Sequence-Specific, RNA–Protein Interactions Overcome Electrostatic Barriers Preventing Assembly of Satellite Tobacco Necrosis Virus Coat Protein

Autor: Arwen R. Pearson, Robert H.A. Coutts, Robert J. Ford, Saskia E. Bakker, Simon E. V. Phillips, Amy M. Barker, Peter G. Stockley, Neil A. Ranson
Rok vydání: 2013
Předmět:
Models
Molecular
ssRNA
single-stranded RNA
Protein Conformation
Molecular Sequence Data
svAUC
sedimentation velocity analytical ultracentrifugation
Protein Data Bank (RCSB PDB)
virus assembly
Sequence (biology)
Genome
Viral
Biology
PS
packaging signal
Article
03 medical and health sciences
Protein structure
Capsid
Structural Biology
PDB
Protein Data Bank
Amino Acid Sequence
Binding site
TCV
turnip crinkle virus
TEM
transmission electron microscopy
Peptide sequence
Molecular Biology
030304 developmental biology
0303 health sciences
Binding Sites
030306 microbiology
Capsomere
RNA
CP
coat protein
Molecular biology
3. Good health
STNV
satellite tobacco necrosis virus
VLP
virus-like particle
smFCS
single-molecule fluorescence correlation spectroscopy
Biophysics
Nucleic Acid Conformation
RNA
Viral
RNA–protein interactions
Capsid Proteins
Tobacco necrosis satellite virus
molecular mechanism
Zdroj: Journal of Molecular Biology
ISSN: 0022-2836
DOI: 10.1016/j.jmb.2013.01.004
Popis: We have examined the roles of RNA–coat protein (CP) interactions in the assembly of satellite tobacco necrosis virus (STNV). The viral genomic RNA encodes only the CP, which comprises a β-barrel domain connected to a positively charged N-terminal extension. In the previous crystal structures of this system, the first 11 residues of the protein are disordered. Using variants of an RNA aptamer sequence isolated against the CP, B3, we have studied the sequence specificity of RNA-induced assembly. B3 consists of a stem–loop presenting the tetra-loop sequence ACAA. There is a clear preference for RNAs encompassing this loop sequence, as measured by the yield of T = 1 capsids, which is indifferent to sequences within the stem. The B3-containing virus-like particle has been crystallised and its structure was determined to 2.3 Å. A lower-resolution map encompassing density for the RNA has also been calculated. The presence of B3 results in increased ordering of the N-terminal helices located at the particle 3-fold axes, which extend by roughly one and a half turns to encompass residues 8–11, including R8 and K9. Under assembly conditions, STNV CP in the absence of RNA is monomeric and does not self-assemble. These facts suggest that a plausible model for assembly initiation is the specific RNA-induced stabilisation of a trimeric capsomere. The basic nature of the helical extension suggests that electrostatic repulsion between CPs prevents assembly in the absence of RNA and that this barrier is overcome by correct placement of appropriately orientated helical RNA stems. Such a mechanism would be consistent with the data shown here for assembly with longer RNA fragments, including an STNV genome. The results are discussed in light of a first stage of assembly involving compaction of the genomic RNA driven by multiple RNA packaging signal–CP interactions.
Graphical Abstract Highlights ► Sequence specificity in satellite virus assembly. ► RNA-induced conformational change in a viral CP. ► RNA binding overcomes an electrostatic barrier to CP assembly. ► RNAs containing multiple preferred stem–loops assemble more efficiently. ► Evidence supports the existence of packaging signals in single-stranded RNA genomes.
Databáze: OpenAIRE
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