Redundant and non-functional guide RNA genes in Trypanosoma brucei are a consequence of multiple genes per minicircle

The mitochondrial mRNA of the parasitic protozoa Trypanosoma brucei is extensively edited by the insertion, and occasional deletion, of uridine residues. The editing is mediated by over 200 guide RNAs (gRNAs) that are encoded in circular DNA molecules called minicircles. There are some 250 different types of minicircle, called classes, with each encoding several gRNAs. Sequencing of gRNAs and minicircles has revealed a surprising amount of both redundancy, where gRNAs from different minicircle classes edit exactly the same part of an mRNA, and non-functionality, where partial or no complementarity is found between gRNA and mRNA. How does this redundancy and non-functionality arise and persist? We propose the following. Minicircle classes that contain several functional gRNA genes can be lost from the population via drift and replaced by more minicircle classes that contain fewer functional gRNA genes, on the condition that the cells keep a full complement of functional gRNAs. We demonstrate this hypothesis in a computer simulation of a model of minicircle evolution. We show that this process leads to an increasing number of minicircle classes and inevitably to only one functional gRNA per minicircle. Moreover, we show that the genome contains more minicircle classes than is actually necessary for cell survival. We also analyse the available minicircle sequence data and conclude that T. brucei is at a transient stage in this process. In addition, ten new putative gRNAs have been discovered.