Functomics Integration Research Team
Team Leader
Seiki KURAMITSU (D.Sci.)
The final goal of this "Structural and Functional Whole-Cell Project of Thermus thermophilus HB8" is to understand the whole cellular biological phenomena on the basis of the structures and functions of all the molecules in the cell. This will enable us to predict every behavior of the cell occuring in response to various kinds of stimuli. As a model organism for genome-wide structural and functional studies, an extremely thermophilic bacterium, T. thermophilus HB8, is exceedingly promising because of the following reasons: (1) This bacterium has a relatively small genome size (2.1 Mbp); (2) gene manupilating tools are available for functional analyses in this bacterium; (3) Proteins from this bacterium show extreme thermostability that is suitable for physicochemical characterizations. In order to understand the whole biological phenomena, we reveals the functions of proteins at a genome-wide scale by using various kinds of bioimaging methodologies, mRNA expression analysis (transcriptomics), protein expression analysis (proteomics), and metabolite analysis (metabolomics). For the genome-wide bioimaging, structural information of each molecule (proteins) is essential. Therefore, we determined the structures of as many proteins as possible. As a result, structures of over 22% of the total proteins (about 460 proteins) in this model organism have been determined. The plasmids for protein expression (2,020 clones) and the plasmids for gene disruption (1,000 clones) are available to the public through the RIKEN BioResource Center. The information about protein expression, purification, crystallization, structure, and functomics data (transcriptomics, proteomics, and metabolomics), is also available at our database or public databases. Distributing these resources, we collaborate with many researchers at RIKEN, other governmental institutes, universities, and companies.
- Systems Biology
- Bioimaging (cellular imaging; molecular imaging)
- Structural Genomics
- Functional Genomics (gene disruptants, transcriptomics, proteomics, metabolomics)
- Functional Discovery of New Proteins
- Nakane, S., Wakamatsu, T., Masui, R., Kuramitsu, S., and Fukui, K.:
"In Vivo, In Vitro, and X-ray Crystallographic Analyses Suggest the Involvement of an Uncharacterized Triose-phosphate Isomerase (TIM) Barrel Protein in Protection Against Oxidative Stress"
J. Biol. Chem. 286, 41636-41646 (2011) - Yamamoto, T., Iino, H., Kim, K., Kuramitsu, S., and Fukui, K.:
"Evidence for ATP-dependent Structural Rearrangement of Nuclease Catalytic Site in DNA Mismatch Repair Endonuclease MutL"
J. Biol. Chem. 286, 42337-42348 (2011) - Wakamatsu, T., Kim, K., Uemura, Y., Nakagawa, N., Kuramitsu, S., and Masui, R.:
"Role of RecJ-Like Protein with 5'-3' Exonuclease Activity in Oligo(deoxy) Nucleotide Degradation"
J. Biol. Chem. 286, 2807-2816 (2011) - Wakamatsu, T., Kitamura, Y., Kotera, Y., Nakagawa, N., Kuramitsu, S., and Masui, R.:
"Structure of RecJ Exonuclease Defines Its Specificity for Single-Stranded DNA"
J. Biol. Chem. 285, 9762-9769 (2010) - Ooga, T., Ohashi, Y., Kuramitsu, S., Koyama, Y., Tomita, M., Soga, T., and Masui, R.:
"Degradation of ppGpp by Nudix Pyrophosphatase Modulates the Transition of Growth Phase in the Bacterium Thermus thermophilus."
J. Biol. Chem. 284, 15449-15456 (2009) - Iino, H., Naitow, H., Nakamura, Y., Nakagawa, N., Agari, Y., Kanagawa, M., Ebihara, A., Shinkai, A., Sugahara, M., Miyano, M., Kamiya, N., Yokoyama, S., Hirotsu, K., and Kuramitsu, S.:
"Crystallization Screening Test for the Whole-Cell Project on Thermus thermophilus HB8"
Acta Cryst. F64, 487-491 (2008) - Mitani, Y., Lezhava, A., Kawai, Y., Kikuchi, T., Oguchi-Katayama, A., Kogo, Y., Itoh, M., Miyagi, T., Takakura, H., Hoshi, K., Kato, C., Arakawa, T., Shibata, K., Fukui, K., Masui, R., Kuramitsu, S., Kiyotani, K., Chalk, A., Tsunekawa, K., Murakami, M., K.:
"Rapid SNP Diagnostics Using Asymmetric Isothermal Amplification and a New Mismatch-Suppression Technology."
Nat. Methods, 4, 257-262 (2007) - Sasaki, H. M., Sekine, S., Sengoku, T., Fukunaga, R., Hattori, M., Utsunomiya, Y., Kuroishi, C., Kuramitsu, S., Shirouzu, M., and Yokoyama, S.:
"Structural and Mutational Studies of the Amino Acid-Editing Domain from Archaeal/Eukaryal Phenylalanyl-tRNA Synthetase"
Proc. Natl. Acad. Sci. USA 103, 14744-14749 (2006) - Hashimoto, Y., Yano, T., Kuramitsu, S., Kagamiyama, H.:
"Disruption of Thermus thermophilus Genes by Homologous Recombination Using a Thermostable Kanamycin-resistant Marker"
FEBS Lett., 506, 231-234 (2001) - Yokoyama, S., Hirota, H., Kigawa, T., Yabuki, T., Shirouzu, M., Terada, T., Ito, Y., Matsuo, Y., Kuroda, Y., Nishimura, Y., Kyogoku, Y., Miki, K., Masui, R., Kuramitsu, S.:
"Structural Genomics Projects in Japan"
Nat. Struct. Biol., 7, 943-945 (2000)
Principal Investigator
- Seiki KURAMITSU
- Team Leader
Staff Scientist
- Mariko OKADA
- Takehiko SHIBATA
- Hideyuki MIYATAKE
- Kenji FUKUI
- Research Scientist
Postdoctoral Fellow
- Hitoshi IINO
- Postdoctoral Researcher
Technical Assistant
- Kayoko MATSUMOTO
- Technical Staff
- Toshi ARIMA
- Technical Staff