made of RNA that replicate through DNA intermediates, and viruses made of both RNA and DNA. Why such diversity? We suggest that viruses may have evolved early and that their genomic diversity reflects the variety of replication strategies available before large DNA genomes became the cellular norm. This leads us to predict that the study of modern viruses will provide further insight into early evolution.
Transitional Genomes as Clues to Early Replication Strategies. If the original role of tRNA-like structures was in replication, as suggested by the single-stranded bacteriophage and plant virus genomes, one might expect to find additional examples of contemporary genomes in which tRNA plays that same role. When we first proposed the genomic tag hypothesis (Weiner and Maizels, 1987), only one other example of tRNA involvement in replication was known: In modern retroviruses, tRNAs function as primers for initiation of cDNA synthesis by the retroviral reverse transcriptase. Over the past few years, additional novel replication strategies have been described that employ tRNA-like structures. These appear to link replication of single-stranded RNA viruses with retroviral replication and with the synthesis of modern chromosomal telomeres. In each of these instances, a genomic RNA replicates via a DNA intermediate. We call these "transitional genomes," because they can be viewed as reenacting the transition from an RNA world to the contemporary DNA world.
Three different sorts of transitional genomes appear to link the function of tRNA in replication of RNA genomes with its role in replication of contemporary DNA genomes, as shown in Figure 4. The example most similar to the (+)-strand RNA viruses Qß and TYMV is the Mauriceville plasmid of Neurospora mitochondria (Maizels and Weiner, 1987; Kuiper and Lambowitz, 1988; Akins et al., 1989). This double-stranded DNA plasmid replicates in a most unusual way. First, rolling-circle transcription of the plasmid generates a multimeric RNA (+)-strand. The multimer is cleaved to produce full-length monomeric RNA transcripts, each with a 3'-terminal tRNA-like structure ending in CCACCA, a genomic tag with a reiterated CCA terminus (see Figure 4). The 3'-terminal genomic tag of the monomeric (+)-strand RNA then serves as the initiation site for replication, but in this case the template is copied not into (-)-strand RNA by an RNA replicase, as for Qß and TYMV, but into cDNA by a reverse transcriptase. Moreover, the reverse transcriptase is encoded by the monomeric (+)-strand RNA, which doubles as an mRNA. The similarities between the replicative strategies of bacteriophage Qß and the Mauriceville plasmid are remarkable: a full-length (+)-strand RNA with a 3'-terminal genomic tag encodes the enzyme which copies the genome starting at the penultimate C of the