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RIKEN Center for Sustainable Resource Science Metabolic Systems Research Team

Team Leader: Masami Hirai (Ph.D.)

Research Summary

Masami  Hirai(Ph.D.)

Metabolism is finely regulated in a complicated way, as it comprises the basis of life. Especially, plant’s and bacterial metabolism is an important base not only for their own lives but also for animal lives and human society by providing nutrient and functional compounds. Aiming at grasping a whole picture of metabolism, we develop metabolomics techniques, predict metabolic reaction network by mathematical modeling using omics data, and explore metabolic gene functions by molecular biology, biochemistry and molecular genetics. We also aim at improvement of plant’s and bacterial productivity of useful metabolites by use of our findings.

Main Research Fields

  • Biological Sciences

Related Research Fields

  • Biology
  • Agricultural Sciences


  • Metabolism
  • Metabolomics
  • Mathematical modelling
  • Plant
  • Secondary metabolism

Selected Publications

  • 1.Okamura, E. and Hirai, M.Y.:
    "Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana."
    Scientific Reports, 7, 3533 (2017)
  • 2.Sawada,Y., Tsukaya, H., Li, Y., Sato, M., Kawade, K. and Hirai, M.Y.:
    "A Novel Method for Single-grain-based Metabolic Profiling of Arabidopsis Seed."
    Metabolomics, 13, 75 (2017)
  • 3.Osanai, T., Shirai, T., Iijima, H., Nakaya, Y., Okamoto, M., Kondo, A. and Hirai, M.Y.:
    "Genetic manipulation of a metabolic enzyme and a transcriptional regulator increasing succinate excretion from unicellular cyanobacterium."
    Frontiers in Microbiology, 6 (2015).
  • 4.Sriyudthsak, K., Sawada, Y., Chiba, Y., Yamashita, Y., Kanaya, S., Onouchi, H., Fujiwara, T., Naito, S., Voit, E.O., Shiraishi, F., and Hirai, M.Y.:
    "A U-system approach for predicting metabolic behaviors and responses based on an alleged metabolic reaction network."
    BMC Syst. Biol. 8 Suppl 5: S4 (2014).
  • 5.Araki, R., Hasumi, A, Nishizawa, O.I., Sasaki, K., Kuwahara, A., Sawada, Y., Totoki, Y., Toyoda, A, Sakaki, Y., Li, Y., Saito, K., Ogawa, T., and Hirai, M.Y.:
    "Novel bioresources for studies of Brassica oleracea: identification of a kale MYB transcription factor responsible for glucosinolate production."
    Plant Biotechnol J. 11: 1017-27 (2013).
  • 6.Kawade, K., Horiguchi, G., Usami, T., Hirai, M.Y., and Tsukaya, H.:
    "ANGUSTIFOLIA3 Signaling Coordinates Proliferation between Clonally Distinct Cells in Leaves."
    Curr Biol. 23: 788-92 (2013).
  • 7.Okazaki, Y. Otsuki, H., Narisawa, T., Kobayashi, M., Sawai, S., Kamide, Y., Kusano, M., Aoki, T., Hirai, M.Y., and Saito, K.:
    "A new class of plant lipid is essential for protection against phosphorus depletion."
    Nature Communications 4, 1510 (2013).
  • 8.Sriyudthsak, K., Shiraishi, F., and Hirai, M.Y.:
    "Identification of a metabolic reaction network from time-series data of metabolite concentrations."
    PLoS One 8, e51212 (2013).
  • 9.Sawada, Y., Akiyama, K., Sakata, A., Kuwahara, A., Otsuki, H., Sakurai, T., Saito, K., and Hirai, M.Y.:
    "Widely targeted metabolomics based on large-scale MS/MS data for elucidating metabolite accumulation patterns in plants."
    Plant Cell Physiol. 50, 37-47 (2009).
  • 10.Hirai, M.Y., Sugiyama, K., Sawada, Y., Tohge, T., Obayashi, T., Suzuki, A., Araki, R., Sakurai, N., Suzuki, H., Aoki, K., Goda, H., Nishizawa, O.I., Shibata, D., and Saito, K.:
    "Omics-based identification of Arabidopsis Myb transcription factors regulating aliphatic glucosinolate biosynthesis."
    Proc. Natl. Acad. Sci. U. S. A. 104, 6478-6483 (2007).

Recent Research Results

Related Links

Lab Members

Principal investigator

Masami Hirai
Team Leader

Core members

Kai Uchida
Research Scientist
Ryoichi Sato
Research Scientist
Yushiro Fuji
Research Scientist
Ryota Akiyama
Special Postdoctoral Researcher
Mai Uzaki
Special Postdoctoral Researcher
Hiromitsu Tabeta
Special Postdoctoral Researcher
Ayuko Kuwahara
Technical Staff I
Muneo Sato
Technical Staff I

Contact Information

C619 Central Research Building, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan

Email: masami.hirai [at] riken.jp