Comparative studies of the endonucleases from two related Xenopus laevis retrotransposons, Tx1L and Tx2L: target site specificity and evolutionary implications

In the genome of the South African frog, Xenopus laevis, there are two comp lex families of transposable elements, Tx1 and Tx2, that have identical ove rall structures, but distinct sequences. In each family there are approxima tely 1500 copies of an apparent DNA-based element (Tx1D and Tx2D). Roughly 10% of these elements in each family are interrupted by a non-LTR retrotran sposon (Tx1L and Tx2L). Each retrotransposon is flanked by a 23-bp target d uplication of a specific D element sequence. In earlier work, we showed tha t the endonuclease domain (Tx1L EN) located in the second open reading fram e (ORF2) of Tx1L encodes a protein that makes a single-strand cut precisely at the expected site within its target sequence, supporting the idea that Tx1L is a site-specific retrotransposon. In this study, we express the endo nuclease domain of Tx2L (Tx2L EN) and compare the target preferences of the two enzymes. Each endonuclease shows some preference for its cognate targe t, on the order of 5-fold over the non- cognate target. The observed discri mination is not sufficient, however, to explain the observation that no cro ss-occupancy is observed - that is, L elements of one family have never bee n found within D elements of the other family. Possible sources of addition al specificity are discussed. We also compare two hypotheses regarding the genome duplication event that led to the contemporary pseudotetraploid char acter of Xenopus laevis in light of the Tx1L and Tx2L data.