Shirai Tomokazu 白井智量

Researcher Number	00639586
Other IDs
Affiliation (Current)	2026: 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, チームディレクター
Affiliation (based on the past Project Information) *help	2021 – 2025: 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, 上級研究員
Review Section/Research Field	Except Principal Investigator Basic Section 59040:Nutrition science and health science-related / Broad Section F / Basic Section 27040:Biofunction and bioprocess engineering-related / Transformative Research Areas, Section (II)
Keywords	Except Principal Investigator 糖代謝フロー / 解糖系 / 呼吸 / エネルギー代謝 / ミトコンドリア / 代謝シミュレーション / 代謝フェロモン / シミュレーション / 細胞間コミュニケーション / 翻訳後修飾 … More / 化学遺伝学 / 内在性代謝物 / 遺伝子発現量解析 / 機械学習 / プラットホーム / プラスミド構成要素 / 遺伝子発現パターン / 遺伝子発現 / プラスミドライブラリィ / 遺伝子導入 / 主成分分析 / 薬剤耐性 / 複製開始起点 / プラスミド / フェニル乳酸 / 大腸菌 / 人工解糖経路 / 無細胞分子システム / ATP合成システム / ノネナール検出 / 統計的因果推論 / システム最適化 / 酵素反応 / 最適化モデル / ATP生産システム / ノネナール Less

Improving mitochondrial function by inhibiting glycolysis
- Principal Investigator
  
  伊藤孝
- Project Period (FY)
  2025 – 2027
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 59040:Nutrition science and health science-related
- Research Institution
  Toyo University
Method for the optimal plasmid selection to produce chemical compounds using Escherichia coli
- Principal Investigator
  
  Shuhei Noda
- Project Period (FY)
  2024
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 27040:Biofunction and bioprocess engineering-related
- Research Institution
  Kobe University
Uncovering hidden functions of intrinsic metabolites using chemical genetics and informatics
- Principal Investigator
  
  吉田稔
- Project Period (FY)
  2023 – 2027
- Research Category
  
  Grant-in-Aid for Scientific Research (S)
- Review Section
  
  Broad Section F
- Research Institution
  Institute of Physical and Chemical Research
Optimization of cell-free molecular systems with computational science approaches
- Principal Investigator
  
  油谷幸代
- Project Period (FY)
  2021 – 2025
- Research Category
  
  Grant-in-Aid for Transformative Research Areas (A)
- Review Section
  
  Transformative Research Areas, Section (II)
- Research Institution
  National Institute of Advanced Industrial Science and Technology

All 2025 2024 2023 2022 2021

All Journal Article Presentation Book

[Book] 微生物を活用した有用物質の製造技術2023
- Author(s)
  白井智量, 森裕太郎
- Total Pages
  6
- Publisher
  CMC出版
- ISBN
  9784781317403
- Data Source
  KAKENHI-PLANNED-21H05230
[Book] Genomics and the Global Bioeconomy (Translational and Applied Genomics) Chapter 3: Computational approaches for smart cell creation in the bioeconomy era.2022
- Author(s)
  Sachiyo Aburatani, Koji Ishiya, Tomokazu Shirai, Yosuke Shida, Wataru Ogasawara, Hiroaki Takaku, and Tomohiro Tamura.
- Total Pages
  23
- Publisher
  ELSEVIER
- ISBN
  9780323916028
- Data Source
  KAKENHI-PLANNED-21H05230
[Journal Article] NHC-Mediated Radical Acylation Catalyzed by Thiamine- and Flavin-Dependent Enzymes.2025
- Author(s)
  Shunsuke Kato, Shuto Fujisawa, Yuto Adachi, Mitsuhiro Bandai, Yutaro Mori, Seiji Mori, Tomokazu Shirai, Takashi Hayashi
- Journal Title
  
  Journal of the American Chemical Society - ACS Publications
  
  Volume: 147 Issue: 17 Pages: 14837-14844
- DOI
  10.1021/jacs.5c04484
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-21H05230
[Journal Article] Structure-based development of novel substrate-type G9a inhibitors as epigenetic modulators for sickle cell disease treatment2024
- Author(s)
  Nishigaya Yosuke、Takase Shohei、Sumiya Tatsunobu、Sato Tomohiro、Niwa Hideaki、Sato Shin、Nakata Akiko、Matsuoka Seiji、Maemoto Yuki、Hashimoto Noriaki、Namie Ryosuke、Honma Teruki、Umehara Takashi、Shirouzu Mikako、Koyama Hiroo、Yoshida Minoru、Ito Akihiro、Shirai Fumiyuki
- Journal Title
  
  Bioorganic & Medicinal Chemistry Letters
  
  Volume: 110 Pages: 129856-129856
- DOI
  10.1016/j.bmcl.2024.129856
- Peer Reviewed
- Data Source
  KAKENHI-PLANNED-23H04882, KAKENHI-PROJECT-23H05473
[Journal Article] Design and construction of artificial metabolic pathways for the bioproduction of useful compounds2024
- Author(s)
  Shirai Tomokazu
- Journal Title
  
  Plant Biotechnology
  
  Volume: 41 Issue: 3 Pages: 261-266
- DOI
  10.5511/plantbiotechnology.24.0721c
- ISSN
  1342-4580, 1347-6114
- Year and Date
  2024-09-25
- Language
  English
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23H05473
[Journal Article] Reduction of H3K9 methylation by G9a inhibitors improves the development of mouse SCNT embryos2024
- Author(s)
  Matoba Shogo、Shikata Daiki、Shirai Fumiyuki、Tatebe Takaki、Hirose Michiko、Nakata Akiko、Watanabe Naomi、Hasegawa Ayumi、Ito Akihiro、Yoshida Minoru、Ogura Atsuo
- Journal Title
  
  Stem Cell Reports
  
  Volume: 19 Issue: 6 Pages: 906-921
- DOI
  10.1016/j.stemcr.2024.04.003
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-WRAPUP-24H02764, KAKENHI-PLANNED-23H04882, KAKENHI-PROJECT-23H05473, KAKENHI-PROJECT-23K20298, KAKENHI-PROJECT-24K21266
[Journal Article] Production of (R)-citramalate by engineered Saccharomyces cerevisiae2024
- Author(s)
  Mitsui Ryosuke、Kondo Akihiko、Shirai Tomokazu
- Journal Title
  
  Metabolic Engineering Communications
  
  Volume: 19 Pages: e00247-e00247
- DOI
  10.1016/j.mec.2024.e00247
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23H05473, KAKENHI-PROJECT-24K17824
[Journal Article] Metabolic and enzymatic engineering approach for the production of 2-phenylethanol in engineered Escherichia coli.2024
- Author(s)
  Shuhei Noda, Yutaro Mori, Yuki Ogawa, Ryosuke Fujiwara, Mayumi Dainin, Tomokazu Shirai, Akihiko Kondo
- Journal Title
  
  Bioresource Technology
  
  Volume: 406 Pages: 130927-130927
- DOI
  10.1016/j.biortech.2024.130927
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05230, KAKENHI-PUBLICLY-23H04565, KAKENHI-PROJECT-23H05473, KAKENHI-PROJECT-23K23153, KAKENHI-PROJECT-24K17572
[Journal Article] Styrene Production in Genetically Engineered Escherichia coli in a Two-Phase Culture2024
- Author(s)
  Noda Shuhei、Fujiwara Ryosuke、Mori Yutaro、Dainin Mayumi、Shirai Tomokazu、Kondo Akihiko
- Journal Title
  
  BioTech
  
  Volume: 13 Issue: 1 Pages: 2-2
- DOI
  10.3390/biotech13010002
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K14777, KAKENHI-PUBLICLY-23H04565, KAKENHI-PROJECT-23K23153, KAKENHI-PROJECT-23H05473
[Journal Article] Integrated pathway mining and selection of an artificial CYP79-mediated bypass to improve benzylisoquinoline alkaloid biosynthesis2024
- Author(s)
  Takenaka Musashi、Kamasaka Kouhei、Daryong Kim、Tsuchikane Keiko、Miyazawa Seiha、Fujihana Saeko、Hori Yoshimi、Vavricka Christopher J.、Hosoyama Akira、Kawasaki Hiroko、Shirai Tomokazu、Araki Michihiro、Nakagawa Akira、Minami Hiromichi、Kondo Akihiko、Hasunuma Tomohisa
- Journal Title
  
  Microbial Cell Factories
  
  Volume: 23 Issue: 1 Pages: 178-178
- DOI
  10.1186/s12934-024-02453-7
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-23H05473
[Journal Article] Discovery of Novel Substrate-Competitive Lysine Methyltransferase G9a Inhibitors as Anticancer Agents2023
- Author(s)
  Yosuke Nishigaya, Shohei Takase, Tatsunobu Sumiya, Ko Kikuzato, Tomohiro Sato, Hideaki Niwa, Shin Sato, Akiko Nakata, Takeshi Sonoda, Noriaki Hashimoto, Ryosuke Namie, Teruki Honma, Takashi Umehara, Mikako Shirouzu, Hiroo Koyama, Minoru Yoshida, Akihiro Ito, Fumiyuki Shirai
- Journal Title
  
  Journal of Medicinal Chemistry
  
  Volume: 66 Issue: 6 Pages: 4059-4085
- DOI
  10.1021/acs.jmedchem.2c02059
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22KJ2790, KAKENHI-PROJECT-19H05640, KAKENHI-PLANNED-23H04882, KAKENHI-PROJECT-23H05473
[Journal Article] Investigation of two metabolic engineering approaches for (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis2023
- Author(s)
  Vikromvarasiri Nunthaphan、Noda Shuhei、Shirai Tomokazu、Kondo Akihiko
- Journal Title
  
  Journal of Biological Engineering
  
  Volume: 17 Issue: 1 Pages: 3-13
- DOI
  10.1186/s13036-022-00320-w
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K23153, KAKENHI-PLANNED-21H05230, KAKENHI-PROJECT-23H05473
[Journal Article] In Silico Design Strategies for the Production of Target Chemical Compounds Using Iterative Single-Level Linear Programming Problems.2022
- Author(s)
  Tomokazu Shirai, Akihiko Kondo.
- Journal Title
  
  Biomolecules
  
  Volume: 12 Issue: 5 Pages: 620-620
- DOI
  10.3390/biom12050620
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05230
[Journal Article] G6P-capturing molecules in the periplasm of Escherichia coli accelerate the shikimate pathway2022
- Author(s)
  Fujiwara, R., Nakano, M., Hirata, Y., Otomo, C., Nonaka, D., Kawada, S., Nakazawa, H., Umetsu, M., Shirai, T., Noda, S.*, Tanaka, T.*, Kondo, A.
- Journal Title
  
  Metabolic Engineering
  
  Volume: 72 Pages: 68-81
- DOI
  10.1016/j.ymben.2022.03.002
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-19H02526, KAKENHI-PROJECT-21K14777, KAKENHI-PROJECT-20H00321, KAKENHI-PROJECT-22KJ2279, KAKENHI-PROJECT-19K15370, KAKENHI-PROJECT-20K22574, KAKENHI-PROJECT-23K23148, KAKENHI-PROJECT-23K23153
[Journal Article] Metabolic engineering design to enhance (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis based on flux balance analysis.2021
- Author(s)
  Vikromvarasiri Nunpathan, Tomokazu Shirai, Akihiko Kondo.
- Journal Title
  
  Microb. Cell Fact.
  
  Volume: 20 Issue: 1 Pages: 196-196
- DOI
  10.1186/s12934-021-01688-y
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05230
[Journal Article] Direct 1,3-butadiene biosynthesis in Escherichia coli via a tailored ferulic acid decarboxylase mutant2021
- Author(s)
  Yutaro Mori, Shuhei Noda, Tomokazu Shirai, Akihiko Kondo
- Journal Title
  
  Nat. Commun.
  
  Volume: 12 Issue: 1 Pages: 2195-2195
- DOI
  10.1038/s41467-021-22504-6
- NAID
  120007035635
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PLANNED-21H05230
[Presentation] Metabolic and enzymatic engineering approach for the production and degradation of biopolymer2024
- Author(s)
  Noda S, Koh S, Katano A, Nonaka D, Mori Y, Fujiwara R, Shirai T, Tanaka T, Taguchi S, Kondo A
- Organizer
  13th International Conference on Biomedical Engineering and Biotechnology
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K23153
[Presentation] Metabolic and enzymatic engineering approach for the aromatic chemical production in Escherichia coli2024
- Author(s)
  Noda S, Ogawa Y, Mori Y, Fujiwara R, Shirai T, Tanaka T, Kondo A
- Organizer
  15th International Conference on Bioscience, Biochemistry and Bioinformatics
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K23153
[Presentation] Butadiene production by constructing an artificial metabolic pathway with enzyme engineering technology.2023
- Author(s)
  Tomokazu Shirai
- Organizer
  Nature Inspires Creativity Engineers (N.I.C.E)
- Invited / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23H05473
[Presentation] ヒストンメチル化酵素G9aの阻害剤による体細胞クローン法の改善2023
- Author(s)
  的場章悟、四方大樹、黒滝陽子、白井文幸、山田祐子、渡邉奈緒美、伊藤昭博、眞貝洋一、佐々木えりか、吉田稔、小倉　淳郎
- Organizer
  第70回日本実験動物学会
- Data Source
  KAKENHI-PROJECT-23H05473
[Presentation] Metabolic Engineering of Escherichia coli for the Production and Degradation of Microbial-Polymer2023
- Author(s)
  Shuhei Noda1,2*, Sangho Koh1, Akinobu Katano3, Daisuke Nonaka3, Yutaro Mori3, Ryosuke Fujiwara, Tomokazu Shirai, Tsutomu Tanaka, Seiichi Taguchi, Akihiko Kondo
- Organizer
  16th Asian Congress on Biotechnology 2023
- Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K23153
[Presentation] 人工代謝経路設計技術を利用した有用化合物の微生物による生産2022
- Author(s)
  白井智量
- Organizer
  第74回日本生物工学会大会シンポジウム
- Invited
- Data Source
  KAKENHI-PLANNED-21H05230
[Presentation] 人工代謝経路設計による微生物を用いた化石資源由来化合物の生産2022
- Author(s)
  白井智量
- Organizer
  日本バイオインフォマティクス学会年会第11回生命医薬情報学連合大会（IIBMP2022）
- Invited
- Data Source
  KAKENHI-PLANNED-21H05230
[Presentation] 人工代謝経路の構築による合成ゴム原料の微生物発酵生産2022
- Author(s)
  白井智量
- Organizer
  第3回天然ゴム研究会
- Invited
- Data Source
  KAKENHI-PLANNED-21H05230
[Presentation] 人工代謝経路設計による有用化合物のバイオ生産に関する研究2021
- Author(s)
  白井智量
- Organizer
  日本化学会第101春季年会シンポジウム
- Invited
- Data Source
  KAKENHI-PLANNED-21H05230

1. Shuhei Noda (30710131)

# of Collaborated Projects: 1 results

# of Collaborated Products: 4 results
2. 油谷幸代 (10361627)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
3. 本田孝祐 (90403162)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
4. 荒木通啓 (40396867)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
5. 吉田稔 (80191617)

# of Collaborated Projects: 1 results

# of Collaborated Products: 2 results
6. 西村慎一 (30415260)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
7. 伊藤昭博 (40391859)

# of Collaborated Projects: 1 results

# of Collaborated Products: 1 results
8. 伊藤孝 (20597124)

# of Collaborated Projects: 1 results

# of Collaborated Products: 0 results
9. TANAKA Tsutomu

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
10. 小倉淳郎

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
11. 藤原良介

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Shirai Tomokazu 白井 智量

Research Projects

Research Products

Co-Researchers

Improving mitochondrial function by inhibiting glycolysis

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Method for the optimal plasmid selection to produce chemical compounds using Escherichia coli

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Uncovering hidden functions of intrinsic metabolites using chemical genetics and informatics

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Optimization of cell-free molecular systems with computational science approaches

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[Book] 微生物を活用した有用物質の製造技術2023

Author(s)

Total Pages

Publisher

ISBN

Data Source

[Book] Genomics and the Global Bioeconomy (Translational and Applied Genomics) Chapter 3: Computational approaches for smart cell creation in the bioeconomy era.2022

Author(s)

Total Pages

Publisher

ISBN

Data Source

[Journal Article] NHC-Mediated Radical Acylation Catalyzed by Thiamine- and Flavin-Dependent Enzymes.2025

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Structure-based development of novel substrate-type G9a inhibitors as epigenetic modulators for sickle cell disease treatment2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Design and construction of artificial metabolic pathways for the bioproduction of useful compounds2024

Author(s)

Journal Title

DOI

ISSN

Year and Date

Language

Data Source

[Journal Article] Reduction of H3K9 methylation by G9a inhibitors improves the development of mouse SCNT embryos2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Production of (R)-citramalate by engineered Saccharomyces cerevisiae2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Metabolic and enzymatic engineering approach for the production of 2-phenylethanol in engineered Escherichia coli.2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Styrene Production in Genetically Engineered Escherichia coli in a Two-Phase Culture2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Integrated pathway mining and selection of an artificial CYP79-mediated bypass to improve benzylisoquinoline alkaloid biosynthesis2024

Author(s)

Shirai Tomokazu 白井智量