Abstract
Potyviruses encode a large polyprotein that undergoes proteolytic processing, producing 10 mature proteins: P1, HC-Pro, P3, 6K1, CI, 6K2, VPg, NIa-Pro, NIb-RdRp, and CP. While P1/HC-Pro and HC-Pro/P3 junctions are cleaved by P1 and HC-Pro, respectively, the remaining seven are processed by NIa-Pro. In this study, we analyzed 135 polyprotein sequences from approved potyvirus species and deduced the consensus amino acid residues at five positions (from −4 to +1, where a protease cleaves between −1 and +1) in each of nine cleavage sites. In general, the newly deduced consensus sequences were consistent with the previous ones. However, seven NIa-Pro cleavage sites showed distinct amino acid preferences despite being processed by the same protease. At position −2, histidine was the dominant amino acid residue in most cleavage sites (57.8–60.7% of analyzed sequences), except for the NIa-Pro/NIb-RdRp junction where it was absent. At position −1, glutamine was highly dominant in most sites (88.2–97.8%), except for the VPg/NIa-Pro junction where glutamic acid was found in all the analyzed proteins (100%). At position +1, serine was the most abundant residue (47.4–86.7%) in five out of seven sites, while alanine (52.6%) and glycine (82.2%) were the most abundant in the P3/6K1 and 6K2/VPg junctions, respectively. These findings suggest that each NIa-Pro cleavage site is finely tuned for differential characteristics of proteolytic reactions. The newly deduced consensus sequences may be useful resources for the development of models and methods to accurately predict potyvirus polyprotein processing sites.
Highlights
A potyvirus produces a large polyprotein that is processed by three proteases (P1, helper component-protease (HC-Pro), and nuclear inclusion-a protease (NIa-Pro)), which recognize and cleave specific sequences
The traditionally accepted consensus recognition sequences for these proteases were deduced based on tens of sequences [12], which included all potyvirus polyproteins available at that time
We analyzed 135 polyprotein sequences derived from approved species to ensure the diversity of input data and robustness of the resulting consensus sequences
Summary
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. To propagate in host cells, most RNA viruses generate multiple proteins from relatively smallsized genomes [1, 2]. RNA viruses rely on the translation machineries of the hosts for protein synthesis because they do not encode or carry components for mRNA translation [1]. Viruses with single RNA genomes that infect eukaryotic cells encounter challenges in the production of multiple proteins because the eukaryotic translation machinery usually produces only one protein from a single mRNA.
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