Viral uncoating is directional: exit of the genomic RNA in a common cold virus starts with the poly-(A) tail at the 3'-end

PLoS Pathog. 2013;9(4):e1003270. doi: 10.1371/journal.ppat.1003270. Epub 2013 Apr 4.

Abstract

Upon infection, many RNA viruses reorganize their capsid for release of the genome into the host cell cytosol for replication. Often, this process is triggered by receptor binding and/or by the acidic environment in endosomes. In the genus Enterovirus, which includes more than 150 human rhinovirus (HRV) serotypes causing the common cold, there is persuasive evidence that the viral RNA exits single-stranded through channels formed in the protein shell. We have determined the time-dependent emergence of the RNA ends from HRV2 on incubation of virions at 56°C using hybridization with specific oligonucleotides and detection by fluorescence correlation spectroscopy. We report that psoralen UV crosslinking prevents complete RNA release, allowing for identification of the sequences remaining inside the capsid. We also present the structure of uncoating intermediates in which parts of the RNA are condensed and take the form of a rod that is directed roughly towards a two-fold icosahedral axis, the presumed RNA exit point. Taken together, in contrast to schemes frequently depicted in textbooks and reviews, our findings demonstrate that exit of the RNA starts from the 3'-end. This suggests that packaging also occurs in an ordered manner resulting in the 3'-poly-(A) tail becoming located close to a position of pore formation during conversion of the virion into a subviral particle. This directional genome release may be common to many icosahedral non-enveloped single-stranded RNA viruses.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Capsid / chemistry
  • Capsid / metabolism
  • Cross-Linking Reagents / pharmacology
  • Ficusin / pharmacology
  • Genome, Viral
  • Humans
  • Nucleic Acid Conformation
  • Poly A / metabolism
  • Protein Conformation
  • RNA, Viral / genetics*
  • RNA, Viral / metabolism*
  • Rhinovirus / genetics
  • Rhinovirus / physiology*
  • Sequence Analysis, RNA
  • Ultraviolet Rays
  • Virus Assembly
  • Virus Internalization*
  • Virus Uncoating* / drug effects
  • Virus Uncoating* / genetics

Substances

  • Cross-Linking Reagents
  • RNA, Viral
  • Poly A
  • Ficusin

Grants and funding

This work was funded by the Austrian Science Foundation (FWF) P #20915-B13. SH and MK were supported by the DK ‘Structure and Interaction of Macromolecules’ funded by the Austrian Science Fund (FWF). 3-D image reconstruction and analysis was carried out by use of the Vienna Scientific Cluster (project 70121). Short stays in the laboratory of our collaborators José Caston and Daniel Luque in Madrid for discussion of the 3D-reconstruction process were funded by ‘Acciones Integradas’ provided by the Österreichischer Austausch Dienst (ÖAD). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.