Retrotransposons and retroviruses: Analysis of the envelope gene

Retroviruses and long terminal repeat (LTR) retrotransposons share a common structural organization. The main difference between these retroelements i s the presence of a functional envelope (env) gene in retroviruses, which i s absent or nonfunctional in LTR retrotransposons. Several similarities bet ween these two groups of retroelements have been detected for the reverse t ranscriptase, gag, and integrase domains. Assuming that each of these domai ns shares a common ancestral sequence, several hypotheses could account for the emergence of retroviruses from LTR retrotransposons. In this context, the positions of elements such as gypsy and the members of the Ty3 subfamil y are not clear, since they are classified as retroviruses but phylogenetic ally they are assigned to the LTR retrotransposon group. We compared the en v gene products of these retroelements and identified two similar motifs in retroviruses and LTR retrotransposons. These two regions do not occur in t he same order. If we assume that they are derived from the same ancestral s equence, this could result from independent acquisition of the various doma ins rather than the single acquisition of the whole env gene. However, we c annot exclude the possibility that the env gene was reorganized after being acquired. Trees based on these regions show that these two groups of eleme nts are clearly distinguished. These trees are similar to those obtained fr om reverse transcriptase or integrase. in trees based on reverse transcript ase, the retroviruses with complete or partial env genes can be distinguish ed from the other LTR retrotransposons.