Structural analysis of a 4414-bp element in Drosophila melanogaster.

We cloned a 4414-bp element from a mutant of Drosophila melanogaster. Its insertion site was 18,929,626 bp. Analysis of the nucleotide and amino acid sequences demonstrated that the element is homologous to Pifo_I, first obtained from D. yabuka, which belongs to the gypsy/Ty3 subfamily. We also obtained a 3754-bp length element from a wild-type fly by PCR, with a pair of primers designed from the conserved region of the 4414-bp length element. The two elements included a pair of long terminal repeats and part of the GAG and ENV proteins, but the POL protein was completely lost. This element is found in the subgenus of D. melanogaster, but it is a degenerate type of Pifo_I and is not infective. Also, a 714-bp region structured in 5.0 tandem repeats of 143 bp each was found in the 5'UTR of the degenerate element; these could interact with transcription factor CF2. Phylogenetic analysis and alignment of amino acids indicated that the Pifo_I element was closer to the ZAM retrotransposon, which gave us some clues to their functional similarity. Based on these data, we propose that there is a relationship between the degenerate element and the mutant phenotype, which would provide a foundation for further research.