Sense and Antisense Transcription Defines Mitochondrial RNA Boundaries in Trypanosomes

Mitochondrial genomes are often transcribed into polycistronic units wherein protein coding regions are punctuated by tRNAs whose excision defines mRNA boundaries. Although maxicircle DNA of trypanosomes lacks tRNA genes, the monophosphorylated 5′ and uniform 3′ termini of mature mRNAs and rRNAs are indicative of the primary transcript partitioning by an endonuclease. We demonstrate that mRNAs and rRNAs are independently transcribed as extended precursors, and processed by antisense RNA-controlled exonucleolytic trimming that delimits the 3′ end. The transcription start-defined 5′ terminus is converted into the monophosphorylated state by the MERS1 pyrophosphohydrolase complex, which also includes a pentatricopeptide repeat subunit. MERS complex acting as “protein cap” stabilizes mRNAs and rRNAs, but not gRNAs retaining 5′ triphosphate. We identify the RNA editing substrate binding complex as the coupling interface between 5′ modification, 3′ processing, and internal mRNA editing. We conclude that mitochondrial genes are transcribed as individual units irrespective of their genomic location.