X-ray structure of empty capsid: insights into the mechanism of uncoating and RNA release in dicistroviruses Free

Abstract

In viruses, uncoating and RNA release are two key steps of successfully infecting a target cell. During these steps, the capsid must undergo the necessary conformational changes to allow RNA egress. Despite their importance, these processes are poorly understood in the family . Here, we used X-ray crystallography to solve the atomic structure of a (TrV) empty particle (Protein Data Bank ID 5L7O), which is the resulting capsid after RNA release. It is observed that the overall shape of the capsid and of the three individual proteins is maintained in comparison with the mature virion. Furthermore, no channels indicative of RNA release are formed in the TrV empty particle. However, the most prominent change in the empty particle when compared with the mature virion is the loss of order in the N-terminal domain of the VP2 protein. In mature virions, the VP2 N-terminal domain of one pentamer is swapped with its twofold related copy in an adjacent pentamer, thereby stabilizing the binding between the pentamers. The loss of these interactions allows us to propose that RNA release may take place through transient flipping-out of pentameric subunits. The lower number of stabilizing interactions between the pentamers and the lack of formation of new holes support this model. This model differs from the currently accepted model for rhinoviruses and enteroviruses, in which genome externalization occurs by extrusion of the RNA through capsid channels.

Loading

Article metrics loading...

/content/journal/jgv/10.1099/jgv.0.000580
2016-10-13
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/jgv/97/10/2769.html?itemId=/content/journal/jgv/10.1099/jgv.0.000580&mimeType=html&fmt=ahah

References

  1. Agirre J., Aloria K., Arizmendi J. M., Iloro I., Elortza F., Sánchez-Eugenia R., Marti G. A., Neumann E., Rey F. A., Guérin D. M. 2011; Capsid protein identification and analysis of mature Triatoma virus (TrV) virions and naturally occurring empty particles. Virology 409:91–101 [View Article][PubMed]
    [Google Scholar]
  2. Agirre J., Goret G., LeGoff M., Sánchez-Eugenia R., Marti G. A., Navaza J., Guérin D. M., Neumann E. 2013; Cryo-electron microscopy reconstructions of triatoma virus particles: a clue to unravel genome delivery and capsid disassembly. J Gen Virol 94:1058–1068 [View Article][PubMed]
    [Google Scholar]
  3. Bakker S. E., Groppelli E., Pearson A. R., Stockley P. G., Rowlands D. J., Ranson N. A. 2014; Limits of structural plasticity in a picornavirus capsid revealed by a massively expanded equine rhinitis a virus particle. J Virol 88:6093–6099 [View Article][PubMed]
    [Google Scholar]
  4. Baxt B., Bachrach H. L. 1980; Early interactions of foot-and-mouth disease virus with cultured cells. Virology 104:42–55 [View Article][PubMed]
    [Google Scholar]
  5. Belnap D. M., Filman D. J., Trus B. L., Cheng N., Booy F. P., Conway J. F., Curry S., Hiremath C. N., Tsang S. K. et al. 2000; Molecular tectonic model of virus structural transitions: the putative cell entry states of poliovirus. J Virol 74:1342–1354 [View Article][PubMed]
    [Google Scholar]
  6. Bennett M. J., Schlunegger M. P., Eisenberg D. 1995; 3D domain swapping: a mechanism for oligomer assembly. Protein Sci 4:2455–2468 [View Article][PubMed]
    [Google Scholar]
  7. Bonning B. C., Miller W. A. 2010; Dicistroviruses. Annu Rev Entomol 55:129–150 [View Article][PubMed]
    [Google Scholar]
  8. Bostina M., Levy H., Filman D. J., Hogle J. M. 2011; Poliovirus RNA is released from the capsid near a twofold symmetry axis. J Virol 85:776–783 [View Article][PubMed]
    [Google Scholar]
  9. Brown F., Cartwright B. 1961; Dissociation of foot-and-mouth disease virus into its nucleic acid and protein components. Nature 192:1163–1164 [View Article][PubMed]
    [Google Scholar]
  10. Bubeck D., Filman D. J., Cheng N., Steven A. C., Hogle J. M., Belnap D. M. 2005; The structure of the poliovirus 135S cell entry intermediate at 10-angstrom resolution reveals the location of an externalized polypeptide that binds to membranes. J Virol 79:7745–7755 [View Article][PubMed]
    [Google Scholar]
  11. Cowtan K., Main P. 1998; Miscellaneous algorithms for density modification. Acta Crystallogr Sect D Biol Crystallogr 54:487–493 [View Article]
    [Google Scholar]
  12. Czibener C., La Torre J. L., Muscio O. A., Ugalde R. A., Scodeller E. A. 2000; Nucleotide sequence analysis of Triatoma virus shows that it is a member of a novel group of insect RNA viruses. J Gen Virol 81:1149–1154 [View Article][PubMed]
    [Google Scholar]
  13. Emsley P., Lohkamp B., Scott W. G., Cowtan K. 2010; Features and development of Coot. Acta Crystallogr Sect D Biol Crystallogr 66:486–501 [View Article]
    [Google Scholar]
  14. Garriga D., Pickl-Herk A., Luque D., Wruss J., Castón J. R., Blaas D., Verdaguer N. 2012; Insights into minor group rhinovirus uncoating: the X-ray structure of the HRV2 empty capsid. PLoS Pathog 8:e1002473 [View Article][PubMed]
    [Google Scholar]
  15. Grant R. A., Hiremath C. N., Filman D. J., Syed R., Andries K., Hogle J. M. 1994; Structures of poliovirus complexes with anti-viral drugs: implications for viral stability and drug design. Curr Biol 4:784–797 [View Article][PubMed]
    [Google Scholar]
  16. Grayson M., Clayton J., Coura J. R., Viñas P. A., Petherick A. 2010; Chagas disease. Nature 115:S3–S22 [CrossRef]
    [Google Scholar]
  17. Hewat E. A., Neumann E., Blaas D. 2002; The concerted conformational changes during human rhinovirus 2 uncoating. Mol Cell 10:317–326 [View Article][PubMed]
    [Google Scholar]
  18. Hewat E. A., Blaas D. 2004; Cryoelectron microscopy analysis of the structural changes associated with human rhinovirus type 14 uncoating. J Virol 78:2935–2942 [View Article][PubMed]
    [Google Scholar]
  19. Kabsch W. 2010; XDS. Acta Crystallogr Sect D Biol Crystallogr 66:125–132 [CrossRef]
    [Google Scholar]
  20. Karplus P. A., Diederichs K. 2012; Linking crystallographic model and data quality. Science 336:1030–1033 [View Article][PubMed]
    [Google Scholar]
  21. Levy H. C., Bostina M., Filman D. J., Hogle J. M. 2010; Catching a virus in the act of RNA release: a novel poliovirus uncoating intermediate characterized by cryo-electron microscopy. J Virol 84:4426–4441 [View Article][PubMed]
    [Google Scholar]
  22. Marti G. A., Echeverría M. G., Susevich M. L., Ceccarelli S., Balsalobre A., Rabinovich G. M. J., Solorzano E., Monroy C. et al. 2013; Exploration for Triatoma virus (TrV) infection in laboratory-reared triatomines of Latin America: a collaborative study*. Int J Trop Insect Sci 33:294–304 [CrossRef]
    [Google Scholar]
  23. Mayo M. A. 2002; Virus taxonomy – Houston 2002. Arch Virol 147:1071–1076 [View Article][PubMed]
    [Google Scholar]
  24. McCoy A. J., Grosse-Kunstleve R. W., Adams P. D., Winn M. D., Storoni L. C., Read R. J. 2007; Phaser crystallographic software. J Appl Crystallogr 40:658–674 [View Article][PubMed]
    [Google Scholar]
  25. Murshudov G. N., Skubák P., Lebedev A. A., Pannu N. S., Steiner R. A., Nicholls R. A., Winn M. D., Long F., Vagin A. A. 2011; REFMAC 5 for the refinement of macromolecular crystal structures. Acta Crystallogr Sect D Biol Crystallogr 67:355–367 [View Article]
    [Google Scholar]
  26. Muscio O. A., La Torre J. L., Scodeller E. A. 1988; Characterization of Triatoma virus, a picorna-like virus isolated from the triatomine bug Triatoma infestans . J Gen Virol 69:2929–2934 [View Article][PubMed]
    [Google Scholar]
  27. Muscio O. A., La Torre J., Bonder M. A., Scodeller E. A. 1997; Triatoma virus pathogenicity in laboratory colonies of Triatoma infestans (Hemiptera: Reduviidae). J Med Entomol 34:253–256 [View Article][PubMed]
    [Google Scholar]
  28. Panjwani A., Strauss M., Gold S., Wenham H., Jackson T., Chou J. J., Rowlands D. J., Stonehouse N. J., Hogle J. M., Tuthill T. J. 2014; Capsid protein VP4 of human rhinovirus induces membrane permeability by the formation of a size-selective multimeric pore. PLoS Pathog 10:e1004294 [View Article][PubMed]
    [Google Scholar]
  29. Pettersen E. F., Goddard T. D., Huang C. C., Couch G. S., Greenblatt D. M., Meng E. C., Ferrin T. E. 2004; UCSF Chimera – a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612 [View Article][PubMed]
    [Google Scholar]
  30. Pickl-Herk A., Luque D., Vives-Adrián L., Querol-Audí J., Garriga D., Trus B. L., Verdaguer N., Blaas D., Castón J. R. 2013; 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 [View Article][PubMed]
    [Google Scholar]
  31. Querido J. F. B., Agirre J., Marti G. A., Guérin D. M. A., Silva M. S. 2013; Molecular techniques for dicistrovirus detection without RNA extraction or purification. Biomed Res Int 2013:218593 [CrossRef]
    [Google Scholar]
  32. Ren J., Wang X., Hu Z., Gao Q., Sun Y., Li X., Porta C., Walter T. S., Gilbert R. J. et al. 2013; Picornavirus uncoating intermediate captured in atomic detail. Nat Commun 4:1929 [View Article][PubMed]
    [Google Scholar]
  33. Rossmann M. G., He Y., Kuhn R. J. 2002; Picornavirus–receptor interactions. Trends Microbiol 10:324–331 [View Article][PubMed]
    [Google Scholar]
  34. Shingler K. L., Yoder J. L., Carnegie M. S., Ashley R. E., Makhov A. M., Conway J. F., Hafenstein S. 2013; The enterovirus 71 A-particle forms a gateway to allow genome release: a cryoEM study of picornavirus uncoating. PLoS Pathog 9:e1003240 [View Article][PubMed]
    [Google Scholar]
  35. Smith T. J., Kremer M. J., Luo M., Vriend G., Arnold E., Kamer G., Rossmann M. G., McKinlay M. A., Diana G. D., Otto M. J. 1986; The site of attachment in human rhinovirus 14 for antiviral agents that inhibit uncoating. Science 233:1286–1293 [View Article][PubMed]
    [Google Scholar]
  36. Smyth M., Tate J., Hoey E., Lyons C., Martin S., Stuart D. 1995; Implications for viral uncoating from the structure of bovine enterovirus. Struct Biol 2:224–231 [View Article]
    [Google Scholar]
  37. Snijder J., Uetrecht C., Rose R. J., Sanchez-Eugenia R., Marti G. A., Agirre J., Guérin D. M., Wuite G. J., Heck A. J., Roos W. H. 2013; Probing the biophysical interplay between a viral genome and its capsid. Nat Chem 5:502–509 [View Article][PubMed]
    [Google Scholar]
  38. Squires G., Pous J., Agirre J., Rozas-Dennis G. S., Costabel M. D., Marti G. A., Navaza J., Bressanelli S., Guérin D. M., Rey F. A. 2013; Structure of the Triatoma virus capsid. Acta Crystallogr D Biol Crystallogr 69:1026–1037 [View Article][PubMed]
    [Google Scholar]
  39. Sánchez-Eugenia R., Goikolea J., Gil-Cartón D., Sánchez-Magraner L., Guérin D. M. A. 2015a; Triatoma virus recombinant VP4 protein induces membrane permeability through dynamic pores. J Virol 89:4645–4654 [View Article]
    [Google Scholar]
  40. Sánchez-Eugenia R., Méndez F., Querido J. F. B., Silva M. S., Guérin D. M., Rodríguez J. F. 2015b; Triatoma virus structural polyprotein expression, processing and assembly into virus-like particles. J Gen Virol 96:64–73 [View Article]
    [Google Scholar]
  41. Tate J., Liljas L., Scotti P., Christian P., Lin T., Johnson J. E. 1999; The crystal structure of cricket paralysis virus: the first view of a new virus family. Nat Struct Biol 6:765–774 [View Article][PubMed]
    [Google Scholar]
  42. Tina K. G., Bhadra R., Srinivasan N. 2007; PIC: protein interactions calculator. Nucleic Acids Res 35:W473–W476 [View Article][PubMed]
    [Google Scholar]
  43. Tuthill T. J., Harlos K., Walter T. S., Knowles N. J., Groppelli E., Rowlands D. J., Stuart D. I., Fry E. E. 2009; Equine rhinitis a virus and its low pH empty particle: clues towards an aphthovirus entry mechanism?. PLoS Pathog 5:e1000620 [View Article][PubMed]
    [Google Scholar]
  44. Wang X., Peng W., Ren J., Hu Z., Xu J., Lou Z., Li X., Yin W., Shen X. et al. 2012; A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71. Nat Struct Mol Biol 19:424–429 [View Article][PubMed]
    [Google Scholar]
  45. Wang X., Ren J., Gao Q., Hu Z., Sun Y., Li X., Rowlands D. J., Yin W., Wang J. et al. 2015; Hepatitis A virus and the origins of picornaviruses. Nature 517:85–88 [View Article][PubMed]
    [Google Scholar]
  46. Xing L., Casasnovas J. M., Cheng R. H. 2003; Structural analysis of human rhinovirus complexed with ICAM-1 reveals the dynamics of receptor-mediated virus uncoating. J Virol 77:6101–6107 [View Article][PubMed]
    [Google Scholar]
  47. Zhang X., Settembre E., Xu C., Dormitzer P. R., Bellamy R., Harrison S. C., Grigorieff N. 2008; Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction. Proc Natl Acad Sci U S A 105:1867–1872 [View Article][PubMed]
    [Google Scholar]
  48. Zhao R., Hadfield A. T., Kremer M. J., Rossmann M. G. 1997; Cations in human rhinoviruses. Virology 227:13–23 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/jgv.0.000580
Loading
/content/journal/jgv/10.1099/jgv.0.000580
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed