Probing pathways of adaptation with continuous evolution

Zhong, Ziwei; Liu, Chang C.

doi:10.1016/j.coisb.2019.02.002

Cited by 3 publications

(4 citation statements)

References 108 publications

(125 reference statements)

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“…The effects of cumulative mutations on enzyme activity can be visualized as a "fitness landscape" in which compounding beneficial changes lead to fitness peaks and detrimental changes cause fitness valleys [21] (Figure 1). Given the existence of fitness valleys, reaching an optimal peak may require "valley crossing" through intermediate steps that are deleterious [22,23]. Traversing valleys can occur by relaxing selective pressure or by introducing multiple mutations simultaneously, effectively skipping over the intermediate, less-fit steps.…”

Section: Directed Evolutionmentioning

confidence: 99%

“…Creating new-to-nature functions. Because continuous directed evolution dramatically improves access to the vast protein design landscape, it can create new-to-nature features more quickly than classic directed evolution [23,61]. Such new features include altered substrate specificity [62] and catalysis of a different type of reaction [8].…”

Section: Future Perspectivesmentioning

confidence: 99%

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Potential for Applying Continuous Directed Evolution to Plant Enzymes: An Exploratory Study

García‐García

Joshi

Patterson

et al. 2020

Life

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Plant evolution has produced enzymes that may not be optimal for maximizing yield and quality in today’s agricultural environments and plant biotechnology applications. By improving enzyme performance, it should be possible to alleviate constraints on yield and quality currently imposed by kinetic properties or enzyme instability. Enzymes can be optimized more quickly than naturally possible by applying directed evolution, which entails mutating a target gene in vitro and screening or selecting the mutated gene products for the desired characteristics. Continuous directed evolution is a more efficient and scalable version that accomplishes the mutagenesis and selection steps simultaneously in vivo via error-prone replication of the target gene and coupling of the host cell’s growth rate to the target gene’s function. However, published continuous systems require custom plasmid assembly, and convenient multipurpose platforms are not available. We discuss two systems suitable for continuous directed evolution of enzymes, OrthoRep in Saccharomyces cerevisiae and EvolvR in Escherichia coli, and our pilot efforts to adapt each system for high-throughput plant enzyme engineering. To test our modified systems, we used the thiamin synthesis enzyme THI4, previously identified as a prime candidate for improvement. Our adapted OrthoRep system shows promise for efficient plant enzyme engineering.

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Section: Directed Evolutionmentioning

confidence: 99%

Section: Future Perspectivesmentioning

confidence: 99%

Potential for Applying Continuous Directed Evolution to Plant Enzymes: An Exploratory Study

García‐García

Joshi

Patterson

et al. 2020

Life

Self Cite

View full text Add to dashboard Cite

show abstract

“…The effects of cumulative mutations on enzyme activity can be visualized as a 'fitness landscape' in which compounding beneficial changes lead to fitness peaks and detrimental changes cause fitness valleys [20] (Figure 1). Given the existence of fitness valleys, reaching an optimal peak may require 'valley crossing' through intermediate steps that are deleterious [21,22]. Traversing valleys can occur by relaxing selective pressure or by introducing multiple mutations simultaneously, effectively skipping over the intermediate, less-fit steps.…”

Section: Directed Evolutionmentioning

confidence: 99%

“…(iv) Creating new-to-nature functions. Because continuous directed evolution dramatically improves access to the vast protein design landscape, it can create new-to-nature features faster than classic directed evolution [22,59]. Such new features include altered substrate specificity [60] and catalysis of a different type of reaction [8].…”

Section: Future Perspectivesmentioning

confidence: 99%

Potential For Applying Continuous Directed Evolution To Plant Enzymes

García‐García

Joshi

Patterson

et al. 2020

Preprint

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SUMMARYPlant evolution has produced enzymes that may not be optimal for maximizing yield and quality in today’s agricultural environments and plant biotechnology applications. By improving enzyme performance, it should be possible to alleviate constraints on yield and quality currently imposed by kinetic properties or enzyme instability. Enzymes can be optimized faster than naturally possible by applying directed evolution, which entails mutating a target gene in vitro and screening or selecting the mutated gene products for the desired characteristics. Continuous directed evolution is a more efficient and scalable version that accomplishes the mutagenesis and selection steps simultaneously in vivo via error-prone replication of the target gene and coupling of the host cell’s growth rate to the target gene’s function. However, published continuous systems require custom plasmid assembly, and convenient multipurpose platforms are not available. We discuss two systems suitable for continuous directed evolution of enzymes, OrthoRep in Saccharomyces cerevisiae and EvolvR in Escherichia coli, and our pilot efforts to adapt each system for high-throughput plant enzyme engineering. To test our modified systems, we used the thiamin synthesis enzyme THI4, previously identified as a prime candidate for improvement. Our adapted OrthoRep system shows promise for efficient plant enzyme engineering.

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