Directed evolution drives the next generation of biocatalysts.

Enzymes are increasingly being used as biocatalysts in the generation of products that have until now been derived using traditional chemical processes. Such products range from pharmaceutical and agrochemical building blocks to fine and bulk chemicals and, more recently, components of biofuels. For a biocatalyst to be effective in an industrial process, it must be subjected to improvement and optimization, and in this respect the directed evolution of enzymes has emerged as a powerful enabling technology. Directed evolution involves repeated rounds of (i) random gene library generation, (ii) expression of genes in a suitable host and (iii) screening of libraries of variant enzymes for the property of interest. Both in vitro screening-based methods and in vivo selection-based methods have been applied to the evolution of enzyme function and properties. Significant developments have occurred recently, particularly with respect to library design, screening methodology, applications in synthetic transformations and strategies for the generation of new enzyme function.

[1]  U. Bornscheuer,et al.  Catalytic promiscuity in biocatalysis: using old enzymes to form new bonds and follow new pathways. , 2004, Angewandte Chemie.

[2]  David R. Liu,et al.  Directed evolution can rapidly improve the activity of chimeric assembly-line enzymes , 2007, Proceedings of the National Academy of Sciences.

[3]  A. Griffiths,et al.  High-throughput screening of enzyme libraries: in vitro evolution of a beta-galactosidase by fluorescence-activated sorting of double emulsions. , 2005, Chemistry & biology.

[4]  Burckhard Seelig,et al.  Selection and evolution of enzymes from a partially randomized non-catalytic scaffold , 2007, Nature.

[5]  Frances H Arnold,et al.  Directed enzyme evolution: climbing fitness peaks one amino acid at a time. , 2009, Current opinion in chemical biology.

[6]  Zhen Qian,et al.  Investigating the Structural and Functional Consequences of Circular Permutation on Lipase B from Candida Antarctica , 2007, Chembiochem : a European journal of chemical biology.

[7]  Nicholas J Turner,et al.  A template-based mnemonic for monoamine oxidase (MAO-N) catalyzed reactions and its application to the chemo-enzymatic deracemisation of the alkaloid (+/-)-crispine A. , 2007, Chemical communications.

[8]  Anthony D. Keefe,et al.  Functional proteins from a random-sequence library , 2001, Nature.

[9]  R. Kazlauskas,et al.  Stereoselective hydrogenation of olefins using rhodium-substituted carbonic anhydrase--a new reductase. , 2009, Chemistry.

[10]  Gavin J. Williams,et al.  Creation of a pair of stereochemically complementary biocatalysts. , 2006, Journal of the American Chemical Society.

[11]  Detlev Belder,et al.  Enantioselective catalysis and analysis on a chip. , 2006, Angewandte Chemie.

[12]  M. Delcourt,et al.  Directed Evolution of Biocatalysts , 2006 .

[13]  Nicholas J Turner,et al.  Directed evolution of enzymes: new biocatalysts for asymmetric synthesis. , 2003, Organic & biomolecular chemistry.

[14]  Gjalt W Huisman,et al.  Enzyme optimization: moving from blind evolution to statistical exploration of sequence-function space. , 2008, Trends in biotechnology.

[15]  Huimin Zhao,et al.  Directed evolution of enzymes and biosynthetic pathways. , 2006, Current opinion in microbiology.

[16]  Ranjini Chatterjee,et al.  Directed evolution of metabolic pathways. , 2006, Trends in biotechnology.

[17]  Nicholas J. Turner,et al.  Deracemization of α‐Methylbenzylamine Using an Enzyme Obtained by In Vitro Evolution , 2002 .

[18]  Sung-Hun Nam,et al.  Design and Evolution of New Catalytic Activity with an Existing Protein Scaffold , 2006, Science.

[19]  Dan S. Tawfik,et al.  Directed enzyme evolution via small and effective neutral drift libraries , 2008, Nature Methods.

[20]  G. Gilardi,et al.  Directed evolution of enzymes for product chemistry. , 2004, Natural product reports.

[21]  Stefan Lutz,et al.  Engineering enzymes by 'intelligent' design. , 2009, Current opinion in chemical biology.

[22]  F. Eisenhaber,et al.  pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model , 2007, Biology Direct.

[23]  Wayne M Patrick,et al.  Novel methods for directed evolution of enzymes: quality, not quantity. , 2004, Current opinion in biotechnology.

[24]  Richard J Fox,et al.  Catalytic effectiveness, a measure of enzyme proficiency for industrial applications. , 2009, Trends in biotechnology.

[25]  Che-Chang Hsu,et al.  Directed evolution of D-sialic acid aldolase to L-3-deoxy-manno-2-octulosonic acid (L-KDO) aldolase. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[26]  Ulrich Schwaneberg,et al.  A screening system for the directed evolution of epoxygenases: importance of position 184 in P450 BM3 for stereoselective styrene epoxidation. , 2006, Angewandte Chemie.

[27]  Nicholas J Turner,et al.  Directed evolution of an amine oxidase possessing both broad substrate specificity and high enantioselectivity. , 2003, Angewandte Chemie.

[28]  Mark E. B. Smith,et al.  Enhancing and Reversing the Stereoselectivity of Escherichia coli Transketolase via Single-Point Mutations , 2008 .

[29]  Manfred T Reetz,et al.  Directed evolution of enantioselective enzymes: iterative cycles of CASTing for probing protein-sequence space. , 2006, Angewandte Chemie.

[30]  Nicholas J Turner,et al.  The structure of monoamine oxidase from Aspergillus niger provides a molecular context for improvements in activity obtained by directed evolution. , 2008, Journal of molecular biology.

[31]  Jan Brezovsky,et al.  Computational tools for designing and engineering biocatalysts. , 2009, Current opinion in chemical biology.

[32]  H. Schoemaker,et al.  Dispelling the Myths--Biocatalysis in Industrial Synthesis , 2003, Science.

[33]  W. Stemmer,et al.  DNA shuffling of a family of genes from diverse species accelerates directed evolution , 1998, Nature.

[34]  Andreas Vogel,et al.  Expanding the substrate scope of enzymes: combining mutations obtained by CASTing. , 2006, Chemistry.

[35]  Frances H. Arnold,et al.  Directed evolution of a para-nitrobenzyl esterase for aqueous-organic solvents , 1996, Nature Biotechnology.

[36]  R. Kazlauskas,et al.  Improving enzyme properties: when are closer mutations better? , 2005, Trends in biotechnology.

[37]  A. Glieder,et al.  Laboratory Evolved Biocatalysts for Stereoselective Syntheses of Substituted Benzaldehyde Cyanohydrins , 2008, Chembiochem : a European journal of chemical biology.

[38]  H. Ohta,et al.  Introduction of single mutation changes arylmalonate decarboxylase to racemase. , 2006, Chemical communications.

[39]  Bernhard Hauer,et al.  Catalytic Promiscuity of Halohydrin Dehalogenase and its Application in Enantioselective Epoxide Ring Opening , 2008, Chembiochem : a European journal of chemical biology.

[40]  Michael W Deem,et al.  Amino acid alphabet size in protein evolution experiments: better to search a small library thoroughly or a large library sparsely? , 2008, Protein engineering, design & selection : PEDS.

[41]  H. Leemhuis,et al.  Directed evolution of enzymes: Library screening strategies , 2009, IUBMB life.

[42]  Dan S. Tawfik,et al.  Directed evolution of an extremely fast phosphotriesterase by in vitro compartmentalization , 2003, The EMBO journal.

[43]  John C Whitman,et al.  Improving catalytic function by ProSAR-driven enzyme evolution , 2007, Nature Biotechnology.

[44]  Manfred T Reetz,et al.  Directed evolution of an enantioselective epoxide hydrolase: uncovering the source of enantioselectivity at each evolutionary stage. , 2009, Journal of the American Chemical Society.

[45]  T. Ward,et al.  Artificial metalloenzymes for asymmetric allylic alkylation on the basis of the biotin-avidin technology. , 2008, Angewandte Chemie.

[46]  John M Woodley,et al.  Directed evolution of biocatalytic processes. , 2005, Biomolecular engineering.

[47]  M. Novič,et al.  Artificial metalloenzyme for enantioselective sulfoxidation based on vanadyl-loaded streptavidin. , 2008, Journal of the American Chemical Society.

[48]  M. Truppo,et al.  Rapid determination of both the activity and enantioselectivity of ketoreductases. , 2008, Angewandte Chemie.

[49]  W. Stemmer Rapid evolution of a protein in vitro by DNA shuffling , 1994, Nature.

[50]  Thomas R Ward,et al.  Artificial enzymes made to order: combination of computational design and directed evolution. , 2008, Angewandte Chemie.

[51]  Nicholas J. Turner Directed Evolution of Enzymes — New Biocatalysts for Organic Synthesis , 2010 .

[52]  H. Hellinga,et al.  Structural reorganization and preorganization in enzyme active sites: comparisons of experimental and theoretically ideal active site geometries in the multistep serine esterase reaction cycle. , 2008, Journal of the American Chemical Society.

[53]  Manfred T Reetz,et al.  Directed evolution of hybrid enzymes: Evolving enantioselectivity of an achiral Rh-complex anchored to a protein. , 2006, Chemical communications.

[54]  Mats Holmquist,et al.  Focusing mutations into the P. fluorescens esterase binding site increases enantioselectivity more effectively than distant mutations. , 2005, Chemistry & biology.

[55]  Frances H. Arnold,et al.  Diversifying Carotenoid Biosynthetic Pathways by Directed Evolution , 2005, Microbiology and Molecular Biology Reviews.

[56]  M. Dawson,et al.  Stereoinversion of β- and γ-substituted α-amino acids using a chemo-enzymatic oxidation–reduction procedure , 2003 .

[57]  N. Turner,et al.  Directed Evolution of Galactose Oxidase: Generation of Enantioselective Secondary Alcohol Oxidases , 2008, Chembiochem : a European journal of chemical biology.

[58]  Patricia C Babbitt,et al.  Evolution of enzymatic activities in the enolase superfamily: stereochemically distinct mechanisms in two families of cis,cis-muconate lactonizing enzymes. , 2009, Biochemistry.

[59]  F. Arnold,et al.  Enantioselective alpha-hydroxylation of 2-arylacetic acid derivatives and buspirone catalyzed by engineered cytochrome P450 BM-3. , 2006, Journal of the American Chemical Society.

[60]  Eric A. Althoff,et al.  De Novo Computational Design of Retro-Aldol Enzymes , 2008, Science.

[61]  John M Woodley,et al.  Biocatalysis for pharmaceutical intermediates: the future is now. , 2007, Trends in biotechnology.

[62]  François Gilardoni,et al.  Tailoring the active site of chemzymes by using a chemogenetic-optimization procedure: towards substrate-specific artificial hydrogenases based on the biotin-avidin technology. , 2005, Angewandte Chemie.

[63]  Manfred T Reetz,et al.  Addressing the Numbers Problem in Directed Evolution , 2008, Chembiochem : a European journal of chemical biology.

[64]  Donald Hilvert,et al.  Stereoselectivity and expanded substrate scope of an engineered PLP-dependent aldolase. , 2006, Angewandte Chemie.

[65]  Dan S. Tawfik,et al.  Advances in laboratory evolution of enzymes. , 2008, Current opinion in chemical biology.

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

[67]  Dan S. Tawfik,et al.  Protein engineers turned evolutionists , 2007, Nature Methods.

[68]  Dan S. Tawfik,et al.  The 'evolvability' of promiscuous protein functions , 2005, Nature Genetics.

[69]  I. Bustos-Jaimes,et al.  Trends and Challenges in Directed Evolution , 2008 .

[70]  Frances H. Arnold,et al.  In Vivo Evolution of Butane Oxidation by Terminal Alkane Hydroxylases AlkB and CYP153A6 , 2008, Applied and Environmental Microbiology.

[71]  Daniel Mink,et al.  Directed evolution of an industrial biocatalyst: 2-deoxy-D-ribose 5-phosphate aldolase. , 2006, Biotechnology journal.

[72]  Roberto A Chica,et al.  Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design. , 2005, Current opinion in biotechnology.

[73]  Ramesh N. Patel Chemo-enzymatic synthesis of pharmaceutical intermediates , 2008, Expert opinion on drug discovery.

[74]  J. W. Frost,et al.  Directed evolution of 2-keto-3-deoxy-6-phosphogalactonate aldolase to replace 3-deoxy-D-arabino-heptulosonic acid 7-phosphate synthase. , 2007, Journal of the American Chemical Society.

[75]  J. Fastrez,et al.  Phage display as a tool for the directed evolution of enzymes. , 2003, Trends in biotechnology.

[76]  Nicholas J Turner,et al.  Directed Evolution of an Amine Oxidase for the Preparative Deracemisation of Cyclic Secondary Amines , 2005, Chembiochem : a European journal of chemical biology.

[77]  Manfred T. Reetz,et al.  Creation of Enantioselective Biocatalysts for Organic Chemistry by In Vitro Evolution , 1997 .

[78]  N. Turner,et al.  A chemo-enzymatic route to enantiomerically pure cyclic tertiary amines. , 2006, Journal of the American Chemical Society.

[79]  Sven Panke,et al.  Trends and innovations in industrial biocatalysis for the production of fine chemicals. , 2004, Current opinion in biotechnology.

[80]  Uwe T Bornscheuer,et al.  Converting an esterase into an epoxide hydrolase. , 2009, Angewandte Chemie.

[81]  Frances H. Arnold,et al.  Directed evolution: Creating biocatalysts for the future , 1996 .

[82]  Frances H Arnold,et al.  Neutral genetic drift can aid functional protein evolution , 2007, 0705.0201.

[83]  Manfred T Reetz,et al.  Greatly reduced amino acid alphabets in directed evolution: making the right choice for saturation mutagenesis at homologous enzyme positions. , 2008, Chemical communications.

[84]  Dan S. Tawfik,et al.  Intense neutral drifts yield robust and evolvable consensus proteins. , 2008, Journal of molecular biology.

[85]  A. Wells,et al.  Enantioselective oxidation of O-methyl-N-hydroxylamines using monoamine oxidase N as catalyst. , 2007, Chemical communications.

[86]  B. Tidor,et al.  Selection of horseradish peroxidase variants with enhanced enantioselectivity by yeast surface display. , 2007, Chemistry & biology.

[87]  C. Schofield,et al.  Mechanisms and structures of crotonase superfamily enzymes – How nature controls enolate and oxyanion reactivity , 2008, Cellular and Molecular Life Sciences.

[88]  G. Grogan Emergent mechanistic diversity of enzyme-catalysed β-diketone cleavage , 2005 .

[89]  N. Turner,et al.  A versatile chemo-enzymatic route to enantiomerically pure β-branched α-amino acids , 2004 .

[90]  K. Hult,et al.  Enzyme promiscuity: mechanism and applications. , 2007, Trends in biotechnology.

[91]  Rainer Merkl,et al.  Computational design of enzymes. , 2008, Chemistry & biology.

[92]  J. Fontecilla-Camps,et al.  The Protein Environment Drives Selectivity for Sulfide Oxidation by an Artificial Metalloenzyme , 2009, Chembiochem : a European journal of chemical biology.

[93]  M. Reetz,et al.  Alternate-site enzyme promiscuity. , 2007, Angewandte Chemie.