Evolutionary convergence in fungal ligninolytic enzymes

The development of similar solutions for the same selective pressure is a common event in biological systems. During the last decades evolutionary convergence has been extensively investigated using bioinformatic tools. Here we track the ability to degrade lignin as a phenotypic trait in fungi, and analyze its evolution in Polyporales, where many wood-rotting species are included. Recent studies on oxidative biodegradation of lignin established the origin of wood-rotting fungi in the Carboniferous period, associated with the production of the first ligninolytic peroxidases. The subsequent evolution of these enzymes in Polyporales is analyzed by ancestral sequence reconstruction and heterologous expression of synthetic genes (ancestral enzyme resurrection). Lignin degradation during the evolution of these organisms started with the production of peroxidases generating Mn³⁺, a diffusible oxidizer acting on the minor phenolic moiety of lignin. Later, these enzymes acquired the ability to oxidize nonphenolic lignin directly at a surface oxidation site, while improving their stability at acidic pH where ligninolysis occurs in nature. However, the appearance of the surface tryptophan responsible for lignin oxidation was not an isolated event in the evolution of ligninolytic peroxidase. Ancestral enzyme resurrection showed the molecular changes that led to the appearance of the same surface oxidation site in two distant peroxidase lineages. By characterization of the resurrected enzymes, we demonstrate convergent evolution at the amino-acid level during the evolution of fungal peroxidases, and track the different changes leading to phylogenetically-distant ligninolytic peroxidases from ancestors lacking the ability to degrade lignin.