Nucleocapsid protein of SARS-CoV-2 phase separates into RNA-rich polymerase-containing condensates

Nat Commun. 2020 Nov 27;11(1):6041. doi: 10.1038/s41467-020-19843-1.

Abstract

The etiologic agent of the Covid-19 pandemic is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The viral membrane of SARS-CoV-2 surrounds a helical nucleocapsid in which the viral genome is encapsulated by the nucleocapsid protein. The nucleocapsid protein of SARS-CoV-2 is produced at high levels within infected cells, enhances the efficiency of viral RNA transcription, and is essential for viral replication. Here, we show that RNA induces cooperative liquid-liquid phase separation of the SARS-CoV-2 nucleocapsid protein. In agreement with its ability to phase separate in vitro, we show that the protein associates in cells with stress granules, cytoplasmic RNA/protein granules that form through liquid-liquid phase separation and are modulated by viruses to maximize replication efficiency. Liquid-liquid phase separation generates high-density protein/RNA condensates that recruit the RNA-dependent RNA polymerase complex of SARS-CoV-2 providing a mechanism for efficient transcription of viral RNA. Inhibition of RNA-induced phase separation of the nucleocapsid protein by small molecules or biologics thus can interfere with a key step in the SARS-CoV-2 replication cycle.

Publication types

  • Research Support, Non-U.S. Gov't
  • Video-Audio Media

MeSH terms

  • Animals
  • Antiviral Agents / pharmacology
  • Antiviral Agents / therapeutic use
  • COVID-19 / epidemiology
  • COVID-19 / virology*
  • COVID-19 Drug Treatment
  • Coronavirus Nucleocapsid Proteins / antagonists & inhibitors
  • Coronavirus Nucleocapsid Proteins / metabolism*
  • Coronavirus RNA-Dependent RNA Polymerase / metabolism
  • HeLa Cells
  • Humans
  • Insecta
  • Intravital Microscopy
  • Microscopy, Fluorescence
  • Molecular Dynamics Simulation
  • Pandemics / prevention & control
  • Phosphoproteins / antagonists & inhibitors
  • Phosphoproteins / metabolism
  • RNA, Viral / antagonists & inhibitors
  • RNA, Viral / metabolism*
  • SARS-CoV-2 / drug effects
  • SARS-CoV-2 / physiology*
  • Viral Transcription / drug effects
  • Viral Transcription / physiology
  • Virus Replication / drug effects
  • Virus Replication / genetics

Substances

  • Antiviral Agents
  • Coronavirus Nucleocapsid Proteins
  • Phosphoproteins
  • RNA, Viral
  • nucleocapsid phosphoprotein, SARS-CoV-2
  • Coronavirus RNA-Dependent RNA Polymerase