Centers & Labs

RIKEN Center for Sustainable Resource Science

Metabolomics Research Group

Group Director: Kazuki Saito (Ph.D.)
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 Field

Biological Sciences

Related Research Fields

Chemistry / Biology / Agricultural sciences / Medicine, dentistry, and pharmacy


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

Selected Publications

  1. 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)
  2. Nakabayashi, R., Hashimoto, K., Toyooka, K. and Saito, K.:
    "Top-down Metabolomic Approaches for Nitrogen-Containing Metabolites"
    Analytical Chemistry, 89, 2698-2703 (2017)
  3. 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)
  4. 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)
  5. 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)
  6. 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)
  7. 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)
  8. Matsuda, F., Okazaki, Y., Oikawa, A., Kusano, M., Nakabayashi, R., Kikuchi, J., Yonemaru, J., Ebana, K., Yano, M. and Saito, K.:
    "Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis"
    Plant J., 70, 624–636 (2012)
  9. Seki, H.*, Sawai, S. *, Ohyama, K. *, Mizutani, M., Ohnishi, T., Sudo, H., Odette Fukushima, E., Akashi, T., Aoki, T., Saito, K., and Muranaka, T.(*equal contribution).:
    "Triterpene functional genomics in licorice for identification of CYP72A154 involved in the biosynthesis of glycyrrhizin"
    Plant Cell, 23, 4112-4123 (2011)
  10. Kusano, M., Redestig, H., Hirai, T., Oikawa, A., Matsuda, F., Fukushima, A., Masanori, A., Watanabe, S., Yano, M., Hiwasa-Tanase, K., Ezura, H., and Saito, K.:
    "Covering chemical diversity of genetically-modified tomatoes using metabolomics for objective substantial equivalence assessment"
    PLoS ONE, 6(2): e16989 (2011)

Lab Members

Principal Investigator

Kazuki Saito
Group Director

Core Members

Keiko Sakakibara
Senior Research Scientist
Naoyuki Umemoto
Senior Research Scientist
Jianwei Tang
Research Scientist
Ryo Nakabayashi
Research Scientist
Yasuhiro Higashi
Research Scientist
Makoto Kobayashi
Technical Staff I
Tomoko Nishizawa
Technical Staff I
Tetsuya Mori
Technical Staff I
Satoko Sugawara
Technical Staff I
Ryosuke Sasaki
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]

Related links

Recent research results