Functomics Biology II Research Team
Team Leader
Yoshitaka BESHHO (Ph.D.)
The mission of this team is to accomplish the complete elucidation of intracellular systems, through structural and functional analyses. We are focusing on the "protein-synthesis (translation)" systems, as essential cellular processes in the central-dogma of life. The protein-synthesis system is the most important cellular operation. Translation is a compiling system, from the genetic information of the DNA to the amino-acid chain of the protein. The translator molecule is "tRNA", the place of translation is the "ribosome", and the rule of translation is the "genetic code". tRNA is a key molecule of the protein synthesis system, and thus we are focusing on the enzymes related to tRNA maturation and aminoacylation. In addition, as an example of a ribosomal system, a quality-control system has been extensively analyzed in the project. Through structural and functional analyses as well as basic research in cell imaging, this research team aims to understand the cellular systems in the extremely thermophilic model organism, Thermus thermophilus HB8.
This team is developing cutting-edge technologies of bio-molecular imaging, facilitated by new generation pulsed coherent X-rays. Coherent imaging is a growing field in optical science. We are developing methods to visualize protein and nucleic-acid complexes and their interactions at higher resolution, by combinations of various technologies. We are developing cutting-edge technologies of bio-molecular imaging, facilitated by new generation pulsed coherent X-rays. Molecular interactions and dynamic reactions will be measured with high quality under almost natural cellular conditions, revealing the complicated molecular mechanisms in living systems. For this purpose, we have successfully elucidated the solution structure of a protein and RNA complex by conventional small angle X-ray scattering. In addition, we performed effective computer simulations using coarse graining models, and designed a nano bio-device toward the biological application of SACLA/XFEL and SPring-8 facilities.
- Structural and functional analyses of proteins involved in protein-sysnthesis systems
- Structural and functional analyses of proteins involved in DNA-repair systems
- Fuctional discovery of functionally-unknwon proteins involved in central-dogma system
- Developmental researches for the bio-molecule imaging with the synchrotoron and XFEL technologies
- Technology development for ultrafine microcrystal structure analysis at the SPring-8 beamlines
- Kitamura A, Sengoku T, Nishimoto M, Yokoyama S, and Bessho Y.:
"Crystal structure of the bifunctional tRNA modification enzyme MnmC from Escherichia coli."
Protein Sci, 20(7):1105-1113, (2011) - Kuratani M., Kasai T., Akasaka R., Higashijima K., Terada T., Kigawa T., Shinkai A., Bessho Y., and Yokoyama S.:
"Crystal structure of Sulfolobus tokodaii Sua5 complexed with L-threonine and AMPPNP."
Proteins, 79(7):2065-2075, (2011) - Hikida Y., Kuratani M., Bessho Y., Sekine S.I., and Yokoyama S.:
"Structure of an archaeal homologue of the bacterial Fmu/RsmB/RrmB rRNA cytosine 5-methyltransferase."
Acta Crystallogr D Biol Crystallogr. 66(Pt12), 1301-1307 (2010) - Kuratani M., Hirano M., Goto-Ito S., Itoh Y., Hikida Y., Nishimoto M., Sekine S., Bessho Y., Ito T., Grosjean H., and Yokoyama S.:
"Crystal structure of Methanocaldococcus jannaschii Trm4 complexed with sinefungin."
J. Mol. Biol. 401, 323-333 (2010) - Bessho Y and Yokoyama S.:
"Enzymatic formation of 5-aminomethyl-uridine derivatives in tRNA."
In: Henri Grosjean (ed) DNA and RNA modification enzymes. Landes Bioscience, Austin, pp.409-425 (2009) - Awai T., Kimura S., Tomikawa C., Ochi A., Ihsanawati, Bessho Y., Yokoyama S., Ohno S., Nishikawa K., Yokogawa T., Suzuki T., and Hori H.:
"Aquifex aeolicus tRNA (N2,N2-guanine)-dimethyltransferase (Trm1) catalyzes transfer of methyl groups not only to guanine 26 but also to guanine 27 in tRNA."
J Biol Chem. 284(31), 20467-20478 (2009) - Ohama T., Inagaki Y., Bessho Y., and Osawa S.:
"Evolving genetic code."
Proc Jpn Acad Ser B Phys Biol Sci. 84(2), 58-74 (2008) - Ihsanawati, Nishimoto M., Higashizima K., Shirouzu M., Grosjean H., Bessho Y. , and Yokoyama S.:
"Crystal structure of tRNA N2, N2-guanosine dimethyltransferase Trm1 from Pyrococcus horikoshii."
J. Mol. Biol. 383, 871-884 (2008) - Agari Y., Sato S., Wakamatsu T., Bessho Y., Ebihara A., Yokoyama S., Kuramitsu S., and Shinkai A.:
"X-ray crystal structure of a hypo- thetical Sua5 protein from Sulfolobus tokodaii strain 7."
Proteins 70, 1108-1111 (2008) - Bessho Y., Shibata R., Sekine S., Murayama K., Higashizima K., Hori-Takemoto C., Shirouzu M., Kuramitsu S., and Yokoyama S.:
"Structural basis for functional mimicry of long-variable- arm tRNA by transfer-messenger RNA."
Proc. Natl. Acad. Sci. USA 104, 8293-8298 (2007)
Principal Investigator
- Yoshitaka BESSHO
- Team Leader
Staff Scientist
- Tsutomu MIKAWA
- Aya KITAMURA
- Research Scientist