A non-LTR retrotransposon from the Hawaiian Drosophila: the LOA element

Abstract

An interspersed sequence has been isolated from the genome of D. silvestris, a species endemic to the Hawaiian Islands. The LOA element is 7.7 kb long and its 3' end consists of (TAA)n tandem repeats. Five different LOA elements were isolated, of which three were truncated at their 5' ends. Large deletions within the elements were frequent. A consensus sequence of the LOA element has been constructed using the nucleotide sequence of three elements. Two overlapping open reading frames (ORF) are present in the LOA element. In ORF1 two 'cys' motifs characteristic for gag proteins are found. The protein translated from ORF2 has similarities with retroviral pol genes. A protein databank search revealed 22% to 25% identity with the reverse transcriptase domains of retrotransposons. This region also shows the pattern of invariant amino acid residues which are most conserved in retroviral reverse transcriptases. In ORF2 an integrase specific 'cys' motif and a conserved sequence of retroviral proteases were identified. Structural similarities with LINE-like elements suggest that the LOA element represents a new non-LTR retrotransposon.