Evolutionary divergence of uric acid catabolic enzymes: structure–function constraints and genomic innovations across taxa

Abstract

Uric acid degradation is a model for understanding how gene duplication, loss, and functional divergence drive metabolic evolution. In hominoids and uricotelic animals, uric acid is the terminal purine catabolite, whereas most other taxa further degrade it to allantoin and beyond. Comparative genomics and structural analyses reveal recurrent duplication and repurposing of key enzymes. 5-Hydroxyisourate hydrolase (HIUase) and transthyretin (TTR) share a common ancestral hydrolase, later diverging through neofunctionalization, while independent gene fusions reshaped the pathway, notably the gene fusion of Urah (HIUase) and Urad (2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, or OHCUd) into single-chain allantoin synthases in plants, diatoms, and bacteria. Elastic network modeling this gene fusion shows uncorrelated motions between the catalytic domains, suggesting its advantage stems from fixed stoichiometry and spatial proximity rather than conformational coupling. Further divergence is seen in enzyme families with complementary substrate specificities, and gene clustering in bacteria and yeast reflects regulatory optimization under nitrogen limitation, paralleling the ureide pathway in legumes. In hominoids, pseudogenization of urate oxidase relaxed constraints on downstream enzymes, elevating serum uric acid, an ancestral adaptation now linked to hyperuricemia. Gut microbiome-mediated degradation and links between Urad variants and cancer risk underscore the pathway’s continuing relevance. Mammalian Urad orthologs show strong sequence conservation. Molecular modeling of the human ortholog demonstrated a conserved fold, consistent with a predominantly α-helical secondary structure content supported by circular dichroism, whereas kinetic characterization revealed the absence of detectable catalytic activity. Building on these principles, evolution-guided protein engineering achieved partial functional interconversion between transthyretins and HIUases without disrupting the ancestral scaffold, revealing purine catabolism’s plasticity as a model for enzyme innovation and the metabolism-disease-protein design interface.