Mitochondrial dual-coding genes in Trypanosoma brucei

Abstract

Trypanosoma brucei is transmitted between mammalian hosts by the tsetse fly. In the mammal, they are exclusively extracellular, continuously replicating within the bloodstream. During this stage, the mitochondrion lacks a functional electron transport chain (ETC). Successful transition to the fly, requires activation of the ETC and ATP synthesis via oxidative phosphorylation. This life cycle leads to a major problem: in the bloodstream, the mitochondrial genes are not under selection and are subject to genetic drift that endangers their integrity. Exacerbating this, T. brucei undergoes repeated population bottlenecks as they evade the host immune system that would create additional forces of genetic drift. These parasites possess several unique genetic features, including RNA editing of mitochondrial transcripts. RNA editing creates open reading frames by the guided insertion and deletion of U-residues within the mRNA. A major question in the field has been why this metabolically expensive system of RNA editing would evolve and persist. Here, we show that many of the edited mRNAs can alter the choice of start codon and the open reading frame by alternative editing of the 5’ end. Analyses of mutational bias indicate that six of the mitochondrial genes may be dual-coding and that RNA editing allows access to both reading frames. We hypothesize that dual-coding genes can protect genetic information by essentially hiding a non-selected gene within one that remains under selection. Thus, the complex RNA editing system found in the mitochondria of trypanosomes provides a unique molecular strategy to combat genetic drift in non-selective conditions.

Trypanosomatid mitochondrial RNA editing: dramatically complex transcript repertoires revealed with a dedicated mapping tool

“…Thus, T-Aligner has allowed the discovery of potential organism-specific mitochondrial genome products. Our results, placed alongside those from Perkinsela ( 12 ) and T. brucei ( 18 , 24 , 37 , 42 ), demonstrate that U-indel RNA editing is universally an extremely chaotic and ‘noisy’ process with ample possibility for functional alternative products. These alternative products could be informative (see, e.g.…”

“…Possessing an inherent possibility for the emergence of radically new protein sequences (currently at background levels) may confer an evolutionary advantage. A mitochondrial gene coding for two radically different transcripts (due to a frameshift introduced by RNA editing, for example) might by advantageous for another reason ( 37 ). If the canonical mitochondrial protein is dispensable at a certain life cycle stage (for instance, bloodstream T. brucei ), the gene would be easily lost due to mutations and genetic drift, but the loss would be prevented if the frameshifted transcript version is functional and indispensable at this life cycle stage.…”

“…Another group of abundant products resulting from one or few alternatively edited sites are extensions, truncations, and alternative sequences of the 5′ ends and 3′ ends of pan-edited mRNAs, such as with L. pyrrhocoris ND8 or L. pyrrhocoris and T. cruzi RPS12. Others’ analyses identified alternative 5′ ends of T. brucei RPS12 ( 24 ) and CR3 and ND7 ( 37 ), the latter even describing the gRNAs likely responsible for such differences. If such alternative products were translated, they could retain at least some function of the canonical product.…”

“…This initial restoration event made the involved short RNAs and enzymatic tools indispensable and precipitated fixation of further mutations to be corrected in a similar manner. Other evolutionary explanations that invoke selective advantage have been proposed for the emergence of U-indel RNA editing ( 35 – 37 ). Evolutionary theories can be evaluated by analyzing similarities and differences of RNA processing events in organisms utilizing them.…”

“…These alternative products could be informative (see, e.g. ( 37 )) when considering the merits of constructive neutral evolution versus conferral of selective advantage as the reason this complex RNA editing process appears in nature.…”