Evolutionary origins of protein novelty across an entire yeast subphylum

Abstract

Genes encoding novel protein sequences are a ubiquitous feature of genomes. They fuel molecular and cellular evolutionary innovations and frequently contribute to species-specific characteristics. We are now unravelling the processes by which they originate, including de novo from noncoding sequences and through extreme divergence, yet how much and what types of novel proteins evolve through each process is still unclear Does the mechanism of origination shape the structural and functional potential of the resulting proteins? Here, we conducted a broad computational investigation of genetic and protein novelty at the scale of the entire subphylum of Saccharomycotina yeasts. We detected more than 5,000 robust de novo genes across 332 species and compared them to more than 10,000 novel genes resulting from extreme sequence divergence, revealing two distinct modes of evolution of novelty. A remarkable 40% of de novo proteins are predicted to localize to mitochondria compared to only 15% of divergent, with the latter also being substantially longer and more disordered. A detailed analysis of conservatively predicted tertiary structures of novel proteins shows that “invention” of novel folds can happen through both processes but is more likely to occur de novo. We also illustrate cases of evolutionary “re-invention” of existing protein folds from non-coding sequences. Our work deepens our understanding of the origins and importance of novel proteins opening new directions for further structural and functional characterization.