Shige H Yoshimura

Summary

Affiliation: Kyoto University
Country: Japan

Publications

  1. ncbi request reprint Condensin architecture and interaction with DNA: regulatory non-SMC subunits bind to the head of SMC heterodimer
    Shige H Yoshimura
    CREST Research Project, Department of Responses to Environmental Signals and Stresses, Graduate School of Biostudies, Kyoto University, Japan
    Curr Biol 12:508-13. 2002
  2. doi request reprint Intermolecular disulfide bonds between nucleoporins regulate karyopherin-dependent nuclear transport
    Shige H Yoshimura
    Graduate School of Biostudies, Kyoto University, Yoshida konoe cho, Sakyo ku, Kyoto 606 8501, Japan
    J Cell Sci 126:3141-50. 2013
  3. doi request reprint Site-specific attachment of a protein to a carbon nanotube end without loss of protein function
    Shige H Yoshimura
    Graduate School of Biostudies, Kyoto University, Yoshida konoe cho, Sakyo ku, Kyoto, 606 8501, Japan
    Bioconjug Chem 23:1488-93. 2012
  4. ncbi request reprint Development of glutathione-coupled cantilever for the single-molecule force measurement by scanning force microscopy
    Shige H Yoshimura
    Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake cho, Sakyo ku, Kyoto 606 8502, Japan
    FEBS Lett 580:3961-5. 2006
  5. ncbi request reprint [Atomic force microscopy as a single-molecule imaging and force measurement tool for the cell nucleus]
    Shige H Yoshimura
    Tanpakushitsu Kakusan Koso 51:1981-8. 2006
  6. ncbi request reprint Molecular mechanisms of DNA end-loop formation by TRF2
    Shige H Yoshimura
    Department of Responses to Environmental Signals and Stresses, Graduate School of Biostudies, Kyoto University, Kitashirawkawa oiwake cho Sakyo ku Kyoto, 606 8502, Japan
    Genes Cells 9:205-18. 2004
  7. ncbi request reprint On-substrate lysis treatment combined with scanning probe microscopy revealed chromosome structures in eukaryotes and prokaryotes
    Shige H Yoshimura
    Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake cho, Sakyo ku, Kyoto 606 8502, Japan
    J Electron Microsc (Tokyo) 52:415-23. 2003
  8. doi request reprint Fluorescence labeling of carbon nanotubes and visualization of a nanotube-protein hybrid under fluorescence microscope
    Shige H Yoshimura
    Graduate School of Biostudies, Kyoto University, Yoshida konoe cho, Sakyo ku, Kyoto 606 8501, Japan
    Biomacromolecules 12:1200-4. 2011
  9. ncbi request reprint Differential degradation of the Na+/K+-ATPase subunits in the plasma membrane
    Shige H Yoshimura
    Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake cho, Sakyo ku, Japan
    Ann N Y Acad Sci 986:378-81. 2003
  10. doi request reprint Fast degradation of the auxiliary subunit of Na+/K+-ATPase in the plasma membrane of HeLa cells
    Shige H Yoshimura
    Graduate School of Biostudies, Kyoto University, Yoshida konoe cho, Sakyo ku, Kyoto, 606 8502, Japan
    J Cell Sci 121:2159-68. 2008

Collaborators

Detail Information

Publications38

  1. ncbi request reprint Condensin architecture and interaction with DNA: regulatory non-SMC subunits bind to the head of SMC heterodimer
    Shige H Yoshimura
    CREST Research Project, Department of Responses to Environmental Signals and Stresses, Graduate School of Biostudies, Kyoto University, Japan
    Curr Biol 12:508-13. 2002
    ..Thus, non-SMC trimers may regulate the ATPase activity of condensin by directly interacting with the globular domains of SMC heterodimer and alter the mode of DNA interaction. A model for the action of heteropentamer is presented...
  2. doi request reprint Intermolecular disulfide bonds between nucleoporins regulate karyopherin-dependent nuclear transport
    Shige H Yoshimura
    Graduate School of Biostudies, Kyoto University, Yoshida konoe cho, Sakyo ku, Kyoto 606 8501, Japan
    J Cell Sci 126:3141-50. 2013
    ..From these results, we propose that the inner channel of the NPC is somehow insulated from the cytoplasm and is more sensitive than the cytoplasm to the intracellular redox state...
  3. doi request reprint Site-specific attachment of a protein to a carbon nanotube end without loss of protein function
    Shige H Yoshimura
    Graduate School of Biostudies, Kyoto University, Yoshida konoe cho, Sakyo ku, Kyoto, 606 8501, Japan
    Bioconjug Chem 23:1488-93. 2012
    ..This procedure can be applied not only to nanotubes, but also to other nanomaterials, and therefore provides a fundamental technique for well-controlled protein conjugation...
  4. ncbi request reprint Development of glutathione-coupled cantilever for the single-molecule force measurement by scanning force microscopy
    Shige H Yoshimura
    Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake cho, Sakyo ku, Kyoto 606 8502, Japan
    FEBS Lett 580:3961-5. 2006
    ..The rupture force between glutathione and GST was approximately 100 pN on average. By using this cantilever, we succeeded in measuring the interaction force between importin alpha and importin beta...
  5. ncbi request reprint [Atomic force microscopy as a single-molecule imaging and force measurement tool for the cell nucleus]
    Shige H Yoshimura
    Tanpakushitsu Kakusan Koso 51:1981-8. 2006
  6. ncbi request reprint Molecular mechanisms of DNA end-loop formation by TRF2
    Shige H Yoshimura
    Department of Responses to Environmental Signals and Stresses, Graduate School of Biostudies, Kyoto University, Kitashirawkawa oiwake cho Sakyo ku Kyoto, 606 8502, Japan
    Genes Cells 9:205-18. 2004
    ..TRF1 also bound to the telomeric DNA as a dimer, but did not mediate DNA loop formation by itself. These results provide a new insight into the molecular mechanism of DNA end-loop formation by TRFs...
  7. ncbi request reprint On-substrate lysis treatment combined with scanning probe microscopy revealed chromosome structures in eukaryotes and prokaryotes
    Shige H Yoshimura
    Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake cho, Sakyo ku, Kyoto 606 8502, Japan
    J Electron Microsc (Tokyo) 52:415-23. 2003
    ..These results suggest that the fundamental mechanism of chromosome packing is common in both prokaryotes and eukaryotes...
  8. doi request reprint Fluorescence labeling of carbon nanotubes and visualization of a nanotube-protein hybrid under fluorescence microscope
    Shige H Yoshimura
    Graduate School of Biostudies, Kyoto University, Yoshida konoe cho, Sakyo ku, Kyoto 606 8501, Japan
    Biomacromolecules 12:1200-4. 2011
    ..By using this technique, we also demonstrated multicolor fluorescence imaging of a nanotube-protein hybrid...
  9. ncbi request reprint Differential degradation of the Na+/K+-ATPase subunits in the plasma membrane
    Shige H Yoshimura
    Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake cho, Sakyo ku, Japan
    Ann N Y Acad Sci 986:378-81. 2003
    ....
  10. doi request reprint Fast degradation of the auxiliary subunit of Na+/K+-ATPase in the plasma membrane of HeLa cells
    Shige H Yoshimura
    Graduate School of Biostudies, Kyoto University, Yoshida konoe cho, Sakyo ku, Kyoto, 606 8502, Japan
    J Cell Sci 121:2159-68. 2008
    ..All these results indicate that the alpha- and beta-subunits of Na(+)/K(+)-ATPase are assembled in the endoplasmic reticulum, but are disassembled in the plasma membrane and undergo different degradation processes...
  11. ncbi request reprint Structural organization of dynamic chromatin
    Kohji Hizume
    Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake cho, Sakyo ku, Kyoto, 606 8502, Japan
    Subcell Biochem 41:3-28. 2007
  12. doi request reprint Molecular dynamics of DNA and nucleosomes in solution studied by fast-scanning atomic force microscopy
    Yuki Suzuki
    Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Sakyo ku, Kyoto, Japan
    Ultramicroscopy 110:682-8. 2010
    ..These observations help us to develop the molecular mechanisms of nucleosome dynamics and also demonstrate the ability of fast-scanning AFM for the analysis of dynamic protein-DNA interaction in sub-seconds time scale...
  13. doi request reprint Molecular mechanisms underlying nucleocytoplasmic shuttling of actinin-4
    Masahiro Kumeta
    Graduate School of Biostudies, Kyoto University, Kyoto 606 8501, Japan
    J Cell Sci 123:1020-30. 2010
    ....
  14. doi request reprint Nuclear architecture and chromatin dynamics revealed by atomic force microscopy in combination with biochemistry and cell biology
    Yasuhiro Hirano
    Kyoto University Graduate School of Biostudies, Yoshida Honmachi, Sakyo ku, Kyoto 606 8501, Japan
    Pflugers Arch 456:139-53. 2008
    ..The new applications of AFM, such as recognition imaging, fast-scanning imaging, and a variety of modified cantilevers, are expected to be powerful techniques to reveal the nanostructure of the nucleus...
  15. pmc Individual binding pockets of importin-beta for FG-nucleoporins have different binding properties and different sensitivities to RanGTP
    Shotaro Otsuka
    Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Yoshida konoe cho, Sakyo ku, Kyoto 606 8501, Japan
    Proc Natl Acad Sci U S A 105:16101-6. 2008
    ..Single-molecule force measurement using the entire molecule of an NPC from a Xenopus oocyte also implies that the reduction of the affinity by RanGTP really occurs at the nucleoplasmic side of the entire NPC...
  16. doi request reprint Karyopherin-independent spontaneous transport of amphiphilic proteins through the nuclear pore
    Masahiro Kumeta
    Graduate School of Biostudies, Kyoto University, Kyoto 606 8501, Japan
    J Cell Sci 125:4979-84. 2012
    ..These results contribute to the understanding of nucleocytoplasmic molecular sorting and the nature of the permeability barrier...
  17. ncbi request reprint Comparative structural biology of the genome: nano-scale imaging of single nucleus from different kingdoms reveals the common physicochemical property of chromatin with a 40 nm structural unit
    Toshiro Kobori
    Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa, Kyoto 606 8502, Japan
    J Electron Microsc (Tokyo) 55:31-40. 2006
    ..A common mechanism could be implied regardless of the intrinsic properties of the eukaryotic genomes...
  18. ncbi request reprint Atomic force microscopy demonstrates a critical role of DNA superhelicity in nucleosome dynamics
    Kohji Hizume
    Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake cho, Sakyo ku, Kyoto, Japan
    Cell Biochem Biophys 40:249-61. 2004
    ..Namely, the negative supercoiling promoted the efficient formation of the nucleosome but the positive supercoiling strongly inhibited it...
  19. pmc Visual analysis of concerted cleavage by type IIF restriction enzyme SfiI in subsecond time region
    Yuki Suzuki
    Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
    Biophys J 101:2992-8. 2011
    ....
  20. ncbi request reprint Linker histone H1 per se can induce three-dimensional folding of chromatin fiber
    Kohji Hizume
    Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake cho, Sakyo ku, Kyoto 606 8502, Japan
    Biochemistry 44:12978-89. 2005
    ..The biological significance of this property of the chromatin architecture will be apparent in the closed segments ( approximately 100 kb) between SAR/MAR regions...
  21. pmc Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy
    Joongbaek Kim
    Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake cho, Sakyo ku, Kyoto 606 8502, Japan
    Nucleic Acids Res 32:1982-92. 2004
    ..Mutant analysis demonstrated that these tight compactions of the nucleoid required a protein, Dps. From these results and previously available information, we propose a structural model of the E.coli nucleoid...
  22. ncbi request reprint Human small G proteins, ObgH1, and ObgH2, participate in the maintenance of mitochondria and nucleolar architectures
    Yasuhiro Hirano
    Graduate School of Biostudies, Kyoto University, Kyoto 606 8502 Japan
    Genes Cells 11:1295-304. 2006
    ..In conclusion, the two human Obg proteins have similar enzymatic activities that can complement bacterial Obg function, but show different cellular function(s) with different intracellular localizations...
  23. pmc Fast-scanning atomic force microscopy reveals the ATP/ADP-dependent conformational changes of GroEL
    Masatoshi Yokokawa
    Laboratory of Plasma Membrane and Nuclear Signaling, Kyoto University Graduate School of Biostudies, Kyoto, Japan
    EMBO J 25:4567-76. 2006
    ....
  24. ncbi request reprint Chromatin reconstitution: development of a salt-dialysis method monitored by nano-technology
    Kohji Hizume
    Laboratory of Plasma Membrane and Nuclear Signaling, Kyoto University Graduate School of Biostudies, Kyoto, Japan
    Arch Histol Cytol 65:405-13. 2002
    ..This enabled the structure-function studies of long chromatin molecules under well-defined conditions...
  25. doi request reprint Antibody-based analysis reveals "filamentous vs. non-filamentous" and "cytoplasmic vs. nuclear" crosstalk of cytoskeletal proteins
    Masahiro Kumeta
    Graduate School of Biostudies, Kyoto University, Kyoto 606 8501, Japan Electronic address
    Exp Cell Res 319:3226-37. 2013
    ..These results suggest the distinct roles of the helix-based cytoskeletal proteins in the nucleus. ..
  26. doi request reprint Fast microscopical dissection of action scenes played by Escherichia coli RNA polymerase
    Yuki Suzuki
    Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Sakyo ku, Kyoto, Japan
    FEBS Lett 586:3187-92. 2012
    ..The present method is potentially applicable to examine a variety of protein-nucleic acid interactions, especially those involved in the process of gene regulation...
  27. pmc Visualization of structural changes accompanying activation of N-methyl-D-aspartate (NMDA) receptors using fast-scan atomic force microscopy imaging
    Yuki Suzuki
    Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kyoto 606 8501, Japan
    J Biol Chem 288:778-84. 2013
    ..A change in receptor size following activation could have important functional implications, in particular by affecting interactions between the NMDA receptor and its extracellular synaptic partners...
  28. ncbi request reprint [Observation of biological samples by atomic force microscopy]
    Masatoshi Yokokawa
    Tanpakushitsu Kakusan Koso 49:1607-14. 2004
  29. pmc Histone and TK0471/TrmBL2 form a novel heterogeneous genome architecture in the hyperthermophilic archaeon Thermococcus kodakarensis
    Hugo Maruyama
    Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
    Mol Biol Cell 22:386-98. 2011
    ..These results show that the archaeal chromosome is organized into heterogeneous structures and that TK0471/TrmBL2 acts as a general chromosomal protein as well as a global transcriptional repressor...
  30. doi request reprint Synthetic RNA-protein complex shaped like an equilateral triangle
    Hirohisa Ohno
    Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake cho, Kitashirakawa, Sakyo ku, Kyoto 606 8502, Japan
    Nat Nanotechnol 6:116-20. 2011
    ..Functional RNA-protein complexes constructed with this approach could have applications in nanomedicine and synthetic biology...
  31. pmc Nucleocytoplasmic shuttling of cytoskeletal proteins: molecular mechanism and biological significance
    Masahiro Kumeta
    Graduate School of Biostudies, Kyoto University, Yoshida konoe cho, Sakyo ku, Kyoto 606 8501, Japan
    Int J Cell Biol 2012:494902. 2012
    ..We propose that such molecular dynamics constitute a form of cytoskeleton-modulated regulation of nuclear functions which is mediated by the translocation of cytoskeletal components in and out of the nucleus...
  32. ncbi request reprint Intermolecular Interaction between Na+/K+-ATPase alpha subunit and glycogen phosphorylase
    Kunio Takeyasu
    Graduate School of Biostudies, Kyoto University, Japan
    Ann N Y Acad Sci 986:522-4. 2003
  33. ncbi request reprint Vacuolar membrane dynamics revealed by GFP-AtVam3 fusion protein
    Tomohiro Uemura
    Graduate School of Biostudies, Kyoto University, Yoshida nihonmatsu cho, Sakyo ku, Kyoto 606 8501, Japan
    Genes Cells 7:743-53. 2002
    ..Our current understanding of the dynamic processes of vacuolar morphogenesis has suffered from the lack of a marker for observing these processes in living cells...
  34. pmc Fast-scan atomic force microscopy reveals that the type III restriction enzyme EcoP15I is capable of DNA translocation and looping
    Neal Crampton
    Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge, United Kingdom
    Proc Natl Acad Sci U S A 104:12755-60. 2007
    ..On the basis of our results, we conclude that EcoP15I uses two distinct mechanisms to communicate between two recognition sites: diffusive DNA loop formation and ATPase-driven translocation of the intervening DNA contour...
  35. pmc Dynamic structures of Bacillus subtilis RecN-DNA complexes
    Humberto Sanchez
    Departamento de Biotecnologia Microbiana, Centro Nacional de Biotecnologia, CSIC, Campus Universidad Autonoma de Madrid, Darwin 3, Cantoblanco, 28049 Madrid, Spain
    Nucleic Acids Res 36:110-20. 2008
    ..Then, the resulting RecA nucleoprotein filaments, on different ssDNA segments, might promote the simultaneous genome-wide homology search...
  36. ncbi request reprint Channel induction by palytoxin in yeast cells expressing Na+,K+-ATPase or its chimera with sarco/endoplasmic reticulum Ca2+-ATPase
    Katsuaki Ito
    Department of Veterinary Pharmacology, Faculty of Agriculture, Miyazaki University, 889 2192, Miyazaki, Japan
    FEBS Lett 543:108-12. 2003
    ..Ouabain inhibited the effect of PTX in NNN or NCN cells but not in ouabain-resistant cells. These data suggest that the channel-forming action of PTX does not depend on the catalytic domain species...
  37. ncbi request reprint Single-molecule detection of phosphorylation-induced plasticity changes during ezrin activation
    Dan Liu
    Division of Cellular Dynamics, Hefei National Laboratory for Physical Sciences, Hefei 230027, China
    FEBS Lett 581:3563-71. 2007
    ....
  38. pmc Following translation by single ribosomes one codon at a time
    Jin Der Wen
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Nature 452:598-603. 2008
    ..Translocation and RNA unwinding are strictly coupled ribosomal functions...