RIKEN Center for Sustainable Resource Science Metabolic Systems Research Team

Team Director: Masami Hirai (Ph.D.)

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Research Summary

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

Keywords

Metabolism
Metabolomics
Mathematical modelling
Plant
Secondary metabolism

Selected Publications

1. Tabeta, H. and Hirai, M.Y.:
"L-2-Aminopimelic acid acts as an auxin mimic to induce lateral root formation across diverse plant species"
FEBS Letters. 598, 1855-1863. (2024)
2. Uzaki, M., Mori, T., Sato, M., Wakazaki, M., Takeda-Kamiya, N., Yamamoto, K., Murakami, A., Guerrero, D.A.S., Shichijo, C., Ohnishi, M., Ishizaki, K., Fukaki, H., O'Connor, S.E., Toyooka, K., Mimura, T. and Hirai, M.Y.:
"Integration of cell differentiation and initiation of monoterpenoid indole alkaloid metabolism in seed germination of Catharanthus roseus"
New Phytol. 242, 1156-1171. (2024)
3. Wang, M., Tabeta, H., Ohtaka, K., Kuwahara, A., Nishihama, R., Ishikawa, T., Toyooka, K., Sato, M., Wakazaki, M., Akashi, H., Tsugawa, H., Shoji, T., Okazaki, Y., Yoshida, K., Sato, R., Ferjani, A., Kohchi, T. and Hirai, M.Y.:
"The phosphorylated pathway of serine biosynthesis affects sperm, embryo, and sporophyte development, and metabolism in Marchantia polymorpha"
Commun Biol. 7, 102. (2024)
4. Kim, J.S., Sato, M., Kojima, M., Asrori, M.I., Uehara-Yamaguchi, Y., Takebayashi, Y., Do, T.N., Do, T.Y., Nguyen, T.K.O., Sakakibara, H., Mochida, K., Ogita, A. and Hirai, M.Y.:
"Multi-omics signatures of diverse plant callus cultures"
Plant Biotechnol. 41, 309-314. (2024)
5. Uchida, K., Kim, J.S., Sato, M., Tabeta, H., Mochida, K. and Hirai, M.Y.
"A metabolome genome-wide association study implicates histidine N-pi-methyltransferase as a key enzyme in N-methylhistidine biosynthesis in Arabidopsis thaliana"
Front. Plant Sci. 14, (2023)
6. Fuji, Y., Uchida, K., Akashi, T., Ohtsuki, T., Matsufuji, H. and Hirai, M.Y.:
"Molecular Identification of UDP-Sugar Dependent Glycosyltransferase and Acyltransferase Involved in the Phenylethanoid Glycoside Biosynthesis Induced by Methyl Jasmonate in Sesamum indicum L"
Plant Cell Physiol. 64, 716-728. (2023)
7. Ito, T., Kitaiwa,T., Nishizono, K.,Umahashi, M., Miyaji, S.,Agake, S., Kuwahara, K., Yokoyama, T., Fushinobu, S., Maruyama-Nakashita, A., Sugiyama, R., Sato, M., Inaba, J., Hirai, M.Y. and Ohkama-Ohtsu, N.:
"Glutathione degradation activity of γ‐glutamyl peptidase 1 manifests its dual roles in primary and secondary sulfur metabolism in Arabidopsis"
Plant J. 111, 1626-1642. (2022)
8. Siriwach, R., Matsuzaki, J., Saito, T., Nishimura, H., Isozaki, M., Isoyama, Y., Sato, M., Arita, M., Akaho, S., Higashide, T., Yano, K., and Hirai, M.Y.:
"Assessment of greenhouse tomato anthesis rate through metabolomics using LASSO regularized linear regression model"
Front. Mol. Biosci. 9, 839051. (2022)
9. Sugiyama, R., Li, R., Kuwahara, A., Nakabayashi, R., Sotta, N., Mori, T., Ito, T., Ohkama-Ohtsu, N., Fujiwara, T., Saito, K., Nakano, R.T., Bednarek, P. and Hirai, M.Y.:
"Retrograde sulfur flow from glucosinolates to cysteine in Arabidopsis thaliana"
PNAS. 118, e2017890118. (2021)
10. Kawade,K., Horiguchi,G., Hirose,Y.,Oikawa,A., Hirai,M.Y., Saito,K., Fujita,T. and Tsukaya,H.
"Metabolic control of gametophore shoot formation through arginine in the moss Physcomitrium patens"
Cell Rep. 32, 108127. (2020)