Improving and repurposing biocatalysts via directed evolution.

Over the last two decades, directed evolution has become a staple in protein engineering and ushered in a new era of industrial biocatalysis. Directed evolution has provided the tools to not only improve the activity of known biocatalysts, but also to endow biocatalysts with chemical reactivities not previously encountered in nature. Here we will discuss the recent successes in the quest to enhance thermostability, stereoselectivity and activity of biocatalysts, as well as to create novel enzymes, over the last two years.

[1]  Fahmi Himo,et al.  Quantum Chemistry as a Tool in Asymmetric Biocatalysis: Limonene Epoxide Hydrolase Test Case , 2013, Angewandte Chemie.

[2]  Frances H Arnold,et al.  Evolutionary history of a specialized p450 propane monooxygenase. , 2008, Journal of molecular biology.

[3]  Henrik Engman,et al.  Engineering protein thermostability using a generic activity-independent biophysical screen inside the cell , 2013, Nature Communications.

[4]  Frances H. Arnold,et al.  Enantioselective Intramolecular C—H Amination Catalyzed by Engineered Cytochrome P450 Enzymes in vitro and in vivo. , 2014 .

[5]  Huimin Zhao,et al.  Inverting the enantioselectivity of P450pyr monooxygenase by directed evolution. , 2010, Chemical communications.

[6]  Indira Wu,et al.  Engineered thermostable fungal Cel6A and Cel7A cellobiohydrolases hydrolyze cellulose efficiently at elevated temperatures , 2013, Biotechnology and bioengineering.

[7]  David P Nannemann,et al.  Assessing directed evolution methods for the generation of biosynthetic enzymes with potential in drug biosynthesis. , 2011, Future medicinal chemistry.

[8]  Manfred T Reetz,et al.  Directed evolution of stereoselective enzymes based on genetic selection as opposed to screening systems. , 2014, Journal of biotechnology.

[9]  Frances H Arnold,et al.  P450-catalyzed asymmetric cyclopropanation of electron-deficient olefins under aerobic conditions. , 2014, Catalysis science & technology.

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[11]  Huimin Zhao,et al.  Recent advances in biocatalyst development in the pharmaceutical industry , 2013 .

[12]  Jasmine L. Gallaher,et al.  Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction , 2010, Science.

[13]  Hein J Wijma,et al.  Directed Evolution Strategies for Enantiocomplementary Haloalkane Dehalogenases: From Chemical Waste to Enantiopure Building Blocks , 2012, Chembiochem : a European journal of chemical biology.

[14]  Uwe T Bornscheuer,et al.  Use of ‘small but smart’ libraries to enhance the enantioselectivity of an esterase from Bacillus stearothermophilus towards tetrahydrofuran‐3‐yl acetate , 2013, The FEBS journal.

[15]  S. Bell,et al.  P450(BM3) (CYP102A1): connecting the dots. , 2012, Chemical Society reviews.

[16]  Eric A. Althoff,et al.  Kemp elimination catalysts by computational enzyme design , 2008, Nature.

[17]  Hein J. Wijma,et al.  Computationally designed libraries for rapid enzyme stabilization , 2014, Protein engineering, design & selection : PEDS.

[18]  G. Huisman,et al.  Engineering the third wave of biocatalysis , 2012, Nature.

[19]  Yolanda Schaerli,et al.  Evolution of enzyme catalysts caged in biomimetic gel-shell beads. , 2014, Nature chemistry.

[20]  Andreas Krause,et al.  Navigating the protein fitness landscape with Gaussian processes , 2012, Proceedings of the National Academy of Sciences.

[21]  Manfred T Reetz,et al.  Regio- and stereoselectivity of P450-catalysed hydroxylation of steroids controlled by laboratory evolution , 2011, Nature Chemistry.

[22]  Frances H Arnold,et al.  Expanding P450 catalytic reaction space through evolution and engineering. , 2014, Current opinion in chemical biology.

[23]  L. Fourage,et al.  Engineering cytochrome P450 BM3 of Bacillus megaterium for terminal oxidation of palmitic acid. , 2014, Journal of biotechnology.

[24]  Andrew Currin,et al.  SpeedyGenes: an improved gene synthesis method for the efficient production of error-corrected, synthetic protein libraries for directed evolution , 2014, Protein engineering, design & selection : PEDS.

[25]  Ritesh Singh,et al.  P450-Catalyzed Intramolecular sp3 C–H Amination with Arylsulfonyl Azide Substrates , 2014, ACS catalysis.

[26]  Tuck Seng Wong,et al.  Polishing the craft of genetic diversity creation in directed evolution. , 2013, Biotechnology advances.

[27]  Son Quang Pham,et al.  Evolving P450pyr hydroxylase for highly enantioselective hydroxylation at non-activated carbon atom. , 2012, Chemical communications.

[28]  Kenji Okano,et al.  Directed evolution of thermotolerant malic enzyme for improved malate production. , 2014, Journal of bioscience and bioengineering.

[29]  Frances H Arnold,et al.  Comparison of random mutagenesis and semi-rational designed libraries for improved cytochrome P450 BM3-catalyzed hydroxylation of small alkanes. , 2012, Protein engineering, design & selection : PEDS.

[30]  Guangyu Yang,et al.  An Improved Single Cell Ultrahigh Throughput Screening Method Based on In Vitro Compartmentalization , 2014, PloS one.

[31]  Aitao Li,et al.  Engineered P450pyr monooxygenase for asymmetric epoxidation of alkenes with unique and high enantioselectivity. , 2013, Chemical communications.

[32]  M. Widersten,et al.  Obtaining optical purity for product diols in enzyme-catalyzed epoxide hydrolysis: contributions from changes in both enantio- and regioselectivity. , 2012, Biochemistry.

[33]  Manfred T Reetz,et al.  Protein engineering of stereoselective Baeyer-Villiger monooxygenases. , 2012, Chemistry.

[34]  Huimin Zhao,et al.  Directed evolution as a powerful synthetic biology tool. , 2013, Methods.

[35]  Stefan Lutz,et al.  Beyond directed evolution--semi-rational protein engineering and design. , 2010, Current opinion in biotechnology.

[36]  S. Camarero,et al.  Engineering Platforms for Directed Evolution of Laccase from Pycnoporus cinnabarinus , 2011, Applied and Environmental Microbiology.

[37]  Manfred T Reetz,et al.  Artificial metalloenzymes as catalysts in stereoselective Diels-Alder reactions. , 2012, Chemical record.

[38]  Nico P E Vermeulen,et al.  Application of engineered cytochrome P450 mutants as biocatalysts for the synthesis of benzylic and aromatic metabolites of fenamic acid NSAIDs. , 2014, Bioorganic & medicinal chemistry.

[39]  Gheorghe-Doru Roiban,et al.  Induced axial chirality in biocatalytic asymmetric ketone reduction. , 2013, Journal of the American Chemical Society.

[40]  Miguel Alcalde,et al.  Development of chimeric laccases by directed evolution , 2012, Biotechnology and bioengineering.

[41]  Yasuhisa Asano,et al.  Tailoring D-amino acid oxidase from the pig kidney to R-stereoselective amine oxidase and its use in the deracemization of α-methylbenzylamine. , 2014, Angewandte Chemie.

[42]  Ivan V Korendovych,et al.  Catalytic efficiency of designed catalytic proteins. , 2014, Current opinion in structural biology.

[43]  Arieh Warshel,et al.  Towards Quantitative Computer‐Aided Studies of Enzymatic Enantioselectivity: The Case of Candida antarctica Lipase A , 2012, Chembiochem : a European journal of chemical biology.

[44]  Ulrich Schwaneberg,et al.  P450 BM3 crystal structures reveal the role of the charged surface residue Lys/Arg184 in inversion of enantioselective styrene epoxidation. , 2013, Chemical communications.

[45]  Manfred T Reetz,et al.  Directed Evolution by Using Iterative Saturation Mutagenesis Based on Multiresidue Sites , 2013, Chembiochem : a European journal of chemical biology.

[46]  Manfred T Reetz,et al.  Enhancing the efficiency of directed evolution in focused enzyme libraries by the adaptive substituent reordering algorithm. , 2012, Chemistry.

[47]  Huimin Zhao,et al.  Directed evolution: an evolving and enabling synthetic biology tool. , 2012, Current opinion in chemical biology.

[48]  Xiang-Qian Peng,et al.  Improved Thermostability of Lipase B from Candida antarctica by Directed Evolution and Display on Yeast Surface , 2012, Applied Biochemistry and Biotechnology.

[49]  Frances H Arnold,et al.  Improved cyclopropanation activity of histidine-ligated cytochrome P450 enables the enantioselective formal synthesis of levomilnacipran. , 2014, Angewandte Chemie.

[50]  Neil Swainston,et al.  GeneGenie: optimized oligomer design for directed evolution , 2014, Nucleic Acids Res..

[51]  Ulrich Schwaneberg,et al.  Regioselective o-hydroxylation of monosubstituted benzenes by P450 BM3. , 2013, Angewandte Chemie.

[52]  Frances H. Arnold,et al.  A Serine-Substituted P450 Catalyzes Highly Efficient Carbene Transfer to Olefins In Vivo , 2013, Nature chemical biology.

[53]  Huimin Zhao,et al.  Directed Evolution: Past, Present and Future. , 2013, AIChE journal. American Institute of Chemical Engineers.

[54]  Manfred T Reetz,et al.  Laboratory evolution of stereoselective enzymes: a prolific source of catalysts for asymmetric reactions. , 2011, Angewandte Chemie.

[55]  Gheorghe-Doru Roiban,et al.  Cytochrome P450 catalyzed oxidative hydroxylation of achiral organic compounds with simultaneous creation of two chirality centers in a single C-H activation step. , 2014, Angewandte Chemie.

[56]  David Baker,et al.  Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase , 2014, Proceedings of the National Academy of Sciences.

[57]  G. Gilardi,et al.  Hydroxylation of non-substituted polycyclic aromatic hydrocarbons by cytochrome P450 BM3 engineered by directed evolution. , 2013, Journal of inorganic biochemistry.

[58]  Qishi Du,et al.  Improving the thermostability of alpha-amylase by combinatorial coevolving-site saturation mutagenesis , 2012, BMC Bioinformatics.

[59]  Donald Hilvert,et al.  Precision is essential for efficient catalysis in an evolved Kemp eliminase , 2013, Nature.

[60]  Miguel Alcalde,et al.  Directed Evolution of Unspecific Peroxygenase from Agrocybe aegerita , 2014, Applied and Environmental Microbiology.

[61]  Gheorghe-Doru Roiban,et al.  Achieving Regio‐ and Enantioselectivity of P450‐Catalyzed Oxidative CH Activation of Small Functionalized Molecules by Structure‐Guided Directed Evolution , 2012, Chembiochem : a European journal of chemical biology.

[62]  Daniel W. Kulp,et al.  Design of a switchable eliminase , 2011, Proceedings of the National Academy of Sciences.

[63]  Frances H. Arnold,et al.  Olefin Cyclopropanation via Carbene Transfer Catalyzed by Engineered Cytochrome P450 Enzymes , 2013, Science.

[64]  Manfred T Reetz,et al.  Laboratory evolution of enantiocomplementary Candida antarctica lipase B mutants with broad substrate scope. , 2013, Journal of the American Chemical Society.

[65]  Zhi Li,et al.  Engineering of p450pyr hydroxylase for the highly regio- and enantioselective subterminal hydroxylation of alkanes. , 2014, Angewandte Chemie.

[66]  Frances H. Arnold,et al.  Cytochrome P450‐Catalyzed Insertion of Carbenoids into N—H Bonds. , 2014 .

[67]  Lixia Tang,et al.  Key Residues for Controlling Enantioselectivity of Halohydrin Dehalogenase from Arthrobacter sp. Strain AD2, Revealed by Structure-Guided Directed Evolution , 2012, Applied and Environmental Microbiology.