Scaling of Protein Function Across the Tree of Life

ABSTRACT Scaling laws are a powerful way to compare genomes because they put all organisms onto a single curve and reveal non-trivial generalities as genomes change in size. The abundance of functional categories in a given genome scales with genome size, suggesting that universal constraints shape category abundance. Here we look across the tree of life to understand how genome evolution may be related to functional scaling. We revisit previous observations of functional genome scaling with an expanded taxonomy by analyzing 3726 bacterial, 220 archaeal, and 79 unicellular eukaryotic genomes. We find that for some functional classes, scaling is best described by multiple exponents, revealing previously unobserved shifts in scaling as genomes grow or contract. Furthermore, scaling varies between phyletic groups and is less universal than previously thought, with scaling shifts varying uniquely between domains and scaling exponents varying uniquely between phyla. We also find that individual phyla frequently span scaling exponents of functional classes, revealing that individual clades can move across scaling exponents. Across the tree of life, variability in functional scaling is not accounted for by genome phylogeny, suggesting that physiological and/or cell plan outweighs phylogeny.