scholarly journals Site-saturation Mutagenesis is more Efficient than DNA Shuffling for the Directed Evolution of β-Fucosidase from β-Galactosidase

2005 ◽  
Vol 352 (3) ◽  
pp. 621-628 ◽  
Author(s):  
Monal R. Parikh ◽  
Ichiro Matsumura
2015 ◽  
Vol 79 ◽  
pp. 965-970 ◽  
Author(s):  
Pei Yao ◽  
Yongjun Lin ◽  
Gaobing Wu ◽  
Yulin Lu ◽  
Tao Zhan ◽  
...  

2017 ◽  
Author(s):  
Anders M. Knight ◽  
S. B. Jennifer Kan ◽  
Russell D. Lewis ◽  
Oliver F. Brandenberg ◽  
Kai Chen ◽  
...  

<p>Stereodivergent syntheses leading to the different stereoisomers of a product are useful in the discovery and testing of drugs and agrochemicals. A longstanding challenge in catalysis, developing sets of stereodivergent catalysts is often solved for enzymes by screening Nature’s diversity for biocatalysts with complementary stereoselectivities. Here, Nature’s protein diversity has been leveraged to develop stereodivergent catalysts for a reaction not known in biology, cyclopropanation via carbene transfer. By screening diverse native and engineered heme proteins, we identified globins and serine-ligated cytochromes P450 with promiscuous activity for cyclopropanation of unactivated alkene substrates. Their activities and stereoselectivities were enhanced by directed evolution: 1-3 rounds of site-saturation mutagenesis and screening generated enzymes that catalyze the stereodivergent cyclopropanation to form each of the four stereoisomers of unactivated alkenes and electron-deficient alkenes with up to 5,400 total turnovers and 98% enantiomeric excess. These fully genetically encoded biocatalysts function in whole <i>E. coli</i> cells in mild, aqueous conditions and provide the first example of enantioselective, intermolecular iron-catalyzed cyclopropanation of unactivated alkenes via carbene transfer.</p>


2017 ◽  
Author(s):  
Anders M. Knight ◽  
S. B. Jennifer Kan ◽  
Russell D. Lewis ◽  
Oliver F. Brandenberg ◽  
Kai Chen ◽  
...  

<p>Stereodivergent syntheses leading to the different stereoisomers of a product are useful in the discovery and testing of drugs and agrochemicals. A longstanding challenge in catalysis, developing sets of stereodivergent catalysts is often solved for enzymes by screening Nature’s diversity for biocatalysts with complementary stereoselectivities. Here, Nature’s protein diversity has been leveraged to develop stereodivergent catalysts for a reaction not known in biology, cyclopropanation via carbene transfer. By screening diverse native and engineered heme proteins, we identified globins and serine-ligated cytochromes P450 with promiscuous activity for cyclopropanation of unactivated alkene substrates. Their activities and stereoselectivities were enhanced by directed evolution: 1-3 rounds of site-saturation mutagenesis and screening generated enzymes that catalyze the stereodivergent cyclopropanation to form each of the four stereoisomers of unactivated alkenes and electron-deficient alkenes with up to 5,400 total turnovers and 98% enantiomeric excess. These fully genetically encoded biocatalysts function in whole <i>E. coli</i> cells in mild, aqueous conditions and provide the first example of enantioselective, intermolecular iron-catalyzed cyclopropanation of unactivated alkenes via carbene transfer.</p>


2009 ◽  
Vol 351 (18) ◽  
pp. 3287-3305 ◽  
Author(s):  
Despina J. Bougioukou ◽  
Sabrina Kille ◽  
Andreas Taglieber ◽  
Manfred T. Reetz

2018 ◽  
Vol 82 (10) ◽  
pp. 1715-1723 ◽  
Author(s):  
Kota Nakatani ◽  
Yuta Katano ◽  
Kenji Kojima ◽  
Teisuke Takita ◽  
Rie Yatsunami ◽  
...  

2017 ◽  
Author(s):  
Gur Pines ◽  
James D. Winkler ◽  
Assaf Pines ◽  
Ryan T. Gill

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.


ChemBioChem ◽  
2010 ◽  
Vol 11 (4) ◽  
pp. 533-538 ◽  
Author(s):  
Zachary Armstrong ◽  
Stephan Reitinger ◽  
Terrence Kantner ◽  
Stephen G. Withers

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