Evolution of Viral Proteins Originated De Novo by Overprinting

Sabath, Niv; Wagner, Andreas; Karlin, David

We identified from the literature a set of 40 overlapping gene pairs for which the expression of a protein product from two reading frames had been experimentally verified. All gene pairs in this data set come from viruses that infect eukaryotes. Among these gene pairs, we selected 29 pairs coming from viruses whose genome encodes an RNA-dependent RNA polymerase (RdRP), to facilitate comparison among clades (see later). We further narrowed the data set to overlapping gene pairs in which we could identify which gene had originated de novo (see procedure described later). In total, we obtained 12 gene pairs that correspond to 12 cases of de novo origin, stemming from 12 families of RNA viruses that met these criteria. The data set shares some genes with a previously published data set (4 cases out of 12: groups 4, 6, 8, and 11 below) (Rancurel et al. 2009 ). The reason why we could include only a minority of the genes published in the Rancurel data set (4 out of 17) is that we restricted ourselves to considering pairs in which both ancestral and de novo proteins had less than 50% amino acid divergence (percentage of identity). Table 1 lists, for each gene pair, the species taxonomy, the genome accession number, the names of the overlapping genes, and their lengths. In the rest of the article, we will refer to each case either by its genus or by the number of its clade, as listed in table 1. Table 3 lists bibliographical evidence about the expression, function, and fitness effect of mutations in the de novo gene.