Abstract
BackgroundTrypanosomes mostly control gene expression by post-transcriptional events such as modulation of mRNA stability and translational efficiency. These mechanisms involve RNA-binding proteins (RBPs), which associate with transcripts to form messenger ribonucleoprotein (mRNP) complexes.ResultsIn this study, we report the identification of mRNA targets for Trypanosoma cruzi U-rich RBP 1 (TcUBP1) and T. cruzi RBP 3 (TcRBP3), two phylogenetically conserved proteins among Kinetoplastids. Co-immunoprecipitated RBP-associated RNAs were extracted from mRNP complexes and binding of RBPs to several targets was confirmed by independent experimental assays. Analysis of target transcript sequences allowed the identification of different signature RNA motifs for each protein. Cis-elements for RBP binding have a stem-loop structure of 30–35 bases and are more frequently represented in the 3'-untranslated region (UTR) of mRNAs. Insertion of the correctly folded RNA elements to a non-specific mRNA rendered it into a target transcript, whereas substitution of the RNA elements abolished RBP interaction. In addition, RBPs competed for RNA-binding sites in accordance with the distribution of different and overlapping motifs in the 3'-UTRs of common mRNAs.ConclusionFunctionally related transcripts were preferentially associated with a given RBP; TcUBP1 targets were enriched in genes encoding proteins involved in metabolism, whereas ribosomal protein-encoding transcripts were the largest group within TcRBP3 targets. Together, these results suggest coordinated control of different mRNA subsets at the post-transcriptional level by specific RBPs.
Highlights
Trypanosomes mostly control gene expression by post-transcriptional events such as modulation of mRNA stability and translational efficiency
Functionally related transcripts were preferentially associated with a given RNA-binding protein (RBP); Trypanosoma cruzi U-rich RBP 1 (TcUBP1) targets were enriched in genes encoding proteins involved in metabolism, whereas ribosomal protein-encoding transcripts were the largest group within T. cruzi RBP 3 (TcRBP3) targets
These results suggest coordinated control of different mRNA subsets at the post-transcriptional level by specific RBPs
Summary
Trypanosomes mostly control gene expression by post-transcriptional events such as modulation of mRNA stability and translational efficiency. Being a single cell that suffers continuous environmental changes, T. cruzi needs to quickly regulate the expression of many genes to allow rapid adaptation (reviewed in references [1] and [2]) Such microorganisms control protein synthesis mostly by post-transcriptional mechanisms. With a single exception [8], no classical promoters have been identified in trypanosomes, and there is no evidence for controlled transcriptional initiation of genes through modulation of RNA polymerase II activity [9] Given these peculiarities, trypanosomes represent an interesting model for studies on mechanisms of post-transcriptional regulation of gene expression [3,10], in which mRNA degradation/stabilization is the main control feature. RNA interference is involved in gene-silencing phenomena in some species of the Trypanosomatidae family [16,17]
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