Protein tandem repeats that produce frameshifts can generate new structural states and functions

Abstract

The genetic code uses three-nucleotide units to encode each amino acid inproteins. Insertions or deletions of nucleotides not divisible by three shiftthe reading frames, resulting in significantly different protein sequences.These events are disruptive but can also create variability important forevolution. Previous studies suggested that the genetic code and genesequences evolve to minimize frameshift effects, maintaining similar physicochemicalproperties to their reference proteins. Here, we focused on tandemrepeat sequences, known as frameshift hotspots. Using cutting-edgebioinformatics tools, we compared reference and frameshifted proteinsequences within tandem repeats across 50 prokaryotic and eukaryotic proteomes.We showed that, in contrast to the general tendency, frameshiftswithin these regions, especially with short repeats, lead to a significantincrease in hydrophobicity and arginine content. Additionally, the frameshifts,particularly in short tandem repeats, rearrange transmembraneregions, potentially converting soluble proteins into membrane proteinsand vice versa. Given their occurrence in rapidly evolving, essential proteins,such changes may promote rapid adaptability. Our large-scale ALPHAFOLDmodeling suggested that frameshift events can generate novelstructures and functions, enabling the synthesis of multiple protein variantswithin the same coding region. Overall, frameshifts cause more drasticchanges in tandem repeat sequences compared to non-repetitive sequencesand therefore can be a primary cause of altered functions, cellular localization,and the development of various pathologies.