BDR researchers coming from diverse research fields are working together to achieve higher goals.

Seminars & Symposia

Seminars & Symposia

BDR hosts annual symposium and regular seminars inviting international scientists in life science.

Careers & Study

Careers & Study

BDR embraces people from diverse backgrounds, and strives to create an open and supportive setting for research.



BDR communicates the appeal and significance of our research to society through the use of various media and activities.



From research, events, people and everything in between, find out what’s going on at RIKEN BDR.

About Us

About Us

Exploring the scientific foundations of life through interdisciplinary approaches to address society’s problems.

Photo of Team leder, Yoshihiro Shimizu

Team Leader
Yoshihiro Shimizu Ph.D.

Laboratory for Cell-Free Protein Synthesis

LocationOsaka / Quantitative Biology Buildings

           and  Kobe / Integrated Innovation Bldg

E-mail yshimizu[at]riken.jp

Recruiting graduate students

Refining technologies for protein/peptide synthesis

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

Selected Publications

Okubo-Kurihara E, Ali A, Hiramoto M, et al.
Tracking metabolites at single-cell resolution reveals metabolic dynamics during plant mitosis.
Plant Physiology 189(2), 459-464 (2022) doi: 10.1093/plphys/kiac093

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