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RIKEN Center for Sustainable Resource Science Metabolomics Research Group

Group Director: Kazuki Saito (Ph.D.)

Research Summary

Kazuki  Saito(Ph.D.)

Metabolomics involves in the identification and quantification of all metabolites in a cell, and correlating these to genomic functions. Metabolome in the plant kingdom is extremely diverse chemically, with estimates indicating as many as 200,000 different types of chemical substances. The various compounds produced by plants are important for the existence of the plant itself, and also play a vital role in our lives as food, industrial materials, energy and medicines. Our group performs high-throughput metabolomics analyses by high-performance mass spectrometry. These non-targeted metabolomic analyses are applied to the identification of unknown gene functions and elucidation of metabolic networks. We are investigating the basic principles behind the wide variety of plant production functions, using Arabidopsis as a model. We are also elucidating the production systems for specialized plant products in crops, medicinal plants and other useful plants at a genome level, regarded as Phytochemical Genomics. Another important aspect of our research is the application of the basic findings from these results to development of sustainable resources.

Main Research Fields

  • Biological Sciences

Related Research Fields

  • Chemistry
  • Biology
  • Agricultural Sciences
  • Medicine, Dentistry & Pharmacy


  • metabolomics
  • functional genomics
  • plant biochemistry
  • specialized (secondary) metabolism
  • mass spectrometry

Selected Publications

  • 1.Tsugawa, H., Nakabayashi, R., Mori, T., Yamada, Y., Takahashi, M., Rai, A., Sugiyama, R., Yamamoto, H., Nakaya, T.,Yamazaki, M., Kooke, R., Bac-Molenaar, J.A., Oztolan-Erol, N., Keurentjes, J.J.B., Arita, M. and Saito, K.:
    "Acheminformatics approach to characterize metabolomes in stable-isotope-labeled organisms."
    Nat. Methods., 16, 295-298 (2019)
  • 2.Knoch, E., Sugawara, S., Mori, T., Poulsen, C., Fukushima, A., Harholt, J., Fujimoto, Y., Umemoto, N. and Saito, K.:
    "The third DWF1 paralog in Solanaceae, sterol D24-isomerase, branching withanolide biosynthesis from the general phytosterol pathway."
    Proc. Natl. Acad. Sci. USA, 115, E8096-E8103 (2018)
  • 3.Higashi, Y., Okazaki, Y., Takano, K., Myouga, F., Shinozaki, K., Knoch, E., Fukushima, A. and Saito, K.:
    "HEAT INDUCIBLE LIPASE1 remodels chloroplastic monogalactosyldiacylglycerol by liberating α-linolenic acid in Arabidopsis leaves under heat stress."
    The Plant Cell, 30, 1887-1905 (2018)
  • 4.Mochida, K., Sakurai, T., Seki, H., Yoshida, T., Takahagi, K., Sawai, S., Uchiyama, H., Muranaka, T. and Saito, K.:
    "Draft genome assembly and annotation of Glycyrrhiza uralensis, a medicinal legume"
    Plant J., 89, 181-194 (2017)
  • 5.Nakabayashi, R., Hashimoto, K., Toyooka, K. and Saito, K.:
    "Top-down Metabolomic Approaches for Nitrogen-Containing Metabolites"
    Analytical Chemistry, 89, 2698-2703 (2017)
  • 6.Matsuda, F., Nakabayashi, R., Yang, Z., Okazaki, Y., Yonemaru, J., Ebana, K., Yano, M. and Saito, K.:
    "Metabolome-genome-wide association study dissects genetic architecture for generating natural variation in rice secondary metabolism"
    Plant J., 81, 13-23 (2015)
  • 7.Sawai, S., Ohyama, K., Yasumoto, S., Seki, H., Sakuma, T., Yamamoto, T., Takebayashi, Y., Kojima, M., Sakakibara, H., Aoki, T., Muranaka, T., Saito, K. and Umemoto, N.:
    "Sterol Side Chain Reductase 2 Is a Key Enzyme in the Biosynthesis of Cholesterol, the Common Precursor of Toxic Steroidal Glycoalkaloids in Potato"
    Plant Cell. 26, 3763-3774 (2014)
  • 8.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 Commun., 26;4:1510. doi: 10.1038/ncomms2512 (2013)
  • 9.Nakabayashi, R., Sawada, Y., Yamada, Y., Suzuki, M., Hirai, M.Y., Sakurai, T and Saito, K.:
    "Combination of Liquid Chromatography-Fourier Transform-Ion Cyclotron Resonance-Mass Spectrometry with 13C-labeling for Chemical Assignment of Sulfur-containing Metabolites in Onion Bulbs"
    Analytical Chemistry, 85, 1310-1315 (2013)
  • 10.Bunsupa, S., Katayama, K., Ikeura, E., Oikawa, A., Toyooka, K., Saito, K. and Yamazaki, M.:
    "Lysine decarboxylase catalyzes the first step of quinolizidine alkaloid biosynthesis and coevolved with alkaloid production in Leguminosae"
    Plant Cell, 24, 1202-1216 (2012)

Recent Research Results

Related Links

Lab Members

Principal investigator

Kazuki Saito
Group Director

Core members

Keiko Sakakibara
Senior Research Scientist
Naoyuki Umemoto
Senior Research Scientist
Tsubasa Shoji
Senior Scientist
Ryo Nakabayashi
Research Scientist
Yasuhiro Higashi
Research Scientist
Tetsuya Mori
Expert Technician
Ryosuke Sasaki
Expert Technician
Makoto Kobayashi
Technical Staff I
Tomoko Nishizawa
Technical Staff I
Satoko Sugawara
Technical Staff I
Kouji Takano
Technical Staff II

Contact Information

C714 Central Research Building, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
Fax: +81-(0)45-503-9489

Email: kazuki.saito [at] riken.jp