Evolution of a fuzzy ribonucleoprotein complex in viral assembly

Area of Science:

• Virology
• Structural Biology
• Molecular Biology

Background:

• SARS-CoV-2 assembly involves the nucleocapsid (N) protein condensing viral RNA into ribonucleoprotein particles (RNPs).
• Previous biochemical and biophysical studies elucidated RNP architectural principles, highlighting cooperative protein-protein and protein-RNA interactions initiated by N protein oligomerization.

Purpose of the Study:

• To investigate the impact of nucleocapsid (N) protein mutations in SARS-CoV-2 variants of concern on RNP formation.
• To understand how these mutations influence viral fitness and host adaptation.

Main Methods:

• Utilized biophysical tools to analyze RNP formation.
• Employed virus-like particle assays to assess RNP assembly.
• Conducted reverse genetics experiments to evaluate the functional consequences of N protein mutations.

Main Results:

• Observed convergent evolution, with independent mutations strengthening existing N protein binding interfaces.
• Identified that the N:P13L mutation in Omicron variants creates a novel self-association interface, enhancing RNP assembly.
• Demonstrated increased viral fitness associated with these mutations.

Conclusions:

• N protein mutations in SARS-CoV-2 variants enhance RNP assembly and viral fitness through strengthened or novel interfaces.
• Hypothesize that polydisperse, fuzzy N-RNA clusters with distributed weak binding interfaces optimize reversible RNA condensation.
• Suggest this mechanism supports viral adaptation and evolution by allowing exploration of a large sequence space.