Pairs of compensatory frameshifting mutations contribute to evolution of protein-coding sequences in vertebrates and insects

Abstract

AbstractInsertions and deletions of lengths not divisible by 3 in protein-coding sequences cause frameshifts that usually induce premature stop codons and may carry a high fitness cost. However, this cost can be circumvented by a second compensatory indel restoring the reading frame. The role of such compensatory frameshifting mutations (CFMs) in evolution has not been studied systematically. Here, we use whole-genome alignments of protein coding genes of 100 vertebrate species, and of 122 insect species, studying the prevalence of CFMs in their divergence. After stringent filtering, we detect a total of 11 high-confidence genes carrying pairs of CFMs, including three human genes:RAB36, ARHGAP6andNCR3LG1.CFMs tended to occur in genes under relaxed negative selection, indicating that they are typically prevented at functionally important genes. In some instances, mutations closely predating or following the CFMs restored the biochemical similarity of the frameshifted segment to the ancestral sequence, possibly reducing or negating the fitness cost of a CFM. Typically, however, the resulting sequence bore no similarity to the ancestral one, indicating that the CFMs can uncover radically novel regions of sequence space. In total, CFMs represent a potentially important and previously overlooked source of novel variation in amino acid sequences.