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RIKEN Center for Biosystems Dynamics Research Laboratory for Cell-Free Protein Synthesis

Team Director: Yoshihiro Shimizu (Ph.D.)

Research Summary

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.

Main Research Fields

  • Biological Sciences

Related Research Fields

  • Biology

Keywords

  • cell-free protein synthesis
  • translation
  • ribosome
  • tRNA

Selected Publications

  • 1. 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/kiac093The webpage will open in a new tab.
  • 2. 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/s42003-020-1074-2The webpage will open in a new tab.
  • 3. 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/s41467-020-15906-5The webpage will open in a new tab.
  • 4. 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/s42003-020-0874-8The webpage will open in a new tab.
  • 5. 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.2018.02.004The webpage will open in a new tab.
  • 6. 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.1615351114The webpage will open in a new tab.
  • 7. 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.1603799113The webpage will open in a new tab.
  • 8. 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.2015.12.052The webpage will open in a new tab.
  • 9. 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.31.67The webpage will open in a new tab.
  • 10. 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.2014.03.042The webpage will open in a new tab.

Related Links

Lab Members

Principal investigator

Yoshihiro Shimizu
Team Director

Core members

Keiko Masuda
Research Scientist
Shoko Harada
Research Scientist
Shota Nishikawa
Research Scientist
Reiko Nakagawa
Technical Scientist
Aya Sato
Technical Staff I
Yumi Mandai
Technical Staff I
Setsuko Tsuboi
Technical Staff I
Akiko Imasato
Research Part-time Worker II
Weng Yu Lai
International Program Associate
Haruto Miyajima
Student Trainee
Yoko Nagatomo
Assistant

Contact Information

Integrated Innovation Building
6-7-1 Minatojima-minamimachi, Chuo-ku, Kobe,
Hyogo 650-0047,
Email: yshimizu@riken.jp

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