Retrotransposons, Endogenous Retroviruses, and the Evolution of Retroelements

Abstract

The retroelements are as diverse an assemblage of related molecular entities as can be found anywhere. With the exception of the retroviruses themselves, retroelements are genetic parasites that inhabit the genomes of all eukaryotes and many prokaryotes. The infectious retroviruses can be considered a highly evolved pinnacle on the complex phylogenetic tree that makes up the retroelements. The root of this tree is believed by many to be an ancient cellular reverse transcriptase gene, as originally proposed by Temin (1980), although this remains controversial. It is useful to consider the retroelements in comparison to the infectious retroviruses. The retroelement types, summarized in Table 1, include the endogenous retroviruses, the retrotransposons, the “retrotranscripts” (including the
Alu
-like sequences and the processed pseudogenes), and the prokaryotic retrons (also known as multicopy single-stranded DNAs [msDNAs]). Retroelements are known primarily as mobile DNA species integrated at various positions in the genomes of their host species, although most of them also have important extrachromosomal DNA forms. From the mitochondrial and chloroplast compartments of various organisms, the mobile group II introns (referred to here as retrointrons) and the retroplasmids are recognized as retroelements. Yet another major grouping of retroelements is the “pararetroviruses,” a group of true viruses with DNA genomes that, in a curious permutation of the retroviral life cycle, replicate via a cellular RNA intermediate but do not normally integrate into the host genome.