Quantitative temporal proteomic analysis of vaccinia virus infection reveals regulation of histone deacetylases by an interferon antagonist

Vaccinia virus (VACV) has numerous immune evasion strategies, including multiple mechanisms of inhibition of IRF-3, NF-κB and type I interferon (IFN) signaling. Here, we use highly multiplexed proteomics to quantify ~9,000 cellular proteins and ~80% of viral proteins at seven time points throughout VACV infection. 265 cellular proteins are downregulated >2 fold by VACV, including putative natural killer cell ligands and IFN-stimulated genes. Two thirds of these viral targets, including the class II histone deacetylase HDAC5, are degraded proteolytically during infection. In follow-up analysis, we demonstrate that HDAC5 restricts replication of both VACV and herpes simplex virus type 1. By generating a protein-based temporal classification of VACV gene expression, we identify protein C6, a multifunctional IFN antagonist, as being necessary and sufficient for proteasomal degradation of HDAC5. Our approach thus identifies both a host antiviral factor and a viral mechanism of innate immune evasion.