Synthetic Biocatalysts for Biomanufacturing

Enzymes as the main form of biocatalysts exhibit obvious advantages for catalyzing reactions, including mild conditions, high specificity, and environmental friendly. Since natural enzymes are rarely suitable for industrial applications, it has spawned the development of enzymes with desired functions and properties. Protein engineering has been applied extensively to improve enzyme properties. The concept of directed evolution of enzymes opened a new chapter of protein modification and design. The most classical strategy is saturation mutations targeting the active sites, including combinational active-site saturation test and iterative saturation mutagenesis, which are introduced based on the preliminary screening to further optimize the screening results. Furthermore, impressively, a series of protein engineering strategies have been developed, like structure-directed mutagenesis and machine learning. At the beginning of the twenty-first century, more biotechnologies emerged and gradually advanced to computational enzyme redesign and de novo design.

In the multiple waves of biocatalyst development, understanding of the protein structure–function relationships has been deepened tremendously with advances in sequencing technology, structural analysis, computing power, and the emergence of advanced algorithms. Moving forward from directed evolution to bioinformatics approaches, structural and molecular mechanism-based rational design and ultimately big data-guided machine learning present a progressive process for exploration in protein engineering. With the increase in discovery of functional enzymes deposited in databases, protein co-evolution, based on multiple sequence alignment analysis, has been applied in gradual development from protein structure prediction to protein function improvement, involving identification of functional sites in the “non-functional regions” far from the active site.

In this special issue, a series of articles by senior experts in this field are presented, providing a state-of-the-art view of synthetic biocatalysts for biomanufacturing. Particularly, this issue begins with the understanding of molecular insights into enzymatic catalysis and enzyme engineering by machine learning-aided directed evolution and site-directed mutagenesis. Next, adoption of protein engineering strategies in enhancing enzymatic activity and stability is discussed. Finally, the applications of biocatalysts in various forms for bio-manufacturing functional carbohydrates, such as N-acetylneuraminic acid, trehalose, and nigerose, are presented. In conclusion, the latest advances in synthetic biocatalysts for biomanufacturing are highlighted in these articles.