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De novo emergence of adaptive membrane proteins from thymine-rich intergenic sequences

By Nikolaos Vakirlis, Omer Acar, Brian Hsu, Nelson Castilho Coelho, S. Branden Van Oss, Aaron Wacholder, Kate Medetgul-Ernar, John Iannotta, Aoife McLysaght, Carlos Camacho, Allyson F. O’Donnell, Trey Ideker, Anne-Ruxandra Carvunis

Posted 29 Apr 2019
bioRxiv DOI: 10.1101/621532 (published DOI: 10.1038/s41467-020-14500-z)

Recent evidence demonstrates that novel protein-coding genes can arise de novo from intergenic loci. This evolutionary innovation is thought to be facilitated by the pervasive translation of intergenic transcripts, which exposes a reservoir of variable polypeptides to natural selection. Do intergenic translation events yield polypeptides with useful biochemical capacities? The answer to this question remains controversial. Here, we systematically characterized how de novo emerging coding sequences impact fitness. In budding yeast, overexpression of these sequences was enriched in beneficial effects, while their disruption was generally inconsequential. We found that beneficial emerging sequences have a strong tendency to encode putative transmembrane proteins, which appears to stem from a cryptic propensity for transmembrane signals throughout thymine-rich intergenic regions of the genome. These findings suggest that novel genes with useful biochemical capacities, such as transmembrane domains, tend to evolve de novo within intergenic loci that already harbored a blueprint for these capacities.

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