Functomics Biology II Research Team
Research Areas
| In cells, a vast amount of DNA damage occurs from UV radiation, various chemical reagents, and errors during DNA replication and genetic recombination. These DNA damages are very harmful, and can result in mutagenesis and even in cell death. To remove these lesions, cells have various types of DNA repair systems, and most of them are common to many organisms, including human. Through the structural and functional analyses as well as basic research for cell imaging, this research team aims to understand the cellular systems of DNA repair systems in an extremely thermophilic model organism, Thermus thermophilus HB8. This team will address the development of single-molecule and whole-cell imaging?technologies, by using the SPring-8 beamline and XFEL, in collaboration with the other two teams in this group and with other research groups. The other methodologies used for imaging are (1) electron microscopy, especially electron tomography for in vivo cell imaging, (2) probe microscopy, which includes atomic force microscopy at video rate, for in vitro imaging, and (3) confocal laser scanning microscopy for in vivo cell imaging of target molecules tagged with thermophilic fluorescent protein domains (super folder GFP, YFP, etc.). These fluorescently-tagged protein domains are also used for in vitro imaging of the target molecules. In addition, as single-molecule imaging analyses, we will attempt to visualize protein-DNA interactions at high resolution. We have started with DNA repair systems as a model, because about 10 proteins involved in this system, which show very high affinity to damaged DNA, have been obtained. Since the proteins from T. thermophilus are stable in a vacuum, we can develop a technology to place a protein molecule onto a DNA molecule in a vacuum. This technology will contribute to single-molecule imaging in the future with XFEL. The cell-wall syntheshis system is also the target for cell imaging. |  Team Leader Yoshitaka BESSHO (Ph.D.) |
Research Subjects
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List of Selected Publications
| (1) | Fukui, K., Nakagawa, N., Kitamura, Y., Nishida, Y., Masui, R., and Kuramitsu, S.: "Crystal Structure of MutS2 Endonuclease Domain and the Mechanism of Homologous Recombination Supression." J. Biol. Chem. 283, 33417-33427 (2008) |
| (2) | Fukui, K., Nishida, M., Nakagawa, N., Masui, R., and Kuramitsu, S.: "Bound Nucleotide Controls the Endonuclease Activity of Mismatch Repair Enzyme MutL." J. Biol. Chem. 283, 12136-12145 (2008) |
| (3) | Ebihara, A., Manzoku, M., Iino, H., Kanagawa, M., Shinkai, A., Yokoyama, S., and Kuramitsu, S.: (2008) "Crystal Structure of Uncharacterized Protein TTHA1756 from Thermus thermophilus HB8: Structural Variety in UPF1050 Family Proteins." Proteins 71, 2097-2101 (2008) |
| (4) | Morita, R., Ishikawa, H., Nakagawa, N., Kuramitsu , S., and Masui, R.: "Crystal Structure of a Putative DNA Methylase TTHA0409 from Thermus thermophilus HB8." Proteins 73, 259-264 (2008) |
| (5) | 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) |
| (6) | Wakamatsu, T., Nakagawa, N., Kuramitsu, S., and Masui, R.: "Structural Basis for Different Substrate Specificities of Two ADP-Ribose Pyrophosphatases from Thermus thermophilus HB8." J. Bacteriol. 190, 1108-1117 (2008) |
| (7) | 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) |
| (8) | Omi, R., Goto, M., Miyahara, I., Manzoku, M., Ebihara, A., and Hirotsu, K.: "Crystal Structure of Monofunctional Histidinol Phosphate Phosphatase from Thermus thermophilus HB8." Biochemistry 46, 12618-12627 (2007) |
| (9) | 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 Crystallogr. D 63, 230-239 (2007) |
| (10) | Ebihara, A., Yao, M., Masui, R., Tanaka, I., Yokoyama, S., and Kuramitsu, S.: "Crystal Structure of Hypothetical Protein TTHB192 from Thermus thermophilus HB8 Reveals a New Protein Family with an RNA Recognition Motif-Like Domain." Protein Sci. 15, 1494-1499 (2006) |