Single nucleotide +1 frameshifts in an apparently functional mitochondrial cytochrome b gene in ants of the genus Polyrhachis.

Twelve of 30 species examined in the ant genus Polyrhachis carry single nucleotide insertions at one or two positions within the mitochondrial cytochrome b (cytb) gene. Two of the sites are present in more than one species. Nucleotide substitutions in taxa carrying insertions show the strong codon position bias expected of functional protein coding genes, with substitutions concentrated in the third positions of the original reading frame. This pattern of evolution of the sequences strongly suggests that they are functional cytb sequences. This result is not the first report of +1 frameshift insertions in animal mitochondrial genes. A similar site was discovered in vertebrates, where single nucleotide frameshift insertions in many birds and a turtle were reported by Mindell et al. (Mol Biol Evol 15:1568, 1998). They hypothesized that the genes are correctly decoded by a programmed frameshift during translation. The discovery of four additional sites gives us the opportunity to look for common features that may explain how programmed frameshifts can arise. The common feature appears to be the presence of two consecutive rare codons at the insertion site. We hypothesize that the second of these codons is not efficiently translated, causing a pause in the translation process. During the stall the weak wobble pairing of the tRNA bound in the peptidyl site of the ribosome, together with an exact Watson-Crick codon-anticodon pairing in the +1 position, allows translation to continue in the +1 reading frame. The result of these events is an adequate level of translation of a full-length and fully functional protein. A model is presented for decoding of these mitochondrial genes, consistent with known features of programmed translational frameshifting in the yeast TY1 and TY3 retrotransposons.