Biosystems design by directed evolution

Abstract

Through iterative rounds of genetic diversification and screening or selection, directed evolution has been widely used to engineer relatively simple biosystems such as nucleic acids and proteins with desired functions. In addition, directed evolution has played an important role in engineering more complex biosystems such as pathways and genomes. Since 2013, directed evolution has been further explored for biosystems design with numerous newly developed techniques that have enabled design and engineering of proteins, pathways, and genomes in a much more effective manner. In this review, we will highlight the abiotic biotransformations arisen from directed evolution and novel strategies for continuous evolution in vivo and ultrahigh‐throughput screening. We will also discuss the future challenges and opportunities of applying directed evolution for biosystems design.

Pervasive cooperative mutational effects on multiple catalytic enzyme traits emerge via long-range conformational dynamics

“…irected evolution constitutes a powerful tool for optimizing protein properties, including activity, substrate scope, selectivity, stability, allostery or binding affinity. By applying iterative rounds of gene mutagenesis, expression and screening (or selection), proteins have been engineered for developing more efficient industrial biocatalytic processes [1][2][3][4] . Directed evolution has also provided important insights into the relationship between protein sequence and function [4][5][6] , yet understanding the intricacies of non-additive epistatic effects remains a challenge 7 .…”

Computational design of noncanonical amino acid-based thioether staples at N/C-terminal domains of multi-modular pullulanase for thermostabilization in enzyme catalysis

“…Enzyme thermostabilization against thermal denaturation has been an urgent and long-standing goal in enzyme design and engineering. Directed evolution [5] is a well-known strategy in protein engineering for enzyme thermostabilization [6] that is generally applicable with the aid of high-throughput screening [7] . Although it is often effective, directed evolution is labor-intensive and time-consuming.…”

“…Although it is often effective, directed evolution is labor-intensive and time-consuming. For instance, multiple rounds of mutation and screening are required to obtain desired variants with obvious improvements in thermostability [7] . During the third wave of biocatalysis, the process of protein thermostabilization via computational design has been promoted based on a large amount of protein structure analysis data and increased bioinformatics tool development [4] , [8] .…”

Pervasive cooperative mutational effects on multiple catalytic enzyme traits emerge via long-range conformational dynamics

“…Directed evolution constitutes a powerful tool for optimizing protein properties including activity, substrate scope, selectivity, stability, allostery or binding affinity. By applying iterative rounds of gene mutagenesis, expression and screening (or selection), proteins have been engineered for developing more efficient industrial biocatalytic processes [1][2][3][4] .…”

“…Epistasis means that the phenotypic consequences of a mutation depend on the genetic background [8][9][10][11] . Epistatic effects can be negative 3 (antagonistic/deleterious) or positive (synergistic/cooperative) if the respective predictive value is smaller or greater in sign/magnitude than the expected value under additivity.…”