Harnessing the Power of SMART Single-Molecule Display for Enzyme Evolution: A Focus on Oxidase

Abstract

For a rapid and cost-effective evolution of tailor-made enzymes, we established a high-throughput in vitro selection platform named SMART (Single-Molecule Assay on Ribonucleic acid by Translated product), integrating mRNA display, next-generation sequencing, and bioinformatics. SMART represents a versatile system where a module termed an auxiliary unit allows enzyme-specific selection under various experimental conditions. Here, we report on the establishment of SMART for oxidases using a model enzyme, Schizosaccharomyces pombed-amino acid oxidase (SpDAAO), and ascorbate peroxidase 2 as the auxiliary enzyme to detect hydrogen peroxide produced by the oxidase, and mediate biotinylation of active single-molecule display complexes. As a proof-of-concept, a library including site-saturation mutagenesis at the catalytic residue Y232 of SpDAAO was subjected to a single SMART selection round, yielding enrichment of the active enzyme variant. The results demonstrate the utility of SMART as a fast, robust, and efficient platform with the potential of customization for other enzyme chemistries through appropriate modifications of the auxiliary unit. Using SMART, desired enzyme variants can be selected in just a few hours by a single person without the need for costly equipment or any bias or limitations.