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

Cubuk, J.; Alston, J. J.; Incicco, J. J.; Singh, S.; Stuchell-Brereton, M. D.; Ward, M. D.; Zimmerman, M. I.; Vithani, N.; Griffith, D.; Wagoner, J. A.; Bowman, G. R.; Hall, K. B.; Soranno, A.; Holehouse, A. S.

doi:10.1101/2020.06.17.158121

bioRxiv · 10.1101/2020.06.17.158121

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

Cubuk, J.·Alston, J. J.·Incicco, J. J.·Singh, S.·Stuchell-Brereton, M. D.·Ward, M. D.·Zimmerman, M. I.·Vithani, N.·Griffith, D.·Wagoner, J. A.·Bowman, G. R.·Hall, K. B.·Soranno, A.·Holehouse, A. S.

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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.

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Cubuk, J., Alston, J. J., Incicco, J. J., Singh, S., Stuchell-Brereton, M. D., Ward, M. D., Zimmerman, M. I., Vithani, N., Griffith, D., Wagoner, J. A., Bowman, G. R., Hall, K. B., Soranno, A., Holehouse, A. S.. 2020-06-18. The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. https://doi.org/10.1101/2020.06.17.158121

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