Evolution-Guided Discovery of Cleavage of Human Proteins by Viral Proteases
Coxsackie virus B3 and encephalomyocarditis virus, which are relevant to human health research, are members of a group called positive-sense single-stranded RNA (+ssRNA) viruses, which is known to translate their RNA genomes as monocistronic polyproteins. These polyproteins contain proteases that are known to fulfill two functions: Cleaving the viral polyprotein into functional protein subunits, and cleaving host proteins. By examining the cleavage sites found within viral polyproteins, homologous sites can be found within host proteins as well. Since infection by viruses can be treated as selection pressure on host immunity proteins, the host proteome can be bioinformatically filtered based on sites of rapid evolution across primate genomes. The predictive power of this pipeline was tested by inserting potential cleavage sites, eight amino acids in size, into a novel reporter system. This evolution-guided model proved sufficient to confer significant vulnerability to cleavage to the reporter construct to CVB3 3C protease, but not to EMCV 3C protease, validating known antagonization targets of CVB3 and discovering new ones as well. Additionally, these two viral proteases exhibited a range of cleavage efficiencies on human proteins and on their own polyproteins, but largely did not cleave each other’s polyproteins. Further investigation and refinement of this model would strengthen its predictive power and allow better insight into the evolution and mechanisms of these disease-causing agents.