Degenerate RNA packaging signals in the genome of satellite tobacco necrosis virus: Implications for the assembly of a T = 1 capsid

Bunka, David H. J., Lane, Stephen W., Lane, Claire L., Dykeman, Eric C., Ford, Robert J., Barker, Amy M., Twarock, Reidun, Phillips, Simon E. V. and Stockley, Peter G. (2011) Degenerate RNA packaging signals in the genome of satellite tobacco necrosis virus: Implications for the assembly of a T = 1 capsid. Journal of Molecular Biology, 413 1: 51-65. doi:10.1016/j.jmb.2011.07.063


Author Bunka, David H. J.
Lane, Stephen W.
Lane, Claire L.
Dykeman, Eric C.
Ford, Robert J.
Barker, Amy M.
Twarock, Reidun
Phillips, Simon E. V.
Stockley, Peter G.
Title Degenerate RNA packaging signals in the genome of satellite tobacco necrosis virus: Implications for the assembly of a T = 1 capsid
Formatted title
Degenerate RNA packaging signals in the genome of satellite tobacco necrosis virus: Implications for the assembly of a T = 1 capsid
Journal name Journal of Molecular Biology   Check publisher's open access policy
ISSN 0022-2836
1089-8638
Publication date 2011-10
Sub-type Article (original research)
DOI 10.1016/j.jmb.2011.07.063
Volume 413
Issue 1
Start page 51
End page 65
Total pages 15
Place of publication London, United Kingdom
Publisher Academic Press
Language eng
Formatted abstract
Using a recombinant, T = 1 Satellite Tobacco Necrosis Virus (STNV)-like particle expressed in Escherichia coli, we have established conditions for in vitro disassembly and reassembly of the viral capsid. In vivo assembly is dependent on the presence of the coat protein (CP) N-terminal region, and in vitro assembly requires RNA. Using immobilised CP monomers under reassembly conditions with “free” CP subunits, we have prepared a range of partially assembled CP species for RNA aptamer selection. SELEX directed against the RNA-binding face of the STNV CP resulted in the isolation of several clones, one of which (B3) matches the STNV-1 genome in 16 out of 25 nucleotide positions, including across a statistically significant 10/10 stretch. This 10-base region folds into a stem–loop displaying the motif ACAA and has been shown to bind to STNV CP. Analysis of the other aptamer sequences reveals that the majority can be folded into stem–loops displaying versions of this motif. Using a sequence and secondary structure search motif to analyse the genomic sequence of STNV-1, we identified 30 stem–loops displaying the sequence motif AxxA. The implication is that there are many stem–loops in the genome carrying essential recognition features for binding STNV CP. Secondary structure predictions of the genomic RNA using Mfold showed that only 8 out of 30 of these stem–loops would be formed in the lowest-energy structure. These results are consistent with an assembly mechanism based on kinetically driven folding of the RNA.
Keyword Stnv
Selex
Genome
Assembly
Signals
Ms2 Coat Protein
3-Dimensional Structure
Mosaic-Virus
Angstrom Resolution
Refined Structure
Crystal-Structure
Aptamers
Complex
Bacteriophage-Ms2
Selection
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: School of Medicine Publications
 
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