Temporal Viral Genome-Protein Interactions Define Distinct Stages of Productive Herpesviral Infection

SUMMARY Herpesviruses utilize multiple mechanisms to redirect host proteins for use in viral processes and to avoid recognition and repression by the host. To investigate the dynamic interactions between HSV-1 DNA and viral and host proteins, we developed an approach to identify proteins that associate with the infecting viral genome from nuclear entry through packaging. We found that input viral DNA progressed within six hours through four temporal stages where the genomes: 1. interacted with intrinsic and DNA damage response proteins, 2. underwent a robust transcriptional switch mediated largely by ICP4, 3. engaged in replication, repair, and continued transcription, and then 4. transitioned to a more transcriptionally inert state engaging de novo synthesized viral structural components while maintaining interactions with replication proteins. Using a combination of genetic, imaging, and proteomic approaches, we provide a new and temporally compressed view of the HSV-1 life cycle based on genome-proteome dynamics.