RIKEN Center for Sustainable Resource Science Biomanufacturing Design Research Team

Team Director: Tomokazu Shirai (Ph.D.)

Japanese Page

Research Summary

We are advancing research in synthetic biology aimed at biomanufacturing, including the bioproduction of valuable compounds derived from fossil resources and the enhancement of plant biomass yields. Our work focuses on designing artificial metabolic pathways for the biosynthesis of useful compounds, constructing artificial enzymes that catalyze non-natural reactions, and enhancing gene functions. We aim to establish efficient design technologies for cellular metabolism to enable high-level production of target compounds. By integrating these efforts with bioprocess design and optimizing the entire production system, we contribute to the realization of a sustainable, resource-circulating society—through initiatives such as greenhouse gas reduction and food security.

Main Research Fields

Engineering

Related Research Fields

Chemistry
Informatics
Biology
Biofunction and bioprocess engineering-related
Applied microbiology-related
System genome science-related

Keywords

Synthetic biology
Metabolic engineering
Bioinformatics
Enzyme engineering
Bioengineering

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.

1. Vikromvarasiri, N., Mitsui, R., Hirasawa, T., Kondo, A., and Shirai T.:
"Examination of the effect of HOG1 deletion on glucose fermentation in Saccharomyces cerevisiae."
Bioresour Technol. 434, 132788. (2025).
2. Mitsui, R., Kondo, A., Shirai, T.:
"Production of (R)-citramalate by engineered Saccharomyces cerevisiae."
Metab. Eng. Commun. 19, e00247 (2024).
3. Vikromvarasiri, N., Noda, S., Shirai T, and Kondo A.:
"Investigation of two metabolic engineering approaches for (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis."
J. Biol. Eng. 17, 3. (2023).
4. Shirai, T., and Kondo, A.:
"In silico design strategies for the production of target chemical compounds using iterative single-level linear programming problems."
Biomolecules, 12, 620. (2022).
5. Vikromvarasiri, N., Shirai, T., and Kondo, A.:
"Metabolic engineering design to enhance (R,R)-2,3-butanediol production from glycerol in Bacillus subtilis based on flux balance analysis."
Microb. Cell Fact., 20, 196. (2021).
6. Mori, Y., Noda, S., Shirai, T., and Kondo, A.:
"Direct 1,3-butadiene biosynthesis in Escherichia coli via a tailored ferulic acid decarboxylase mutant."
Nat. Commun., 12, 2195. (2021).
7. Noda, S., Mori, Y., Oyama, S., Kondo, A., Araki, M., and Shirai T.:
"Reconstruction of metabolic pathway for isobutanol production in Escherichia coli."
Microb Cell Fact., 18, 124. (2019).
8. Mori, Y., and Shirai, T.:
"Designing artificial metabolic pathways, construction of target enzymes, and analysis of their function."
Curr. Opin. Biotechnol., 54, 41-44. (2018).
9. Shirai, T., Osanai, T., and Kondo, A.:
"Designing intracellular metabolism for production of target compounds by introducing a heterologous metabolic reaction based on a Synechosystis sp. 6803 genome-scale model."
Microb. Cell. Fact., 15, 13. (2016).
10. Shirai, T., Matsuda, F., Okamoto, M., and Kondo, A.:
"Evaluation of control mechanisms for Saccharomyces cerevisiae central metabolic reactions using metabolome data of eight single-gene deletion mutants."
Appl. Microbiol. Biotechnol., 97, 3569-77. (2013).

Lab Members

Principal investigator

Tomokazu Shirai: Team Director

Contact Information

English 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan

Visiting the Lab

Email: tomokazu.shirai@riken.jp