The SARS-CoV-2 nucleocapsid phosphoprotein forms mutually exclusive condensates with RNA and the membrane-associated M protein

• Published in: Nature communications 2021-01, Vol.12 (1), p.502-502, Article 502
• Main Authors: Lu, Shan, Ye, Qiaozhen, Singh, Digvijay, Cao, Yong, Diedrich, Jolene K., Yates, John R., Villa, Elizabeth, Cleveland, Don W., Corbett, Kevin D.
• Format: Article
• Language: English
• Subjects: 101/58; 14; 14/28; 14/63; 631/326/596/4130; 631/45/500; 82/83; Arginine; Binding; Capsids; Cell Membrane - virology; Compartments; Condensates; Coronavirus Nucleocapsid Proteins - chemistry; Coronavirus Nucleocapsid Proteins - genetics; Coronavirus Nucleocapsid Proteins - metabolism; COVID-19 - genetics; COVID-19 - metabolism; COVID-19 - virology; Dimerization; DNA Helicases - genetics; DNA Helicases - metabolism; Domains; Genomes; Genomics; Granular materials; Humanities and Social Sciences; Humans; Immune response; Liquid phases; M protein; Membrane proteins; Membranes; multidisciplinary; N protein; Nucleocapsids; Packaging; Phase separation; Phosphoproteins - chemistry; Phosphoproteins - genetics; Phosphoproteins - metabolism; Phosphorylation; Physical properties; Poly-ADP-Ribose Binding Proteins - genetics; Poly-ADP-Ribose Binding Proteins - metabolism; Protein Binding; Protein Domains; Proteins; Ribonucleic acid; RNA; RNA Helicases - genetics; RNA Helicases - metabolism; RNA Recognition Motif Proteins - genetics; RNA Recognition Motif Proteins - metabolism; RNA, Viral - genetics; RNA, Viral - metabolism; SARS-CoV-2 - chemistry; SARS-CoV-2 - genetics; SARS-CoV-2 - metabolism; Science; Science (multidisciplinary); Serine; Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Viral Matrix Proteins - chemistry; Viral Matrix Proteins - genetics; Viral Matrix Proteins - metabolism; Virions
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-20768-y

The multifunctional nucleocapsid (N) protein in SARS-CoV-2 binds the ~30 kb viral RNA genome to aid its packaging into the 80–90 nm membrane-enveloped virion. The N protein is composed of N-terminal RNA-binding and C-terminal dimerization domains that are flanked by three intrinsically disordered regions. Here we demonstrate that the N protein’s central disordered domain drives phase separation with RNA, and that phosphorylation of an adjacent serine/arginine rich region modulates the physical properties of the resulting condensates. In cells, N forms condensates that recruit the stress granule protein G3BP1, highlighting a potential role for N in G3BP1 sequestration and stress granule inhibition. The SARS-CoV-2 membrane (M) protein independently induces N protein phase separation, and three-component mixtures of N + M + RNA form condensates with mutually exclusive compartments containing N + M or N + RNA, including annular structures in which the M protein coats the outside of an N + RNA condensate. These findings support a model in which phase separation of the SARS-CoV-2 N protein contributes both to suppression of the G3BP1-dependent host immune response and to packaging genomic RNA during virion assembly. The SARS-CoV-2 nucleocapsid (N) protein binds the viral RNA genome and contains two ordered domains flanked by three intrinsically-disordered regions. Here, the authors show that RNA binding induces liquid-liquid phase separation of N, which is driven by its central intrinsically-disordered region and is modulated by phosphorylation. The SARS-CoV-2 Membrane (M) protein also phase-separates with N, and three-component mixtures of N + M + RNA form mutually exclusive compartments containing N + M or N + RNA.