The complete structure of VIPER, an unsual LTR retroelement present in Trypanosomes but not in Leishmania major

LEVIN, MARIANO J.; ROBLEDO, GERMÁN; LORENZI, HERNAN A.; MULINARI, SHAI; ROCHA, CRISTIAN

Seattle, Washington

Encuentro; TriTryp Genomes Meeting; 2004

Seattle Biomedical Research Institute

VIPER was initially characterized as a 2,359 bp long retroelement of Trypanosoma cruzi associated with SIRE (Short interspersed Repetitive Element). Sequence comparisons of its RT-RNAseH domains determine its classification in the family of LTR. Analysis of different CL-Brener genomic sequences allowed the identification of a 4,480 bp long VIPER that includes an ORF for a gag protein, next to it an ORF encoding for a tyrosine recombinase and the previously mentioned RT-RNAseH ORF. This structure is unusual for a LTR retrotransposon because it lacks the long terminal repeats that are replaced at the 5´ end by the first 182 bp of SIRE and at the 3´ end by the SIRE´s last 226 pb. Using BLAST we were able to identify VIPER-like retroelements in Trypanosoma brucei. Further analysis demonstrated that in T. brucei VIPER is found within 5´ and 3´ sequences that bare homology with SIRE. Sequence comparisons revealed a C-rich stretch within SIRE, the putative target of the tyrosine recombinase.