initiates cDNA synthesis without a primer—a feat previously thought to be impossible for a DNA polymerase. This suggests that the transition from RNA to DNA genomes did not require invention of a novel priming activity, but simply the transformation of an RNA polymerase into a DNA polymerase. The ability of Qß replicase to misincorporate DNA bases in the presence of Mn2+ (Blumenthal and Carmichael, 1979) suggests that such a transformation is not implausible.
From Template to Primer. In Qß, TYMV, and the Mauriceville retroplasmid, tRNA is the template for replication. In contrast, tRNA functions not as template but as primer in other transitional genomes which probably arose later. Examples of such genomes are cauliflower mosaic virus (CaMV) and vertebrate retroviruses. The CaMV genome is a circular duplex DNA that replicates as an extrachromosomal element without ever integrating into chromosomal DNA (see Figure 4). Transcription of the viral genome initiates at a unique regulatory region which, like a retroviral long terminal repeat (LTR), consists of an RNA polymerase II promoter just upstream from a polyadenylation signal. The polyadenylation signal is too close to the promoter to function efficiently, so transcription bypasses the signal the first time around and generates a terminally redundant transcript that is slightly longer than full length. This terminally redundant genomic (+)-strand RNA is then converted to a cDNA by the CaMV-encoded reverse transcriptase using tRNA as the primer (Hohn et al., 1985; Covey and Turner, 1986; Sanfacon and Hohn, 1990). The CaMV replication scheme is very similar to that used by retroviruses (also shown in Figure 4), except that subsequent integration of retroviral DNA into the host chromosome generates a DNA provirus with a copy of the regulatory region at either end (hence, LTR). The terminally redundant DNA provirus is topologically equivalent to the circular CaMV genome, and transcription from the upstream promoter of the provirus to the distal polyadenylation signal generates the terminally redundant genomic RNA. Transcription of diverse, but related (Xiong and Eickbush, 1990), retroviral elements is also primed by tRNA (Kikuchi et al., 1986; Chapman et al., 1992).
Specificity and Catalysis Reside in Separate Polymerase Domains. The suggestion that tRNA functioned first as template for the initiation of replication and later as primer is consistent with the domain structure of contemporary polymerases. Many polymerases have two structural domains, one that is catalytic and another that determines template specificity. The classical example of this separation of functions is the σ factor of E. coli RNA polymerase (reviewed by Jaehning, 1991). Similarly, in Qß replicase it is elongation factor Tu that recognizes that