In 1964, Howard Temin (1) first proposed that genetic information might actually flow in reverse (i.e. from RNA to DNA) in some organisms. The subsequent codiscovery of RNAdependent DNA polymerases (reverse transcriptases) by Temin and Mizutani (2) and Baltimore (3) solidified this revolutionary idea and provided a key to the identification of a large group of evolutionarily related mobile genetic elements that encode their own reverse transcriptases and replicate through RNA intermediates (DNA -> RNA -> DNA; 4-6). These exist across broad phylogenetic boundaries (bacteria, algae, plants, fungi, insects, birds, fish, and mammals) and include bacterial episomal elements (msDNA), mitochondrial retroplasmids and group II introns, interspersed repeated sequences [long terminal repeat (LTR) retrotransposons and non-LTR long interspersed nuclear elements (LINE)-like elements], and replicating viruses (retroviruses, hepadnaviruses, and caulimoviruses). Comparisons of genome organizations, replication mechanisms, and reverse transcriptase sequences and functions clearly point to evolutionary relationships among retroelements (6-9). Although the temporal order of retroelement evolution is controversial (6), it has been suggested that retroelements were evolutionary links between ancient RNA and DNA worlds (10). A hallmark of retroelements is their genetic heterogeneity. This was discovered first (11) and is best documented (12-15) for retroviruses that have been shown to exist as complex mixtures of genetically heterogeneous virions (quasispecies) that are ever-changing. Studies of nonviral retrotransposons and mitochondrial retroplasmids suggest that genetic variation is also a property of other retroelements (16-23; GenBank data base). The frequency of genetic variants within a population of retroelements may be influenced by many factors, including mutation rate, the number of retrotransposition cycles, selection, population size, competition, and random sampling (24). The distinction between mutation frequency (i.e., the proportion of mutants in a population at any given time) and mutation rate (i.e., the number of de novo mutations arising per nucleotide per cycle of replication) is very important if one is to understand underlying mechanisms of genetic variation (25). Recent studies using recombinant and clonally purified retroviruses have permitted the quantitation of mutation rates after a single cycle of replication in the absence of strong selection (reviewed in ref. 15). These studies show that retroviruses, like other RNA viruses, mutate at very high rates (0.05-1 mutation per genome per replication cycle), resulting in base substitutions, frameshifts, genetic rearrangements, and hypermutations. Although it has long been suspected that other retroelements also mutate at high rates (16, 17), technical difficulties have precluded a rigorous quantitation of these rates.
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