Use of DNA, RNA, and chimeric templates by a viral RNA-dependent RNA polymerase: Evolutionary implications for the transition from the RNA to the DNAworld

All polynucleotide polymerases have a similar structure and mechanism of ca talysis, consistent with their evolution from one progenitor polymerase, Vi ral RNA-dependent RNA polymerases (RdRp) are expected to have properties co mparable to those from this progenitor and therefore may offer insight into the commonalities of all classes of polymerases, We examined RNA synthesis by the brome mosaic virus RdRp on DNA, RNA, and hybrid templates and found that precise initiation of RNA synthesis can take place from all of these templates. Furthermore, initiation can take place from either internal or p enultimate initiation sites. Using a template competition assay, we found t hat the BMV RdRp interacts with DNA only three- to fourfold less well than it interacts with RNA. Moreover, a DNA molecule with a ribonucleotide at po sition -11 relative to the initiation nucleotide was able to interact with RdRp at levels comparable to that observed with RNA. These results suggest that relatively few conditions were needed for an ancestral RdRp to replica te DNA genomes.