Viral proteomics: The emerging cutting-edge of virus research

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

The Y2H system has been widely applied in the study of global proteome interaction of various viruses. The most recent virus interaction screening database includes T7 bacteriophage, VV, and KSHV & varicella-zoster virus. As early as 1996, Bartel et al. [38] used the yeast two-hybrid system on a genome-wide scale to identify 25 interactions among the proteins of Escherichia coli and bacteriophage T7. Among these, a set of six interactions connected proteins that function in DNA replication and DNA packaging. Several of the interactions reflect intramolecular associations of different domains of the same polypeptide, suggesting an important role of the two-hybrid assay in the analysis of protein folding. McCraith et al. [39] performed a comprehensive two-hybrid analysis to detect interactions among proteins of vaccinia virus. They constructed an array of yeast transformants that comprised each of the 266 putative viral ORFs as Gal4 activation domain hybrid proteins. The array was individually mated to transformants containing each ORF as a Gal4-DNA-binding domain hybrid. Diploids expressing the two-hybrid reporter genes were defined. Of the 70000 combinations, 37 protein-protein interactions were found, including 28 that were previously unannotated. The interacting proteins could be functionally categorized into DNA replication, transcription, virion structure and morphogenesis, and virus-host interactions. Another study investigated intraviral protein interactions in herpes viral proteins, KSHV, and varicella-zoster virus (VZV). Eightynine ORFs from the KHSV genome were tested for 12000 viral protein interactions, leading to the detection of 123 nonredundant interacting protein pairs. Of the 69 ORFs in VZV and 10000 tested bait-prey pairs, 173 nonredundant intraviral protein interactions were found. A database of all predicted viral intraprotein interactions and previously established viral protein-human cellular protein interactions has been set up. This database facilitated the prediction of 20 interactions between eight KSHV and 20 human proteins [28] . These studies illustrate that the global yeast two-hybrid screening of protein-protein interactions can be applied to the analysis of emerging, more complex, genomes.