A general RNA-templated RNA extension activity of E. coli RNA polymerase

Multi-subunit "DNA-dependent" RNA polymerases (RNAPs) have noncanonical activity on RNA templates. Such RNAPs replicate RNA pathogens, such as hepatitis delta virus (HDV) and viroids, and contribute to cellular gene regulation. Despite the broad biological significance of these processes, our understanding of the underlying RNAP mechanisms remains incomplete. Using E. coli RNAP, a multi-subunit RNAP, as a simple model, we describe here the general RNA-templated RNA extension activity of that enzyme. In this activity, the 3' end of an added RNA template appears to fold back and base pair upstream in the template, creating an intramolecular primer-template duplex as short as 1-2 base pairs. The RNAP extends this intramolecular duplex, incorporating nucleotides complementary to the template. RNA-templated RNA extension occurred in minutes and did not appear to be suppressed by the presence of a promoter-containing DNA template. With one exception, every RNA template we tested could be extended by the enzyme, highlighting the general nature of this reaction. These data define a general activity of a cellular RNAP. Unrestricted, this activity could contribute to emergence and replication of RNA-based agents such as HDV and viroids; if highly regulated, the activity could limit these same elements.