Biocatalyst development by directed evolution.

Biocatalysis has emerged as a great addition to traditional chemical processes for production of bulk chemicals and pharmaceuticals. To overcome the limitations of naturally occurring enzymes, directed evolution has become the most important tool for improving critical traits of biocatalysts such as thermostability, activity, selectivity, and tolerance towards organic solvents for industrial applications. Recent advances in mutant library creation and high-throughput screening have greatly facilitated the engineering of novel and improved biocatalysts. This review provides an update of the recent developments in the use of directed evolution to engineer biocatalysts for practical applications.

[1]  J. Kingma,et al.  Improved enantioselective conversion of styrene epoxides and meso-epoxides through epoxide hydrolases with a mutated nucleophile-flanking residue , 2009 .

[2]  E. Farinas,et al.  Directed evolution of CotA laccase for increased substrate specificity using Bacillus subtilis spores. , 2010, Protein engineering, design & selection : PEDS.

[3]  G. F. Joyce,et al.  Microfluidic compartmentalized directed evolution. , 2010, Chemistry & biology.

[4]  Chacko S Chakiath,et al.  Thermal Stabilization of Erwinia chrysanthemi Pectin Methylesterase A for Application in a Sugar Beet Pulp Biorefinery , 2009, Applied and Environmental Microbiology.

[5]  K. Rajagopal,et al.  Single-step overlap-primer-walk polymerase chain reaction for multiple mutagenesis without overlap extension. , 2008, Analytical biochemistry.

[6]  E. Hardiman,et al.  Directed Evolution of a Thermophilic β-glucosidase for Cellulosic Bioethanol Production , 2010, Applied biochemistry and biotechnology.

[7]  C. Imamura,et al.  Enhancement of Thermal Stabilization of Formaldehyde Dehydrogenase from Pseudomonas putida by Directed Evolution , 2010, Bioscience, biotechnology, and biochemistry.

[8]  Huimin Zhao,et al.  Protein engineering in designing tailored enzymes and microorganisms for biofuels production. , 2009, Current opinion in biotechnology.

[9]  Yosephine Gumulya,et al.  Iterative saturation mutagenesis accelerates laboratory evolution of enzyme stereoselectivity: rigorous comparison with traditional methods. , 2010, Journal of the American Chemical Society.

[10]  Yosephine Gumulya,et al.  Increasing the stability of an enzyme toward hostile organic solvents by directed evolution based on iterative saturation mutagenesis using the B-FIT method. , 2010, Chemical communications.

[11]  J. Keasling,et al.  Engineering microbial biofuel tolerance and export using efflux pumps , 2011, Molecular systems biology.

[12]  Jan Marienhagen,et al.  Advances in generating functional diversity for directed protein evolution. , 2009, Current opinion in chemical biology.

[13]  Zhu Yi,et al.  Three amino acid changes contribute markedly to the thermostability of β-glucosidase BglC from Thermobifida fusca. , 2011, Bioresource technology.

[14]  J. Kaur,et al.  Engineering of Bacillus lipase by directed evolution for enhanced thermal stability: effect of isoleucine to threonine mutation at protein surface , 2011, Molecular Biology Reports.

[15]  F. Arnold,et al.  Optimizing non-natural protein function with directed evolution. , 2011, Current opinion in chemical biology.

[16]  S. Savvides,et al.  Development and application of a screening assay for glycoside phosphorylases. , 2010, Analytical biochemistry.

[17]  Ahmad S. Khalil,et al.  Synthetic biology: applications come of age , 2010, Nature Reviews Genetics.

[18]  J. Bäckvall,et al.  Directed evolution of an enantioselective lipase with broad substrate scope for hydrolysis of alpha-substituted esters. , 2010, Journal of the American Chemical Society.

[19]  Huimin Zhao.  Highlights of biocatalysis and biomimetic catalysis , 2011 .

[20]  M. Kataoka,et al.  Directed evolution of an aminoalcohol dehydrogenase for efficient production of double chiral aminoalcohols. , 2011, Journal of bioscience and bioengineering.

[21]  Carla C. C. R. de Carvalho,et al.  Enzymatic and whole cell catalysis: finding new strategies for old processes , 2011 .

[22]  M. Murphy,et al.  Directed evolution of copper nitrite reductase to a chromogenic reductant. , 2010, Protein engineering, design & selection : PEDS.

[23]  V. Urlacher,et al.  Engineering cytochrome P450 monooxygenase CYP 116B3 for high dealkylation activity , 2010, Biotechnology Letters.

[24]  S. Bozonnet,et al.  A high-throughput screening system for the evaluation of biomass-hydrolyzing glycoside hydrolases. , 2010, Bioresource technology.

[25]  P. Engel,et al.  Efficient screening for new amino acid dehydrogenase activity: directed evolution of Bacillus sphaericus phenylalanine dehydrogenase towards activity with an unsaturated non-natural amino acid. , 2009, Journal of biotechnology.

[26]  Gang Li,et al.  Improving the decolorization for textile dyes of a metagenome-derived alkaline laccase by directed evolution , 2011, Applied Microbiology and Biotechnology.

[27]  Huimin Zhao,et al.  Directed evolution of specific receptor-ligand pairs for use in the creation of gene switches. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[28]  A. Abate,et al.  Ultrahigh-throughput screening in drop-based microfluidics for directed evolution , 2010, Proceedings of the National Academy of Sciences.

[29]  Guangyu Yang,et al.  Switch of substrate specificity of hyperthermophilic acylaminoacyl peptidase by combination of protein and solvent engineering , 2011, Protein & Cell.

[30]  Huimin Zhao,et al.  Synthetic biology: putting synthesis into biology , 2010, Wiley interdisciplinary reviews. Systems biology and medicine.

[31]  Yanhe Ma,et al.  Directed evolution of a thermophilic endoglucanase (Cel5A) into highly active Cel5A variants with an expanded temperature profile. , 2011, Journal of Biotechnology.

[32]  Dan S. Tawfik,et al.  Incorporating Synthetic Oligonucleotides via Gene Reassembly (ISOR): a versatile tool for generating targeted libraries. , 2007, Protein engineering, design & selection : PEDS.

[33]  M. Reetz,et al.  Laboratory evolution of robust and enantioselective Baeyer-Villiger monooxygenases for asymmetric catalysis. , 2009, Journal of the American Chemical Society.

[34]  U. Bornscheuer,et al.  Protein engineering of carboxyl esterases by rational design and directed evolution. , 2009, Protein and peptide letters.

[35]  P. Kim,et al.  Escherichia coli arabinose isomerase and Staphylococcus aureus tagatose-6-phosphate isomerase: which is a better template for directed evolution of non-natural substrate isomerization? , 2010, Journal of microbiology and biotechnology.

[36]  I. S. Pretorius,et al.  Microbial Cellulose Utilization: Fundamentals and Biotechnology , 2002, Microbiology and Molecular Biology Reviews.

[37]  Manfred T Reetz,et al.  Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes , 2007, Nature Protocols.

[38]  Burckhard Seelig,et al.  mRNA display for the selection and evolution of enzymes from in vitro-translated protein libraries , 2011, Nature Protocols.

[39]  S. Withers,et al.  Fluorescence activated cell sorting as a general ultra-high-throughput screening method for directed evolution of glycosyltransferases. , 2010, Journal of the American Chemical Society.

[40]  W. V. van Zyl,et al.  Heterologous expression of a Clostridium minicellulosome in Saccharomyces cerevisiae. , 2009, FEMS yeast research.

[41]  H. Ogino,et al.  Enhancement of the organic solvent‐stability of the LST‐03 lipase by directed evolution , 2009, Biotechnology progress.

[42]  M. Sung,et al.  Simultaneous improvement of catalytic activity and thermal stability of tyrosine phenol‐lyase by directed evolution , 2009, The FEBS journal.

[43]  Guangyu Yang,et al.  Discrimination of Esterase and Peptidase Activities of Acylaminoacyl Peptidase from Hyperthermophilic Aeropyrum pernix K1 by a Single Mutation* , 2006, Journal of Biological Chemistry.

[44]  G. Phillips,et al.  Expanding the Nucleotide and Sugar 1-Phosphate Promiscuity of Nucleotidyltransferase RmlA via Directed Evolution* , 2011, The Journal of Biological Chemistry.

[45]  Yasushi Morikawa,et al.  Directed evolution of endoglucanase III (Cel12A) from Trichoderma reesei , 2009, Applied Microbiology and Biotechnology.

[46]  A. Ballesteros,et al.  Evolving thermostability in mutant libraries of ligninolytic oxidoreductases expressed in yeast , 2010, Microbial cell factories.

[47]  M. Himmel,et al.  Outlook for cellulase improvement: screening and selection strategies. , 2006, Biotechnology advances.

[48]  Manuel Ferrer,et al.  Metagenomic era for biocatalyst identification. , 2010, Current opinion in biotechnology.

[49]  Ryan D. Woodyer,et al.  Single-step bioconversion for the preparation of L-gulose and L-galactose. , 2010, Carbohydrate research.

[50]  Huimin Zhao,et al.  Engineering microbial factories for synthesis of value-added products , 2011, Journal of Industrial Microbiology & Biotechnology.

[51]  Wim Soetaert,et al.  Creating lactose phosphorylase enzymes by directed evolution of cellobiose phosphorylase. , 2009, Protein engineering, design & selection : PEDS.

[52]  S. Withers,et al.  Designer enzymes for glycosphingolipid synthesis by directed evolution. , 2009, Nature chemical biology.

[53]  M. Dadashipour,et al.  Functional expression of a plant hydroxynitrile lyase in Escherichia coli by directed evolution: creation and characterization of highly in vivo soluble mutants. , 2011, Protein engineering, design & selection : PEDS.

[54]  Xiao‐Zhou Zhang,et al.  Engineering of Clostridium phytofermentans Endoglucanase Cel5A for Improved Thermostability , 2010, Applied and Environmental Microbiology.

[55]  Frances H Arnold,et al.  A family of thermostable fungal cellulases created by structure-guided recombination , 2009, Proceedings of the National Academy of Sciences.

[56]  Bernhard Hauer,et al.  Structure-guided directed evolution of alkenyl and arylmalonate decarboxylases. , 2009, Angewandte Chemie.

[57]  M. Asther,et al.  Automated assay for screening the enzymatic release of reducing sugars from micronized biomass , 2010, Microbial cell factories.

[58]  Michael H Hecht,et al.  Novel proteins: from fold to function. , 2011, Current opinion in chemical biology.

[59]  Lai-Xi Wang,et al.  Enzymatic transglycosylation for glycoconjugate synthesis. , 2009, Current opinion in chemical biology.

[60]  James A. Stapleton,et al.  A Cell-Free Microtiter Plate Screen for Improved [FeFe] Hydrogenases , 2010, PloS one.

[61]  Christian Wandrey,et al.  Industrial Biocatalysis: Past, Present, and Future , 2000 .

[62]  David Baker,et al.  Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series. , 2010, Journal of molecular biology.

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

[64]  Nikolaos E. Labrou,et al.  Random mutagenesis methods for in vitro directed enzyme evolution. , 2009 .

[65]  Stephen R. Decker,et al.  High-Throughput Screening Techniques for Biomass Conversion , 2009, BioEnergy Research.

[66]  M. Dion,et al.  Digital screening methodology for the directed evolution of transglycosidases. , 2008, Protein engineering, design & selection : PEDS.

[67]  Rafael Molina,et al.  A one-pot, simple methodology for cassette randomisation and recombination for focused directed evolution. , 2008, Protein engineering, design & selection : PEDS.

[68]  M. Himmel,et al.  The potential of cellulases and cellulosomes for cellulosic waste management. , 2007, Current opinion in biotechnology.

[69]  Yi Tang,et al.  Directed evolution and structural characterization of a simvastatin synthase. , 2009, Chemistry & biology.

[70]  S. Withers,et al.  Ultrahigh‐Throughput FACS‐Based Screening for Directed Enzyme Evolution , 2009, Chembiochem : a European journal of chemical biology.

[71]  Kenji Miyamoto,et al.  Dramatically improved catalytic activity of an artificial (S)-selective arylmalonate decarboxylase by structure-guided directed evolution. , 2011, Chemical communications.

[72]  Ramesh N. Patel.  Biocatalysis: Synthesis of Key Intermediates for Development of Pharmaceuticals , 2011 .

[73]  S. Withers,et al.  New approaches to enzymatic glycoside synthesis through directed evolution. , 2010, Carbohydrate research.

[74]  David R. Liu,et al.  A System for the Continuous Directed Evolution of Biomolecules , 2011, Nature.

[75]  M. Widersten,et al.  Structure-function relationships of epoxide hydrolases and their potential use in biocatalysis. , 2010, Biochimica et biophysica acta.

[76]  E. Bayer,et al.  The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. , 2004, Annual review of microbiology.

[77]  M. Reetz,et al.  Induced allostery in the directed evolution of an enantioselective Baeyer–Villiger monooxygenase , 2010, Proceedings of the National Academy of Sciences.

[78]  N. Tamura,et al.  Purification, characterization, and directed evolution study of a vitamin D3 hydroxylase from Pseudonocardia autotrophica. , 2009, Biochemical and biophysical research communications.

[79]  Paul N. Devine,et al.  Biocatalytic Asymmetric Synthesis of Chiral Amines from Ketones Applied to Sitagliptin Manufacture , 2010, Science.

[80]  H. Schoemaker,et al.  Improvement of an Acid Phosphatase/DHAP‐Dependent Aldolase Cascade Reaction by Using Directed Evolution , 2009, Chembiochem : a European journal of chemical biology.

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

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

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

[84]  Manfred T Reetz,et al.  Directed evolution of enantioselective enzymes: an unconventional approach to asymmetric catalysis in organic chemistry. , 2009, The Journal of organic chemistry.

[85]  Huimin Zhao,et al.  Recent advances in biocatalysis by directed enzyme evolution. , 2006, Combinatorial chemistry & high throughput screening.

[86]  U. Bornscheuer,et al.  Enzymatic Synthesis of Optically Active Tertiary Alcohols: Expanding the Biocatalysis Toolbox , 2008, Chembiochem : a European journal of chemical biology.

[87]  Bruce E Dale,et al.  High-throughput microplate technique for enzymatic hydrolysis of lignocellulosic biomass. , 2008, Biotechnology and bioengineering.

[88]  K. Maurer,et al.  Engineering of choline oxidase from Arthrobacter nicotianae for potential use as biological bleach in detergents , 2010, Applied Microbiology and Biotechnology.

[89]  Charles Junghanns,et al.  Harnessing the power of enzymes for environmental stewardship. , 2012, Biotechnology advances.

[90]  Tomas Hudlicky,et al.  Applications of biotransformations and biocatalysis to complexity generation in organic synthesis. , 2009, Chemical Society reviews.

[91]  Ryan D. Woodyer,et al.  Directed evolution toward improved production of L-ribose from ribitol. , 2010, Combinatorial chemistry & high throughput screening.

[92]  Takeo Tomita,et al.  Enhancement of the latent 3-isopropylmalate dehydrogenase activity of promiscuous homoisocitrate dehydrogenase by directed evolution. , 2010, The Biochemical journal.

[93]  Zhanglin Lin,et al.  Morphing activity between structurally similar enzymes: from heme-free bromoperoxidase to lipase. , 2009, Biochemistry.

[94]  L. Casper,et al.  Dispelling the Myths , 2002 .

[95]  Ronny Martínez,et al.  A Flow Cytometry–Based Screening System for Directed Evolution of Proteases , 2011, Journal of biomolecular screening.

[96]  Frances H. Arnold,et al.  Molecular evolution by staggered extension process (StEP) in vitro recombination , 1998, Nature Biotechnology.

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

[98]  M. Reetz,et al.  Revisiting the lipase from Pseudomonas aeruginosa: directed evolution of substrate acceptance and enantioselectivity using iterative saturation mutagenesis. , 2011, Chemphyschem : a European journal of chemical physics and physical chemistry.

[99]  E. Bokma,et al.  Directed evolution of a bacterial efflux pump: Adaptation of the E. coli TolC exit duct to the Pseudomonas MexAB translocase , 2006, FEBS letters.

[100]  K. Miyazaki,et al.  Directed Evolution of the Actinomycete Cytochrome P450 MoxA (CYP105) for Enhanced Activity , 2009, Bioscience, biotechnology, and biochemistry.

[101]  Akihiko Kondo,et al.  Cocktail δ-integration: a novel method to construct cellulolytic enzyme expression ratio-optimized yeast strains , 2010, Microbial cell factories.

[102]  Giuseppe Manco,et al.  Improving the promiscuous nerve agent hydrolase activity of a thermostable archaeal lactonase. , 2010, Bioresource technology.

[103]  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.

[104]  Huimin Zhao,et al.  Yeast Surface Display of Trifunctional Minicellulosomes for Simultaneous Saccharification and Fermentation of Cellulose to Ethanol , 2009, Applied and Environmental Microbiology.

[105]  Manfred T Reetz,et al.  Manipulating the stereoselectivity of limonene epoxide hydrolase by directed evolution based on iterative saturation mutagenesis. , 2010, Journal of the American Chemical Society.

[106]  V. Faraco,et al.  Random mutants of a Pleurotus ostreatus laccase as new biocatalysts for industrial effluents bioremediation , 2010, Journal of applied microbiology.

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

[108]  Uwe T Bornscheuer,et al.  Thermostabilization of an esterase by alignment-guided focussed directed evolution. , 2010, Protein engineering, design & selection : PEDS.

[109]  Huimin Zhao,et al.  Evolution in Reverse: Engineering a D‐Xylose‐Specific Xylose Reductase , 2008, Chembiochem : a European journal of chemical biology.

[110]  Robert Kourist,et al.  Complete inversion of enantioselectivity towards acetylated tertiary alcohols by a double mutant of a Bacillus subtilis esterase. , 2008, Angewandte Chemie.

[111]  David Baker,et al.  Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution. , 2011, Journal of molecular biology.

[112]  Robert Kourist,et al.  Biocatalytic synthesis of optically active tertiary alcohols , 2011, Applied Microbiology and Biotechnology.