The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA

• Published in: Nature communications Vol. 12; no. 1; p. 1936
• Main Authors: Cubuk, Jasmine, Alston, Jhullian J., Incicco, J. Jeremías, Singh, Sukrit, Stuchell-Brereton, Melissa D., Ward, Michael D., Zimmerman, Maxwell I., Vithani, Neha, Griffith, Daniel, Wagoner, Jason A., Bowman, Gregory R., Hall, Kathleen B., Soranno, Andrea, Holehouse, Alex S.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 29.03.2021; Nature Publishing Group; Nature Portfolio
• Subjects: 631/114/2397; 631/57/2265; 631/57/2269; Binding Sites; Broken symmetry; Coronavirus Nucleocapsid Proteins - chemistry; Coronavirus Nucleocapsid Proteins - metabolism; COVID-19 - virology; Dimerization; Genomes; Humanities and Social Sciences; Liquid phases; Molecular Dynamics Simulation; multidisciplinary; N protein; Nucleocapsids; Packaging; Phase separation; Phosphoproteins - chemistry; Phosphoproteins - metabolism; Polymers; Protein Conformation; Protein Domains; Proteins; Ribonucleic acid; RNA; RNA, Viral - chemistry; RNA, Viral - metabolism; RNA-binding protein; SARS-CoV-2 - chemistry; SARS-CoV-2 - metabolism; Science; Science (multidisciplinary); Severe acute respiratory syndrome; Severe acute respiratory syndrome coronavirus 2; Spectroscopy; Spectrum analysis
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-21953-3

The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. The two folded domains interact minimally such that full-length N protein is a flexible and multivalent RNA-binding protein. N protein also undergoes liquid-liquid phase separation when mixed with RNA, and polymer theory predicts that the same multivalent interactions that drive phase separation also engender RNA compaction. We offer a simple symmetry-breaking model that provides a plausible route through which single-genome condensation preferentially occurs over phase separation, suggesting that phase separation offers a convenient macroscopic readout of a key nanoscopic interaction. SARS-CoV-2 nucleocapsid (N) protein is responsible for viral genome packaging. Here the authors employ single-molecule spectroscopy with all-atom simulations to provide the molecular details of N protein and show that it undergoes phase separation with RNA.