Laboratory for Cell-Free Protein Synthesis | RIKEN BDR

Laboratory for Cell-Free Protein Synthesis

Team Leader

Yoshihiro ShimizuPh.D.

Photo of principal investigator

  • Location:Osaka / Quantitative Biology Buildings
  • E-mail:yshimizu[at]riken.jpPlease replace [at] with @.
  • Lab Website

Refining technologies for protein/peptide synthesis

Research Summary

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, analyzing, 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 Theme

  • Analyses of a cellular protein synthesis system
  • Protein production by the PURE system
  • Development of proteomics tools using the PURE system
  • Construction of a self-replication model for cell-free protein synthesis

Main Publications List

  • Hibi K, Amikura K, Sugiura N, et al.
    Reconstituted cell-free protein synthesis using in vitro transcribed tRNAs.
    Communications Biology 3. 350 (2020). doi: 10.1038/s42003-020-1074-2
  • Susaki EA, Shimizu C, Kuno A, et al.
    Versatile whole-organ/body staining and imaging based on electrolyte-gel properties of biological tissues
    Nature Communications 11. 1982 (2020) doi: 10.1038/s41467-020-15906-5
  • Shimojo M, Amikura K, Masuda K, et al.
    In vitro reconstitution of functional small ribosomal subunit assembly for comprehensive analysis of ribosomal elements in E. coli.
    Communications Biology 3. 142 (2020) doi: 10.1038/s42003-020-0874-8
  • Narumi R, Masuda K, Tomonaga T, et al.
    Cell-free synthesis of stable isotope-labeled internal standards for targeted quantitative proteomics.
    Synthetic and Systems Biotechnology 3. 97-104 (2018) doi:10.1016/j.synbio.2018.02.004
  • Matsuura T, Tanimura N, Hosoda K, et al.
    Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling.
    Proceedings of the National Academy of Sciences of the United States of America 114(8). E1336-E1344 (2017) doi:10.1073/pnas.1615351114
  • Narumi R, Shimizu Y, Ukai-Tadenuma M, et al.
    Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins.
    Proceedings of the National Academy of Sciences of the United States of America 113(24). E3461-E3467 (2016) doi:10.1073/pnas.1603799113
  • Sunagawa GA, Sumiyama K, Ukai-Tadenuma M, et al.
    Mammalian Reverse Genetics without Crossing Reveals Nr3a as a Short-Sleeper Gene.
    Cell Reports 14(3). 662-677 (2016) doi:10.1016/j.celrep.2015.12.052
  • Tanaka Y, Shimizu Y.
    Integration of a Reconstituted Cell-free Protein-synthesis System on a Glass Microchip.
    Analytical Sciences 31(2). 67-71 (2015) doi : 10.2116/analsci.31.67
  • Susaki EA, Tainaka K, Perrin D, et al.
    Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis.
    Cell 157(3). 726-739 (2014) doi:10.1016/j.cell.2014.03.042
  • Shimizu Y.
    Biochemical aspects of bacterial strategies for handling the incomplete translation processes.
    Frontiers in Microbiology 5. 1 (2014) doi:10.3389/fmicb.2014.00170
  • Shimizu Y, Kuruma Y, Kanamori T, Ueda T.
    The PURE System for Protein Production.
    Methods in Molecular Biology 1118. 275-284 (2014) doi:10.1007/978-1-62703-782-2_19
  • Shimizu Y.
    ArfA Recruits RF2 into Stalled Ribosomes.
    Journal of Molecular Biology 423(4). 624-631 (2012) doi:10.1016/j.jmb.2012.08.007
  • Kihira K, Shimizu Y, Shomura Y, et al.
    Crystal structure analysis of the translation factor RF3 (release factor 3).
    FEBS Letters 586(20). 3705-3709 (2012) doi:10.1016/j.febslet.2012.08.029

All Publications