An overview of the vaccinia virus infectome: a survey of the proteins of the poxvirus-infected cell.

We have quantitatively profiled the proteins of vaccinia virus-infected HEK293T cells early and late during vaccinia virus infection. Proteins corresponding to 4,326 accessions were identified, the products of 3,798 genes. One hundred thirty-six of the proteins were vaccinia virus-encoded (∼64% of the known vaccinia virus proteome). The remaining accessions were from the host cell. A total of 3,403 of the 4,326 accessions could be confidently quantitated at the precursor peptide level. Although vaccinia virus gene products spanned the entire abundance dynamic range of the cellular proteome, nearly all of the proteome dynamics observed as a result of infection were manifest in the virus gene products with very little plasticity in the host cell proteome. The vaccinia virus gene products could be grouped into four kinetic classes (i.e., four combinations of pre- and postreplicative expression). These protein kinetic classes reflected, almost entirely, the corresponding gene classes within the recently characterized vaccinia virus transcriptome map. The few cellular gene products that showed notable changes in abundance upon vaccinia virus infection were concentrated largely in just a few functional groups. After all of the quantitated cellular gene products were assigned to Gene Ontology (GO)-specific groups, quantitation values for a number of these GO-specific groups were significantly skewed toward over- or underabundance with respect to the global distribution of quantitation values. Quantitative analysis of host cell functions reflected several known facets of virus infection, along with some novel observations.