Viral proteomics: The emerging cutting-edge of virus research

Zhou, ShengTao; Liu, Rui; Zhao, Xia; Huang, CanHua; Wei, YuQuan

Chronologically, the first proteome of a DNA virus particle to be sequenced was an ictalurid fish herpes virus, the channel catfish virus, in 1995. Purified virions were solubilized with NP-40, separated by gel electrophoresis, electroblotted, and the bands digested with different proteases including trypsin, Lys-C, Arg-C, or glu-C to generate a broad spectrum of peptide fragments. The fragments were subsequently analyzed using MALDI-MS. The peptide mass fingerprint was used to search the Swiss-Prot database, and a total of 16 primary structural proteins, including mature capsid proteins, protein kinases, C3HC4 zinc-binding protein, and actin were identified [9] . More importantly, the above-mentioned combined strategy of MS and sequence database searching has now become widely applied for the analysis of in the proteomes of such DNA virions as poxviruses and herpes viruses. With regard to poxviruses, although the complete genomic sequences of most poxviruses have been available for some time, only a limited number of studies have attempted to comprehensively profile the protein composition of poxvirus virions [25] . Early proteomics studies attempted to analyze the protein composition of purified vaccinia virus (VV). However, they were unable to perform a complete structural analysis of all the protein components of the virions, probably because the limited availability of advanced purification methodologies and the limitations of the technologies available for protein identification at the time. Recently, three different groups with different approaches, instruments, and digestion protocols reported the comprehensive structural analysis of the protein composition of the infectious mature virion of VV [10] [11] [12] . For instance, Resch et al. [10] detected 80 vaccinia virus-encoded proteins, representing 37% of the 218 genes annotated in the complete genome sequence, using denaturation with SDS or urea, fractionation with solid-phase extraction columns, and analysis by LC-ESI-LTQ Fourier transform MS. Among them were 13 proteins were not previously described as being part of the virion. H5, F8, E3, E6, and A6 were not previously reported as being virion-associated proteins, while N1, C22, A11, A19, M1, A50, E9, and F4 had been described as absent or unlikely to be associated with the virion.