Metabolic networks—complex systems of chemical reactions within cells—offer new clues about the earliest stages of enzyme evolution. Enzymes are proteins that act as catalysts in these reactions, enabling life's essential processes like breaking down molecules for energy or building complex compounds. These enzymes are encoded by genes, and by comparing genes across all living organisms, scientists trace back to the last universal common ancestor (LUCA), a hypothetical organism thought to exist around 4 billion years ago. LUCA is believed to be the ancestor of all life on Earth. However, even LUCA's proteins were complex enough to support the basic functions of a living cell. Traditional gene comparison methods struggle to explain how these complex proteins evolved before LUCA. As a result, researchers are turning to alternative approaches, such as examining the evolution of enzymes involved in metabolic reactions, which are the chemical processes that sustain life. Metabolic reactions are interconnected, forming a layered system where the output of one reaction becomes the input for another. This complexity suggests that studying these layers can reveal insights into early metabolic systems and the environments in which the first life forms existed. Dr. Liam M. Longo, a researcher at the Earth-Life Science Institute (ELSI) in Japan, highlights the significance of this approach. Alongside colleagues Harrison B. Smith and Tatsuya Corlett, Longo led a study to reconstruct the history of enzymes by analyzing the layers of metabolism. Their research, published in the Proceedings of the National Academy of Sciences, used extensive databases of metabolic reactions and protein structures to build a model of how enzymes might have evolved over time. The team analyzed 4,294 metabolites and 7,678 reactions involving 4,331 enzymes, identifying 396 distinct protein structures. They constructed a model called "enzyme-gated network expansion," starting with simple molecules believed to have existed before LUCA. The model suggested that many of the earliest enzymes had α/β structures, which are different from the more common α-only or β-only structures found in modern enzymes. This finding suggests that α/β structures might have played a crucial role in early metabolic processes, possibly due to their ability to bind phosphate, a key component in many biochemical reactions. One of the study’s most intriguing findings was how enzymes adapted to the rise of oxygen in Earth’s atmosphere due to photosynthesis. While some new enzymes evolved, many oxygen-related enzymes were variations of older ones, showing that adaptation and refunctionalization were key strategies in enzyme evolution. These results provide a clearer picture of the likely structures and functions of the first enzymes and how different protein folds evolved over time. By combining this approach with studies of highly conserved structures like ribosomes, scientists may gain deeper insights into the evolution of enzymes and metabolism. This research marks an important step toward understanding the integrated history of protein evolution, linking enzymes, cofactors, and metabolic reactions in a unified framework.