Kotaro Nakanishi received his B.S. degree from Tokyo University of Science in 2000 and his M.S. degree from the University of Tokyo in 2003. Kotaro obtained his D.Sc. in 2007 from Tokyo Institute of Technology where he studied aminoacyl-tRNA synthetase and tRNA modification enzyme using X-ray crystallography with Osamu Nureki. Then he joined the laboratory of Dinshaw Patel in the Memorial Sloan-Kettering Cancer Center, and determined the crystal structures of Argonaute and Dicer. He was awarded Japan Society for the Promotion of Science (JSPS) for Young Scientist, JSPS for Research Abroad, and Human Frontier Science Program for Long-term Fellow. In recognition of his works, Kotaro received RNA Society/Scaringe Award in 2012. He will join the Ohio State University in August of 2013.
Our research interest focuses on elucidating the mechanism of microRNA-mediated gene regulations underlying cell type determination. After processed by microprocessor and Dicer, microRNA duplexes are loaded into another key player, Argonaute protein. Then one of the strands serves as a guide to recruit the RNA-induced silencing complex, RISC, to the target mRNAs, thereby triggering target cleavage, translational repression or mRNA decay. Our long-term goal is to take crystallographic snapshots of each step such that we understand the molecular basis at the atomic resolution.
Another interest is a completely different subject but still relevant to our research: developing a new tag capable of increasing the solubility of the interested proteins and of facilitating crystal packing.
* These authors contributed equally to the works.
Nakanishi, K.*, Weinberg, D.E.*, Bartel, D.P., & Patel, D.J. (2012) Structure of yeast Argonaute with guide RNA. Nature 486, 368-374.
Weinberg, D.E.*, Nakanishi, K.*, Patel, D.J., & Bartel, D.P. (2011) The inside-out mechanism of Dicers from budding yeasts. Cell 146, 262-276.
Nakanishi, K., Bonnefond, L., Kimura, S., Suzuki, T., Ishitani, R., & Nureki, O. (2009) Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase. Nature 461, 1144-1148.
Nakanishi, K., Ogiso, Y., Nakama, T., Fukai, S., & Nureki, O. (2005) Structural basis for anticodon recognition by methionyl-tRNA synthetase. Nat. Struct. Mol. Biol. 12, 931-932.
Nakanishi, K., Fukai, S., Ikeuchi, Y., Soma, A., Sekine, Y., Suzuki, T., & Nureki, O. (2005) Structural basis for lysidine formation by ATP pyrophosphatase accompanied by a lysine specific loop and a tRNA-recognition domain. Proc. Natl. Acad. Sci. U. S. A. 24, 7487-7492.