title: The short interspersed repetitive element of Trypanosoma cruzi, SIRE, is part of VIPER, an unusual retroelement related to long terminal repeat retrotransposons.
abstract: The short interspersed repetitive element (SIRE) of Trypanosoma cruzi was first detected when comparing the sequences of loci that encode the TcP2beta 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 consensus nucleotide sequence and structure for the element, consisting of three regions (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 polyadenylation site in 63% of the cases. This study led to the characterization of VIPER (vestigial interposed retroelement), a 2,326-bp-long unusual retroelement. 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 connected by a 1,924-bp-long fragment that carries a unique ORF encoding a complete reverse transcriptase-RNase H gene whose 15 C-terminal amino acids derive from codons specified by SIRE's region II. The amino acid sequence of VIPER's reverse transcriptase-RNase H shares significant homology to that of long terminal repeat retrotransposons. The fact that SIRE and VIPER sequences are found only in the T. cruzi genome may be of relevance for studies concerning the evolution and the genome flexibility of this protozoan parasite.
authors.affiliation: Laboratorio de Biología Molecular de la Enfermedad de Chagas, Instituto de Investigaciones en Ingenieria Genética y Biologia Molecular, Vuelta de Obligado 2490, 1428 Buenos Aires, Argentina.
authors.forename: M
authors.initials: M
authors.lastname: Vazquez
authors.forename: C
authors.initials: C
authors.lastname: Ben-Dov
authors.forename: H
authors.initials: H
authors.lastname: Lorenzi
authors.forename: T
authors.initials: T
authors.lastname: Moore
authors.forename: A
authors.initials: A
authors.lastname: Schijman
authors.forename: M J
authors.initials: MJ
authors.lastname: Levin
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D016384:Consensus Sequence; D016054:DNA, Protozoan; D015870:Gene Expression; D008969:Molecular Sequence Data; D015800:Protozoan Proteins / Q000235:genetics*; D018626:Retroelements; D012269:Ribosomal Proteins / Q000235:genetics*; D017386:Sequence Homology, Amino Acid; D020086:Short Interspersed Nucleotide Elements; D013045:Species Specificity; D020079:Terminal Repeat Sequences; D014349:Trypanosoma cruzi / Q000235:genetics*
chemical_list: D016054:DNA, Protozoan; D015800:Protozoan Proteins; D018626:Retroelements; D012269:Ribosomal Proteins