Dr. Hideaki YOSHIMURA

E-mail:
hideaki[at]chem.s.u-tokyo.ac.jp
Office:
Room 06, Chem East Building（campus map）
Tel:
03-5841-4376 (ext: 24376)
Research and Professional Experience
1997–2001
Department of Industrial Chemistry, Faculty of Engineering, Kyoto University
2001–2003
Department of Molecular Engineering, Graduate School of Engineering, Kyoto University
2003–2007
Department of Structural Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies
2007–2009
Postdoctoral Researcher, JST-ICORP, Institute of Frontier Medical Sciences, Kyoto University
2009–2015
Project Assistant Professor, Department of Chemistry, School of Science, The University of Tokyo
2015–
Assistant Professor, Department of Chemistry, School of Science, The University of Tokyo
Awards
2016
Presentation Award (International Symposium on Pure and Applied Chemistry, Kuching, Malaysia)
2015
RSC Best Presentation Award (Royal Society of Chemistry Tokyo International Conference 2015)
2012
CSJ Presentation Award
2006
CSJ Student Presentation Award
Research Interests

Investigation of the mechanisms in life phenomena through analysis and manipulation of molecular motions in living cells.

Main targets: signal transduction, mRNAs, noncoding RNAs

Research keywords
  • Single molecule imaging
  • Fluorescence microscopy
  • Live cell imaging
  • Fluorescent probe
  • Molecular design
  • Molecular manipulation
  • RNA
  • Signal transduction
  • Biomolecular assemblies
Publications
  • G. Ado, N. Noda, H. T. Vu, A. D. Mahapatra, K. P. Arista, H. Yoshimura, D. M. Packwood, F. Ishidate, S. Sato, T. Ozawa and M. Uesugi,
    Discovery of a phase-separating small molecule that selectively sequesters tubulin in cells.
    Chem. Sci., in press. DOI: 10.1039/D1SC07151C
  • Triple-color single-molecule imaging for analysis of the role of receptor oligomers in signal transduction.
    H. Yoshimura*
    * corresponding author
    Biophys. Physicobiol., in press.
  • Long-term single cell bioluminescence imaging with C-3 position protected coelenterazine analogues.
    Y. Mizui, M. Eguchi, M. Tanaka, Y. Ikeda, H. Yoshimura*, T. Ozawa, D. Citterio, Y. Hiruta*
    * corresponding author
    Org. Biomol. Chem., 19, 579-586 (2021). DOI: 10.1039/d0ob02020f
  • Potential of Single-Molecule Live-Cell Imaging for Chemical Translational Biology.
    H Yoshimura*
    * corresponding author
    ChemBioChem, 22, 2941-2945 (2021). DOI: 10.1002/cbic.202100258
  • Signaling activations through G-protein-coupled-receptor aggragations.
    M. Watabe, H. Yoshimura, S. N. V. Arjunan, K. Kaizu, K. Takahashi
    Phys. Rev. E, 102, 032413 (2020). DOI:10.1103/PhysRevE.102.032413
  • Synergetic roles of Formyl Peptide Receptor 1 oligomerization in ligand-induced signal transduction.
    T. Nishiguchi, H. Yoshimura, R.S. Kasai, T. K. Fujiwara, T. Ozawa
    ACS Chem. Biol., 15, 2577-2587 (2020). DOI: 10.1021/acschembio.0c00631
  • Photocleavable Cadherin Inhibits Cell-to-Cell Mechanotransduction by Light.
    M. Endo, T. Iwawaki, H. Yoshimura, and T. Ozawa
    ACS Chem. Biol., 14, 2206-2214 (2019). DOI: 10.1021/acschembio.9b00460
  • A Robust Split-Luciferase-Based Cell Fusion Screening for Discovering Myogenesis-Promoting Molecules
    Q. Li, H. Yoshimura, M. Komiya, K. Tajiri, M. Uesugi, Y. Hata, T. Ozawa
    Analyst, 143, 3472-3480 (2018). DOI: 10.1039/C8AN00285A
  • Unique Roles of β-Arrestin in GPCR Trafficking Revealed by Photoinducible Dimerizers.
    O. Takenouchi, H. Yoshimura, T. Ozawa
    Sci. Rep., 8, 677 (2018). DOI: 10.1038/s41598-017-19130-y
  • Protein dynamics of the oxygen sensor protein HemAT as revealed by time-resolved step-scan FTIR spectroscopy.
    A. Pavlou, H. Yoshimura, S. Aono, E. Pinakoulaki
    Biophys. J., 114, 584-591 (2018). DOI: 10.1016/j.bpj.2017.12.012
  • Live Cell Imaging of Endogenous RNAs Using Pumilio Homology Domain Mutants: Principles and Applications.
    H. Yoshimura*
    *corresponding author
    Biochemistry, 57, 200-208 (2018). DOI: 10.1021/acs.biochem.7b00983
  • Real-time fluorescence imaging of single-molecule endogenous non-coding
    RNA in living cells.
    H. Yoshimura and T. Ozawa,
    Methods Mol. Biol., 1649, 337-347 (2018).DOI: 10.1007/978-1-4939-7213-5_22
  • Probing the role of the heme distal and proximal environment in ligand dynamics in the signal transducer protein HemAT by time-resolved step-scan FTIR and resonance Raman spectroscopy.
    A. Pavlou, A. Loullis, H. Yoshimura, S. Aono, E. Pinakoulaki,
    Biochemistry, 56, 5309-5317 (2017). DOI: 10.1021/acs.biochem.7b00558
  • Spatiotemporal analysis with a genetically encoded fluorescent RNA probe reveals TERRA function around telomeres.
    T. Yamada, H. Yoshimura, R. Shimada, M. Hattori, M. Eguchi, T. K. Fujiwara, A. Kusumi, T. Ozawa,
    Sci. Rep. 6, 38910 (2016). DOI: 10.1038/srep38910
  • Monitoring of RNA dynamics in living cells using PUM-HD and fluorescent protein reconstitution technique.
    H. Yoshimura and T. Ozawa,
    Methods Enzymol., 572, 65-85 (2016). DOI: 10.1016/bs.mie.2016.03.018
  • Genetically Encoded Fluorescent Probe for Imaging Apoptosis in Vivo with Spontaneous GFP Complementation.
    Y. Nasu, Y. Asaoka, M. Namae, H. Nishina, H. Yoshimura, T. Ozawa,
    Anal. Chem.    , 88, 838-844 (2016). DOI: 10.1021/acs.analchem.5b03367
  • Development of red-shifted mutants derived from luciferase of Brazilian click beetle Pyrearinus termitilluminans
    T. Nishiguchi, T. Yamada, Y. Nasu, M. Ito, H. Yoshimura, T. Ozawa
    J. Biomed. Opt.,20, 101205 (2015).DOI: 10.1117/1.jbo.20.10.101205
  • Simultaneous time-lamination imaging of protein association using a split fluorescent timer protein.
    A. Takamura, M Hattori, H. Yoshimura, T Ozawa
    Anal. Chem., 87, 3366-3372 (2015). DOI: 10.1021/ac504583t
  • Method of split-reporter reconstitution for the analysis of biomolecules
    H. Yoshimura, T. Ozawa
    Chem. Rec, 14, 492-501 (2014). DOI: 10.1002/tcr.201402001
  • Bioluminescent Probes to Analyze Ligand-induced Phosphatidylinositol
    3,4,5-trisphosphate Production with Split Luciferase Complementation
    L.Z. Yang, Y. Nasu, M. Hattori, H. Yoshimura, A. Kanno, T. Ozawa,
    Anal. Chem., 85, 11352-11359 (2013). DOI: 10.1021/ac402278f
  • Advances in fluorescence and bioluminescence imaging
    T. Ozawa, H. Yoshimura and S.B. Kim,
    Anal. Chem.,85, 590-609 (2013). DOI: 10.1021/ac3031724
  • Fluorescent probes for imaging endogenous β-actin mRNA in living cells using fluorescent protein-tagged pumilio.
    H. Yoshimura, A. Inaguma, T. Yamada and T. Ozawa
    ACS Chem. Biol., 7, 999-1005 (2012). DOI: 10.1021/cb200474a
  • Visualization of non-engineered single mRNAs in living cells using genetically encoded fluorescent probes.
    T. Yamada, H. Yoshimura, A. Inaguma and T. Ozawa,
    Anal. Chem., 83, 5708-5714 (2011). DOI: 10.1021/ac2009405

    • *The above two articles are introduced in "RNA imaging in situ" (Technology Feature; Nat. Methods, 9 787-790 (2012))

  • Hydrogen bonding interaction on the heme-bound ligand in the heme-based O2 sensor protein,
    M. Nishimura, H. Yoshimura, K. Ozawa, S. Yoshioka, M. Kubo, T. Kitagawa and S. Aono,
    J. Porphyrins Phthalocyanines, 12, 142-148 (2008). DOI: 10.1142/S1088424608000182

  • Protein conformation changes of HemAT-Bs upon ligand binding probed by ultraviolet resonance Raman spectroscopy.
    S. F. EI-Mashtoly, Y. Gu, H. Yoshimura, S. Yoshioka, S. Aono, T. Kitagawa,
    J. Biol. Chem., 283, 6942-6946 (2008). DOI: 10.1074/jbc.M709209200

  • The signal transduction mechanism of HemAT-Bs through the proximal heme pocket revealed by time-resolved resonance Raman spectroscopy.
    H. Yoshimura, S. Yoshioka, Y. Mizutani and S. Aono,
    Biochem. Biophys. Res. Commun., 307, 1053-1057 (2007). DOI: 10.1016/j.bbrc.2007.04.041

  • Two ligand binding sites in the O2-sensing signal transducer HemAT: implications for ligand recognition/discrimination and signaling,
    E. Pinakoulaki, H. Yoshimura, V. Daskalakis, S. Yoshioka, S. Aono and C. Varotsis,
    Proc. Natl. Acad. Sci. USA, 103, 14796-14801 (2006). DOI: 10.1073/pnas.0604248103

  • Specific hydrogen-bonding networks responsible for selective O2 sensing of the oxygen sensor protein HemAT from Bacillus subtilis,
    H. Yoshimura, S. Yoshioka, K. Kobayashi, T. Ohta, T. Uchida, M. Kubo, T. Kitagawa and S. Aono,
    Biochemistry, 45, 8301-8307 (2006). DOI: 10.1021/bi060315c

  • Recognition and discrimination of gases by the oxygen-sensing signal transducer protein HemAT as revealed by FTIR spectroscopy,
    E. Pinakoulaki, H. Yoshimura, S. Yoshioka, S. Aono and C. Varotsis,
    Biochemistry, 45, 7763-7766 (2006). DOI: 10.1021/bi0604072

  • Non-covalent modification of the heme-pocket of apomyoglobin by a 1,10-phenanthroline derivative,
    Y. Hitomi, H. Mukai, H. Yoshimura, T. Tanaka and T. Funabiki,
    Bioorg. Med. Chem. Lett., 16, 248-251 (2006). DOI: 10.1016/j.bmcl.2005.10.016

  • Biophysical properties of a c-type heme in chemotaxis signal transducer protein DcrA,
    S. Yoshioka, K. Kobayashi, H. Yoshimura, T. Uchida, T. Kitagawa and S. Aono,
    Biochemistry, 44, 15406.-15413 (2005). DOI: 10.1021/bi0513352

  • Oxygen-sensing mechanism of HemAT from Bacillus subtilis: a resonance Raman spectroscopic study,
    T. Ohta, H. Yoshimura, S. Yoshioka, S. Aono and Teizo Kitagawa,
    J. Am. Chem. Soc., 126, 15000-15001 (2004). DOI: 10.1021/ja046896f
Books
  • Optical monitoring of single molecule dynamics of RNA in living cells
    Hideaki Yoshimura*, Takeaki Ozawa
    * corresponding author
    Springer Series in Chemical Physics,"Progress in Photon Science", in press
  • A Split-Luciferase-Based Cell Fusion Assay for Evaluating the Myogenesis-Promoting Effects of Bioactive Molecules
    Q. Li, H Yoshimura*, T. Ozawa
    * corresponding author
    Methods in Mol. Biol., 2274, 79-87 (2021). DOI: 10.1007/978-1-0716-1258-3_8
  • Quantitative Analysis of Membrane Receptor Trafficking Manipulated by Optogenetic Tools
    O. Takenouchi, H Yoshimura*, T. Ozawa
    * corresponding author
    Methods in Mol. Biol., 2274, 15-23 (2021). DOI: 10.1007/978-1-0716-1258-3_2
  • Optical Control of G Protein-Coupled Receptor Activated in Living Cells
    Hideaki Yoshimura, Takeaki Ozawa
    Springer Series in Chemical Physics,"Progress in Photon Science: Recent Advances", Chapter 7, pp.129-138, Springer (2018). DOI: 10.1007/978-3-030-05974-3_7