RNA-Seq reveals that overexpression of TcUBP1 switches the gene expression pattern toward that of the infective form of Trypanosoma cruzi

Trypanosomes regulate gene expression mainly by using posttranscriptional mechanisms. Key factors responsible for carrying out this regulation are RNA-binding proteins, affecting subcellular localization, translation, and/or transcript stability. Trypanosoma cruzi U-rich RNA-binding protein 1 (TcUBP1) is a small protein that modulates the expression of several surface glycoproteins of the trypomastigote infective stage of the parasite. Its mRNA targets are known, but the impact of its overexpression at the transcriptome level in the insect-dwelling epimastigote cells has not yet been investigated. Thus, in the present study, by using a tetracycline-inducible system, we generated a population of TcUBP1-overexpressing parasites and analyzed its effect by RNA-Seq methodology. This allowed us to identify 793 up- and 371 downregulated genes with respect to the wildtype control sample. Among the upregulated genes, it was possible to identify members coding for the TcS superfamily, MASP, MUCI/II, and protein kinases, whereas among the downregulated transcripts, we found mainly genes coding for ribosomal, mitochondrial, and synthetic pathway proteins. RNA-Seq comparison with two previously published datasets revealed that the expression profile of this TcUBP1-overexpressing replicative epimastigote form resembles the transition to the infective metacyclic trypomastigote stage. We identified novel cis-regulatory elements in the 3′-untranslated region of the affected transcripts and confirmed that UBP1m, a signature TcUBP1 binding element previously characterized in our laboratory, is enriched in the list of stabilized genes. We can conclude that the overall effect of TcUBP1 overexpression on the epimastigote transcriptome is mainly the stabilization of mRNAs coding for proteins that are important for parasite infection.