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 understanding the whole biological phenomena on the basis of the structure and function of all the molecules in the cell. This enables the prediction of the cell response in any environment. As a model organism for the structural and functional studies, an extremely thermophilic bacterium, T. thermophilus HB8, is very promising, because of the small genome size (2.1 Mbp), the availability of genetic tools for functional analysis, and the thermostability of its proteins. Using the structural and functional information of the molecules, this research group aims to reveal the functional information on a genome-wide scale by using bioimaging methods and analyzing mRNA expression (transcriptomics), protein expression (proteomics) and metabolite dynamics (metabolomics). This research aims to establish the basis of the prediction for the biological responses. For whole-cell imaging, structural information for each molecule will be very useful. Therefore, we determined the structures of as many proteins as possible. The structures of over 22% of the total proteins (about 460 proteins) in this model organism have been determined. The plasmids for protein expression (1,700 clones) and the plasmids for gene disruption (1,000 clones) are available to the public through the RIKEN BioResource Center. Some of the information about protein production (protein expression and purification), crystallization, structure, and functomics (transcriptomics, proteomics, and metabolomics), is also available from our database and public databases. By using these resources, we collaborate with many researchers at RIKEN, universities, and companies.
- Systems Biology
- Bioimaging (cellular imaging; molecular imaging)
- Structural Genomics
- Functional Genomics (gene disruptants, transcriptomics, proteomics, metabolomics)
- Functional Discovery of New Proteins
- 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) - Kondo,N., Ebihara, A., Ru, H., Kuramitsu, S., Iwamoto, A., Rao, Z., and Matsuda, Z.
"Thermus thermophilus-Derived Protein Tags That Aid in Preparation of Insoluble Viral Proteins."
Anal. Biochem. 385, 278-285 (2009) - 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) - Kondo, N., Nishikubo, T., Wakamatsu, T., Ishikawa, H., Nakagawa, N., Kuramitsu, S., Masui, R.
"Insights Into Different Dependence of dNTP Triphosphohydrolase on Metal Ion Species From Intracellular Ion Concentrations in Thermus thermophilus"
Extremophiles, 12, 217-223 (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., Kamataki, T., Oka, T., Shimada, H., Cizdziel, P. E., Hayashizaki, Y.
"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