RIKEN Center for Sustainable Resource Science Chemical Genomics Research Group
Group Director: Minoru Yoshida (D.Agr.)
Research Summary

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
Keywords
- 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