Discovery and characterization of a lactonase in gut microbiota that initiates the metabolism of ellagic acid

Ellagic acid (EA), a natural plant polyphenol, and its metabolite urolithin (Uro) exhibit significant bioactivity, with Uro being recognized as the active compound responsible for the in vivo effects of EA. Although specific intestinal microorganisms that can metabolize EA have been discovered, the corresponding biochemical routes and genetic mechanisms involved in these processes have yet to be fully elucidated. In this study, we employed bioinformatics, biochemical assays, and genetic analyses to discover and characterize an EA lactonase (EAL) from the intestinal bacterium Gordonibacter urolithinfaciens DSM 27213. EAL specifically catalyzes the cleavage of the ester bond in EA, yielding Uro-M5. Notably, EAL and its extensive homologs form a unique subclass within the lactonase and amidohydrolase families. Structural predictions indicate that the active pocket of EAL comprises a propeller-like structure formed by seven {beta}-strands. Additionally, molecular modeling analyses further revealed that EA establishes specific interactions with key catalytic residues within the enzymes binding site. These insights enhance our understanding of the role of intestinal microbial communities in metabolizing plant-derived phenolic compounds, potentially shaping health outcomes and disease management through dietary interventions. Significance StatementEllagic acid (EA), which is abundant in the human gut microbiome, can be metabolized by gut microbes into urolithin A (Uro-A), however, the biochemical mechanisms underlying these transformations remain incompletely understood. In this study, we identified and characterized an EA lactonase (EAL) from the gut bacterium Gordonibacter urolithinfaciens DSM 27213, which serves as a key enzyme in the initial metabolic breakdown of EA. We elucidate the function, distribution, and structure of the EAL. This discovery advances our understanding of Uro-A production within the human body and may provide a foundation for further investigations into the relationship between Uros and human health.