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SR System Biology Research Group
Seiki KURAMITSU
Group Director
Seiki KURAMITSU (D.Sci.)
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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.

Research Subject

  1. Whole-Cell Project of a Model Organism, Thermus thermophilus HB8.
  2. System biological analyses of transcription, Protein synthesis, and DNA repair systems in the cell.
  3. Functional identification of unknown functional protein (gene).
  4. Cell imaging / Biomolecular imaging, based on the synchrotoron and XFEL technologies.

Related links

  1. RIKEN SPring-8 Center Website_Laboratories PageNew Window
  2. Structual-Biological Whole Cell Project PageNew Window
  3. DNA BANK PageNew Window

Press release

May 27, 2008
Efficient protein three dimensional structure analysis in the world's top speed assisted by three types of automated crystallization robots, supporting the progress of the Structural-Biological Whole Cell Project.
August 28, 2008
Finding a new transcription factor from high temperature thermophilic bacteria, whicn functions when faced with a life crisis
November 18, 2008
Elucidation of the regulatory mechanism of DNA recombination inducing genomic transformation, by controlling definitive choice to induce evolutional or non-evolutional transformation

RIKEN RESEARCH

September 26, 2008
Crystal quest brings success
Study obtains protein structures more efficiently using a combination of techniques New Window
December 26, 2008
The recession gene
A master switch allows bacteria, already living in extreme environments, to survive times of crisis New Window

List of Selected Publications

  1. 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)
  2. 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)
  3. 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).
  4. 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).
  5. 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).
  6. 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).
  7. 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).
  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."
    Nature Struct. Biol. 7, 943-945 (2000).

Members

Principal Investigator

Seiki KURAMITSU
Group Director


Functomics Integration Research TeamSeiki KURAMITSU (D.Sci.)
Functomics Biology I Research TeamAkeo SHINKAI (Ph.D.)
Functomics Biology II Research TeamYoshitaka BESSHO (Ph.D.)


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