Determination of host proteins composing the microenvironment of coronavirus replicase complexes by proximity-labeling

Elife. 2019 Jan 11:8:e42037. doi: 10.7554/eLife.42037.


Positive-sense RNA viruses hijack intracellular membranes that provide niches for viral RNA synthesis and a platform for interactions with host proteins. However, little is known about host factors at the interface between replicase complexes and the host cytoplasm. We engineered a biotin ligase into a coronaviral replication/transcription complex (RTC) and identified >500 host proteins constituting the RTC microenvironment. siRNA-silencing of each RTC-proximal host factor demonstrated importance of vesicular trafficking pathways, ubiquitin-dependent and autophagy-related processes, and translation initiation factors. Notably, detection of translation initiation factors at the RTC was instrumental to visualize and demonstrate active translation proximal to replication complexes of several coronaviruses. Collectively, we establish a spatial link between viral RNA synthesis and diverse host factors of unprecedented breadth. Our data may serve as a paradigm for other positive-strand RNA viruses and provide a starting point for a comprehensive analysis of critical virus-host interactions that represent targets for therapeutic intervention.

Keywords: coronavirus; human; infectious disease; microbiology; mouse; proximity labeling; replicase complex; translation; vesicular transport; virus; virus-host interaction.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Cell Line
  • Coronavirus / genetics
  • Coronavirus / metabolism*
  • Coronavirus / physiology
  • Coronavirus Infections / metabolism*
  • Coronavirus Infections / virology
  • Cytoplasm / metabolism
  • Cytoplasm / virology
  • Fibroblasts / metabolism
  • Fibroblasts / ultrastructure
  • Fibroblasts / virology
  • Host-Pathogen Interactions
  • Humans
  • Mice
  • Microscopy, Electron, Transmission
  • Protein Biosynthesis
  • RNA, Viral / genetics
  • RNA, Viral / metabolism*
  • RNA-Dependent RNA Polymerase / genetics
  • RNA-Dependent RNA Polymerase / metabolism*
  • Virus Replication*


  • RNA, Viral
  • RNA-Dependent RNA Polymerase