2025/03/03 by Antonio Muñoz‐Mérida, A. Jesús Muñoz‐Pajares · 1 voice
Computer Science · #Evolutionary Algorithms and Applications
paper · doi:10.1093/molbev/msag121
openalex publication_date 2025/03/03 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/31
Protein function evolution provides a powerful lens to uncover biological complexity. Here, we introduce the concept of the pan-functionome-the full set of protein functions encoded by the proteome of individuals belonging to a taxonomic group-and explore its evolutionary implications. By analyzing over 1,000 annotated proteomes across major branches of life, we identify systematic differences in functional composition that reflect deep evolutionary patterns. The number of biological processes per protein increases nonlinearly over time, with functional diversification rather than protein expansion driving organismal complexity. Distinct taxonomic divisions invest differently in biological processes, highlighting signatures of multicellularity, metabolism, and stress response. Phylogenetic analyses suggest that the evolution of protein functions follows a non-neutral model. Furthermore, functional profiles allow robust taxonomic classification and reveal unique adaptations in individual organisms. Our findings suggest that the functionome provides a complementary perspective on evolution, with potential applications in taxonomy, evolutionary biology, and comparative genomics.