The untranslated regions of genes from Trypanosoma cruzi: perspectives for functional characterization of strains and isolates

Abstract

The abundance of polycistronic transcription for protein-coding genes in the kinetoplastid protozoa has influenced profoundly the way in which we think about regulating levels of protein expression in eukaryotes. In contrast to most eukaryotes where the primary level of control may be exerted at transcription initiation, kinetoplastids show little regulation at this checkpoint. Genes transcribed at equal rates can yield mRNA(s) that differ in abundance in lifestage-and cell cycle-specific patterns. The most abundant mechanism of control is post transcriptional (Clayton 2002), affecting the stability of the mRNA through interactions of RNA-binding proteins with cis-elements in the 5'-and 3'-untranlslated regions (UTRs) of the mRNA. Regulation of mRNA levels at the level of trans-splicing is indicated by intergenic sequences that do not end up in stable RNA. The perspective by Brandão highlights the wealth of information that remains to be interpreted in the three kinetoplastid genome sequences.The current rush of activity is focused downstream from the conceptual translations of protein sequence, as these should give insights into the more immediately tangible aspects of the parasites' biology. Broader interest will return inevitably to understanding the basic mechanisms of regulating protein levels that are mediated through signals embedded in the RNA structure. The forward approach to understanding regulated expression lies in the identification of regulatory elements in mRNAs (Mahmood et al. 1999, Boucher et al. 2002 and subsequent purification of binding activities (Mittra & Ray 2004). The 'reverse genetic' approach defines the targets and biological effects of binding by proteins identified in silico. The kinetoplastids possess an abundance of proteins related to RNA-binding proteins (D'Orso et al. 2003, De Gaudenzi et al. 2005, Caro et al. 2006) that are candidates for regulatory functions.Brandão and Fernandes' approach to analyzing the UTRs of the Trypanosoma cruzi calmodulin genes (Brandão & Fernandes 2006) illustrates practical applications of UTR gazing, classification of isolates and a means to predict clinical outcomes of infection with different parasites. The former goal is feasible for defining at least five of the six subdivisions recognized currently in T. cruzi (Brisse et al. 2000, Westenberger et al. 2005. The latter goal remains a major and worthy challenge for the clinicians and molecular diagnosticians, for whom the function of the diagnostic gene is not relevant. Differences in the intergenic regions chosen for study are unlikely to show direct correlations with biological patterns. To relate the primary sequence differences to pathogenesis, molecular biologists may have to focus on mRNA whose protein products relate to the multiple steps of entry into the vertebrate and invertebrate hosts, replication in diverse anatomical environments, survival through the onslaught of simple and complex immune systems, and transmission to the next host in the cycle.How does the field proceed from here? ...

Antileishmanial Chemotherapy through Clemastine Fumarate Mediated Inhibition of the Leishmania Inositol Phosphorylceramide Synthase

“…The majority of mutations were found in the UTRs (14 and 12, respectively), perhaps indicating that these affect regulatory elements such as noncoding RNAs present in these regions in Leishmania . Notably, in Leishmania and other kinetoplastids, UTRs are involved in transcription and gene expression; , therefore, these mutations could influence enzyme content. The total number of variants identified is provided (Table S3), and the high number of SNPs found across the genomes of the selected clones (cl.C and cl.D compared with parental wild type) complicates our interpretation of these polymorphisms.…”

Gene Editing in Trypanosomatids: Tips and Tricks in the CRISPR-Cas9 Era

“…In T. brucei, the 3′-UTR is considered the main regulator of gene expression [58,[61][62][63][64]; but regulatory elements have also been described in the 5' UTRs [78]. Likewise, several studies in Leishmania and T. cruzi have described the presence of regulatory elements in the UTRs of several genes influencing mRNA stability and translation efficiency [79][80][81].…”