Unit Leader

Yoshihiro Shimizu (Ph.D.)

To understand life, it is indispensable to understand the function and the structure of proteins that play essential roles inside and outside of cells. Laboratory for Cell-Free Protein Synthesis aims to develop the PURE system, a reconstituted cell-free protein synthesis system, to contribute to the development of techniques for manipulating, analysing, and modeling proteins by establishing a method for diverse protein production without restraint. We are also trying to incorporate into the PURE system the ability for self-replication by synthesizing PURE system components autonomously. Using these techniques, we hope to design and control living systems.

Research Topics

• Protein production by the PURE system
• Construction of a self-replication model for cell-free protein synthesis
• Cell-free protein synthesis on micro-devices

Selected Publications

• Matsuura, T., Tanimura, N., Hosoda, K., Yomo, T. & Shimizu, Y.
  "Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling"
  Proc. Natl. Acad. Sci. U.S.A. 114, E1336-E1344 (2017) doi:10.1073/pnas.1615351114
• Narumi, R., Shimizu, Y., Ukai-Tadenuma, M., Ode, K. L., Kanda, G. N., Shinohara, Y., et al.
  "Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins"
  Proc. Natl. Acad. Sci. U.S.A. 113, E3461-E3467 (2016) doi:10.1073/pnas.1603799113
• Tanaka, Y. & Shimizu, Y.
  "Integration of a Reconstituted Cell-free Protein-synthesis System on a Glass Microchip"
  Anal. Sci. 31, 67-71 (2015)
• Susaki, E. A., Tainaka, K., Perrin, D., Kishino, F., Tawara, T., Watanabe, T. M., et al.
  "Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis"
  Cell 157, 726-739 (2014) doi:10.1016/j.cell.2014.03.042
• Shimizu, Y.
  "Biochemical aspects of bacterial strategies for handling the incomplete translation processes"
  Front. Microbiol. 5, 1 (2014) doi:10.3389/fmicb.2014.00170
• Shimizu, Y.
  "ArfA Recruits RF2 into Stalled Ribosomes"
  J. Mol. Biol. 423, 624-631 (2012) doi:10.1016/j.jmb.2012.08.007
• Kihira, K., Shimizu, Y., Shomura, Y., Shibata, N., Kitamura, M., Nakagawa, A., et al.
  "Crystal structure analysis of the translation factor RF3 (release factor 3)"
  FEBS Lett. 586, 3705-3709 (2012) doi:10.1016/j.febslet.2012.08.029
• Shimizu, Y. & Ueda, T.
  "SmpB triggers GTP hydrolysis of elongation factor Tu on ribosomes by compensating for the lack of codon-anticodon interaction during trans- translation initiation"
  J. Biol. Chem. 281, 15987-15996 (2006) doi:10.1074/jbc.M512165200
• Shimizu, Y., Kanamori, T. & Ueda, T.
  "Protein synthesis by pure translation systems"
  Methods 36, 299-304 (2005) doi:10.1016/j.ymeth.2005.04.006
• Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K., et al.
  "Cell-free translation reconstituted with purified components"
  Nat. Biotechnol. 19, 751-755 (2001) doi:10.1038/90802