Further characterization of Trypanosoma cruzi strains through a simple sequence repeat (SSR) of ferredoxin-NADP+ reductase 5' UTR.

Abstract

Trypanosoma cruzi displays clonal expansion, and genetic exchanges have contributed to the current complexity of its population (Machado and Ayala, 2001). Several clustering schemes have been proposed to aid the understanding of T. cruzi genetic nomenclature, including: zymodemes (Miles et al., 1978), two major phylogenetic lineages (Souto et al., 1996), discrete typing units (Brisse et al., 2000) and haplotype analysis (de Freitas et al., 2006). This clustering scheme shed light on T. cruzi population structure and also advanced the analysis of Chagas disease epidemiology. However, except for kDNA or the schizodeme analysis (Morel et al., 1980), no other molecular marker has been successfully deployed to narrow the characterization of particular strains and extend information beyond T. cruzi population structure. We have approached this question by looking at the untranslated regions (UTRs) in T. cruzi (Brandao, 2006; Brandao and Fernandes, 2006; Brandao and Jiang, 2009). In general, UTRs tend to accumulate mutations at rates higher than the respective open reading frame (ORF) (Makalowski and Boguski, 1998). Thus, molecular clusters for T. cruzi strains could be detected by inspecting UTR sequences. We have inspected UTR from low copy number genes such as ferredoxin-NADP+ reductase and reasoned that its 5′ UTR might be used for this purpose. Ferredoxin-NADP+ reductase is present in a wide range of organisms and modulates redox metabolic pathways such as the one involved in electron transfer (Paladini et al., 2009). In T. cruzi CL Brener, a search in its genome sequence (www.tritrypdb.org) shows that ferredoxin-NADP+ reductase is single copy, displaying an ORF and 5′ UTR of 2004 and 130 bp in length, respectively (according to sequence in GenBank accession no. {"type":"entrez-nucleotide","attrs":{"text":"AY206009","term_id":"37782788","term_text":"AY206009"}}AY206009). Here, we discuss that it contains two segments that are useful for characterization of strains: a simple sequence repeat (SSR) which allows a narrow analysis at the strain level and an upstream open reading frame (uORF) that identifies two of the major T. cruzi populations.