関連論文

Subteam 1

Adachi, T., Ichikawa, K., Miyata, T., Makino, F., Tanaka, F., Namba, K., Sowa, K. Improved direct bioelectrochemical fructose oxidation with surfactant-free heterotrimeric fructose dehydrogenase variant truncating heme 1c and C-terminal hydrophobic regions. ACS Electrochem. 2025 in press. https://doi.org/10.1021/acselectrochem.5c00106

Tokunou, Y., Yamazaki, T., Fujikawa, T., Okamoto, A. Decoding in-cell respiratory enzyme dynamics by label-free in situ electrochemistry. Proc. Natl. Acad. Sci. U S A 2025, 22(12):e2418926122. doi: 10.1073/pnas.2418926122.

Toya, Y., Imada, T., Ishibashi, M., Kawamoto, Y., Isshiki, K., Shibai, A., Furusawa, C., Shimizu, H. Growth inhibition by ppc deletion is rescued by isocitrate dehydrogenase mutations in Escherichia coli.　FEMS Microbiol. Lett. 2025, 10, 372, fnaf013. doi: 10.1093/femsle/fnaf013.
https://doi.org/10.1093/femsle/fnaf013

Ichikawa, K., Adachi, T., Kitazumi, Y., Shirai, O., Sowa, K. Quantitative elucidation of catalytic reaction of truncated aldehyde dehydrogenase based on linear free energy relationship. ACS Catal. 2025, 15, 9, 7283–7295. https://doi.org/10.1021/acscatal.4c07978.

Suzuki, Y., Kitazumi, Y., Shirai, O., Sowa, K. Downsizing effect on direct electron transfer-type bioelectrocatalysis by D-fructose dehydrogenase with structural insight. Biosci. Biotechnol. Biochem. 2025, 89(7) 925–933. https://doi.org/10.1093/bbb/zbaf043

Tanaka, K., Kondo, A., Hasunuma, T. Minimized dark consumption of Calvin cycle intermediates facilitates the initiation of photosynthesis in Synechocystis sp. PCC 6803. Plant Cell Physiol. 2024, 5(11):1812-1820. doi: 10.1093/pcp/pcae102.

Suzuki, Y., Sowa, K., Kitazumi, Y., Shirai, O. Enhancement of direct electron transfer by aromatic thiol modification with truncated D-fructose dehydrogenase. 2024, Electrochim. Acta 502, 144804. https://doi.org/10.1016/j.electacta.2024.144804.

Bamba, T., Munakata, R., Ushiro, Y., Kumokita, R., Tanaka, S., Hori, Y., Kondo, A., Yazaki, K., Hasunuma, T. De novo production of the bioactive phenylpropanoid artepillin C using membrane-bound prenyltransferase in Komagataella phaffii. ACS Synth. Biol. 2024, 13(12):4040-4049. doi: 10.1021/acssynbio.4c00472.

Ciemniecki, J. A., Ho, C. L., Horak, R. D., Okamoto, A. Newman, D.K. Mechanistic study of a low-power bacterial maintenance state using high-throughput electrochemistry. Cell 2024, 187(24), 6882-6895. doi: 10.1016/j.cell.2024.09.042.

Ueno, K., Sawada, S., Ishibashi, M., Kanda, Y., Shimizu, H., Toya, Y. Identification of a novel NADPH generation reaction in the pentose phosphate pathway in Escherichia coli using mBFP. J. Bacteriol. 2024, 206(11), e0027624. doi: 10.1128/jb.00276-24.

Fukawa, E., Suzuki, Y., Adachi, T., Miyata, T., Makino, F., Tanaka, H., Namba, K., Sowa, K., Kitazumi, Y., Shirai, O. Structural and electrochemical elucidation of biocatalytic mechanisms in direct electron transfer-type D-fructose dehydrogenase. Electrochim. Acta 2024, 490, 144271.https://www.sciencedirect.com/science/article/pii/S0013468624005139

Toya, Y., Shimizu, H. Coupling and uncoupling growth and product formation for producing chemicals. Curr. Opin. Biotechnol. 2024, 87, 103133. https://doi.org/10.1016/j.copbio.2024.103133

Tanaka, K., Bamba, T., Kondo, A., Hasunuma, T. Metabolomics-Based Development of bioproduction processes toward industrial-scale production. Curr. Opin. Biotechnol. 2024, 85, 103057.  https://doi.org/10.1016/j.copbio.2023.103057

Subteam 2

Shiraishi, K., Kitamura, B., Aramaki, K., Sakai, Y., Hoseki, J. Improvement of a FRET-based redox probe Redoxfluor through circular permutation and effects of substitution of cysteine residues on its redox properties. J. Biochem. 2025 May 14: mvaf023. https://doi.org/10.1093/jb/mvaf023

Katayama, S., Shiraishi, K., Kaji, K., Kawabata, K., Tamura, N., Tani, A., Yurimoto, H., Sakai, Y. Methanol chemoreceptor MtpA- and flagellin protein FliC-dependent methylotaxis contributes to the spatial colonization of PPFM in the phyllosphere. ISME Commun. 2025, ycaf092, https://doi.org/10.1093/ismeco/ycaf092

Seike, T., Takekata, H., Kono, K., Sakata, N., Kotani, H., Furusawa, C., Matsuda, F. Discovery and identification of a novel yeast species, Hanseniaspora drosophilae sp. nov., from Drosophila in Okinawa, Japan. Int. J. Syst. Evol. Microbiol. 2025, 75(2), 006661. https://doi.org/10.1099/ijsem.0.006661

Tominaga, M., Kawakami, K., Ogawa, H, Nakamura, T, Kondo, A., Ishii, J. Production of borneol, camphor, and bornyl acetate using engineered Saccharomyces cerevisiae. Metab. Eng. Commun. 2025, 20, e00259. https://doi.org/10.1016/j.mec.2025.e002592

Seike, T., Takekata, H., Sakata, N., Furusawa, C., Matsuda, F. Yamadazyma thunbergiae sp. nov., a novel yeast species associated with Bengal clock vines and soil in Okinawa, Japan. Int. J. Syst. Evol. Microbiol. 2024, 74(10), 006537. 
https://doi.org/10.1099/ijsem.0.006537

Tominaga, M., Shima, Y., Nozaki, K., Ito, Y., Someda, M., Shoya, Y., Hashii, N., Obata, C., Matsumoto-Kitano, M., Suematsu, K., Matsukawa, T., Hosoya, K., Hashiba, N., Kondo, A., Ishii, J. Designing strong inducible synthetic promoters in yeasts. Nat. Commun. 2024, 15(1):10653. doi: 10.1038/s41467-024-54865-z.

Yoshimoto, S., Aoki, S., Ishikawa, M., Suzuki, A., Hori, K. Size‑dependent ability of AtaA to immobilize cells in Acinetobacter sp. Tol 5. Sci. Rep. 2024, 14:21039. https://doi.org/10.1038/s41598-024-71920-3

Takafuji, Y., Fischer, T., Miyazaki, K., Honda, K. Complete Genome Sequences of Thermus thermophilus strains isolated from Shirahama Hot Spring in Japan. Microbiol. Resour. Announc. 2024, e00316-24. https://doi.org/10.1128/mra.00316-24

Yamada, R., Yamamoto, C., Sakaguchi, R., Matsumoto, T., Ogino, H. Development of a metabolic engineering technology to simultaneously suppress the expression of multiple genes in yeast and application in carotenoid production. World J. Microbiol. Biotechnol. 2024, 40 (7), 227.  DOI：10.1007/s11274-024-04034-7.

Yamada, R., Ando, K., Sakaguchi, R., Matsumoto, T., Ogino, H. Induction of point and structural mutations in engineered yeast Saccharomyces cerevisiae improve carotenoid production. World J. Microbiol. Biotechnol. 2024, 40 (7), 230. DOI：10.1007/s11274-024-04037-4.

Subteam 3

Hirasawa, T., Satoh, Y., Koma, D. Production of aromatic amino acids and their derivatives by Escherichia coli and Corynebacterium glutamicum. World J. Microbiol. Biotechnol. 2025, 41 (2), 65. doi: 10.1007/s11274-025-04264-3.

Matsuda, F., Kamiyama, A., Yamasaki, K., Seike, T., Okahashi, N. ΔΔG method for elucidating key control reactions from relative quantification metabolome data: Comparative analysis of yeast glycolysis. Anal. Chem. 2025, 97(12), 6391-6398. https://pubs.acs.org/doi/10.1021/acs.analchem.4c04480

Mitsunobu, H., Kita, Y., Nambu-Nishida, Y., Miyazaki, S., Nakajima, K., Taoka, K. Kondo, A., Nishida, K. Development of a highly efficient base editing system for Lactobacilli to improve probiotics and dissect essential functions. Appl. Microbiol. Biotechnol. 2025, 109, 96. doi: 10.1007/s00253-025-13489-z.

Himeoka, Y., Furusawa C. Perturbation-response analysis of in silico metabolic dynamics in nonlinear regime: Hard-coded responsiveness in the cofactors and network sparsity. eLife 2025. https://doi.org/10.7554/eLife.98800.3

Kosaka, Y., Miyawaki, Y., Mori, M., Aburaya, S., Nishizawa, C., Chujo, T., Niwa, T., Miyazaki, T., Sugita, T., Fukuyama, M., Taguchi, H., Tomizawa, K., Sugase, K., Ueda, M., Aoki, W. Autonomous ribosome biogenesis in vitro. Nat. Commun. 2025, 16(1), 514.  doi: 10.1038/s41467-025-55853-7.

Ojima-Kato, T. Advances in recombinant protein production in microorganisms and functional peptide tags. Biosci. Biotechnol. Biochem. 2024, 89(1), 1-10. https://academic.oup.com/bbb/article/89/1/1/7853146

Nishikawa, Y., Fujikawa, R., Nakano, H., Kanamori, T., Ojima-Kato, T. Effect of translation enhancing nascent SKIK peptide on the arrest peptides containing consecutive proline. ACS Synth. Biol. 2024, 13(12), 3908-3916. doi: 10.1021/acssynbio.4c00221.

Himeoka, Y., Horiguchi, SA, Kobayashi TJ Theoretical basis for cell deaths. Phy. Rev. Res. 2024, 6, 043217. DOI:https://doi.org/10.1103/PhysRevResearch.6.043217

Harazono, Y., Shimono, H., Hata, K., Mitsuyama, T., Horinouchi, T. Evaluation of microplate handling accuracy for applying robotic arms in laboratory automation. SLAS Technol. 2024, 29(6):100200.
doi: 10.1016/j.slast.2024.100200.
https://doi.org/10.1016/j.slast.2024.100200

Taniguchi, T.; Okahashi N.; Matsuda, F. 13C-metabolic flux analysis reveals metabolic rewiring in HL-60 neutrophil-like cells through differentiation and immune stimulation. Metab. Eng. Commun. 2024, 18, p. e00239.  DOI：10.1016/j.mec.2024.e00239.