Do Viruses Exchange Genes across Superkingdoms of Life?

Malik, Shahana S.; Azem-e-Zahra, Syeda; Kim, Kyung Mo; Caetano-Anollés, Gustavo; Nasir, Arshan

The ABE group was the largest Venn group for viruses of the three superkingdoms (i.e., 93 ABE FSFs out of 98 total FSFs in archaeoviruses, 319 out of 441 in bacterioviruses, and 315 out of 449 in eukaryoviruses, Figure 2) . The ABE domains are, by definition, detected in the proteomes of all three superkingdoms and are more likely to evolve vertically and hold a deep history Caetano-Anollés, 2013, 2015) . Indeed, ABE domains were widespread in cellular species (median f -value > 0.6 for all, Figure 5 ) and were enriched in "cell-like" functions such as metabolism, information, DNA repair, among others, and occasionally viral proteins (Tables S2-S4) . Therefore, the ABE group stands in contrast to the "viral-like" nature of the other Venn groups, especially, B and E FSFs that had limited spread in cellular proteomes ( Table 1) . The presence of a large number of universal "cell-like" proteins in viral proteomes is therefore intriguing and worthy of exploration. It suggests two possible scenarios. First, the detection of ABE FSFs in viral proteomes effectively transforms ABE into an ABEV group, which now represents a large core of (near)-universal FSF domains shared by both cells and viruses. The mere existence of this FSF core supports an early "cell-like" phase in the evolution of modern viruses, an idea that has recently become popular (Nasir et al., 2012a,b) following the discovery of several "giant viruses" that overlap parasitic cells in physical and genome size (La Scola et al., 2003; Philippe et al., 2013; Legendre et al., 2014 Legendre et al., , 2015 . Under this proposal, viruses are secondarily acellular as they either "escaped" or "reduced" from primordial cells before these cells diversified into superkingdoms (Nasir and Caetano-Anollés, 2015, see Schulz et al., 2017 for an opposite view). In an alternative second scenario, the ABEV group points to recent HGTs occurring between viruses and cells in either direction, more likely from cell-to-virus considering the cell-like nature of ABE FSFs. It is important to note that a single HGT event is sufficient to invoke transformation from the ABE to the ABEV group. For example, ABE FSFs can be transferred directly from Archaea to archaeoviruses, from Bacteria to bacterioviruses, and Eukarya to eukaryoviruses, in addition to indirect crosssuperkingdom genetic transfers. All of these transfers suffice for ABE to ABEV transformation.