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SR System Biology Research Group
Research Areas
The final goal of this research project is the understanding of all fundamental biological phenomena in a cell based on three-dimensional structure and function of all molecules. As a model organism for the structural and functional studies, an extremely thermophilic bacterium, Thermus thermophilus HB8, is very promising, because of the small genome size (2 Mbp), the availability of genetic tools for functional analysis, and the thermostability of its proteins. Using the protein structural information, this research group aims to reveal the functional information on a genome-wide scale by analyzing mRNA expression (transcriptomics), protein expression (proteomics) and metabolite dynamics (metabolomics). This research aims to establish the next basis of the prediction of the biological responses.   Seiki KURAMITSU
Group Director
Seiki KURAMITSU (D. Sci.)
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Research Subjects
(1) Functional identification of unknown functional protein (gene)
(2) System biological analyses of transcription, DNA repair, and oxidative stress protection systems
(3) Cell imaging
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List of Selected Publications
(1) Kondo, N., Nishikubo, T., Wakamatsu, T., Ishikawa, H., Nakagawa, N., Kuramitsu, S., and Masui, R.:
"Insights into Different Dependence of dNTP Triphosphohydrolase on Meta Ion Species from Intracellular Ion Concentrations in Thermus thermophilus."
Extremophiles 12, 217-223 (2008).
(2) 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).
(3) Fukui, K., Takahata, Y., Nakagawa, N., Kuramitsu, S., and Masui, R.:
"Analysis of a Nuclease Activity of Catalytic Domain of Thermus thermophilus MutS2 by High-Accuracy Mass Spectrometry."
Nucleic Acids Res. 35, e100 (2007).
(4) Shinkai, A., Ohbayashi, N., Terada, T., Shirouzu, M., Kuramitsu, S., and Yokoyama, S.:
"Identification of Promoters Recognized by RNA Polymerase-sigmaE Holoenzyme from Thermus thermophilus HB8."
J. Bacteriol. 189, 8758-8764 (2007).
(5) 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).
(6) 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).
(7) Hanawa-Suetsugu, K., Sekine, S., Sakai, H., Hori-Takemoto, C., Terada, T., Unzai, S., Tame, J.R.H., Kuramitsu, S., Shirouzu, M., and Yokoyama, S.:
"Crystal Structure of Elongation Factor P from Thermus thermophilus HB8."
Proc. Natl. Acad. Sci. USA101, 9595-9600 (2004).
(8) Hoseki, J., Okamoto, A., Takada, N., Suenaga, A., Futatsugi, N., Konagaya, A., Taigi, M., Yano, T., Kuramitsu, S., and Kagamiyama, H.:
"Increased Rigidity of Domain Structures Enhances the Stability of a Mutant Enzyme Created by Directed Evolution."
Biochemistry 42, 14469-14475 (2003).
(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."
Nature Struct. Biol. 7, 943-945 (2000).




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