title: Revealing the density of encoded functions in a viral RNA.
abstract: We present direct experimental evidence that assembly of a single-stranded RNA virus occurs via a packaging signal-mediated mechanism. We show that the sequences of coat protein recognition motifs within multiple, dispersed, putative RNA packaging signals, as well as their relative spacing within a genomic fragment, act collectively to influence the fidelity and yield of capsid self-assembly in vitro. These experiments confirm that the selective advantages for viral yield and encapsidation specificity, predicted from previous modeling of packaging signal-mediated assembly, are found in Nature. Regions of the genome that act as packaging signals also function in translational and transcriptional enhancement, as well as directly coding for the coat protein, highlighting the density of encoded functions within the viral RNA. Assembly and gene expression are therefore direct molecular competitors for different functional folds of the same RNA sequence. The strongest packaging signal in the test fragment, encodes a region of the coat protein that undergoes a conformational change upon contact with packaging signals. A similar phenomenon occurs in other RNA viruses for which packaging signals are known. These contacts hint at an even deeper density of encoded functions in viral RNA, which if confirmed, would have profound consequences for the evolution of this class of pathogens.
authors: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom;
authors: Nikesh
authors: N
authors: Patel
authors: York Centre for Complex Systems Analysis, and Departments of Mathematics and Biology, University of York, York YO10 5DD, United Kingdom;
authors: Eric C
authors: EC
authors: Dykeman
authors: Division of Biology, Imperial College London, London SW7 2AZ, United Kingdom;
authors: Robert H A
authors: RH
authors: Coutts
authors: Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norfolk NR4 7UH, United Kingdom; and.
authors: George P
authors: GP
authors: Lomonossoff
authors: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom;
authors: David J
authors: DJ
authors: Rowlands
authors: Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxon OX11 0FA, United Kingdom.
authors: Simon E V
authors: SE
authors: Phillips
authors: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom;
authors: Neil
authors: N
authors: Ranson
authors: York Centre for Complex Systems Analysis, and Departments of Mathematics and Biology, University of York, York YO10 5DD, United Kingdom;
authors: Reidun
authors: R
authors: Twarock
authors: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom;
authors: Roman
authors: R
authors: Tuma
authors: Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; p.g.stockley@leeds.ac.uk.
authors: Peter G
authors: PG
authors: Stockley
mesh_terms: D036022:Capsid Proteins / Q000378:metabolism; D012328:RNA Viruses / Q000235:genetics* / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D055672:Static Electricity
chemical_list: D036022:Capsid Proteins; D012367:RNA, Viral
keywords: packaging signal; satellite tobacco necrosis virus; single-molecule fluorescence correlation spectroscopy; virus assembly
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