Informatics analysis on selectivity and diversity of enzymatic reaction

• Project/Area Number: 26430198
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: System genome science
• Research Institution: Kobe University
• Principal Investigator: araki michihiro 神戸大学, 科学技術イノベーション研究科, 特命准教授 (40396867)
• Project Period (FY): 2014-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000); Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2014: ¥2,600,000 (Direct Cost: ¥2,000,000、Indirect Cost: ¥600,000)
• Keywords: バイオインフォマティクス / 合成生物学 / 代謝工学

Outline of Final Research Achievements

In constructing a novel metabolic pathway, selection of enzyme gene candidates required for metabolic pathways, whether unknown or known, is an important task. In this research, in order to more efficiently select such enzyme genes, we reconstructed a new enzyme reaction database that integrated information diffused in each database in a form suitable for this purpose. Based on this, we have developed biological and chemical information analysis and machine learning methods that can support selection of representative gene sequences while considering selectivity and diversity of enzyme genes.

Research Products

• [Journal Article] A Systematic Approach to Time-series Metabolite Profiling and RNA-seq Analysis of Chinese Hamster Ovary Cell Culture (2017)
  • Author(s): Hsu, HH., Araki, M., Mochizuki, M., Hori, Y., Murata, M., Kahar, P., Yoshida, T., Hasunuma, T. and Kondo A.
  • Journal Title: Scientific Reports Volume: 7 Issue: 1 Pages: 43518-43518
  • DOI: 10.1038/srep43518
  • NAID: 120006346139
  • Peer Reviewed / Open Access
• [Journal Article] Application of LC-MS/MS analysis for time-lapse amino acid metabolomics analysis in CHO cell culture (2017)
  • Author(s): Hsu, H.H., Hasunuma, T., Araki, M., Yoshida, T., Hori, Y., Murata, M., Kondo, A.
  • Journal Title: Shimadzu Journal Volume: 5 Pages: 17-17
  • Peer Reviewed
• [Journal Article] Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems (2016)
  • Author(s): Nishida, K., Arazoe, T., Yachie, N., Banno, S., Kakimoto, M., Tabata, M., Mochizuki, M., Miyabe, A., Araki, M., Hara, K.Y., Shimatani, Z. and Kondo, A.
  • Journal Title: Science Volume: 353 Issue: 6305 Pages: 6305-6305
  • DOI: 10.1126/science.aaf8729
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Improvement of oxidized glutathione fermentation by thiol redox metabolism engineering in Saccharomyces cerevisiae (2015)
  • Author(s): Hara, K.Y., Aoki, N., Kobayashi, J., Kiriyama, K., Nishida, K., Araki, M., Kondo, A.
  • Journal Title: Appl. Microbiol. Biotechnol. Volume: 99 Issue: 22 Pages: 9771-9778
  • DOI: 10.1007/s00253-015-6847-z
  • Peer Reviewed
• [Journal Article] Evaluation of genes involved in oxidative phosphorylation in yeast by developing a simple and rapid method to measure mitochondrial ATP synthetic activity. (2015)
  • Author(s): Ye X, Morikawa K, Ho SH, Araki M, Nishida K, Hasunuma T, Hara KY, Kondo A.
  • Journal Title: Microbial Cell Factories Volume: 14 Issue: 1 Pages: 56-56
  • DOI: 10.1186/s12934-015-0239-z
  • Peer Reviewed / Open Access
• [Journal Article] M-path: A Compass for Navigating Potential Metabolic Pathways (2015)
  • Author(s): Araki, M., Cox III, RS., Makiguchi, H., Ogawa, T., Taniguchi, T., Miyaoku, K., Nakatsui M., Hara, K.Y., Kondo, A.
  • Journal Title: Bioinformatics Volume: 31 Issue: 6 Pages: 905-911
  • DOI: 10.1093/bioinformatics/btu750
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Development of bio-based fine chemical production through synthetic bioengineering (2014)
  • Author(s): Hara, K.Y., Araki, M., Okai, N., Wakai, S., Hasunuma, T., Kondo, A.
  • Journal Title: Microbial Cell Factories Volume: 13 Issue: 1 Pages: 173-173
  • DOI: 10.1186/s12934-014-0173-5
  • Peer Reviewed / Open Access
• [Presentation] 代謝経路デザインの限界 (2017)
  • Author(s): 荒木通啓
  • 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）
  • Invited
• [Presentation] Development of Design Platform for Metabolic Pathways (2016)
  • Author(s): Ogawa, T., Makiguchi, H. and Araki, M
  • Organizer: 生命医薬情報学連合大会2016年大会
  • Place of Presentation: 東京国際交流館プラザ平成（東京都）
  • Year and Date: 2016-09-29
• [Presentation] In Silico代謝設計ツールの開発とその展開 (2016)
  • Author(s): 荒木通啓
  • Organizer: 農芸化学会2016年度大会
  • Place of Presentation: 札幌コンベンションセンター（北海道・札幌市）
  • Year and Date: 2016-03-30
  • Invited
• [Presentation] 大腸菌における1,4-ブタンジオール人工生合成経路の構築 (2016)
  • Author(s): 江口晃一、工藤基徳、荒木通啓、石井純、山本浩明、近藤昭彦
  • Organizer: 農芸化学会2016年度大会
  • Place of Presentation: 札幌コンベンションセンター（北海道・札幌市）
  • Year and Date: 2016-03-30
• [Presentation] インシリコ代謝経路設計基盤の展開 (2016)
  • Author(s): 荒木通啓、牧口大旭、小川哲平、近藤昭彦
  • Organizer: 日本薬学会第136回年会
  • Place of Presentation: パシフィコ横浜（神奈川県・横浜市）
  • Year and Date: 2016-03-28
• [Presentation] 代謝デザインの展開 (2016)
  • Author(s): 荒木通啓
  • Organizer: 第1回デザイン生命工学研究会
  • Place of Presentation: 東京工業大学（神奈川県・横浜市）
  • Year and Date: 2016-03-08
  • Invited
• [Presentation] Expanding the Scope of Metabolic Pathway In Silico (2016)
  • Author(s): Michihiro Araki
  • Organizer: The 7th International Symposium of Innovative BioProduction Kobe (iBioK)
  • Place of Presentation: 神戸大学（兵庫県・神戸市）
  • Year and Date: 2016-01-27
  • Invited
• [Presentation] スマートセル開発に向けたIT/AI技術の展望 (2016)
  • Author(s): 荒木通啓
  • Organizer: 産業構造審議会 商務流通情報分科会 バイオ小委員会（第4回）
  • Place of Presentation: 経済産業省（東京都）
  • Invited
• [Presentation] バイオプロセスデザインプラットフォームの構築 (2016)
  • Author(s): 牧口 大旭、小川 哲平、荒木通啓
  • Organizer: 第39回日本分子生物学会
  • Place of Presentation: パシフィコ横浜（神奈川県、横浜市）
• [Presentation] M-Path＆PathPod：バイオプロセスデザインプラットフォームと統合型パスウェイデータベースシステム (2015)
  • Author(s): 牧口大旭、小川哲平、近藤昭彦、荒木通啓
  • Organizer: 第38回分子生物学会
  • Place of Presentation: 神戸国際会議場（兵庫県・神戸市）
  • Year and Date: 2015-12-02
• [Presentation] M-path Database: Navigating Potential Metabolic Pathways (2015)
  • Author(s): 小川哲平、牧口大旭、中津井雅彦、Cox III, RS.、近藤昭彦、荒木通啓
  • Organizer: M-path Database: Navigating Potential Metabolic Pathways
  • Place of Presentation: 京都大学（京都府・宇治市）
  • Year and Date: 2015-10-29
• [Presentation] Development of M-path platform for Navigating Potential Metabolic Pathways (2015)
  • Author(s): Ogawa, T., Makiguchi, H., Cox III, RS., Nakatsui M., Kondo, A., and Araki, M.
  • Organizer: ISMB 2015
  • Place of Presentation: the Convention Centre Dublin【Dublin（Ireland）】
  • Year and Date: 2015-07-10
• [Presentation] New approach for Metabolomics pathway analysis (2015)
  • Author(s): Oshida, T., Ogawa, T., Yokoi, Y., Fukamachi, Y., Araki, M., Makiguchi, H.
  • Organizer: ASMS2015
  • Place of Presentation: America's Center【St. Louis（USA）】
  • Year and Date: 2015-05-31
• [Presentation] M-path: Construction of a Database for Expanded Metabolic Pathways (2014)
  • Author(s): Ogawa, T., Makiguchi, H., Cox III, RS., Nakatsui M., Kondo, A., Taniguchi, T., Miyaoku, K. and Araki, M.
  • Organizer: Active Enzyme Molecule 2014
  • Place of Presentation: Toyama International Conference Center, Toyama
  • Year and Date: 2014-12-17 – 2014-12-19
• [Presentation] Meta-synthetic metabolism: in silico design of novel amino acids from all-organism data (2014)
  • Author(s): Cox III, RS., Nakatsui M., Makiguchi, H., Ogawa, T., Kondo, A., Araki, M.
  • Organizer: GIW ISCB-ASIA 2014
  • Place of Presentation: CBRC, Tokyo
  • Year and Date: 2014-12-15 – 2014-12-17
• [Presentation] M-path: 拡張代謝パスウェイデータベースの構築 (2014)
  • Author(s): 牧口大旭、小川哲平、中津井雅彦、Cox III, RS.、近藤昭彦、谷口岳志、宮奥康平、荒木通啓
  • Organizer: 第37回分子生物学会
  • Place of Presentation: パシフィコ横浜、横浜
  • Year and Date: 2014-11-26
• [Presentation] 代謝設計基盤（M-path）によるバイオ合成スコープの拡張 (2014)
  • Author(s): 荒木通啓
  • Organizer: 合成生物工学シンポジウム
  • Place of Presentation: 神戸大学、神戸
  • Year and Date: 2014-11-25
  • Invited
• [Presentation] バイオプロセス合成経路データベース"M-path"の構築 (2014)
  • Author(s): 小川哲平、牧口大旭、谷口岳志、宮奥康平、中津井雅彦、Cox III, RS.、近藤昭彦、荒木通啓
  • Organizer: 第３回生命医薬情報学連合大会
  • Place of Presentation: 仙台国際センター、仙台
  • Year and Date: 2014-10-02 – 2014-10-04
• [Presentation] Computational platform for designing synthetic metabolic pathways (2014)
  • Author(s): Michihiro Araki
  • Organizer: 7th International Congress on Biocatalysis
  • Place of Presentation: Hamburg University of Technology, Hamburg, Germany
  • Year and Date: 2014-09-03
  • Invited
• [Presentation] Mpath: Computationally-Aided Design of Synthetic Metabolic Pathways (2014)
  • Author(s): Cox III, RS., Nakatsui M., Makiguchi, H., Ogawa, T., Kondo, A., Araki, M.
  • Organizer: SEED2014
  • Place of Presentation: Manhattan Beach, LA, USA
  • Year and Date: 2014-07-14 – 2014-07-17
• [Book] 合成生物工学によるモノづくり微生物のデザインに向けて (2015)
  • Author(s): 石井純、荒木通啓、中津井雅彦、崎濱 由梨、柘植 陽太、蓮沼 誠久、近藤 昭彦
  • Total Pages: 5
  • Publisher: 生物工学会誌
• [Book] データベースからの再発見 (2014)
  • Author(s): 荒木通啓
  • Total Pages: 1
  • Publisher: 生物工学会誌（バイオミディア）
• [Remarks] M-path EN
  • URL: http://bp.scitec.kobe-u.ac.jp/m-path/en