Directed Evolution of an Enantioselective Enoate-Reductase: Testing the Utility of Iterative Saturation Mutagenesis

Directed evolution has emerged as a powerful method for engineering essentially any catalytic parameter of enzymes for application in synthetic organic chemistry and biotechnology, including thermostability, substrate scope, and enantioselectivity. Enantioselectivity is especially crucial when applying biocatalysts to synthetic organic chemistry. This contribution focuses on recent methodology developments in laboratory evolution of stereoselective enzymes, hydrolases, and monooxygenases serving as the enzymes. Specifically, iterative saturation mutagenesis (ISM) has been developed as an unusually effective method to evolve enhanced or reversed enantioselectivity, broader substrate scope, and/or higher thermostability of enzymes.

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Refactoring the Genetic Code for Increased Evolvability

10.1101/128058 ◽

2017 ◽

Author(s):

Gur Pines ◽

James D. Winkler ◽

Assaf Pines ◽

Ryan T. Gill

Keyword(s):

Genetic Code ◽

Directed Evolution ◽

Single Gene ◽

Point Mutations ◽

Saturation Mutagenesis ◽

Mutagenic Potential ◽

Single Nucleotide ◽

Common Error ◽

Mutational Landscape ◽

Genetic Codes

AbstractThe standard genetic code is robust to mutations and base-pairing errors during transcription and translation. Point mutations are most likely to be synonymous or preserve the chemical properties of the original amino acid. Saturation mutagenesis experiments suggest that in some cases the best performing mutant requires a replacement of more than a single nucleotide within a codon. These replacements are essentially inaccessible to common error-based laboratory engineering techniques that alter single nucleotide per mutation event, due to the extreme rarity of adjacent mutations. In this theoretical study, we suggest a radical reordering of the genetic code that maximizes the mutagenic potential of single nucleotide replacements. We explore several possible genetic codes that allow a greater degree of accessibility to the mutational landscape and may result in a hyper-evolvable organism serving as an ideal platform for directed evolution experiments. We then conclude by evaluating potential applications for recoded organisms within the synthetic biology field.Significance StatementThe conservative nature of the genetic code prevents bioengineers from efficiently accessing the full mutational landscape of a gene using common error-prone methods. Here we present two computational approaches to generate alternative genetic codes with increased accessibility. These new codes allow mutational transition to a larger pool of amino acids and with a greater degree of chemical differences, using a single nucleotide replacement within the codon, thus increasing evolvability both at the single gene and at the genome levels. Given the widespread use of these techniques for strain and protein improvement along with more fundamental evolutionary biology questions, the use of recoded organisms that maximize evolvability should significantly improve the efficiency of directed evolution, library generation and fitness maximization.

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