Functomics Integration Research Team
Research Areas
| The final goal of this 鉄tructural and Functional Whole-Cell Project of Thermus thermophilus HB8琶s 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 21% 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. |  Team Leader Seiki KURAMITSU (D.Sci.)  |
Research Subjects
| (1) | Systems Biology |  |
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| (2) | Bioimaging | |||
| (3) | Structural Genomics | |||
| (4) | Functional Genomics (gene disruptants, transcriptomics, proteomics, metabolomics) | |||
| (5) | Functional Discovery of New Proteins |
List of Selected Publications
| (1) | 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) |
| (2) | Kondo, N., Nishikubo, T., Wakamatsu, T., Ishikawa, H., Nakagawa, N., Kuramitsu, S., and 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) |
| (3) | Kondo, N., Nishikubo, T., Wakamatsu, T., Ishikawa, H., Nakagawa, N., Kuramitsu, S., and 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) |
| (4) | 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., and Hayashizaki, Y.: "Rapid SNP Diagnostics Using Asymmetric Isothermal Amplification and a New Mismatch-Suppression Technology." Nat. Methods, 4, 257-262 (2007) |
| (5) | Kondo, N., Nakagawa, N., Ebihara, A., Chen, L., Liu, Z.-J., Wang, B.-C., Yokoyama, S.,Kuramitsu, S., and Masui, R.: "Structure of dNTP-Inducible dNTP Triphosphohydrolase: Insight into Broad Specificity for dNTPs and Triphosphohydrolase-Type Hydrolysis." Acta Cryst. D63, 230-239 (2007) |
| (6) | Kosaka, H., Hoseki, J., Nakagawa, N., Kuramitsu, S., and Masui, R.: "Crystal Structure of Family 5 Uracil-DNA Glycosylase Bound to DNA." J. Mol. Biol., 373, 839-850 (2007) |
| (7) | 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) |
| (8) | Nakai, T., Nakagawa, N., Maoka, N., Masui, R., Kuramitsu, S., and Kamiya, N.: "Structure of P-protein of the Glycine Cleavage System: Implications for Nonketoic Hyperglycinemia." EMBO J., 24, 1523-1536 (2005) |
| (9) | Hashimoto, Y., Yano, T., Kuramitsu, S., and Kagamiyama, H.: "Disruption of Thermus thermophilus Genes by Homologous Recombination Using a Thermostable Kanamycin-resistant Marker." FEBS Lett., 506, 231-234 (2001) |
| (10) | 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., and Kuramitsu, S.: "Structural Genomics Projects in Japan." Nat. Struct. Biol., 7, 943-945 (2000) |