title: A two-stage mechanism of viral RNA compaction revealed by single molecule fluorescence.
abstract: Long RNAs often exist as multiple conformers in equilibrium. For the genomes of single-stranded RNA viruses, one of these conformers must include a compacted state allowing the RNA to be confined within the virion. We have used single molecule fluorescence correlation spectroscopy to monitor the conformations of viral genomes and sub-fragments in the absence and presence of coat proteins. Cognate RNA-coat protein interactions in two model viruses cause a rapid collapse in the hydrodynamic radii of their respective RNAs. This is caused by protein binding at multiple sites on the RNA that facilitate additional protein-protein contacts. The collapsed species recruit further coat proteins to complete capsid assembly with great efficiency and fidelity. The specificity in RNA-coat protein interactions seen at single-molecule concentrations reflects the packaging selectivity seen for such viruses in vivo. This contrasts with many in vitro reassembly measurements performed at much higher concentrations. RNA compaction by coat protein or polycation binding are distinct processes, implying that defined RNA-coat protein contacts are required for assembly.
authors: Astbury Centre for Structural Molecular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK.
authors: Alexander
authors: A
authors: Borodavka
authors: Roman
authors: R
authors: Tuma
authors: Peter G
authors: PG
authors: Stockley
mesh_terms: D036022:Capsid Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D002412:Cations / Q000737:chemistry / Q000378:metabolism; D016679:Genome, Viral; D017909:Levivirus / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D009690:Nucleic Acid Conformation; D011485:Protein Binding / Q000235:genetics; D059370:RNA Folding / Q000235:genetics* / Q000502:physiology; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D013050:Spectrometry, Fluorescence / Q000379:methods*; D025641:Tobacco necrosis satellite virus / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D014771:Virion / Q000235:genetics / Q000378:metabolism; D019065:Virus Assembly / Q000235:genetics* / Q000502:physiology
chemical_list: D036022:Capsid Proteins; D002412:Cations; D012367:RNA, Viral
keywords: RNA folding; single molecule fluorescence; viral genomes