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RIKEN Center for Sustainable Resource Science Chemical Genomics Research Group

Group Director: Minoru Yoshida (D.Agr.)

Research Summary

Minoru  Yoshida(D.Agr.)

Identification of novel small molecular ligands is essential to understand diverse biological phenomena and to control the biological systems by chemical methods. This project focuses on the development of useful molecular ligands that are expected to contribute to an advance in environmental and resource sciences by employing chemical libraries that consist of microbial metabolites and/or synthetic compounds. In particular, we search into novel active compounds by constructing a variety of phenotypic screening systems using genetically modified animal, plant and yeast cells, and in vitro screening systems using various target proteins that include enzymes for metabolism and epigenetics. In addition, we construct new platforms for developing high throughput screening systems. Our goal is to identify and provide unique molecular ligands that are useful for chemical biology research aiming at exploiting new area of environmental and resource sciences.

Main Research Fields

  • Biology

Related Research Fields

  • Chemistry


  • Chemical Biology
  • Epigenetics
  • Mode of Action
  • Transcriptional Regulation
  • Chemical Screening for Drug Discovery

Selected Publications

  • 1.Matsumoto, K., Kose, S., Kuwahara, I., Yoshimura, M., Imamoto, N., Yoshida, M.:
    "Y-box protein-associated acidic protein (YBAP1/C1QBP) affects the localization and cytoplasmic functions of YB-1."
    Sci. Rep., 8, 6198 (2018)
  • 2.Takase, S., Kurokawa, R., Arai, D., Kanemoto Kanto, K,, Okino, T., Nakao, Y., Kushiro, T., Yoshida, M., Matsumoto, K.:
    "A quantitative shRNA screen identifies ATP1A1 as a gene that regulates cytotoxicity by aurilide B."
    Sci. Rep., 7, 2002 (2017)
  • 3.Piotrowski, J.S., Li, S.C., Deshpande, R., Simpkins, S.W., Nelson, J., Yashiroda, Y., Barber, J.M., Safizadeh, H., Wilson, E., Okada, H., Gebre, A.A., Kubo, K., Torres, N., Leblanc, M.B., Andrusiak, K., Okamoto, R., Yoshimura, M., van Leeuwen, J., Shirahige, K., Baryshnikova, A., Brown, G., Saito, T., Costanzo, M., Andrews, B., Ohya, Y., Osada, H., Yoshida, M., Myers, C.L., Boone, C.:
    "Functional annotation of chemical libraries across diverse biological processes."
    Nat. Chem. Biol., 13, 982-993 (2017)
  • 4.Nakaoka, S., Sasaki, K., Ito, A., Nakao, Y., Yoshida, M.:
    "A genetically encoded FRET probe to detect intranucleosomal histone H3K9 or H3K14 acetylation using BRD4, a BET family member."
    ACS Chem. Biol., 11, 729-33 (2016)
  • 5.Sun, X., Hirai, G., Ueki, M., Hirota, H., Wang, Q., Hongo, Y., Nakamura, T., Hitora, Y., Takahashi, H., Sodeoka, M., Osada, H., Hamamoto, M., Yoshida, M., Yashiroda, Y.:
    "Identification of novel secreted fatty acids that regulate nitrogen catabolite repression in fission yeast."
    Sci. Rep., 6, 20856 (2016)
  • 6.Ling, F., Niu, R., Hatakeyama, R., Goto, Y., Shibata, T., and Yoshida, M.:
    "ROS stimulate mitochondrial allele segregation towards homoplasmy in human cells."
    Mol. Biol. Cell, 27, 1684-93 (2016)
  • 7.Ito, A., Shimazu, T., Maeda, S., Shah, A.A., Tsunoda, T., Iemura, S., Natsume, T., Suzuki, T., Motohashi, H., Yamamoto, M., Yoshida, M.:
    "The subcellular localization and activity of cortactin is regulated by acetylation and interaction with Keap1."
    Sci. Signal., 8, ra120 (2015)
  • 8.Arita, Y., Nishimura, S., Ishitsuka, R., Kishimoto, T., Ikenouchi, J., Ishii, K., Umeda, M., Matsunaga, S., Kobayashi, T., Yoshida, M.:
    "Targeting cholesterol in a liquid-disordered environment by theonellamides modulates cell membrane order and cell shape."
    Chem. Biol., 222, 604-610 (2015)
  • 9.Feldman, J.L., Dittenhafer-Reed, K.E., Kudo, N., Thelen, J.N., Ito, A., Yoshida, M., Denu, J.M.:
    "Kinetic and structural basis for acyl-group selectivity and NAD(+) dependence in sirtuin-catalyzed deacylation."
    Biochemistry, 54, 3037-3050 (2015)
  • 10.Hirohama, M., Kumar, A., Fukuda, I., Matsuoka, S., Igarashi, Y., Saitoh, H., Takagi, M., Shin-Ya, K., Honda, K., Kondoh, Y., Saito, T., Nakao, Y., Osada, H., Zhang, K.Y., Yoshida, M., Ito, A.:
    "Spectomycin B1 as a novel SUMOylation inhibitor that directly binds to SUMO E2."
    ACS Chem. Biol., 8, 2635-2642 (2013)

Related Links

Lab Members

Principal investigator

Minoru Yoshida
Group Director

Core members

Ken Matsumoto
Senior Research Scientist
Akihisa Matsuyama
Senior Research Scientist
Feng Ling
Senior Research Scientist
Yoko Yashiroda
Senior Research Scientist
Tilman Hans Jorg Schneider-Poetsch
Research Scientist
Kazuki Sasaki
Research Scientist
Shin-ya Okamoto
Research Scientist
Norio Kudo
Research Scientist
Takashi Ito
Research Scientist
Masaki Matsuoka
Postdoctoral Researcher
Jagat Krishna Chhipi Shrestha
Postdoctoral Researcher
Kazumi Fukatsu
Visiting Researcher
Fereshteh Azadeh
Junior Research Associate
Rumi Kurokawa
Technical Staff I
Mayumi Arata
Technical Staff I
Atsushi Hashimoto
Technical Staff II
Megumi Takase
Technical Staff II

Contact Information

2-1 Hirosawa, Wako, Saitama 351-0198, Japan
Tel: +81-(0)48-467-9516
Fax: +81-(0)48-462-4676

Email: yoshidam [at] riken.jp