Computationally Guided Characterization of Carboxylic Acid Reductases for Expanding Aldehyde Bioproduction

While industrial biosynthesis has primarily focused on overproduction of naturally-occuring metabolites, there is an urgent need to expand our biochemical capabilities toward chemical structures that do not occur in nature. To diversify the types of chemicals that can be made by biological synthesis, we must rely on enzyme promiscuity to catalyze reactions on non-native substrates for which limited data currently exists. Aldehydes are commonly used in polymerization chemistry as well as many flavoring and perfume additives; however, the diversity of aldehydes is low in native metabolomes, particularly compared to related structures like alcohols and carboxylic acids. We use a dual computational and experimental approach to assess enzyme reactivity for a range of enzymes that reduce carboxylic acids to aldehydes. Using two of our own computational tools, the biochemical network simulator BNICE and the enzyme prediction tool SimZyme, we were able to identify a group of enzymes that convert carboxylic acids to aldehydes, mostly through a thermodynamically favorable, conserved phosphopantetheine-mediated reduction. We then expanded the scope to homologues of the original enzymes. We are now able to give an expanded view of several carboxylic acid precursors that can be converted to aldehydes, as well as which enzymes have preferences for different carboxylic-acid-containing substrates. By exploring the catalytic limits of these enzymes we are able to provide novel insight for the production of diverse bio-aldehydes.