Smart Cell Engineering and Bioproduction Research Unit Research Achievements

Bio-Based Fuel and Chemical Research Group

  1. Tanaka, K., Shirai, T., Vavricka, CJ., Matsuda, M., Kondo, A., Hasunuma, T.
    Dark accumulation of downstream glycolytic intermediates confers robust initiation of photosynthesis in cyanobacteria. Plant Physiology, in press.
  2. Kahar, P., Itomi, A., Tsuboi, H., Ishizaki, M., Yasuda, M., Kihira, C., Otsuka, H., Azmi, N.b., Matsumoto, H., Ogino, C., Kondo, A.
    (2022/07) The flocculant Saccharomyces cerevisiae strain gains robustness via alteration of the cell wall hydrophobicity, Metabolic Engineering, 72, 82-96
  3. Vavricka, CJ., Takahashi, S., Watanabe, N., Takenaka, M., Matsuda, M., Yoshida, T., Suzuki, R., Kiyota, H., Li, J., Minami, H., Ishii, J., Tsuge, K., Araki, M., Kondo, A., Hasunuma, T.
    (03/2022) Machine learning discovery of missing links that mediate alternative branches to plant alkaloids. Nature Communications, 13, 1405.
  4. Bamba, T., Guirimand, G., Kondo, A., Hasunuma, T.
    (02/2022) Enzyme display technology for lignocellulosic biomass valorization by yeast cell factories. Current Opinion in Green and Sustainable Chemistry, 33: 100584.
  5. Kahar, P., Rachmadona, N., Pangestu, R., Palar, R., Nugroho Adi, DT., Juanssilfero, AB., Yopi, Manurung, I., Hama, S., Ogino, C.
    (01/2022) An integrated biorefinery strategy for the utilization of palm-oil wastes. Bioresource Technology, 344(B): 126266.
  6. Kato, Y., Inabe, K., Hidese, R., Kondo, A., Hasunuma, T.
    (01/2022) Metabolomics-based engineering for biofuel and bio-based chemical production in microalgae and cyanobacteria: A review. Bioresource Technology, 344(A): 126196.
  7. Kawaguchi, H., Takada, K., Elkasaby, T., Pangestu, R., Toyoshima, M., Kahar, P., Ogino, C., Kaneko, T., Kondo, A.
    (01/2022) Recent advances in lignocellulosic biomass white biotechnology for bioplastics. Bioresource Technology, 344(B): 126165.
  8. Ismail, KSK., Matano, Y., Sakihama, Y., Inokuma, K., Nambu, Y., Hasunuma, T., Kondo, A.
    (01/2022) Pretreatment of extruded Napier grass by hydrothermal process with dilute sulfuric acid and fermentation using a cellulose-hydrolyzing and xylose-assimilating yeast for ethanol production. Bioresource Technology, 343, 126071.
  9. Guirimand, G., Kulagina, N., Papon, N., Hasunuma, T., Courdavault, V.
    (05/2021) Innovative tools and strategies for optimizing yeast cell factories. Trends in Biotechnology, 39(5), 488-504.
  10. Shoji, S., Yamaji, T., Makino, H., Ishii, J., Kondo, A.
    (05/2021) Metabolic design for selective production of nicotinamide mononucleotide from glucose and nicotinamide. Metabolic Engineering, 65, 167-177.
  11. Mori, Y., Noda, S., Shirai, T., Kondo, A.
    (04/2021) Direct 1,3-butadiene biosynthesis in Escherichia coli via a tailored ferulic acid decarboxylase mutant. Nature Communications, 12: 2195.
  12. Tominaga, M., Nozaki, K., Umeno, D., Ishii, J., Kondo, A.
    (03/2021) Robust and flexible platform for directed evolution of yeast genetic switches. Nature Communications, 12: 1846.
  13. Nishida, K., Kondo, A.
    (01/2021) CRISPR-derived genome editing technologies for metabolic engineering. Metabolic Engineering, 63, 141-147.
  14. Ito, Y., Terai, G., Ishigami, M., Hashiba, N., Nakamura, Y., Bamba, T., Kumokita, R., Hasunuma, T., Asai, K., Ishii, J., Kondo, A.
    (12/2020) Exchange of endogenous and heterogeneous yeast terminators in Pichia pastoris to tune mRNA stability and gene expression. Nucleic Acids Research, 48(22), 13000-13012.
  15. Zhang, S., Wakai, S., Sasakura, N., Tsutsumi, H., Hata, Y., Ogino, C., Kondo, A.
    (09/2020) Pyruvate metabolism redirection for biological production of commodity chemicals in aerobic fungus Aspergillus oryzae. Metabolic Engineering, 61, 225-237.
  16. Vavricka, CJ., Hasunuma, T., Kondo, A.
    (01/2020) Dynamic metabolomics for engineering biology: Accelerating learning cycles for bioproduction. Trends in Biotechnology, 38(1), 68-82.
  17. Inokuma, K., Kurono, H., den Haan, R., van Zyl, W. H., Hasunuma, T., Kondo, A.
    (01/2020) Novel strategy for anchorage position control of GPI-attached proteins in the yeast cell wall using different GPI-anchoring domains. Metabolic Engineering, 57, 110-117.

Biologics Research Group

  1. Ito, Y., Terai, G., Ishigami, M., Hashiba, N., Nakamura, Y., Bamba, T., Kumokita, R., Hasunuma, T., Asai, K., Ishii, J.*, Kondo, A. * (2020) Exchange of endogenous and heterogeneous yeast terminators in Pichia pastoris to tune mRNA stability and gene expression, Nucleic Acids Research, 48(22), 13000-13012
  2. Nakamura, Y., Asama R., Tabata, T., Morita, K., Maruyama, T., Kondo, A., Ishii, J. * (2020) Comparative analyses of site-directed mutagenesis of human melatonin MTNR1A and MTNR1B receptors using a yeast fluorescent biosensor, Biotechnology and Bioengineering, 118(2), 863-876 DOI:10.1002/bit.27609
  3. Higashiyama, K., Yuan, Y., Hashiba, N., Masumi-Koizumi, K., Yusa, K., Uchida, K. (2023) Quantitation of residual host cell DNA in recombinant adeno-associated virus using droplet digital PCR, Human Gene Therapy, doi: 10.1089/hum.2023.006.
  4. Kono, K., Kataoka, K., Yuan, Y., Yusa, K., Uchida, K., Sato Y. (2020) A highly sensitive method for the detection of recombinant PERV-A/C env RNA using next generation sequencing technologies. Scientific Reports 10, 21935　DOI:https://doi.org/10.1038/s41598-020-78890-2
  5. Yusa, K., Yuan Y., Uchida, K. (2000) Viral safety testing for biopharmaceuticals: Current and future prospects Translat Regulat Sci. 2(3): 94–99; doi: 10.33611/trs.2020-017
  6. Kono, K., Kataoka, K., Yuan, Y., Yusa, K., Uchida, K., Sato, Y. (2021) Infectivity assessment of porcine endogenous retrovirus using high-throughput sequencing technologies. Biologicals. 71:1-8.

Functional Food and Agrobio Research Group

  1. Hayashi, D., Mouchlis, V. D., Okamoto, S., Namba, T., Wang, L., Li, S., Ueda, S., Yamanoue, M., Tachibana, H., Arai, H., Ashida, H., Dennis, E. A., & Shirai, Y. (2022). Vitamin E functions by association with a novel binding site on the 67 kDa laminin receptor activating diacylglycerol kinase. Journal of Nutritional Biochemistry 110, 109129-109131.
  2. Yamamoto, M., Yoshioka, Y., Kitakaze, T., Yamashita, Y., & Ashida, H. (2022). Preventive effects of black soybean polyphenols on non-alcoholic fatty liver disease in three different mouse models. Food & Function, 13(2), 1000–1014.
  3. Okada, N., Sugiyama, K., Shichi, S., Shirai, Y., Goto, K., Sakane, F., Kitamura, H., & Taketomi, A. (2022). Combination therapy for hepatocellular carcinoma with diacylglycerol kinase alpha inhibition and anti-programmed cell death-1 ligand blockade. Cancer Immunology, Immunotherapy : CII, 71(4), 889–903.
  4. Sanjaya, A., Muramatsu, R., Sato, S., Suzuki, M., Sasaki, S., Ishikawa, H., Fujii, Y., Asano, M., Itoh, R. D., Kanamaru, K., Ohbu, S., Abe, T., Kazama, Y., & Fujiwara, M. T. (2021). Arabidopsis EGY1 is critical for chloroplast development in leaf epidermal guard cells. Plants, 10(6), 1254.
  5. Shiraiwa, M., Kitakaze, T., Yamashita, Y., Ukawa, Y., Mukai, K., & Ashida, H. (2022). Pectolinarigenin induces antioxidant enzymes through Nrf2/ARE pathway in HepG2 cells. Antioxidants, 11(4), 675.
  6. Yoshioka, Y., Kono, R., Kuse, M., Yamashita, Y., & Ashida, H. (2022). Phenylpropanoids and neolignans isolated from Myristica fragrans enhance glucose uptake in myotubes. Food & Function, 13(7), 3879–3893.
  7. Hironao, K. Y., Ashida, H., & Yamashita, Y. (2022). Black soybean seed coat polyphenol ameliorates the abnormal feeding pattern induced by high-fat diet consumption. Frontiers in Nutrition, 9, 1006132.
  8. Sanjaya, A., Kazama, Y., Ishii, K., Muramatsu, R., Kanamaru, K., Ohbu, S., Abe, T., & Fujiwara, M. T. (2021). An Argon-ion-induced pale green mutant of Arabidopsis exhibiting rapid disassembly of mesophyll chloroplast grana. Plants, 10(5), 848.
  9. Ueda, S., Takashima, Y., Gotou, Y., Sasaki, R., Nakabayashi, R., Suzuki, T., Sasazaki, S., Fukuda, I., Kebede, B., Kadowaki, Y., Tamura, M., Nakanishi, H., & Shirai, Y. (2022). Application of mass spectrometry for determining the geographic production area of wagyu beef. Metabolites, 12(9), 777.
  10. Koyama, R., Ishibashi, M., Fukuda, I., Okino, A., Osawa, R., & Uno, Y. (2022). Pre- and post-harvest conditions affect polyphenol content in strawberry (Fragaria × ananassa). Plants, 11(17), 2220.
  11. Tanaka, E., Mitani, T., Nakashima, M., Yonemoto, E., Fujii, H., & Ashida, H. (2022). Theobromine enhances the conversion of white adipocytes into beige adipocytes in a PPARγ activation-dependent manner. Journal Nutritional Biochemistry, 100, 108898.
  12. Hashimoto, T., Kiyota, M., & Kanazawa, K. (2021). Protective effect of boysenberry juice on ferric nitrilotriacetate-induced renal injury in mice. European Journal of Medicinal Plants, 32(4), 76-81.
  13. Honda, K., Yasuhara, A., Saneyasu, T., & Kamisoyama, H. (2021). Enzymatically-synthesized glycogen induces cecal glucagon-like peptide-1 production and suppresses food intake in mice. Journal of Nutritional Science and Vitaminology, 67(4), 217–224.
  14. Hashimoto, T., Kobayashi, M., & Kanazawa, K. (2021) 6-Methylsulfinylhexyl isothiocyanate inhibits cell cycle progression in quiescent JB6 cells stimulated with epidermal growth factor. Annual Research & Review in Biology, 36(6), 19-28.
  15. Kano, T., Tsumagari, R., Nakashima, A., Kikkawa, U., Ueda, S., Yamanoue, M., Takei, N., & Shirai, Y. (2021). RalA, PLD and mTORC1 are required for kinase-independent pathways in DGKβ-induced neurite outgrowth. Biomolecules, 11(12), 1814.
  16. Hashimoto, T., Shang, W., & Kanazawa, K. (2021) Artepillin C inhibits cell proliferation by cell cycle arrest at G0/G1 phase accompanied by up-regulation of p27Kip1 in human hepatoma HepG2 cells. Journal of Complementary and Alternative Medical, 14(1), 30-43.
  17. Koyama, R., Yoshimoto, A., Ishibashi, M., Itoh, H., & Uno, Y. (2021). Enzymatic activities and gene transcript levels associated with the augmentation of antioxidant constituents during drought stress in lettuce. Horticulturae, 7(11), 444.
  18. Matsui, S., Akazawa, H., Tsujikawa, Y., Fukuda, I., Suzuki, Y., Yamamoto, Y., Mukai, T., Shirai, Y., & Osawa, R. (2021). Milk oligosaccharide-mediated cross-feeding between Enterococcus gallinarum and lactobacilli in the gut microbiota of infant rats. Bioscience of Microbiota, Food and Health, 40(4), 204–211.
  19. Tsumagari, R., Maruo, K., Nakao, T., Ueda, S., Yamanoue, M., & Shirai, Y. (2021). Motor dyscoordination and alteration of functional correlation between DGKγ and PKCγ in senescence-accelerated mouse prone 8 (SAMP8). Frontiers in Aging Neuroscience, 13, 573966.
  20. Akazawa, H., Tsujikawa, Y., Fukuda, I., Suzuki, Y., Choi, M., Katayama, T., Mukai, T., & Osawa, R. (2021). Isolation and identification of milk oligosaccharide-degrading bacteria from the intestinal contents of suckling rats. Bioscience of Microbiota, Food and Health, 40(1), 27–32.
  21. Yoshioka, Y., Samukawa, Y., Yamashita, Y., & Ashida, H. (2020). 4-Hydroxyderricin and xanthoangelol isolated from Angelica keiskei prevent dexamethasone-induced muscle loss. Food & Function, 11(6), 5498–5512.
  22. Kitakaze, T., Makiyama, A., Nakai, R., Kimura, Y., & Ashida, H. (2020). Kaempferol modulates TCDD- and t-BHQ-induced drug-metabolizing enzymes and luteolin enhances this effect. Food & Function, 11(4), 3668–3680.
  23. Nishiyama, K., Takaki, T., Sugiyama, M., Fukuda, I., Aiso, M., Mukai, T., Odamaki, T., Xiao, J. Z., Osawa, R., & Okada, N. (2020). Extracellular vesicles produced by Bificobacterium longum export mucin-binding proteins. Applied and Environmental Microbiology, 86(19), e01464-20.
  24. Kitakaze, T., Jiang, H., Nomura, T., Hironao, K. Y., Yamashita, Y., & Ashida, H. (2020). Kaempferol promotes glucose uptake in myotubes through a JAK2-dependent pathway. Journal of Agricultural and Food Chemistry, 68(47), 13720-13729.
  25. Yamashita, Y., Nakamura, A., Nanba, F., Saito, S., Toda, T., Nakagawa, J., & Ashida, H. (2020). Black soybean improves vascular function and blood pressure: A randomized, placebo controlled, crossover trial in Humans. Nutrients, 12(9), 2755.
  26. Tsumagari, R., Maruo, K., Kakizawa, S., Ueda, S., Yamanoue, M., Saito, H., Suzuki, N., & Shirai, Y. (2020). Precise regulation of the basal PKCγ activity by DGKγ is crucial for motor coordination. International Journal of Molecular Sciences 21; 7866.
  27. Seki, K., Komatsu, K., Tanaka, K., Hiraga, M., Kajiya-Kanegae, H., Matsumura, H., & Uno, Y. (2020). A CIN-like TCP transcription factor (LsTCP4) having retrotransposon insertion associates with a shift from Salinas type to Empire type in crisphead lettuce (Lactuca sativa L.). Horticulture Research, 7, 15.
  28. Hayashi, D., Wang, L., Ueda, S., Yamanoue, M., Ashida, H., & Shirai, Y. (2020). The mechanisms of ameliorating effect of a green tea polyphenol on diabetic nephropathy based on diacylglycerol kinase α. Scientific Reports, 10(1), 11790.

Review Article

  1. Hayashi, D., & Shirai, Y. (2022). The role of diacylglycerol kinase in the amelioration of diabetic nephropathy. Molecules 27, 6784-6799.
  2. Hashimoto, T., Kobayashi, M., & Kanazawa, K. (2021). Inhibition of 6-methylsulfinylhexyl isothiocyanate for cell cycle progression in quiescent JB6 cells stimulated with fetal bovine serum, accompanied by suppression of cyclin A2 expression. In: New Innovations in Chemistry and Biochemistry Volume 5, (Eds. by Hassanien, M.F.R.), Chapter 5, 43-59.
  3. Yamashita, Y., Sakakibara, H., Toda, T., & Ashida, H. (2020). Insights into the potential benefits of black soybean (Glycine max L.) polyphenols in lifestyle diseases. Food & Function, 11, 7321-7339.