scholarly journals Neutral Genetic Drift-Based Engineering of a Sucrose-Utilizing Enzyme toward Glycodiversification

ACS Catalysis ◽  
2018 ◽  
Vol 9 (2) ◽  
pp. 1241-1252 ◽  
Author(s):  
David Daudé ◽  
Alizée Vergès ◽  
Emmanuelle Cambon ◽  
Stéphane Emond ◽  
Samuel Tranier ◽  
...  
Keyword(s):  
Genetic Drift ◽  
Neutral Genetic Drift

scholarly journals Shuffling the Neutral Drift of Unspecific Peroxygenase inSaccharomyces cerevisiae

2018 ◽  
Vol 84 (15) ◽  
Author(s):  
Javier Martin-Diaz ◽  
Carmen Paret ◽  
Eva García-Ruiz ◽  
Patricia Molina-Espeja ◽  
Miguel Alcalde
Keyword(s):  
Genetic Drift ◽  
Dna Recombination ◽  
Dna Shuffling ◽  
Content Type ◽  
Neutral Drift ◽  
Oxygenase Activity ◽  
Improved Stability ◽  
Neutral Mutations ◽  
Neutral Genetic Drift

ABSTRACTUnspecific peroxygenase (UPO) is a highly promiscuous biocatalyst, and its selective mono(per)oxygenase activity makes it useful for many synthetic chemistry applications. Among the broad repertory of library creation methods for directed enzyme evolution, genetic drift allows neutral mutations to be accumulated gradually within a polymorphic network of variants. In this study, we conducted a campaign of genetic drift with UPO inSaccharomyces cerevisiae, so that neutral mutations were simply added and recombinedin vivo. With low mutational loading and an activity threshold of 45% of the parent's native function, mutant libraries enriched in folded active UPO variants were generated. After only eight rounds of genetic drift and DNA shuffling, we identified an ensemble of 25 neutrally evolved variants with changes in peroxidative and peroxygenative activities, kinetic thermostability, and enhanced tolerance to organic solvents. With an average of 4.6 substitutions introduced per clone, neutral mutations covered approximately 10% of the protein sequence. Accordingly, this study opens new avenues for UPO design by bringing together neutral genetic drift and DNA recombinationin vivo.IMPORTANCEFungal peroxygenases resemble the peroxide shunt pathway of cytochrome P450 monoxygenases, performing selective oxyfunctionalizations of unactivated C-H bonds in a broad range of organic compounds. In this study, we combined neutral genetic drift andin vivoDNA shuffling to generate highly functional peroxygenase mutant libraries. The panel of neutrally evolved peroxygenases showed different activity profiles for peroxygenative substrates and improved stability with respect to temperature and the presence of organic cosolvents, making the enzymes valuable blueprints for emerging evolution campaigns. This association of DNA recombination and neutral drift is paving the way for future work in peroxygenase engineering and, from a more general perspective, to any other enzyme system heterologously expressed inS. cerevisiae.

scholarly journals Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution

2007 ◽  
Vol 2 (1) ◽  
pp. 17 ◽  
Author(s):  
Jesse D Bloom ◽  
Philip A Romero ◽  
Zhongyi Lu ◽  
Frances H Arnold
Keyword(s):  
Genetic Drift ◽  
Functional Evolution ◽  
Protein Functions ◽  
Neutral Genetic Drift

Neutral genetic drift: an investigation using Cartesian Genetic Programming

2015 ◽  
Vol 16 (4) ◽  
pp. 531-558 ◽  
Author(s):  
Andrew James Turner ◽  
Julian Francis Miller
Keyword(s):  
Genetic Programming ◽  
Genetic Drift ◽  
Cartesian Genetic Programming ◽  
Neutral Genetic Drift

scholarly journals Recombination Can Evolve in Large Finite Populations Given Selection on Sufficient Loci

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2249-2258 ◽  
Author(s):  
Mark M Iles ◽  
Kevin Walters ◽  
Chris Cannings
Keyword(s):  
Experimental Evidence ◽  
Genetic Drift ◽  
Finite Population ◽  
Selective Advantage ◽  
Indirect Selection ◽  
Small Populations ◽  
Finite Populations ◽  
Population Sizes ◽  
Population Recombination

AbstractIt is well known that an allele causing increased recombination is expected to proliferate as a result of genetic drift in a finite population undergoing selection, without requiring other mechanisms. This is supported by recent simulations apparently demonstrating that, in small populations, drift is more important than epistasis in increasing recombination, with this effect disappearing in larger finite populations. However, recent experimental evidence finds a greater advantage for recombination in larger populations. These results are reconciled by demonstrating through simulation without epistasis that for m loci recombination has an appreciable selective advantage over a range of population sizes (am, bm). bm increases steadily with m while am remains fairly static. Thus, however large the finite population, if selection acts on sufficiently many loci, an allele that increases recombination is selected for. We show that as selection acts on our finite population, recombination increases the variance in expected log fitness, causing indirect selection on a recombination-modifying locus. This effect is enhanced in those populations with more loci because the variance in phenotypic fitnesses in relation to the possible range will be smaller. Thus fixation of a particular haplotype is less likely to occur, increasing the advantage of recombination.

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