujiwara T, Naito S, Voit EO, Shiraishi F, Hirai MY
  • Journal Title: BMC Systems Biology Volume: 8 Issue: S5
  • DOI: 10.1186/1752-0509-8-s5-s4
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] BST-loglem: Parameter and Network Estimations Based on BST Modeling Using LOESS, Granger Causality and Levenberg-Marquardt Method (2013)
  • Author(s): Sriyudthsak K, Shiraishi F, Hirai MY
  • Journal Title: TSB2013 Conference Proceedings Volume: - Pages: 94-98
  • Peer Reviewed
• [Journal Article] Estimation of kinetic parameters in an S-system equation model for ametabolic reaction system using the Newton-Raphson method (2013)
  • Author(s): Michio Iwata, Kansuporn Sriyudthsak, Masami Yokota Hirai and Fumihide Shiraishi
  • Journal Title: Mathematical Biosciences Volume: VOL.248 Pages: 11-21
  • DOI: 10.1016/j.mbs.2013.11.002
  • Peer Reviewed
• [Journal Article] SS-mPMG and SS-GA : tools for finding pathways and dynamic simulation of metabolic networks. (2013)
  • Author(s): Tetsuo Katsuragi, Naoaki Ono, Keiichi Yasumoto, Masami Y. Hirai, Kansuporn Sriyudthsak, Yuji Sawada, Yui Yamashita, Yukako Chiba, Hitoshi Onouchi, Toru Fujiwara, Satoshi Naito
  • Journal Title: Plant and Cell Physiology Volume: 54 Issue: 5 Pages: 728-739
  • DOI: 10.1093/pcp/pct052
  • Peer Reviewed
• [Presentation] Prediction of unknown regulation in a metabolic pathway using omics time-series data. (2016)
  • Author(s): シユタサ カンスポーン，澤田有司， 桑原亜由子，佐藤心郎，尾之内 均，内藤哲，平井優美
  • Organizer: 第57回日本植物生理学会年会
  • Place of Presentation: 盛岡
  • Year and Date: 2016-03-19
• [Presentation] 時系列オミクスデータに基づく代謝ネットワーク解析 (2016)
  • Author(s): 平井優美
  • Organizer: CRESTシンポジウム「トランスオミクスによる生命システムの解明」
  • Place of Presentation: 東京
  • Year and Date: 2016-03-04
  • Invited
• [Presentation] オミクス時系列データに基づく代謝経路 と制御の予測 (2015)
  • Author(s): シユタサ カンスポーン、桑原 亜由子、 澤田 有司、佐藤 心郎、尾之内 均、 内藤 哲、平井 優
  • Organizer: 第33回日本植物細胞分子生物学会（東京）大会・シンポジウム
  • Place of Presentation: 東京
  • Year and Date: 2015-08-11
• [Presentation] Understanding of plant metabolism via metabolomics-based mathematical modeling (2014)
  • Author(s): Masami Y. Hirai
  • Organizer: GIW/ISCB-Asia 2014
  • Place of Presentation: Plaza Heisei, Tokyo International Exchange Center
  • Year and Date: 2014-12-15
  • Invited
• [Presentation] メタボロミクスによる植物の代謝制御機構の解明 (2014)
  • Author(s): 平井優美
  • Organizer: 第87回日本生化学会大会シンポジウム「代謝とシステムバイオロジー」
  • Place of Presentation: 国立京都国際会館
  • Year and Date: 2014-10-17
  • Invited
• [Presentation] A simple method for constructing a mathematical model to predict metabolic behaviors (2013)
  • Author(s): Kansuporn SRIYUDTHSAK, Michio IWATA, Masami Yokota HIRAI, Fumihide SHIRAISHI
  • Organizer: 日本バイオインフォマティクス学会2013年年会(JSBi)
  • Place of Presentation: 東京
• [Presentation] メタボロームデータを用いた代謝の数理モデリング
  • Author(s): 平井 優美
  • Organizer: 第36回日本分子生物学会年会 ワークショップ：トランスオミクスへ向けた定量生物学
  • Place of Presentation: 神戸
  • Invited
• [Presentation] メタボロミクスによる植物科学研究―農作物への展開―
  • Author(s): 平井 優美
  • Organizer: 2013植物科学シンポジウム：持続可能資源の開発に向けた植物科学
  • Place of Presentation: 東京
  • Invited
• [Presentation] グルコシノレート生合成を制御 するMYB転写因子の機能解析
  • Author(s): 平井 優美、李 一蒙、荒木 良一、澤田 有司、西澤 治、斉藤 和季、小川 俊也
  • Organizer: 第31回植物細胞分子生物学会年会
  • Place of Presentation: 札幌
• [Presentation] 代謝産物量の経時変化のデータを用いた代謝の数理モデリング手法の開発
  • Author(s): シユタサ カンスポーン、 澤田 有司、千葉 由佳子、山下 由衣、岩田 通夫、尾之内 均、内藤 哲、白石 文秀、平井 優美
  • Organizer: 植物学会第77回大会
  • Place of Presentation: 札幌
• [Presentation] A new technique for constructing a large-scale kinetic model to comprehensively understand metabolic regulatory mechanisms
  • Author(s): Kansuporn SRIYUDTHSAK, Yuji Sawada, Yukako Chiba, Yui Yamashita, Shigehiko Kanaya, Hitoshi Onouchi, Toru Fujiwara, Satoshi Naito, Fumihide Shiraishi, Masami Yokota Hirai
  • Organizer: 第55回日本植物生理学会年会
  • Place of Presentation: 富山
• [Remarks] PASMet
  • URL: http://pasmet.riken.jp/