Chaperone Activity of SARS-CoV-2 Nucleocapsid Protein: RNA Annealing and Destabilization Mechanisms

The recent global COVID-19 pandemic has prompted new research in coronaviruses. Despite the discovery of effective vaccines and therapeutic interventions, coronaviruses remain a threat to humans as the emergence of novel variants or new pathogenic coronaviruses is possible. The N protein or nucleocapsid protein, belonging to the virus’ essential proteins, is mainly involved in the compaction and protection of the viral genome. Here, we show that the SARS-CoV-2 N protein is a very efficient chaperone protein of nucleic acids that aggregates nucleic acids and anneals well-folded and complementary oligonucleotides hairpins in vitro. Using fluorescence and gel shift electrophoresis methods, we showed the high ability of the protein to destabilize nucleic acid secondary structure and to anneal nucleic acid strands. This last activity needs the full-length protein as we demonstrate that protein fragments, while they could display some activities, are considerably less efficient. However, the ability of the full-length protein to destabilize small double-stranded RNAs is poor. Our results show that the N protein possesses a chaperone activity similar to the HIV-1 NCp7 and NCp9 nucleocapsid proteins known as powerful nucleic acid chaperons.