title: The VIPER elements of trypanosomes constitute a novel group of tyrosine recombinase-enconding retrotransposons.
abstract: VIPER was initially characterized as a 2326bp LTR-like retroelement associated to SIRE, a short interspersed repetitive element specific of Trypanosoma cruzi. It carried a single ORF that coded for a putative reverse transcriptase-RNAse H protein, suggesting that it could be a truncated copy of a longer retroelement. Herein we report the identification and characterization of a complete 4480bp long VIPER in the T. cruzi genome. The complete VIPER harbored three non-overlapped domains encoding for a GAG-like, a tyrosine recombinase and a reverse transcriptase-RNAse H proteins. VIPER elements were also found in the genomes of Trypanosoma brucei and Trypanosoma vivax, but not in Leishmania sp. On the basis of its reverse transcriptase phylogeny, VIPER was classified as an LTR retroelement. However, VIPER was structurally related to the tyrosine recombinase encoding retroelements, DIRS and Ngaro. Phylogenetic analysis showed that VIPER's tyrosine recombinase grouped with the transposases RCI1 of Escherichia coli and Ye24 and Ye72 of Haemophilus influenzae within a major branch of prokaryotic recombinases. Taken together, VIPER's structure, the nature of its tyrosine recombinase, the unique features of its reverse transcriptase catalytic consensus motif and the fact that it was found in Trypanosomes, an early branching eukaryote, suggest that VIPER may be the closest relative of the founder element of the tyrosine recombinase encoding retrotransposons known up to date. Our analysis revealed that tyrosine recombinase-encoding retroelements were originated as early in evolution as non-LTR retroelements and suggests that VIPER, Ngaro and DIRS elements may constitute a third group of retrotransposons, distinct from both LTR and non-LTR retroelements.
authors.affiliation: Laboratorio de Biologia Molecular de la Enfermedad de Chagas (LaBMECh) INGEBI, National Research Council (CONICET), Centro de Genomica Aplicada (CeGA), University of Buenos Aires, Vuelta de Obligado 2490 2P, 1428, Buenos Aires, Argentina.
authors.forename: Hernan A
authors.initials: HA
authors.lastname: Lorenzi
authors.forename: German
authors.initials: G
authors.lastname: Robledo
authors.forename: Mariano J
authors.initials: MJ
authors.lastname: Levin
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology; D004254:DNA Nucleotidyltransferases / Q000235:genetics; D015683:Gene Products, gag / Q000235:genetics; D018503:Genome, Protozoan; D006193:Haemophilus influenzae / Q000235:genetics; D007891:Leishmania / Q000235:genetics; D008969:Molecular Sequence Data; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012194:RNA-Directed DNA Polymerase / Q000235:genetics; D045522:Recombinases / Q000235:genetics*; D018626:Retroelements / Q000235:genetics*; D016914:Ribonuclease H / Q000235:genetics; D017385:Sequence Homology; D014346:Trypanosoma brucei brucei / Q000235:genetics; D014349:Trypanosoma cruzi / Q000235:genetics*; D016689:Trypanosoma vivax / Q000235:genetics
chemical_list: D015683:Gene Products, gag; D045522:Recombinases; D018626:Retroelements; D004254:DNA Nucleotidyltransferases; C077570:Site-specific recombinase; D012194:RNA-Directed DNA Polymerase; D016914:Ribonuclease H