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

Jasmine Cubuk, Jhullian J. Alston, J. Jeremías Incicco, Sukrit Singh, Melissa D. Stuchell-Brereton, Michael D. Ward, Maxwell I. Zimmerman, Neha Vithani, Daniel Griffith, Jason A. Wagoner, Gregory R. Bowman, Kathleen B. Hall, Andrea Soranno () and Alex S. Holehouse ()
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Jasmine Cubuk: Washington University School of Medicine
Jhullian J. Alston: Washington University School of Medicine
J. Jeremías Incicco: Washington University School of Medicine
Sukrit Singh: Washington University School of Medicine
Melissa D. Stuchell-Brereton: Washington University School of Medicine
Michael D. Ward: Washington University School of Medicine
Maxwell I. Zimmerman: Washington University School of Medicine
Neha Vithani: Washington University School of Medicine
Daniel Griffith: Washington University School of Medicine
Jason A. Wagoner: Stony Brook University
Gregory R. Bowman: Washington University School of Medicine
Kathleen B. Hall: Washington University School of Medicine
Andrea Soranno: Washington University School of Medicine
Alex S. Holehouse: Washington University School of Medicine

Nature Communications, 2021, vol. 12, issue 1, 1-17

Abstract: Abstract 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.

Date: 2021
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DOI: 10.1038/s41467-021-21953-3

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