Strategies for directed and adapted evolution as part of microbial strain engineering

Abstract

The industrial production of chemicals by microorganisms usually requires improvements to the enzymes, pathways, and strain that go beyond the capacity of innate enzymes. To achieve these phenotypes and overcome our limited capacity to de novo design these parts, directed and adaptive evolutionary approaches are used to explore new functions. This review highlights the recent advances in both sequence diversity generation and selection strategies from traditional in vitro mutagenesis to novel in vivo continuous evolution applications. The focus here is on comparison of the different gene diversity methods in an attempt to distinguish the best strategy for protein or strain engineering for a given goal. Furthermore, the important role that screening and selection can play in advancing directed and adapted evolution is discussed. © 2018 Society of Chemical Industry

Biosensor-Coupled In Vivo Mutagenesis and Omics Analysis Reveals Reduced Lysine and Arginine Synthesis To Improve Malonyl-Coenzyme A Flux in Saccharomyces cerevisiae

“…Compared to traditional mutagenesis approaches such as physical and chemical mutagenesis and the construction of the genome modification library ( 14 ) or gene regulation library ( 15 , 16 ), in vivo mutagenesis can achieve continuous mutagenesis during the cultivation ( 17 ). Coupling in vivo mutagenesis with adaptive evolution linked continuous evolution and selection simultaneously and thus has significantly accelerated evolution.…”

Fine‐tuning the (2S)‐naringenin synthetic pathway using an iterative high‐throughput balancing strategy

“…To improve the titer of target chemicals, researchers first focused on screening for high‐activity enzymes in plants, animals, fungi, and bacteria (Jendresen et al, ; Santos et al, ). If the screened enzymes cannot satisfy present requirements of metabolic engineering, then protein engineering strategies, like directed evolution (S. Zhou & Alper, ; S. Zhou et al, ) and computer‐aided methods (Ebert & Pelletier, ; Fang, Zhang, Du, & Chen, ; Verma, Schwaneberg, & Roccatano, ), are typically performed to further improve the properties of the target enzymes. However, high‐efficiency biosynthetic pathways are through the use and regulated expression of high‐activity enzymes.…”

Dextran Aldehyde in Biocatalysis: More Than a Mere Immobilization System

“…Fortunately, there are many ways to enhance enzyme capabilities; for instance, the development of metagenomics tools has permitted the exploitation of all biodiversity, including non-cultivable microorganisms or even no longer existing ones [57][58][59][60]. On the other hand, directed evolution allows for mimicking natural evolution by specifically improving the target property of the desired enzyme [61][62][63][64][65]. Finally, chemical modification and enzyme immobilization [66][67][68][69][70] are evolving in order to allow the development of more specific and directed enzymatic modifications.…”