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.痘苗病毒（Vaccinia virus, VACV）拥有多种免疫逃逸策略，可通过多种机制抑制IRF-3、NF-κB及I型干扰素（IFN）信号通路。本研究采用高度多重蛋白质组学技术，在痘苗病毒感染的7个时间点中，定量检测了约9000种宿主细胞蛋白与80%左右的病毒蛋白。研究发现，共有265种宿主细胞蛋白被痘苗病毒表达下调超过2倍，其中包括推定的自然杀伤细胞配体与干扰素刺激基因（IFN-stimulated genes）。上述265种宿主蛋白中有三分之二在感染过程中被蛋白水解降解，其中包括II型组蛋白去乙酰化酶HDAC5。在后续验证实验中，本研究证实HDAC5可同时抑制痘苗病毒与1型单纯疱疹病毒的复制。本研究通过构建痘苗病毒基因表达的蛋白质时间维度分类体系，鉴定出蛋白C6——一种多功能干扰素拮抗剂——是介导HDAC5发生蛋白酶体降解的必需且充分条件。因此，本研究的研究策略同时鉴定出了一种宿主抗病毒因子与一套病毒介导的先天免疫逃逸机制。