Kyushu University Academic Staff Educational and Research Activities Database
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Yuki Soma Last modified date:2023.07.31

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Academic Degree
Ph. D.
Country of degree conferring institution (Overseas)
Field of Specialization
Synthetic Biology, Metabolic Engineering, Metabolomics
ORCID(Open Researcher and Contributor ID)
Total Priod of education and research career in the foreign country
Research Interests
  • Development and application of quantitative metabolomic analysis methods
    keyword : metabolomics, metabolic engineering, mass spectrometry
  • Metabolic flux regulation by synthetic genetic circuit
    keyword : genetic circuit, metabolic flux regulation, quorum sensing, metabolomics
Academic Activities
1. Yuki Soma, Keigo Tsuruno, Masaru Wada, Atsushi Yokota, Taizo Hanai, Metabolic flux redirection from a central metabolic pathway toward a synthetic pathway using a metabolic toggle switch, METABOLIC ENGINEERING, 10.1016/j.ymben.2014.02.008, 23, 175-184, 2014.05.
2. Yuki Soma, Taizo Hanai, Self-induced metabolic state switching by a tunable cell density sensor for microbial isopropanol production, METABOLIC ENGINEERING, 10.1016/j.ymben.2015.04.005, 30, 7-15, 2015.07.
3. Yuki Soma, Yuri Fujiwara, Takuya Nakagawa, Keigo Tsuruno, Taizo Hanai, Reconstruction of a metabolic regulatory network in Escherichia coli for purposeful switching from cell growth mode to production mode in direct GABA fermentation from glucose, METABOLIC ENGINEERING, 10.1016/j.ymben.2017.08.002, 43, Pt A, 54-63, 2017.09, [URL], gamma-aminobutyric acid (GABA) is a drug and functional food additive and is used as a monomer for producing the biodegradable plastic, polyamide 4. Recently, direct GABA fermentation from glucose has been developed as an alternative to glutamate-based whole cell bioconversion. Although total productivity in fermentation is determined by the specific productivity and cell amount responsible for GABA production, the optimal metabolic state for GABA production conflicts with that for bacterial cell growth. Herein, we demonstrated metabolic state switching from the cell growth mode based on the metabolic pathways of the wild type strain to a GABA production mode based on a synthetic metabolic pathway in Escherichia coli through rewriting of the metabolic regulatory network and pathway engineering. The GABA production mode was achieved by multiple strategies such as conditional interruption of the TCA and glyoxylate cycles, engineering of GABA production pathway including a bypass for precursor metabolite supply, and upregulation of GABA transporter. As a result, we achieved 3-fold improvement in total GABA production titer and yield (4.8 g/L, 49.2% (mol/mol glucose)) in batch fermentation compared to the case without metabolic state switching (1.6 g/L, 16.4% (mol/mol glucose)). This study reports the highest GABA production performance among previous reports on GABA fermentation from glucose using engineered E. coli..
4. Hiroshi Honjo, Kenshiro Iwasaki, Yuki Soma, K. Tsuruno, Hiroyuki Hamada, T. Hanai, Synthetic microbial consortium with specific roles designated by genetic circuits for cooperative chemical production, Metabolic Engineering, 10.1016/j.ymben.2019.08.007, 55, 268-275, 2019.09.
5. Kosuke Hata, Yuki Soma, Toshiyuki Yamashita, Masatomo Takahashi, Kuniyo Sugitate, Takeshi Serino, Hiromi Miyagawa, Kenichi Suzuki, Kayoko Yamada, Takatomo Kawamukai, Teruhisa Shiota, Yoshihiro Izumi, Takeshi Bamba, Calibration-Curve-Locking Database for Semi-Quantitative Metabolomics by Gas Chromatography/Mass Spectrometry, Metabolites, 10.3390/metabo11040207, 11, 4, 207-207, 2021.03, [URL].
6. Yan-Yu Chen, Yuki Soma, Masahito Ishikawa, Masatomo Takahashi, Yoshihiro Izumi, Takeshi Bamba, Katsutoshi Hori, Metabolic alteration of Methylococcus capsulatus str. Bath during a microbial gas-phase reaction, Bioresource Technology, 10.1016/j.biortech.2021.125002, 330, 125002-125002, 2021.06, [URL], This study demonstrates the metabolic alteration of Methylococcus capsulatus (Bath), a representative bacterium among methanotrophs, in microbial gas-phase reactions. For comparative metabolome analysis, a bioreactor was designed to be capable of supplying gaseous substrates and liquid nutrients continuously. Methane degradation by M. capsulatus (Bath) was more efficient in a gas-phase reaction operated in the bioreactor than in an aqueous phase reaction operated in a batch reactor. Metabolome analysis revealed remarkable alterations in the metabolism of cells in the gas-phase reaction; in particular, pyruvate, 2-ketoglutarate, some amino acids, xanthine, and hypoxanthine were accumulated, whereas 2,6-diaminopimelate was decreased. Based on the results of metabolome analysis, cells in the gas-phase reaction seemed to alter their metabolism to reduce the excess ATP and NADH generated upon increased availability of methane and oxygen. Our findings will facilitate the development of efficient processes for methane-based bioproduction with low energy consumption..
7. Yuki Soma, Masatomo Takahashi, Yuri Fujiwara, Tamaki Shinohara, Yoshihiro Izumi, Taizo Hanai, Takeshi Bamba, Design of Synthetic Quorum Sensing Achieving Induction Timing-Independent Signal Stabilization for Dynamic Metabolic Engineering of E. coli, ACS Synthetic Biology, 10.1021/acssynbio.1c00008, 10, 6, 1384-1393, 2021.06, [URL], Dynamic metabolic engineering that harnesses synthetic biological tools is a next-generation strategy for microbial chemical and fuel production. We previously reported a synthetic quorum sensing system combined with a metabolic toggle switch (QS-MTS) in E. coli. It autonomously redirected endogenous metabolic flux toward the synthetic metabolic pathway and improved biofuel production. However, its functions and effects on host metabolism were attenuated by induction timing delay. Here, we redesigned the QS-MTS to stabilize QS signaling efficiency and metabolic regulation. We performed a metabolome analysis to clarify the effects of QS-MTS redesign on host metabolism. We compared the contributions of conventional and redesigned QS-MTS to fed-batch fermentation. The redesigned QS-MTS was more conducive than the conventional QS-MTS to long-term processes such as fed-batch fermentation. Here, we present a circuit redesign for metabolic flux control based on dynamic characteristic evaluation and metabolome analysis..
1. , [URL].
2. Yuki Soma, Design of synthetic genetic circuit for dynamic metabolic engineering, 8thASIAN SYMPOSIUM ON INNOVATIVE BIO-PRODUCTION SINGAPORE (i-BioS), 2017.12, [URL].
3. Yuki Soma, Yuri Fujiwara, Taizo Hanai, Yoshihiro Izumi, Takeshi Bamba, Reprogramming of Collective Microbial Cell Behavior, The 27th Hot Spring Harbor International Symposium, 2017.10.
4. Yuki Soma, Metabolomics on designed metabolic dynamics by synthetic genetic circuits, The 26th Hot Spring Harbor International Symposium, 2016.11.
Membership in Academic Society
  • Japan Society for Environmental Biotechnology
  • American Society for Mass Spectrometry
  • The Society of Biotechnology, Japan