Machine learning reveals signatures of promiscuous microbial amidases for micropollutant biotransformations

Abstract

Organic micropollutants, including pharmaceuticals, personal care products, pesticides, and food additives, are widespread in the environment, causing potentially toxic effects. Human waste is a direct source of micropollutants, with the majority of pharmaceuticals being excreted through urine. Urine contains its own microbiota with the potential to catalyze micropollutant biotransformations. Amidase signature (AS) enzymes are known for their promiscuous activity in micropollutant biotransformations, but the potential for AS enzymes from the urinary microbiota to transform micropollutants is not known. Moreover, the characterization of AS enzymes to identify key chemical and enzymatic features associated with biotransformation profiles is critical for developing benign-by-design chemicals and micropollutant removal strategies. Here, to uncover the signatures of AS enzyme–substrate specificity, we tested 17 structurally diverse compounds against a targeted enzyme library consisting of 40 AS enzyme homologues from diverse urine microbial isolates. The most promiscuous enzymes were active on nine different substrates, while 16 enzymes had activity on at least one substrate and exhibited diverse substrate specificities. Using an interpretable gradient boosting machine learning model, we identified chemical and amino acid features associated with AS enzyme biotransformations. Key chemical features from our substrates included the molecular weight of the amide carbonyl substituent and the number of formal charges in the molecule. Four of the identified amino acid features were located in close proximity to the substrate tunnel entrance. Overall, this work highlights the understudied potential of urine-derived microbial AS enzymes for micropollutant biotransformation and offers insights into substrate and protein features associated with micropollutant biotransformations for future environmental applications.