Using continuous directed evolution to improve enzymes for plant applications

• Published in: Plant physiology (Bethesda) Vol. 188; no. 2; pp. 971 - 983
• Main Authors: García-García, Jorge D, Van Gelder, Kristen, Joshi, Jaya, Bathe, Ulschan, Leong, Bryan J, Bruner, Steven D, Liu, Chang C, Hanson, Andrew D
• Format: Journal Article
• Language: English
• Published: United States American Society of Plant Biologists 04.02.2022; Oxford University Press
• Subjects: BASIC BIOLOGICAL SCIENCES; Directed Molecular Evolution - methods; Enzymes - genetics; Plant Breeding - methods; Plant Proteins - genetics; Regular Issue Content; Saccharomyces cerevisiae - genetics
• ISSN: 0032-0889; 1532-2548; 1532-2548
• DOI: 10.1093/plphys/kiab500

Continuous directed evolution of enzymes and other proteins in microbial hosts is capable of outperforming classical directed evolution by executing hypermutation and selection concurrently in vivo, at scale, with minimal manual input. Provided that a target enzyme’s activity can be coupled to growth of the host cells, the activity can be improved simply by selecting for growth. Like all directed evolution, the continuous version requires no prior mechanistic knowledge of the target. Continuous directed evolution is thus a powerful way to modify plant or non-plant enzymes for use in plant metabolic research and engineering. Here, we first describe the basic features of the yeast (Saccharomyces cerevisiae) OrthoRep system for continuous directed evolution and compare it briefly with other systems. We then give a step-by-step account of three ways in which OrthoRep can be deployed to evolve primary metabolic enzymes, using a THI4 thiazole synthase as an example and illustrating the mutational outcomes obtained. We close by outlining applications of OrthoRep that serve growing demands (i) to change the characteristics of plant enzymes destined for return to plants, and (ii) to adapt (“plantize”) enzymes from prokaryotes—especially exotic prokaryotes—to function well in mild, plant-like conditions.