UCSF

The nucleocapsid (N) protein of coronaviruses serves two major functions: compaction of the RNA genome in the virion and regulation of viral gene transcription. It is not clear how the N protein mediates such distinct functions. The N protein contains two RNA-binding domains surrounded by regions of intrinsic disorder. Phosphorylation of the central disordered region promotes the protein’s transcriptional function, but the underlying mechanism is not known. Here we show that the N protein of SARS-CoV-2, together with viral RNA, forms biomolecular condensates and ordered RNA packaging units that are both regulated by phosphorylation. Unmodified N protein forms partially ordered gel-like condensates and discrete 15-nm viral ribonucleoprotein (vRNP) complexes based on multivalent RNA-protein and protein-protein interactions. Phosphorylation reduces these interactions, generating a more liquid-like droplet and a less compact vRNP. We propose that distinct oligomeric states support the two functions of the N protein: unmodified protein forms a structured oligomer that is suited for nucleocapsid assembly, and phosphorylated protein forms a liquid-like compartment for viral genome processing.