Combing Directed Enzyme Evolution with Metabolic Engineering to Develop Efficient Microbial Cell Factories

The booming field of synthetic biology and metabolic engineering provides promising approaches for sustainable manufacturing of chemicals from renewable feedstocks with microbial cell factories. Classical metabolic engineering strategies mainly focus on altering gene expression levels and enzyme concentrations to improve the metabolic fluxes of specific pathways. However, the impact and limitations of enzyme properties, which are usually ignored in classical metabolic engineering efforts, can hinder further optimization of microbial cell factories. Protein engineering and directed evolution are powerful tools for modifying proteins to achieve desirable properties, and they have been integrated into metabolic engineering efforts to build highly efficient metabolic pathways and optimal industrial chassis. In this review, we present traditional and data-driven strategies and techniques of directed evolution, including random library design, semirational design, smart library design, and in vivo continuous evolution. We also discuss how these directed evolution strategies have been applied in metabolic engineering toward superphenotypes that cannot be achieved through simple gene overexpression or knockout. Finally, we discuss the challenges of applying protein engineering in metabolic engineering and the prospects for accelerating the directed evolution workflow using the state-of-art technologies.