An unusual vertebrate LTR retrotransposon from the cod Gadus morhua

摘要

The pursuit of genome sequencing projects has added impetus to the discovery and analysis of the repetitive DNA sequences that are present in all eukaryotes. Much interest has been focused on retroelements, elements propagated via an RNA intermediate, as these are the most abundant form of repetitive DNA in eukaryote genomes. One class of these elements is the retrotransposons, which can further be subdivided into two major groups: those that possess long terminal repeats (LTRs) and those that do not. The LTR retrotransposons contain open reading frames (ORFs) which encode the proteins (GAG and POL) required for the reverse transcription of the element mRNA and integration of the resulting cDNA into the host genome. The classification of LTR retroelements is currently under intense analysis, and several schemes have recently been proposed (Bowen and McDonald 1999; Hull 1999; Pringle 1999; Cook et al. 2000). The phylogenetic analyses of LTR retrotransposons based on the predicted amino acid sequences of their reverse transcriptases (RTs) indicate that they fall into at least four major groups: the two extensively reviewed Tyl/copia and Ty3/gypsy groups, the BEL-like group that includes several newly discovered elements (Cook et al. 2000), and the retroviruses. The Tyl/copia retroelement can be distinguished from members of the other three groups not only on the basis of their RT sequences, but also on the basis of the order of amino acid motifs within their POL ORFs. The order of domains in the POL ORF of Tyl/copia elements is protease, integrase, RT/RNase H, while in Ty3/gypsy elements, Bel elements, and the retroviruses, the order is protease, RT/RNase H, integrase. It has been proposed that the difference in the orders of the POL domains be the main defining feature in the classification of LTR-containing retroelements (Bowen and MacDonald 1999; Hull 1999; Pringle 1999). Such a scheme is debatable, however, in that phylogenetic analyses suggest similar divergence between the BEL elements, the Ty3/gypsy elements, and the Tyl/copia elements.