Pairs of Mutually Compensatory Frameshifting Mutations Contribute to Protein Evolution

Area of Science:

• Evolutionary Biology
• Genetics
• Molecular Biology

Background:

• Insertions and deletions (indels) not divisible by three in protein-coding genes cause frameshifts, often leading to premature stop codons and high fitness costs.
• Compensatory indels can restore the reading frame, potentially mitigating the fitness cost of frameshifts.
• The evolutionary significance of pairs of compensatory frameshifting mutations (pCFMs) remains largely uninvestigated.

Purpose of the Study:

• To systematically investigate the prevalence and evolutionary role of pCFMs in protein-coding genes.
• To identify genes and species exhibiting pCFMs and analyze their characteristics.

Main Methods:

• Whole-genome alignments of protein-coding genes from 100 vertebrate and 122 insect species were analyzed.
• Identification and stringent quality filtering of candidate pCFM genes were performed.
• Analysis of amino acid sequence similarity before and after pCFMs compared to ancestral sequences and random sequences.

Main Results:

• A total of 624 candidate pCFM genes were detected across the studied species.
• Six genes, including three human genes (RAB36, ARHGAP6, NCR3LG1), passed stringent quality filtering.
• pCFMs often resulted in significant divergence from ancestral amino acid sequences, suggesting exploration of novel protein space rather than simple restoration of biochemical similarity.

Conclusions:

• pCFMs represent a previously overlooked source of novel amino acid sequence variation.
• These mutation pairs can facilitate evolutionary innovation by enabling access to new protein sequence possibilities.
• The findings highlight the importance of considering frameshifting mutations in evolutionary studies.