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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. Yonekura-Sakakibara, K., Yamamura, M., Matsuda, F., Ono, E., Nakabayashi, R., Sugawara, S., Mori, T., Tobimatsu, Y., Umezawa, T. and Saito, K.:
    "Seed-coat protective neolignans are produced by the dirigent protein AtDP1 and the laccase AtLAC5 in Arabidopsis"
    Plant Cell, 33, 129–152, doi.org/10.1093/plcell/koaa014 (2021)
  • 2. Rai, A., Hirakawa, H., Nakabayashi, R., Kikuchi, S., Hayashi, K., Rai, M., Tsugawa, H., Nakaya, T., Mori, T., Nagasaki, H., Fukushi, R., Kusuya, Y., Takahashi, H., Uchiyama, H., Toyoda, A., Hikosaka, S., Goto, E., Saito, K. and Yamazaki, M.:
    "Chromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis"
    Nature Commun., 12, 405, doi: 10.1038/s41467-020-20508-2 (2021)
  • 3. Nakabayashi, R., Mori, T., Takeda, N., Toyooka, K., Sudo, H., Tsugawa, H. and Saito, K.:
    "Metabolomics With 15N Labeling for Characterizing Missing Monoterpene Indole Alkaloids in Plants"
    Anal. Chem., 92, 5670-5675 (2020)
  • 4. Waki, T., Mameda, R., Nakano, T., Yamada, S., Terashita, M., Ito, K., Tenma, N., Li, Y., Fujino, N., Uno, K., Yamashita, S., Aoki, Y., Denessiouk, K., Kawai, Y., Sugawara, S., Saito, K., Yonekura-Sakakibara, K., Morita, Y., Hoshino, A., Takahashi, S. and Nakayama, T.:
    "A Conserved Strategy of Chalcone Isomerase-Like Protein to Rectify Promiscuous Chalcone Synthase Specificity"
    Nature Commun., 11, 870, doi: 10.1038/s41467-020-14558-9 (2020)
  • 5. 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"
    Nature Methods., 16, 295-298 (2019)
  • 6. 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 Δ24-isomerase, branching withanolide biosynthesis from the general phytosterol pathway"
    Proc. Natl. Acad. Sci. USA, 115, E8096-E8103 (2018)
  • 7. 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"
    Plant Cell, 30, 1887-1905 (2018)
  • 8. 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)
  • 9. Nakabayashi, R., Hashimoto, K., Toyooka, K. and Saito, K.:
    "Top-down Metabolomic Approaches for Nitrogen-Containing Metabolites"
    Anal. Chem., 89, 2698-2703 (2017)
  • 10. 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)

Recent Research Results

Related Links

Lab Members

Principal investigator

Kazuki Saito
Group Director

Core members

Naoyuki Umemoto
Senior Scientist
Tsubasa Shoji
Senior Scientist
Amit Rai
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