Degradation of the unstable EP1 mRNA in Trypanosoma brucei involves initial destruction of the 3′-untranslated region

Kinetoplastid protozoa regulate their gene expression primarily through control of mRNA degradation and translation. We describe here the degradation of three reporter rnRNAs in Trypanosoma brucei. One mRNA had the 3'-untranslated region (3'-UTR) from the developmentally regulated EP1 mRNA, which is abundant in the procyclic (tsetse fly) form of them parasite but is almost undetectable in the bloodstream form. This untranslated region includes a 26 nt U-rich sequence that causes extreme RNA instability in the bloodstream form. The two other RNAs, which are not developmentally regulated, had either the actin 3'-UTR, or a version of the EP1 sequence lacking the 26 nt bloodstream-form instability element. All RNAs had poly(A) tails similar to 200 nt long, in both bloodstream and procyclic forms. Degradation of the two constitutively expressed mRNAs involved deadenylation and degradation by both 5'-->3' and 3'-->5' exonucleases. In contrast, in bloodstream forms, the 3'-end of the RNA bearing the blood-stream-form instability element disappeared very rapidly after transcription inhibition and partially deadenylated intermediates were not seen. Them instability element may cause extremely rapid deadenylation, or it may be targeted by an endonuclease.