Virus-Driven Proximity Proteomics Identifies p400 as a Restriction Factor Poised on Incoming Viral Genomes

Abstract

Immediate-early viral proteins must rapidly counteract host defenses directed at incoming viral genomes, yet the protein interaction networks that mediate this remain unresolved. This gap persists largely because immediate-early proteins are expressed at low abundance during this stage of infection, making them challenging to investigate with standard approaches. Here, we present a virus-driven proximity proteomics framework to investigate immediate-early phase virus-host interactions in an authentic infection context. An isogenic P2A control virus untethers a miniTurbo biotin ligase from the viral protein under investigation, effectively modeling bait abundance and background changes from a matched infection context. Continuous biotin labeling from the earliest hours of infection further amplifies detection of transient, low-abundance interactions characteristic of this phase. Using the adenovirus E1A hub protein as a benchmark, we recovered the majority of known E1A interactors and identified over 150 high-confidence interactions. Applying this strategy to the immediate-early phase, we resolved the E1A interactome and identified the p400 chromatin remodeling complex as its dominant target. We show p400 associates with incoming viral genomes, represses gene expression, and regulates persistent infection. These data identify p400 as a poised host restriction factor and establish a temporally resolved proximity proteomics strategy transferable to other immediate-early viral proteins.