Journal Article

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

Holehouse, Alex S., Ward, Michael D., Hall, Kathleen B., Incicco, J. Jeremías, Alston, Jhullian J., Vithani, Neha, Stuchell-Brereton, Melissa D., Wagoner, Jason A., Soranno, Andrea, Singh, Sukrit, Zimmerman, Maxwell I., Griffith, Daniel, Bowman, Gregory R., Cubuk, Jasmine

2021

Overview

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.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 631/114/2397 / 631/57/2265 / 631/57/2269 / Binding Sites / Broken symmetry / Coronavirus Nucleocapsid Proteins - chemistry / Coronavirus Nucleocapsid Proteins - metabolism / COVID-19 / 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 coronavirus 2 / Spectroscopy / Spectrum analysis