The history of enzyme evolution embedded in metabolism

Phylogenetic reconstructions are a primary record of protein evolution. But what other records can attest to the deep history of enzymes, and what tools are needed to decode their meaning? Here, we demonstrate that the history of enzyme discovery and reuse is embedded within the web of interdependencies that constitute contemporary, biosphere-scale metabolism. Using a simple network analysis approach, we reconstruct both the relative temporal ordering of enzyme domain emergence and, where possible, the first reactions that they catalyzed. These network-based histories were found to be broadly concordant with phyletic information, suggesting that the two approaches reflect related generative processes. When enzyme emergence is initiated after the discovery of nucleotide cofactors, a predominantly stepwise trajectory of domain discovery is recovered. We find that the earliest enzyme-mediated metabolisms were dominated by α/β domains, likely due to their high discoverability and functional potential under constraint. Finally, we quantify how the protein universe responded to a major transition, the biological production of molecular oxygen, by preferentially reusing pre-existing enzyme domains. This work presents a self-consistent model of metabolic and enzyme evolution, essential progress towards integrating multiple, independent records into a unified history of protein evolution.