Center for Sustainable Resource Science Environment-Oriented Metabolism RIKEN ECL Research Unit
RIKEN ECL Unit Leader: Yoko Chiba (Ph.D.)
Research Summary
Metabolism is a fundamental mechanism that enables life. Our research unit aims to elucidate the design principles of metabolism through comparative analyses of metabolic pathways and enzymes across diverse organisms. We focus on organisms adapted to environments distinct from those of model organisms, identifying previously unknown central metabolic pathways and exploring the origins of these differences by considering environmental conditions, intracellular physicochemical constraints, and “metabolic context”. By articulating metabolism as the mechanism that has sustained life for four billion years, we seek to contribute to sustainable human societal activities.
Main Research Fields
- Biological Sciences
Related Research Fields
- Chemistry
- Agricultural Sciences
- Biology
- Applied microbiology
- Applied biochemistry
- Functional biochemistry
Keywords
- Metabolism
- Microorganism
- Enzyme
- Non-model organisms
- Kinetics
Selected Publications
Papers with an asterisk(*) are based on research conducted outside of RIKEN.
- 1.
Chiba, Y., Ooka, H.:
"How to enhance enzymatic reaction rates? The Sabatier principle and beyond"
Bioscience, Biotechnology, and Biochemistry, 90, 300-305 (2026) - 2.
Wakashima, T., Kume, K., Chiba, Y.:
"Wood-Ljungdahl pathway and the reductive glycine pathway in Desulfobacterota"
Frontiers in Microbiology 16, 1708584 (2026) - 3.
Chiba, Y., Sumida, T., Kameya, M., Fukuyama, Y., Wakashima, T., Shimamura, S., Kamikawa, R., Chikaraishi, Y., Nunoura, T.:
"Impact of acetate on CO2 fixation pathways in thermophilic and hydrogenotrophic bacteria"
ISME communications 5, ycaf227 (2025) - 4.
Chiba, Y., Ooka, H., Wintzer, M. E., Tsunematsu, N., Nogawa, T., Suzuki, T., Dohmae, N., Nakamura, R.:
"Rationalizing the influence of the binding affinity on the activity of phosphoserine phosphatases"
Angewandte Chemie International Edition 63, e202318635 (2024) - 5.
Ooka, H., Chiba, Y., Nakamura, R.:
"Thermodynamic principle to enhance enzymatic activity using the substrate affinity"
Nature Communications 14, 4860 (2023) - 6.
*Chiba, Y., Yoshida, A., Shimamura, S., Kameya, M., Tomita, T., Nishiyama, M., Takai, K.:
"Discovery and analysis of a novel type of the serine biosynthetic enzyme phosphoserine phosphatase in Thermus thermophilus"
The FEBS Journal 286, 726-736 (2019) - 7.
*Kim, K., Chiba, Y., Kobayashi, A., Arai, H., Ishii, M.:
"Phosphoserine phosphatase is required for serine and one-carbon unit synthesis in Hydrogenobacter thermophilus"
Journal of bacteriology 199, 10.1128/jb. 00409-00417 (2017) - 8.
*Chiba, Y., Kamikawa, R., Nakada-Tsukui, K., Saito-Nakano, Y., Nozaki, T.:
"Discovery of PPi-type phosphoenolpyruvate carboxykinase genes in eukaryotes and bacteria"
Journal of Biological Chemistry 290, 23960-23970 (2015) - 9.
*Chiba,Y., Oshima, K., Arai, H., Ishii, M., Igarashi, Y.:
"Discovery and analysis of cofactor-dependent phosphoglycerate mutase homologs as novel phosphoserine phosphatases in Hydrogenobacter thermophilus"
Journal of Biological Chemistry 287, 11934-11941 (2012) - 10.
*Chiba, Y., Terada, T., Kameya, M., Shimizu, K., Arai, H., Ishii, M., Igarashi, Y.:
"Mechanism for folate‐independent aldolase reaction catalyzed by serine hydroxymethyltransferase"
The FEBS Journal 279, 504-514（2012）
Related Links
Lab Members
Principal investigator
- Yoko Chiba
- RIKEN ECL Unit Leader
Careers
| Position | Deadline |
|---|---|
| Seeking a Research Scientist or a Postdoctoral Researcher (25-1655) | Open until filled |
Contact Information
Sustainable Resource Science Building
2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
Email: yoko.chiba.ey@riken.jp