ICAM-1 induced rearrangements of capsid and genome prime rhinovirus 14 for activation and uncoating

Jazyk angličtina Země Spojené státy americké Médium print

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/pmid33947819

Most rhinoviruses, which are the leading cause of the common cold, utilize intercellular adhesion molecule-1 (ICAM-1) as a receptor to infect cells. To release their genomes, rhinoviruses convert to activated particles that contain pores in the capsid, lack minor capsid protein VP4, and have an altered genome organization. The binding of rhinoviruses to ICAM-1 promotes virus activation; however, the molecular details of the process remain unknown. Here, we present the structures of virion of rhinovirus 14 and its complex with ICAM-1 determined to resolutions of 2.6 and 2.4 Å, respectively. The cryo-electron microscopy reconstruction of rhinovirus 14 virions contains the resolved density of octanucleotide segments from the RNA genome that interact with VP2 subunits. We show that the binding of ICAM-1 to rhinovirus 14 is required to prime the virus for activation and genome release at acidic pH. Formation of the rhinovirus 14-ICAM-1 complex induces conformational changes to the rhinovirus 14 capsid, including translocation of the C termini of VP4 subunits, which become poised for release through pores that open in the capsids of activated particles. VP4 subunits with altered conformation block the RNA-VP2 interactions and expose patches of positively charged residues. The conformational changes to the capsid induce the redistribution of the virus genome by altering the capsid-RNA interactions. The restructuring of the rhinovirus 14 capsid and genome prepares the virions for conversion to activated particles. The high-resolution structure of rhinovirus 14 in complex with ICAM-1 explains how the binding of uncoating receptors enables enterovirus genome release.

Zobrazit více v PubMed

Jacobs S. E., Lamson D. M., St George K., Walsh T. J., Human rhinoviruses. Clin. Microbiol. Rev. 26, 135–162 (2013). PubMed PMC

Fendrick A. M., Monto A. S., Nightengale B., Sarnes M., The economic burden of non-influenza-related viral respiratory tract infection in the United States. Arch. Intern. Med. 163, 487–494 (2003). PubMed

Bertino J. S., Cost burden of viral respiratory infections: Issues for formulary decision makers. Am. J. Med. 112 (suppl. 6A), 42S–49S (2002). PubMed

Palmenberg A. C., et al. ., Sequencing and analyses of all known human rhinovirus genomes reveal structure and evolution. Science 324, 55–59 (2009). PubMed PMC

Greve J. M., et al. ., The major human rhinovirus receptor is ICAM-1. Cell 56, 839–847 (1989). PubMed

Uncapher C. R., DeWitt C. M., Colonno R. J., The major and minor group receptor families contain all but one human rhinovirus serotype. Virology 180, 814–817 (1991). PubMed

Hofer F., et al. ., Members of the low density lipoprotein receptor family mediate cell entry of a minor-group common cold virus. Proc. Natl. Acad. Sci. U.S.A. 91, 1839–1842 (1994). PubMed PMC

Bochkov Y. A., et al. ., Cadherin-related family member 3, a childhood asthma susceptibility gene product, mediates rhinovirus C binding and replication. Proc. Natl. Acad. Sci. U.S.A. 112, 5485–5490 (2015). PubMed PMC

Wells A. I., Coyne C. B., Enteroviruses: A gut-wrenching game of entry, detection, and evasion. Viruses 11, 460 (2019). PubMed PMC

Bergelson J. M., et al. ., Decay-accelerating factor (CD55), a glycosylphosphatidylinositol-anchored complement regulatory protein, is a receptor for several echoviruses. Proc. Natl. Acad. Sci. U.S.A. 91, 6245–6248 (1994). PubMed PMC

Nishimura Y., et al. ., Human P-selectin glycoprotein ligand-1 is a functional receptor for enterovirus 71. Nat. Med. 15, 794–797 (2009). PubMed

Staring J., et al. ., KREMEN1 is a host entry receptor for a major group of enteroviruses. Cell Host Microbe 23, 636–643.e5 (2018). PubMed

Su P. Y., et al. ., Cell surface sialylation affects binding of enterovirus 71 to rhabdomyosarcoma and neuroblastoma cells. BMC Microbiol. 12, 162 (2012). PubMed PMC

Mendelsohn C. L., Wimmer E., Racaniello V. R., Cellular receptor for poliovirus: Molecular cloning, nucleotide sequence, and expression of a new member of the immunoglobulin superfamily. Cell 56, 855–865 (1989). PubMed

Bergelson J. M., et al. ., Isolation of a common receptor for Coxsackie B viruses and adenoviruses 2 and 5. Science 275, 1320–1323 (1997). PubMed

Yamayoshi S., et al. ., Scavenger receptor B2 is a cellular receptor for enterovirus 71. Nat. Med. 15, 798–801 (2009). PubMed

Tuthill T. J., Groppelli E., Hogle J. M., Rowlands D. J., Picornaviruses. Curr. Top. Microbiol. Immunol. 343, 43–89 (2010). PubMed PMC

Basavappa R., et al. ., Role and mechanism of the maturation cleavage of VP0 in poliovirus assembly: Structure of the empty capsid assembly intermediate at 2.9 A resolution. Protein Sci. 3, 1651–1669 (1994). PubMed PMC

Holland J. J., Kiehn E. D., Specific cleavage of viral proteins as steps in the synthesis and maturation of enteroviruses. Proc. Natl. Acad. Sci. U.S.A. 60, 1015–1022 (1968). PubMed PMC

Procházková M., et al. ., Virion structures and genome delivery of honeybee viruses. Curr. Opin. Virol. 45, 17–24 (2020). PubMed

Rossmann M. G., et al. ., Structure of a human common cold virus and functional relationship to other picornaviruses. Nature 317, 145–153 (1985). PubMed

Harrison S. C., Olson A. J., Schutt C. E., Winkler F. K., Bricogne G., Tomato bushy stunt virus at 2.9 A resolution. Nature 276, 368–373 (1978). PubMed

Verdaguer N., Blaas D., Fita I., Structure of human rhinovirus serotype 2 (HRV2). J. Mol. Biol. 300, 1179–1194 (2000). PubMed

Oliveira M. A., et al. ., The structure of human rhinovirus 16. Structure 1, 51–68 (1993). PubMed

Smyth M., Pettitt T., Symonds A., Martin J., Identification of the pocket factors in a picornavirus. Arch. Virol. 148, 1225–1233 (2003). PubMed

Pickl-Herk A., et al. ., Uncoating of common cold virus is preceded by RNA switching as determined by X-ray and cryo-EM analyses of the subviral A-particle. Proc. Natl. Acad. Sci. U.S.A. 110, 20063–20068 (2013). PubMed PMC

Levy H. C., Bostina M., Filman D. J., Hogle J. M., Catching a virus in the act of RNA release: A novel poliovirus uncoating intermediate characterized by cryo-electron microscopy. J. Virol. 84, 4426–4441 (2010). PubMed PMC

Garriga D., et al. ., Insights into minor group rhinovirus uncoating: The X-ray structure of the HRV2 empty capsid. PLoS Pathog. 8, e1002473 (2012). PubMed PMC

Wang X., et al. ., A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71. Nat. Struct. Mol. Biol. 19, 424–429 (2012). PubMed PMC

Shingler K. L., et al. ., The enterovirus 71 A-particle forms a gateway to allow genome release: A cryoEM study of picornavirus uncoating. PLoS Pathog. 9, e1003240 (2013). PubMed PMC

Seitsonen J. J., et al. ., Structural analysis of coxsackievirus A7 reveals conformational changes associated with uncoating. J. Virol. 86, 7207–7215 (2012). PubMed PMC

Belnap D. M., et al. ., Molecular tectonic model of virus structural transitions: The putative cell entry states of poliovirus. J. Virol. 74, 1342–1354 (2000). PubMed PMC

Buchta D., et al. ., Enterovirus particles expel capsid pentamers to enable genome release. Nat. Commun. 10, 1138 (2019). PubMed PMC

Ren J., et al. ., Picornavirus uncoating intermediate captured in atomic detail. Nat. Commun. 4, 1929 (2013). PubMed PMC

Bauer L., Lyoo H., van der Schaar H. M., Strating J. R., van Kuppeveld F. J., Direct-acting antivirals and host-targeting strategies to combat enterovirus infections. Curr. Opin. Virol. 24, 1–8 (2017). PubMed PMC

Smith T. J., et al. ., The site of attachment in human rhinovirus 14 for antiviral agents that inhibit uncoating. Science 233, 1286–1293 (1986). PubMed

van de Stolpe A., van der Saag P. T., Intercellular adhesion molecule-1. J. Mol. Med. (Berl.) 74, 13–33 (1996). PubMed

Casasnovas J. M., Stehle T., Liu J. H., Wang J. H., Springer T. A., A dimeric crystal structure for the N-terminal two domains of intercellular adhesion molecule-1. Proc. Natl. Acad. Sci. U.S.A. 95, 4134–4139 (1998). PubMed PMC

Chothia C., Jones E. Y., The molecular structure of cell adhesion molecules. Annu. Rev. Biochem. 66, 823–862 (1997). PubMed

Wang J., Springer T. A., Structural specializations of immunoglobulin superfamily members for adhesion to integrins and viruses. Immunol. Rev. 163, 197–215 (1998). PubMed

Harpaz Y., Chothia C., Many of the immunoglobulin superfamily domains in cell adhesion molecules and surface receptors belong to a new structural set which is close to that containing variable domains. J. Mol. Biol. 238, 528–539 (1994). PubMed

Kolatkar P. R., et al. ., Structural studies of two rhinovirus serotypes complexed with fragments of their cellular receptor. EMBO J. 18, 6249–6259 (1999). PubMed PMC

Xiao C., et al. ., Discrimination among rhinovirus serotypes for a variant ICAM-1 receptor molecule. J. Virol. 78, 10034–10044 (2004). PubMed PMC

Xiao C., et al. ., Interaction of coxsackievirus A21 with its cellular receptor, ICAM-1. J. Virol. 75, 2444–2451 (2001). PubMed PMC

Olson N. H., et al. ., Structure of a human rhinovirus complexed with its receptor molecule. Proc. Natl. Acad. Sci. U.S.A. 90, 507–511 (1993). PubMed PMC

Xing L., Casasnovas J. M., Cheng R. H., Structural analysis of human rhinovirus complexed with ICAM-1 reveals the dynamics of receptor-mediated virus uncoating. J. Virol. 77, 6101–6107 (2003). PubMed PMC

Hoover-Litty H., Greve J. M., Formation of rhinovirus-soluble ICAM-1 complexes and conformational changes in the virion. J. Virol. 67, 390–397 (1993). PubMed PMC

Hogle J. M., Chow M., Filman D. J., Three-dimensional structure of poliovirus at 2.9 A resolution. Science 229, 1358–1365 (1985). PubMed

Muckelbauer J. K., et al. ., Structure determination of coxsackievirus B3 to 3.5 A resolution. Acta Crystallogr. D Biol. Crystallogr. 51, 871–887 (1995). PubMed

Hendry E., et al. ., The crystal structure of coxsackievirus A9: New insights into the uncoating mechanisms of enteroviruses. Structure 7, 1527–1538 (1999). PubMed

Xiao C., et al. ., The crystal structure of coxsackievirus A21 and its interaction with ICAM-1. Structure 13, 1019–1033 (2005). PubMed

McFadden E. R. Jr. et al. ., Thermal mapping of the airways in humans. J. Appl. Physiol. 58, 564–570 (1985). PubMed

Xing L., et al. ., Distinct cellular receptor interactions in poliovirus and rhinoviruses. EMBO J. 19, 1207–1216 (2000). PubMed PMC

McClelland A., et al. ., Identification of monoclonal antibody epitopes and critical residues for rhinovirus binding in domain 1 of intercellular adhesion molecule 1. Proc. Natl. Acad. Sci. U.S.A. 88, 7993–7997 (1991). PubMed PMC

Sun M. A., et al. ., Prediction of reversible disulfide based on features from local structural signatures. BMC Genomics 18, 279 (2017). PubMed PMC

Register R. B., Uncapher C. R., Naylor A. M., Lineberger D. W., Colonno R. J., Human-murine chimeras of ICAM-1 identify amino acid residues critical for rhinovirus and antibody binding. J. Virol. 65, 6589–6596 (1991). PubMed PMC

Verdaguer N., Fita I., Reithmayer M., Moser R., Blaas D., X-ray structure of a minor group human rhinovirus bound to a fragment of its cellular receptor protein. Nat. Struct. Mol. Biol. 11, 429–434 (2004). PubMed

Li Q., Yafal A. G., Lee Y. M., Hogle J., Chow M., Poliovirus neutralization by antibodies to internal epitopes of VP4 and VP1 results from reversible exposure of these sequences at physiological temperature. J. Virol. 68, 3965–3970 (1994). PubMed PMC

Lewis J. K., Bothner B., Smith T. J., Siuzdak G., Antiviral agent blocks breathing of the common cold virus. Proc. Natl. Acad. Sci. U.S.A. 95, 6774–6778 (1998). PubMed PMC

Škubník K., et al. ., Capsid opening enables genome release of iflaviruses. Sci. Adv. 7, eabd7130 (2021). PubMed PMC

Bostina M., Levy H., Filman D. J., Hogle J. M., Poliovirus RNA is released from the capsid near a twofold symmetry axis. J. Virol. 85, 776–783 (2011). PubMed PMC

Strauss M., Levy H. C., Bostina M., Filman D. J., Hogle J. M., RNA transfer from poliovirus 135S particles across membranes is mediated by long umbilical connectors. J. Virol. 87, 3903–3914 (2013). PubMed PMC

Zheng S. Q., et al. ., MotionCor2: Anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017). PubMed PMC

Zhang K., Gctf: Real-time CTF determination and correction. J. Struct. Biol. 193, 1–12 (2016). PubMed PMC

Wagner T., et al. ., SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun. Biol. 2, 218 (2019). PubMed PMC

Scheres S. H., A Bayesian view on cryo-EM structure determination. J. Mol. Biol. 415, 406–418 (2012). PubMed PMC

Russo C. J., Henderson R., Ewald sphere correction using a single side-band image processing algorithm. Ultramicroscopy 187, 26–33 (2018). PubMed PMC

de la Rosa-Trevín J. M., et al. ., Scipion: A software framework toward integration, reproducibility and validation in 3D electron microscopy. J. Struct. Biol. 195, 93–99 (2016). PubMed

Vilas J. L., et al. ., MonoRes: Automatic and accurate estimation of local resolution for electron microscopy maps. Structure 26, 337–344.e4 (2018). PubMed

Ramírez-Aportela E., et al. ., Automatic local resolution-based sharpening of cryo-EM maps. Bioinformatics 36, 765–772 (2020). PubMed PMC

Kleywegt G. J., Jones T. A., xdlMAPMAN and xdlDATAMAN–Programs for reformatting, analysis and manipulation of biomacromolecular electron-density maps and reflection data sets. Acta Crystallogr. D Biol. Crystallogr. 52, 826–828 (1996). PubMed

Potterton E., Briggs P., Turkenburg M., Dodson E., A graphical user interface to the CCP4 program suite. Acta Crystallogr. D Biol. Crystallogr. 59, 1131–1137 (2003). PubMed

Pettersen E. F., et al. ., UCSF Chimera–A visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004). PubMed

Dong Y., et al. ., Antibody-induced uncoating of human rhinovirus B14. Proc. Natl. Acad. Sci. U.S.A. 114, 8017–8022 (2017). PubMed PMC

Murshudov G. N., et al. ., REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr. D Biol. Crystallogr. 67, 355–367 (2011). PubMed PMC

Emsley P., Cowtan K., Coot: Model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004). PubMed

Adams P. D., et al. ., PHENIX: A comprehensive python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010). PubMed PMC

Croll T. I., ISOLDE: A physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D Struct. Biol. 74, 519–530 (2018). PubMed PMC

Chen V. B., et al. ., MolProbity: All-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010). PubMed PMC

Barad B. A., et al. ., EMRinger: Side chain-directed model and map validation for 3D cryo-electron microscopy. Nat. Methods 12, 943–946 (2015). PubMed PMC

Xiao C., Rossmann M. G., Interpretation of electron density with stereographic roadmap projections. J. Struct. Biol. 158, 182–187 (2007). PubMed PMC

Madeira F., et al. ., The EMBL-EBI search and sequence analysis tools APIs in 2019. Nucleic Acids Res. 47, W636–W641 (2019). PubMed PMC

Waterhouse A. M., Procter J. B., Martin D. M., Clamp M., Barton G. J., Jalview Version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009). PubMed PMC

Najít záznam

Citační ukazatele

Nahrávání dat ...

Možnosti archivace

Nahrávání dat ...