Canonical and noncanonical MDG4 (Gypsy) sequences contained in Drosophila melanogaster genome

Abstract

Transposable genetic elements constitute an essential component of eukaryotic genome. LTR-retrotransposons of the group Gypsy , many of which are considered as endogenous retroviruses of invertebrates, are of special interest [1,2]. The transposable genetic element MDG4 ( gypsy ) is the best studied retrotransposon of Drosophila melanogaster. Earlier, we demonstrated the existence of MDG4 subfamilies, differing in their ability for transpositions. Both these subfamilies, which were named "active" and "inactive," with different efficiency form new copies in transformed cultured cells of D. hydei. However, only the active MDG4 can undergo transpositions in D. melanogaster lines, whereas no transposition of the inactive MDG4 was detected in any line studied [3,4]. Structural differences between the two MDG4 subfamilies can be detected even at the level of restriction maps (Fig. 1). For example, all MDG4 copies cloned from the insertion mutagenesis systems contain the sites for the restriction endonucleases Hind III (4483), Mlu I (5335), and Cla I (6939) in the coding region and the sites for Xba I (430, 7417) in the long terminal repeats (LTRs) [3]. Because, unlike the active MDG4 variant, the inactive MDG4 is present in the genome of all Drosophila lines studied, it is probably the most ancient variant. To approach the question on MDG4 evolution, we decided to study all sequences of D. melanogaster genome that shared a significant extent of homology with this retrotransposon. Experiments were performed with the D. melanogaster line G32, the genome of which contains unusual MDG4 variants [6].As a result of screening of the genomic library of the D. melanogaster line G32, 28 clones homologous to the MDG4 sequence were selected. Only four out of the 28 clones contained the full-length variants of this retrotransposon: two active copies, one inactive copy, and one unusual copy that contained facultative restriction sites for Hind III (4483) and Xba I (430 and 7417) but had no sites for Mlu I (5335) and Cla I (6939). Probably, this copy occurred as a result of recombination processes. Another four sequences cloned from the genome of line G32 contained copies of a poorly studied retrotransposon gtwin , which is classified in the group of LTR-retrotransposons Gypsy and shares a significant degree of homology with MDG4. The other clones contained sequences whose structure also considerably differed from MDG4 structure.To reveal sequences homologous to MDG4, we created a genomic library of line G32 on the basis of bacteriophage λ . Genomic DNA of λ GEM11 was treated with the specific restriction endonuclease BamH I,