A novel sphingomyelin/cholesterol domain‐specific probe reveals the dynamics of the membrane domains during virus release and in Niemann‐Pick type C

We identified a novel, nontoxic mushroom protein that specifically binds to a complex of sphingomyelin (SM), a major sphingolipid in mammalian cells, and cholesterol (Chol). The purified protein, termed nakanori, labeled cell surface domains in an SM‐ and Chol‐dependent manner and decorated specific lipid domains that colocalized with inner leaflet small GTPase H‐Ras, but not K‐Ras. The use of nakanori as a lipid‐domain–specific probe revealed altered distribution and dynamics of SM/Chol on the cell surface of Niemann‐Pick type C fibro‐blasts, possibly explaining some of the disease phenotype. In addition, that nakanori treatment of epithelial cells after influenza virus infection potently inhibited virus release demonstrates the therapeutic value of targeting specific lipid domains for anti‐viral treatment. —Makino, A., Abe, M., Ishitsuka, R., Murate, M., Kishimoto, T., Sakai, S., Hullin‐Matsuda, F., Shimada, Y., Inaba, T., Miyatake, H., Tanaka, H., Kurahashi, A., Pack, C.‐G., Kasai, R. S., Kubo, S., Schieber, N. L., Dohmae, N., Tochio, N., Hagiwara, K., Sasaki, Y., Aida, Y., Fujimori, F., Kigawa, T., Nishibori, K., Parton, R. G., Kusumi, A., Sako, Y., Anderluh, G., Yamashita, M., Kobayashi, T., Greimel, P., Kobayashi, T. A novel sphingomyelin/cholesterol domain‐specific probe reveals the dynamics of the membrane domains during virus release and in Niemann‐Pick type C. FASEB J. 31, 1301–1322 (2017) www.fasebj.org

[1]  Johannes Söding,et al.  Automatic Prediction of Protein 3D Structures by Probabilistic Multi-template Homology Modeling , 2015, PLoS Comput. Biol..

[2]  P. Greimel,et al.  Evaluation of aegerolysins as novel tools to detect and visualize ceramide phosphoethanolamine, a major sphingolipid in invertebrates , 2015, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[3]  K. Iwabuchi,et al.  Transbilayer distribution of lipids at nano scale , 2015, Journal of Cell Science.

[4]  Neval Yilmaz,et al.  Visualization of the heterogeneous membrane distribution of sphingomyelin associated with cytokinesis, cell polarity, and sphingolipidosis , 2015, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[5]  G. Fairn,et al.  Molecular probes to visualize the location, organization and dynamics of lipids , 2014, Journal of Cell Science.

[6]  V. Malhotra,et al.  Sphingomyelin homeostasis is required to form functional enzymatic domains at the trans-Golgi network , 2014, The Journal of cell biology.

[7]  M. Kraft,et al.  Imaging lipids with secondary ion mass spectrometry. , 2014, Biochimica et biophysica acta.

[8]  P. Courtoy,et al.  Endogenous sphingomyelin segregates into submicrometric domains in the living erythrocyte membrane[S] , 2014, Journal of Lipid Research.

[9]  Toshihide Kobayashi,et al.  Imaging local sphingomyelin-rich domains in the plasma membrane using specific probes and advanced microscopy. , 2014, Biochimica et biophysica acta.

[10]  T. Balla,et al.  A novel probe for phosphatidylinositol 4-phosphate reveals multiple pools beyond the Golgi , 2014, The Journal of cell biology.

[11]  Vesna Hodnik,et al.  Tracking Cholesterol/Sphingomyelin-Rich Membrane Domains with the Ostreolysin A-mCherry Protein , 2014, PloS one.

[12]  Y. Ohsumi,et al.  Yeast and mammalian autophagosomes exhibit distinct phosphatidylinositol 3-phosphate asymmetries , 2014, Nature Communications.

[13]  N. Dohmae,et al.  Binding of a pleurotolysin ortholog from Pleurotus eryngii to sphingomyelin and cholesterol-rich membrane domains[S] , 2013, Journal of Lipid Research.

[14]  G. Anderluh,et al.  Membrane Damage by an α-Helical Pore-forming Protein, Equinatoxin II, Proceeds through a Succession of Ordered Steps* , 2013, The Journal of Biological Chemistry.

[15]  G. Anderluh,et al.  The sensing of membrane microdomains based on pore-forming toxins. , 2013, Current medicinal chemistry.

[16]  V. Malhotra,et al.  Sphingomyelin organization is required for vesicle biogenesis at the Golgi complex , 2012, The EMBO journal.

[17]  A. Miyawaki,et al.  A Role for Sphingomyelin-Rich Lipid Domains in the Accumulation of Phosphatidylinositol-4,5-Bisphosphate to the Cleavage Furrow during Cytokinesis , 2012, Molecular and Cellular Biology.

[18]  A. Shevchenko,et al.  Quantitative analysis of the lipidomes of the influenza virus envelope and MDCK cell apical membrane , 2012, The Journal of cell biology.

[19]  J. Segovia,et al.  Cholesterol-rich lipid rafts are required for release of infectious human respiratory syncytial virus particles. , 2012, Virology.

[20]  S. Grinstein,et al.  High-resolution mapping reveals topologically distinct cellular pools of phosphatidylserine , 2011, The Journal of cell biology.

[21]  A. Miyawaki,et al.  Fluorescent probes for superresolution imaging of lipid domains on the plasma membrane , 2011 .

[22]  T. Kigawa,et al.  A practical method for cell-free protein synthesis to avoid stable isotope scrambling and dilution. , 2011, Analytical biochemistry.

[23]  Eric R. Prossnitz,et al.  Full characterization of GPCR monomer–dimer dynamic equilibrium by single molecule imaging , 2011, The Journal of cell biology.

[24]  M. Matsuda,et al.  Heterogeneity of Phosphatidic Acid Levels and Distribution at the Plasma Membrane in Living Cells as Visualized by a Förster Resonance Energy Transfer (FRET) Biosensor* , 2010, The Journal of Biological Chemistry.

[25]  P. Greimel,et al.  Phosphatidylglucoside forms specific lipid domains on the outer leaflet of the plasma membrane. , 2010, Biochemistry.

[26]  J. Lakey,et al.  A Toxin-based Probe Reveals Cytoplasmic Exposure of Golgi Sphingomyelin* , 2010, The Journal of Biological Chemistry.

[27]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[28]  Kai Simons,et al.  Lipid Rafts As a Membrane-Organizing Principle , 2010, Science.

[29]  J. Mancheño,et al.  Sticholysins, two pore-forming toxins produced by the Caribbean Sea anemone Stichodactyla helianthus: their interaction with membranes. , 2009, Toxicon : official journal of the International Society on Toxinology.

[30]  Makoto Inoue,et al.  Automated system for high-throughput protein production using the dialysis cell-free method. , 2009, Protein expression and purification.

[31]  David S. Goodsell,et al.  AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility , 2009, J. Comput. Chem..

[32]  D. Marsh,et al.  Cholesterol-induced fluid membrane domains: a compendium of lipid-raft ternary phase diagrams. , 2009, Biochimica et biophysica acta.

[33]  D. Lingwood,et al.  Order of lipid phases in model and plasma membranes , 2009, Proceedings of the National Academy of Sciences.

[34]  A. Bax,et al.  TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts , 2009, Journal of biomolecular NMR.

[35]  I. C. Leão,et al.  Deficiency of Niemann-Pick Type C-1 Protein Impairs Release of Human Immunodeficiency Virus Type 1 and Results in Gag Accumulation in Late Endosomal/Lysosomal Compartments , 2009, Journal of Virology.

[36]  R. Parton,et al.  A Single Method for Cryofixation and Correlative Light, Electron Microscopy and Tomography of Zebrafish Embryos , 2009, Traffic.

[37]  Toshihide Kobayashi,et al.  The Use of Lipid‐Binding Toxins to Study the Distribution and Dynamics of Sphingolipids and Cholesterol , 2008 .

[38]  J. Lakey,et al.  Molecular Determinants of Sphingomyelin Specificity of a Eukaryotic Pore-forming Toxin* , 2008, Journal of Biological Chemistry.

[39]  Tony Yeung,et al.  Membrane Phosphatidylserine Regulates Surface Charge and Protein Localization , 2008, Science.

[40]  M. Tokunaga,et al.  Highly inclined thin illumination enables clear single-molecule imaging in cells , 2008, Nature Methods.

[41]  T. Kigawa,et al.  A robust two-step PCR method of template DNA production for high-throughput cell-free protein synthesis , 2007, Journal of Structural and Functional Genomics.

[42]  Takashi Kumasaka,et al.  Mail-in data collection at SPring-8 protein crystallography beamlines , 2008 .

[43]  L. McGinnes,et al.  Incorporation of Functional HN-F Glycoprotein-Containing Complexes into Newcastle Disease Virus Is Dependent on Cholesterol and Membrane Lipid Raft Integrity , 2007, Journal of Virology.

[44]  Peter Güntert,et al.  KUJIRA, a package of integrated modules for systematic and interactive analysis of NMR data directed to high-throughput NMR structure studies , 2007, Journal of biomolecular NMR.

[45]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[46]  Koichi Furukawa,et al.  Gangliosides GM1 and GM3 in the living cell membrane form clusters susceptible to cholesterol depletion and chilling. , 2007, Molecular biology of the cell.

[47]  T. Kigawa,et al.  Improving cell-free protein synthesis for stable-isotope labeling , 2007, Journal of biomolecular NMR.

[48]  M. Tamura,et al.  Microenvironment and effect of energy depletion in the nucleus analyzed by mobility of multiple oligomeric EGFPs. , 2006, Biophysical journal.

[49]  Y. Umezawa,et al.  Imaging diacylglycerol dynamics at organelle membranes , 2006, Nature Methods.

[50]  Y. Henis,et al.  Clustering of Raft-Associated Proteins in the External Membrane Leaflet Modulates Internal Leaflet H-Ras Diffusion and Signaling , 2006, Molecular and Cellular Biology.

[51]  P. Várnai,et al.  Live cell imaging of phosphoinositide dynamics with fluorescent protein domains. , 2006, Biochimica et biophysica acta.

[52]  L. Pike.  Rafts defined: a report on the Keystone symposium on lipid rafts and cell function Published, JLR Papers in Press, April 27, 2006. , 2006, Journal of Lipid Research.

[53]  Takashi Kumasaka,et al.  RIKEN structural genomics beamlines at the SPring-8; high throughput protein crystallography with automated beamline operation , 2006, Journal of Structural and Functional Genomics.

[54]  Leslie M Loew,et al.  Characterization and application of a new optical probe for membrane lipid domains. , 2006, Biophysical journal.

[55]  S. Narumiya,et al.  Local Change in Phospholipid Composition at the Cleavage Furrow Is Essential for Completion of Cytokinesis* , 2005, Journal of Biological Chemistry.

[56]  E. Ikonen,et al.  Defective insulin receptor activation and altered lipid rafts in Niemann-Pick type C disease hepatocytes. , 2005, The Biochemical journal.

[57]  L. Cantley,et al.  PtdIns(4,5)P2 Functions at the Cleavage Furrow during Cytokinesis , 2005, Current Biology.

[58]  J. Hancock,et al.  Ras plasma membrane signalling platforms. , 2005, The Biochemical journal.

[59]  Johannes Söding,et al.  The HHpred interactive server for protein homology detection and structure prediction , 2005, Nucleic Acids Res..

[60]  Toshihide Kobayashi,et al.  Spatial and Functional Heterogeneity of Sphingolipid-rich Membrane Domains* , 2005, Journal of Biological Chemistry.

[61]  Anil Verma,et al.  Quantitative electron microscopy and fluorescence spectroscopy of the membrane distribution of influenza hemagglutinin , 2005, The Journal of cell biology.

[62]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[63]  Toshihide Kobayashi,et al.  Recognition of sphingomyelin by lysenin and lysenin-related proteins. , 2004, Biochemistry.

[64]  H. Mimuro,et al.  Pleurotolysin, a Novel Sphingomyelin-specific Two-component Cytolysin from the Edible Mushroom Pleurotus ostreatus, Assembles into a Transmembrane Pore Complex* , 2004, Journal of Biological Chemistry.

[65]  Y. Ioannou,et al.  Reduced sensitivity of Niemann-Pick C1-deficient cells to θ-toxin (perfringolysin O): sequestration of toxin to raft-enriched membrane vesicles , 2004, Histochemistry and Cell Biology.

[66]  Lolke de Haan,et al.  Cholera toxin: A paradigm for multi-functional engagement of cellular mechanisms (Review) , 2004, Molecular membrane biology.

[67]  S. Munro.  Lipid Rafts Elusive or Illusive? , 2003, Cell.

[68]  Juan A Hermoso,et al.  Crystal and electron microscopy structures of sticholysin II actinoporin reveal insights into the mechanism of membrane pore formation. , 2003, Structure.

[69]  Petra Schwille,et al.  Probing Lipid Mobility of Raft-exhibiting Model Membranes by Fluorescence Correlation Spectroscopy* , 2003, Journal of Biological Chemistry.

[70]  H. Kimura-Suda,et al.  Oligomerization and Pore Formation of a Sphingomyelin-specific Toxin, Lysenin* , 2003, Journal of Biological Chemistry.

[71]  K. Fujimoto,et al.  Cinnamycin (Ro 09-0198) Promotes Cell Binding and Toxicity by Inducing Transbilayer Lipid Movement* , 2003, The Journal of Biological Chemistry.

[72]  Gregor Anderluh,et al.  Two-step Membrane Binding by Equinatoxin II, a Pore-forming Toxin from the Sea Anemone, Involves an Exposed Aromatic Cluster and a Flexible Helix* , 2002, The Journal of Biological Chemistry.

[73]  P. Cosson,et al.  Separation and Characterization of Late Endosomal Membrane Domains* , 2002, The Journal of Biological Chemistry.

[74]  Frederick R Maxfield,et al.  Plasma membrane microdomains. , 2002, Current opinion in cell biology.

[75]  Akihiro Kusumi,et al.  Phospholipids undergo hop diffusion in compartmentalized cell membrane , 2002, The Journal of cell biology.

[76]  Y. Henis,et al.  Activated K-Ras and H-Ras display different interactions with saturable nonraft sites at the surface of live cells , 2002, The Journal of cell biology.

[77]  G. Anderluh,et al.  Cytolytic peptide and protein toxins from sea anemones (Anthozoa: Actiniaria). , 2002, Toxicon : official journal of the International Society on Toxinology.

[78]  J. Slot,et al.  Immunoelectron Microscopic Localization of Cholesterol Using Biotinylated and Non-cytolytic Perfringolysin O , 2002, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[79]  E. Ikonen,et al.  Mass spectrometric analysis reveals an increase in plasma membrane polyunsaturated phospholipid species upon cellular cholesterol loading. , 2001, Biochemistry.

[80]  E. Ikonen,et al.  Roles of lipid rafts in membrane transport. , 2001, Current opinion in cell biology.

[81]  C. Potrich,et al.  Effects of lipid composition on membrane permeabilization by sticholysin I and II, two cytolysins of the sea anemone Stichodactyla helianthus. , 2001, Biophysical journal.

[82]  K. Higaki,et al.  Isolation of NPC1-deficient Chinese hamster ovary cell mutants by gene trap mutagenesis. , 2001, Journal of biochemistry.

[83]  Robert G. Parton,et al.  GTP-dependent segregation of H-ras from lipid rafts is required for biological activity , 2001, Nature Cell Biology.

[84]  Andrew Pekosz,et al.  Influenza Virus Assembly and Lipid Raft Microdomains: a Role for the Cytoplasmic Tails of the Spike Glycoproteins , 2000, Journal of Virology.

[85]  C. Der,et al.  Understanding Ras: 'it ain't over 'til it's over'. , 2000, Trends in cell biology.

[86]  L. Nicholson,et al.  Protein dynamics measurements by TROSY-based NMR experiments. , 2000, Journal of magnetic resonance.

[87]  P. Scheiffele,et al.  Influenza Viruses Select Ordered Lipid Domains during Budding from the Plasma Membrane* , 1999, The Journal of Biological Chemistry.

[88]  K Wüthrich,et al.  TROSY in triple-resonance experiments: new perspectives for sequential NMR assignment of large proteins. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[89]  R. Parton,et al.  A lipid associated with the antiphospholipid syndrome regulates endosome structure and function , 1998, Nature.

[90]  M. Umeda,et al.  Lysenin, a Novel Sphingomyelin-specific Binding Protein* , 1998, The Journal of Biological Chemistry.

[91]  R. Riek,et al.  Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[92]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[93]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[94]  Bruce A. Johnson,et al.  NMR View: A computer program for the visualization and analysis of NMR data , 1994, Journal of biomolecular NMR.

[95]  E. Nanba,et al.  Altered sensitivities to potential inhibitors of cholesterol biosynthesis in Niemann-Pick type C fibroblasts. , 1993, Cell structure and function.

[96]  R. Parton,et al.  Sphingolipid transport from the trans‐Golgi network to the apical surface in permeabilized MDCK cells , 1992, FEBS letters.

[97]  T. E. Thompson,et al.  Interaction of cholesterol with various glycerophospholipids and sphingomyelin. , 1990, Biochemistry.

[98]  G. Karlström,et al.  Phase equilibria in the phosphatidylcholine-cholesterol system. , 1987, Biochimica et biophysica acta.

[99]  E. Lissi,et al.  Effect of sphingomyelin and cholesterol on the interaction of St II with lipidic interfaces. , 2007, Toxicon : official journal of the International Society on Toxinology.

[100]  Toshihide Kobayashi,et al.  A lipid-specific toxin reveals heterogeneity of sphingomyelin-containing membranes. , 2004, Biophysical journal.

[101]  J. Slotte,et al.  Cholesterol interactions with phospholipids in membranes. , 2002, Progress in lipid research.

[102]  G. Anderluh,et al.  Structure-function studies of tryptophan mutants of equinatoxin II, a sea anemone pore-forming protein. , 2000, The Biochemical journal.

[103]  R. Palmiter,et al.  Late endosomal membranes rich in lysobisphosphatidic acid regulate cholesterol transport , 1999, Nature Cell Biology.

[104]  Z. Otwinowski,et al.  [20] Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[105]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.