Bioinformatic analysis: Retroposon sequences containing multiple putative endonucleases

Among the retroposons, the source of the endonuclease activity is known to be variable. We investigated whether any retroposon genomes encode potential multiple endonuclease functions. Amino acid alignments were generated to reveal the presence of the characterized ordered-series-of-motifs (OSM) that define four different endonuclease functions. These endonuclease functions include a retroviral-like integrase (IN), an apurinic-apyrimidinic endonuclease (APE), the PDD endonuclease recently identified in the R2BM retroposon and an HNH endonuclease signature conserved by the group 11 intron sequences. The results indicate that the spliced l eader associated conserved sequences (SLACS) of T. brucei, c ruzi-associated retrotransposon (CZAR) of Trypanosoma cruzi, two crithidia retrotransposable elements (CRE); CRE1 and CRE2 of Crithidia fasciculata , and certain ING retroposon sequences of Trypanosoma brucei contain multiple putative endonuclease functions