Team Leader
Yoshihiro Shimizu
Ph.D.
Laboratory for Cell-Free Protein 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 Wed Jun 01 00:00:00 JST 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 Tue Dec 01 00:00:00 JST 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 Sun Nov 01 00:00:00 JST 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 Thu Oct 01 00:00:00 JST 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 Sat Dec 01 00:00:00 JST 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 Fri Dec 01 00:00:00 JST 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 Thu Dec 01 00:00:00 JST 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 Tue Nov 01 00:00:00 JST 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 Tue Dec 01 00:00:00 JST 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 Mon Dec 01 00:00:00 JST 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 Sat Nov 01 00:00:00 JST 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 Wed Oct 01 00:00:00 JST 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 Sat Dec 01 00:00:00 JST 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 Thu Nov 01 00:00:00 JST 2012
doi: 10.1016/j.febslet.2012.08.029