A phylogenomic data-driven exploration of viral origins and evolution

Nasir, Arshan; Caetano-Anollés, Gustavo

The "DNA/RNA polymerases" FSF (e.8.1), which includes T7 RNA polymerase, RNA-dependent RNA polymerase of plus-sense and dsRNA viruses, reverse transcriptase, DNA polymerase I, and the catalytic domain of Y-family DNA polymerase, was detected in six of the seven subgroups (the exception being ssDNA viruses, which replicate by using the host's polymerase). In turn, "S-adenosyl-L-methionine dependent methyltransferases" (c.66.1) FSF was detected in five of the seven viral subgroups, except retrotranscribing viruses. Three additional FSFs, the "P-loop containing NTP hydrolase" (c.37.1), the "Ribonuclease H-like" (c.55.3) and the "Positive stranded ssRNA viruses" (b.121.4), were detected in four of the seven viral subgroups ( Table 4 ). The c.37.1 FSF is one of the most abundant and widespread FSFs in modern cells. The c.55.3 superfamily includes many proteins involved in informational processes (including replication and translation) that are universal among cellular proteomes. This FSF was relatively widespread in viral subgroups but was absent in the proteomes of plus-ssRNA, dsRNA, and dsDNA-RT viruses. It was especially abundant in ssRNA-RT (79% of proteomes) and dsDNA (58%) viruses. The c.55.3 FSF also includes the catalytic domain of retroviral integrase, which is an important target to silence retroviral gene expression (53) and is medically important. In turn, b.121.4 is the jelly-roll fold, which is one of the most common topologies observed in viral capsid proteins (3, 54) . Finally, 10 FSFs were present in three of the six viral subgroups, whereas 52 were shared by two subgroups (Fig. 4A , Venn diagram, and Table 4 ).