The short interspersed repetitive element of Trypanosoma cruzi, SIRE, is part of VIPER, an unusual retroelement related to long terminal repeat retrotransposons

The short interspersed repetitive element (SIRE) of Trypanosoma cruzi was f irst detected when comparing the sequences of loci that encode the TcP2 bet a genes. It is present in about 1,500-3,000 copies per genome, depending on the strain, and it is distributed in all chromosomes. An initial analysis of SIRE sequences from 21 genomic fragments allowed us to derive a consensu s nucleotide sequence and structure for the element, consisting of three re gions (I, II, and III) each harboring distinctive features. Analysis of 158 transcribed SIREs demonstrates that the consensus is highly conserved. The sequences of 51 cDNAs show that SIRE is included in the 3' end of several mRNAs, always transcribed from the sense strand, contributing the polyadeny lation site in 63% of the cases. This study led to the characterization of VIPER (vestigial interposed retroelement), a 2,326-bp-long unusual retroele ment. VIPER's 5' end is formed by the first 182 bp of SIRE, whereas its 3' end is formed by the last 220 bp of the element. Both SIRE moieties are con nected by a 1,924-bp-long fragment that carries a unique ORF encoding a com plete reverse transcriptase-RNase H gene whose 15 C-terminal amino acids de rive from codons specified by SIRE's region II. The amino acid sequence of VIPER's reverse transcriptase-RNase H shares significant homology to that o f long terminal repeat retrotransposons. The fact that SIRE and VIPER seque nces are found only in the T. cruzi genome may be of relevance for studies concerning the evolution and the genome flexibility of this protozoan paras ite.