Sindbis virus nucleocapsid assembly: RNA folding promotes capsid protein dimerization

Area of Science:

• Virology
• Structural Biology
• Molecular Biology

Background:

• Sindbis virus nucleocapsid assembly initiates with capsid protein recognition of a specific RNA encapsidation signal.
• Previous studies localized the signal to a 132-nucleotide region and mapped RNA binding to the capsid protein's central domain.
• The mechanism linking RNA binding to ordered capsid protein oligomerization and assembly remained unclear.

Purpose of the Study:

• To investigate the molecular mechanism by which Sindbis virus capsid protein binding to the encapsidation signal leads to nucleocapsid core assembly.
• To characterize the interaction between the capsid protein and its cognate RNA signal.

Main Methods:

• Development of a mobility shift assay to study the RNA-protein interaction.
• Characterization of a 32 amino acid peptide mimicking capsid protein RNA recognition.
• Mutational analysis of the encapsidation signal RNA and observation of RNA conformational changes.

Main Results:

• A 32 amino acid peptide specifically recognized the Sindbis virus encapsidation signal RNA with high affinity (K(d)(app) = 12 nM).
• Capsid protein binding induced a conformational change in the RNA and led to peptide dimerization.
• Efficient binding required specific RNA secondary structures, particularly two purine-rich loops, but not specific base identities within helices.

Conclusions:

• The encapsidation signal RNA adopts a highly folded structure upon capsid protein binding.
• This RNA folding process is critical for directing the initial events of nucleocapsid assembly.
• A model is proposed where RNA structural transitions nucleate capsid protein oligomerization and viral core formation.