Thermo-sensing by mRNA with low-complexity and complementary untranslated sequences in trypanosomes
Parasitic African trypanosomes experience temperature fluctuations due to fever symptomatic of infection, during developmental life cycle transitions in insect vectors and mammalian hosts, or due to diurnal shift. Since trypanosomes exhibit almost exclusive polycistronic transcription, gene expression regulation is dominated by post-transcriptional controls mediated by mRNA 3'-untranslated regions (3'-UTRs). Heat-shock responses have not been described in detail at the transcriptomic or proteomic level, however, and mechanisms underpinning thermo-sensing remain largely uncharacterised. We quantified >9,300 transcripts, and >5,900 proteins in bloodstream form Trypanosoma brucei after growth at 34C, 37C or 40C for six hours. Increased protein abundance correlated with temperature for several hundred genes, encoding both the classical heat-shock proteins, and a second cohort including developmentally regulated genes. Transcript abundance also increased for genes close to transcription initiation sites, but this had minimal impact on protein abundance. Notably, the classical heat-shock response was characterised by both increased mRNA and protein abundance, while increased protein abundance dominated for the second cohort, suggesting translation control. Analysis of 3'-UTRs from post-transcriptionally regulated genes, using motif searching and machine learning, revealed enrichment of (UUA)4 motifs associated with heat-shock proteins, and enrichment of poly-purine and poly-pyrimidine tracts associated with translationally controlled genes. To determine whether these low-complexity sequences increased RNA secondary structure, we disrupted the RNA interference machinery and repeated transcriptomic profiling, essentially using argonaute as an in cellulo probe for native double-stranded RNA (dsRNA). As predicted, thermo-sensitive mRNAs displayed signatures of thermo-sensitive dsRNA formation. Thus, we provide transcriptomic and proteomic profiles of the heat-shock and thermo-sensing response in the African trypanosome. Thermo-sensitive UTRs are enriched in low-complexity and complementary sequences, supporting a post-transcriptional zipper hypothesis whereby sequences that regulate mRNA stability and/or translation are progressively unmasked as temperature increases.