Temporal analysis of the plasma membrane proteome after vaccinia virus infection sheds light on virus strategies to evade the immune response

Abstract

Abstract Vaccinia virus (VACV) is a poxvirus and the vaccine used to protect against variola virus and related orthopoxviruses. VACV encodes multiple proteins whose function is to evade the host immune response, contributing to an immune suppressive environment at the site of infection. There is, however, an incomplete understanding of how this immune suppression by VACV is consistent with a strong induction of immunological memory. There is especially little known about the relationship between NK cells and VACV, such as which ligands trigger NK activation and whether VACV uses strategies to interfere with the NK cell response. The purposes of this study is to clarify these open questions. Here, we performed a quantitative proteomic analysis of membrane-associated proteins from VACV-infected cells at various time points. Using tandem mass-tag spectrometry we detected about 70 viral proteins and 900 membrane-associated host proteins. Analysis revealed that VACV infection rapidly altered the expression of proteins with immune functions, downregulated the surface expression of plexins, ephrins, cadherins and selectively downregulated MHC-I proteins. Moreover, VACV prevented the upregulation of stress-induced ligands and death receptors. Finally, the kinetics of expression of VACV proteins at the surface of the infected cell were analysed. Collectively, these data constitute a valuable resource for the study of VACV and its interaction with the host immune response, provide insights into the interaction of NK cells with VACV, suggest novel VACV immune evasion mechanisms and shed light on which host factors are required to raise a protective immunological memory.