Directed evolution: tailoring biocatalysts for industrial applications

References

• Abécassis V, Pompon D, Truan G. 2000. High efficiency family shuffling based on multi-step PCR and in vivo DNA recombination in yeast: Statistical and functional analysis of a combinatorial library between human cytochrome P450 1A1 and 1A2. Nucleic Acids Res 28: E88.
   PubMed Web of Science ®Google Scholar
• Aharoni A, Gaidukov L, Khersonsky O, McQ Gould S, Roodveldt C, Tawfik DS. 2005. The ‘evolvability’ of promiscuous protein functions. Nat Genet 37: 73–76.
   PubMed Web of Science ®Google Scholar
• Badalassi F, Wahler D, Klein G, Crotti P, Reymond JL. 2000. A versatile periodate-coupled fluorogenic assay for hydrolytic enzymes. Angew Chem Int Ed 39: 4067.
   Google Scholar
• Baik SH, Ide T, Yoshida H, Kagami O, Harayama S. 2003. Significantly enhanced stability of glucose dehydrogenase by directed evolution. Appl Microbiol Biotechnol 61: 329–335.
   PubMed Web of Science ®Google Scholar
• Bessler C, Schmitt J, Maurer KH, Schmid RD. 2003. Directed evolution of a bacterial α-amylase: Toward enhanced pH-performance and higher specific activity. Protein Sci 12: 2141–2149.
   PubMed Web of Science ®Google Scholar
• Bloom JD, Arnold FH. 2009. In the light of directed evolution: Pathways of adaptive protein evolution. Proc Natl Acad Sci USA 106 Suppl 1: 9995–10000.
   PubMed Web of Science ®Google Scholar
• Bougioukou DJ, Kille S, Taglieber A, Reetz MT. 2009. Directed evolution of an enantioselective enoate-reductase: Testing the utility of iterative saturation mutagenesis. Adv Synth Catal 351: 3287–3305.
   Google Scholar
• Bommarius AS, Blum JK, Abrahamson MJ. 2011. Status of protein engineering for biocatalysts: How to design an industrially useful biocatalyst. Curr Opin Chem Biol 15: 194–200.
   PubMed Web of Science ®Google Scholar
• Boersma YL, Dröge MJ, Quax WJ. 2007. Selection strategies for improved biocatalysts. FEBS J 274: 2181–2195.
   PubMed Web of Science ®Google Scholar
• Bosma T, Damborský J, Stucki G, Janssen DB. 2002. Biodegradation of 1,2,3-trichloropropane through directed evolution and heterologous expression of a haloalkane dehalogenase gene. Appl Environ Microbiol 68: 3582–3587.
   PubMed Web of Science ®Google Scholar
• Brouzes E, Medkova M, Savenelli N, Marran D, Twardowski M, Hutchison JB, Rothberg JM, Link DR, Perrimon N, Samuels ML. 2009. Droplet microfluidic technology for single-cell high-throughput screening. Proc Natl Acad Sci USA 106: 14195–14200.
   PubMed Web of Science ®Google Scholar
• Böttcher D, Bornscheuer U T.. 2010. Protein engineering of microbial enzymes. Curr Opin Microbiol 13: 274–282.
   PubMed Web of Science ®Google Scholar
• Cadwell RC, Joyce GF. 1992. Randomization of genes by PCR mutagenesis. PCR Methods Appl 2: 28–33.
   PubMedGoogle Scholar
• Camps M, Naukkarinen J, Johnson BP, Loeb LA. 2003. Targeted gene evolution in Escherichia coli using a highly error-prone DNA polymerase I. Proc Natl Acad Sci USA 100: 9727–9732.
   PubMedGoogle Scholar
• Castro GR, Knubovets T. 2003. Homogeneous biocatalysis in organic solvents and water-organic mixtures. Crit Rev Biotechnol 23: 195–231.
   PubMed Web of Science ®Google Scholar
• Chatterjee R, Yuan L. 2006. Directed evolution of metabolic pathways. Trends Biotechnol 24: 28–38.
   Google Scholar
• Chen G, Hayhurst A, Thomas JG, Harvey BR, Iverson BL, Georgiou G. 2001. Isolation of high-affinity ligand-binding proteins by periplasmic expression with cytometric screening (PECS). Nat Biotechnol 19: 537–542.
   PubMed Web of Science ®Google Scholar
• Cheriyan M, Walters MJ, Kang BD, Anzaldi LL, Toone EJ, Fierke CA. 2011. Directed evolution of a pyruvate aldolase to recognize a long chain acyl substrate. Bioorg Med Chem 19: 6447–6453.
   Google Scholar
• Cherry JR, Lamsa MH, Schneider P, Vind J, Svendsen A, Jones A, Pedersen AH. 1999. Directed evolution of a fungal peroxidase. Nat Biotechnol 17: 379–384.
   PubMed Web of Science ®Google Scholar
• Christmann A, Wentzel A, Meyer C, Meyers G, Kolmar H. 2001. Epitope mapping and affinity purification of monospecific antibodies by Escherichia coli cell surface display of gene-derived random peptide libraries. J Immunol Methods 257: 163–173.
   Google Scholar
• Cipolla L. 2004. Combinatorial libraries of biocatalysts: Application and screening. Comb Chem High Throughput Screen 7: 101–114.
   Google Scholar
• Coco WM. 2003. RACHITT: Gene family shuffling by random chimeragenesis on transient templates. Methods Mol Biol 231: 111–127.
   Google Scholar
• Coco WM, Encell LP, Levinson WE, Crist MJ, Loomis AK, Licato LL, Arensdorf JJ, Sica N, Pienkos PT, Monticello DJ. 2002. Growth factor engineering by degenerate homoduplex gene family recombination. Nat Biotechnol 20: 1246–1250.
   Google Scholar
• Coco WM, Levinson WE, Crist MJ, Hektor HJ, Darzins A, Pienkos PT, Squires CH, Monticello DJ. 2001. DNA shuffling method for generating highly recombined genes and evolved enzymes. Nat Biotechnol 19: 354–359.
   PubMed Web of Science ®Google Scholar
• Crameri A, Raillard SA, Bermudez E, Stemmer WP. 1998. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature 391: 288–291.
   PubMed Web of Science ®Google Scholar
• Dalby PA. 2011. Strategy and success for the directed evolution of enzymes. Curr Opin Struct Biol 21: 473–480.
   Google Scholar
• Delagrave S, Murphy DJ. 2003. In vitro evolution of proteins for drug development. Assay Drug Dev Technol 1: 187–198.
   Google Scholar
• Deng QW, Luo WS, Donnenberg MS. 2007. Rapid site site-directed domain scanning mutagenesis of enteropathogenic Escherichia coli espD. Biol Proced Online, 18–26.
   Google Scholar
• Dougherty MJ, Arnold FH. 2009. Directed evolution: New parts and optimized function. Curr Opin Biotechnol 20: 486–491.
   PubMed Web of Science ®Google Scholar
• Eggert T, Funke SA, Rao NM, Acharya P, Krumm H, Reetz MT, Jaeger KE. 2005. Multiplex-PCR-based recombination as a novel high-fidelity method for directed evolution. Chembiochem 6: 1062–1067.
   PubMed Web of Science ®Google Scholar
• Eijsink VG, Gåseidnes S, Borchert TV, van den Burg B. 2005. Directed evolution of enzyme stability. Biomol Eng 22: 21–30.
   PubMedGoogle Scholar
• Emond S, André I, Jaziri K, Potocki-Véronèse G, Mondon P, Bouayadi K, Kharrat H, Monsan P, Remaud-Simeon M. 2008. Combinatorial engineering to enhance thermostability of amylosucrase. Protein Sci 17: 967–976.
   Google Scholar
• Esvelt KM, Carlson JC, Liu DR. 2011. A system for the continuous directed evolution of biomolecules. Nature 472: 499–503.
   PubMed Web of Science ®Google Scholar
• Farinas ET. 2006. Fluorescence activated cell sorting for enzymatic activity. Comb Chem High Throughput Screen 9: 321–328.
   Google Scholar
• Fong S, Machajewski TD, Mak CC, Wong C. 2000. Directed evolution of D-2-keto-3-deoxy-6-phosphogluconate aldolase to new variants for the efficient synthesis of D- and L-sugars. Chem Biol 7: 873–883.
   PubMedGoogle Scholar
• Fox RJ, Davis SC, Mundorff EC, Newman LM, Gavrilovic V, Ma SK, Chung LM, Ching C, Tam S, Muley S, Grate J, Gruber J, Whitman JC, Sheldon RA, Huisman GW. 2007. Improving catalytic function by ProSAR-driven enzyme evolution. Nat Biotechnol 25: 338–344.
   PubMed Web of Science ®Google Scholar
• Frankel A, Millward SW, Roberts RW. 2003. Encodamers: Unnatural peptide oligomers encoded in RNA. Chem Biol 10: 1043–1050.
   Google Scholar
• Fujii R, Kitaoka M, Hayashi K. 2006a. Error-prone rolling circle amplification: The simplest random mutagenesis protocol. Nat Protoc 1: 2493–2497.
   Google Scholar
• Fujii R, Kitaoka M, Hayashi K. 2006b. RAISE: A simple and novel method of generating random insertion and deletion mutations. Nucleic Acids Res 34: e30.
   Google Scholar
• Garcia-Ruiz E, Gonzalez-Perez D, Ruiz-Dueñas FJ, Martínez AT, Alcalde M. 2012. Directed evolution of a temperature, peroxide and alkaline pH tolerant versatile peroxidase. Biochem J 441: 487–498.
   PubMed Web of Science ®Google Scholar
• Gibbs MD, Nevalainen KM, Bergquist PL. 2001. Degenerate oligonucleotide gene shuffling (DOGS): A method for enhancing the frequency of recombination with family shuffling. Gene 271: 13–20.
   PubMed Web of Science ®Google Scholar
• Guo HH, Choe J, Loeb LA. 2004. Protein tolerance to random amino acid change. Proc Natl Acad Sci USA 101: 9205–9210.
   PubMed Web of Science ®Google Scholar
• Harvey BR, Georgiou G, Hayhurst A, Jeong KJ, Iverson BL, Rogers GK. 2004. Anchored periplasmic expression, a versatile technology for the isolation of high-affinity antibodies from Escherichia coli-expressed libraries. Proc Natl Acad Sci USA 101: 9193–9198.
   PubMed Web of Science ®Google Scholar
• Heinzelman P, Snow CD, Wu I, Nguyen C, Villalobos A, Govindarajan S, Minshull J, Arnold FH. 2009a. A family of thermostable fungal cellulases created by structure-guided recombination. Proc Natl Acad Sci USA 106: 5610–5615.
   PubMed Web of Science ®Google Scholar
• Heinzelman P, Snow CD, Smith MA, Yu X, Kannan A, Boulware K, Villalobos A, Govindarajan S, Minshull J, Arnold FH. 2009b. SCHEMA recombination of a fungal cellulase uncovers a single mutation that contributes markedly to stability. J Biol Chem 284: 26229–26233.
   Google Scholar
• Heinzelman P, Komor R, Kanaan A, Romero P, Yu X, Mohler S, Snow C, Arnold F. 2010. Efficient screening of fungal cellobiohydrolase class I enzymes for thermostabilizing sequence blocks by SCHEMA structure-guided recombination. Protein Eng Des Sel 23: 871–880.
   PubMed Web of Science ®Google Scholar
• Herman A, Tawfik DS. 2007. Incorporating Synthetic Oligonucleotides via Gene Reassembly (ISOR): A versatile tool for generating targeted libraries. Protein Eng Des Sel 20: 219–226.
   PubMed Web of Science ®Google Scholar
• Hidalgo A, Schliessmann A, Molina R, Hermoso J, Bornscheuer UT. 2008. A one-pot, simple methodology for cassette randomisation and recombination for focused directed evolution. Protein Eng Des Sel 21: 567–576.
   Google Scholar
• Hiraga K, Arnold FH. 2003. General method for sequence-independent site-directed chimeragenesis. J Mol Biol 330: 287–296.
   PubMed Web of Science ®Google Scholar
• Hoffmeister D, Yang J, Liu L, Thorson JS. 2003. Creation of the first anomeric D/L-sugar kinase by means of directed evolution. Proc Natl Acad Sci USA 100: 13184–13189.
   PubMed Web of Science ®Google Scholar
• Jäckel C, Kast P, Hilvert D. 2008. Protein design by directed evolution. Annu Rev Biophys 37: 153–173.
   PubMed Web of Science ®Google Scholar
• Jaeger KE, Eggert T, Eipper A, Reetz MT. 2001. Directed evolution and the creation of enantioselective biocatalysts. Appl Microbiol Biotechnol 55: 519–530.
   PubMed Web of Science ®Google Scholar
• Jochens H, Stiba K, Savile C, Fujii R, Yu JG, Gerassenkov T, Kazlauskas RJ, Bornscheuer UT. 2009. Converting an esterase into an epoxide hydrolase. Angew Chem Int Ed Engl 48: 3532–3535.
   Google Scholar
• Josh J. 2006. Autodisplay: Efficient bacterial surface display of recombinant proteins. Appl Microbiol Biotechnol 69: 607–614.
   Google Scholar
• Josephson K, Hartman MC, Szostak JW. 2005. Ribosomal synthesis of unnatural peptides. J Am Chem Soc 127: 11727–11735.
   PubMed Web of Science ®Google Scholar
• Jürgens C, Strom A, Wegener D, Hettwer S, Wilmanns M, Sterner R. 2000. Directed evolution of a (βα)8-barrel enzyme to catalyze related reactions in two different metabolic pathways. Proc Natl Acad Sci USA 97: 9925–9930.
   PubMed Web of Science ®Google Scholar
• Kampen MDV, Egmond MR. 2000. Directed evolution: From a staphylococcal lipase to a phospholipase. Eur J Lipid Sci Technol 102, 717–726.
   Google Scholar
• Kauffmann I, Schmidt-Dannert C. 2001. Conversion of Bacillus thermocatenulatus lipase into an efficient phospholipase with increased activity towards long-chain fatty acyl substrates by directed evolution and rational design. Protein Eng 14: 919–928.
   Google Scholar
• Kawarasaki Y, Griswold KE, Stevenson JD, Selzer T, Benkovic SJ, Iverson BL, Georgiou G. 2003. Enhanced crossover SCRATCHY: Construction and high-throughput screening of a combinatorial library containing multiple non-homologous crossovers. Nucleic Acids Res 31: e126.
   Google Scholar
• Kelly RM, Dijkhuizen L, Leemhuis H. 2009. Starch and α-glucan acting enzymes, modulating their properties by directed evolution. J Biotechnol 140: 184–193.
   PubMed Web of Science ®Google Scholar
• Kelly RM, Leemhuis H, Rozeboom HJ, van Oosterwijk N, Dijkstra BW, Dijkhuizen L. 2008. Elimination of competing hydrolysis and coupling side reactions of a cyclodextrin glucanotransferase by directed evolution. Biochem J 413: 517–525.
   PubMed Web of Science ®Google Scholar
• Khersonsky O, Röthlisberger D, Dym O, Albeck S, Jackson CJ, Baker D, Tawfik DS. 2010. Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series. J Mol Biol 396: 1025–1042.
   PubMed Web of Science ®Google Scholar
• Kikuchi M, Ohnishi K, Harayama S. 2000. An effective family shuffling method using single-stranded DNA. Gene 243: 133–137.
   PubMed Web of Science ®Google Scholar
• Kim YW, Choi JH, Kim JW, Park C, Kim JW, Cha H, Lee SB, Oh BH, Moon TW, Park KH. 2003. Directed evolution of Thermus maltogenic amylase toward enhanced thermal resistance. Appl Environ Microbiol 69: 4866–4874.
   PubMed Web of Science ®Google Scholar
• Kim YS, Jung HC, Pan JG. 2000. Bacterial cell surface display of an enzyme library for selective screening of improved cellulase variants. Appl Environ Microbiol 66: 788–793.
   Google Scholar
• Kirschner A, Bornscheuer UT. 2008. Directed evolution of a Baeyer-Villiger monooxygenase to enhance enantioselectivity. Appl Microbiol Biotechnol 81: 465–472.
   Google Scholar
• Kitamura K, Kinoshita Y, Narasaki S, Nemoto N, Husimi Y, Nishigaki K. 2002. Construction of block-shuffled libraries of DNA for evolutionary protein engineering: Y-ligation-based block shuffling. Protein Eng 15: 843–853.
   Google Scholar
• Komeda HNI, Asano Y. 2003. Enhancement of the thermostability and catalytic activity D-stereospecific amino- acid amidase from Ochrobactrum anthropi SV3 by directed evolution. J Mol Catal B-Enzym 21: 283–290.
   Google Scholar
• Korkegian A, Black ME, Baker D, Stoddard BL. 2005. Computational thermostabilization of an enzyme. Science 308: 857–860.
   Google Scholar
• Kumar R, Rajagopal K. 2008. Single-step overlap-primer-walk polymerase chain reaction for multiple mutagenesis without overlap extension. Anal Biochem 377: 105–107.
   Google Scholar
• Lassila JK, Keeffe JR, Oelschlaeger P, Mayo SL. 2005. Computationally designed variants of Escherichia coli chorismate mutase show altered catalytic activity. Protein Eng Des Sel 18: 161–163.
   Google Scholar
• Leemhuis H, Stein V, Griffiths AD, Hollfelder F. 2005. New genotype-phenotype linkages for directed evolution of functional proteins. Curr Opin Struct Biol 15: 472–478.
   PubMed Web of Science ®Google Scholar
• Li HM, Mei LH, Urlacher VB, Schmid RD. 2008. Cytochrome P450 BM-3 evolved by random and saturation mutagenesis as an effective indole-hydroxylating catalyst. Appl Biochem Biotechnol 144: 27–36.
   PubMed Web of Science ®Google Scholar
• Liang J, Mundorff E, Voladri R, Jenne S, Gilson L, Conway A, Krebber A, Wong J, Huisman G, Truesdell S, Lalonde J. 2010. Highly enantioselective reduction of a small heterocyclic ketone: Biocatalytic reduction of tetrahydrothiophene-3-one to the corresponding (R)-alcohol. Org Process Res Dev 14: 188–192.
   Web of Science ®Google Scholar
• Lipovsek D, Plückthun A. 2004. In-vitro protein evolution by ribosome display and mRNA display. J Immunol Methods 290: 51–67.
   PubMed Web of Science ®Google Scholar
• Loo SW, Siemerink MA, Perrakis G, Kaper T, Kengen SW, van der Oost J. 2009. Improving low-temperature activity of Sulfolobus acidocaldarius 2-keto-3-deoxygluconate aldolase. Archaea 2: 233–239.
   Google Scholar
• Lutz S, Ostermeier M, Benkovic SJ. 2001a. Rapid generation of incremental truncation libraries for protein engineering using α-phosphothioate nucleotides. Nucleic Acids Res 29: E16.
   Web of Science ®Google Scholar
• Lutz S, Ostermeier M, Moore GL, Maranas CD, Benkovic SJ. 2001b. Creating multiple-crossover DNA libraries independent of sequence identity. Proc Natl Acad Sci USA 98: 11248–11253.
   PubMed Web of Science ®Google Scholar
• Ma SK, Gruber J, Davis C, Newman L, Gray D, Wang A, Grate J, Huisman GW, Sheldon RA. 2010. A green-by-design biocatalytic process for atorvastatin intermediate. Green Chem 12: 81–86.
   Web of Science ®Google Scholar
• Machielsen R, Leferink NG, Hendriks A, Brouns SJ, Hennemann HG, Daussmann T, van der Oost J. 2008. Laboratory evolution of Pyrococcus furiosus alcohol dehydrogenase to improve the production of (2S,5S)-hexanediol at moderate temperatures. Extremophiles 12: 587–594.
   Google Scholar
• Mandai T, Fujiwara S, Imaoka S. 2009. Construction and engineering of a thermostable self-sufficient cytochrome P450. Biochem Biophys Res Commun 384: 61–65.
   PubMed Web of Science ®Google Scholar
• Marrs B, Delagrave S, Murphy D. 1999. Novel approaches for discovering industrial enzymes. Curr Opin Microbiol 2: 241–245.
   Google Scholar
• Matsuura T, Miyai K, Trakulnaleamsai S, Yomo T, Shima Y, Miki S, Yamamoto K, Urabe I. 1999. Evolutionary molecular engineering by random elongation mutagenesis. Nat Biotechnol 17: 58–61.
   PubMed Web of Science ®Google Scholar
• May O, Nguyen PT, Arnold FH. 2000. Inverting enantioselectivity by directed evolution of hydantoinase for improved production of L-methionine. Nat Biotechnol 18: 317–320.
   PubMed Web of Science ®Google Scholar
• Meyer MM, Silberg JJ, Voigt CA, Endelman JB, Mayo SL, Wang ZG, Arnold FH. 2003. Library analysis of SCHEMA-guided protein recombination. Protein Sci 12: 1686–1693.
   PubMed Web of Science ®Google Scholar
• Miyazaki K. 2003. Creating random mutagenesis libraries by megaprimer PCR of whole plasmid (MEGAWHOP). Methods Mol Biol 231: 23–28.
   Google Scholar
• Miele A, Giardina P, Notomista E, Piscitelli A, Sannia G, Faraco V. 2010. A semi-rational approach to engineering laccase enzymes. Mol Biotechnol 46: 149–156.
   Google Scholar
• McHunu NP, Singh S, Permaul K. 2009. Expression of an alkalo-tolerant fungal xylanase enhanced by directed evolution in Pichia pastoris and Escherichia coli. J Biotechnol 141: 26–30.
   PubMed Web of Science ®Google Scholar
• Ness JE, Kim S, Gottman A, Pak R, Krebber A, Borchert TV, Govindarajan S, Mundorff EC, Minshull J. 2002. Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently. Nat Biotechnol 20: 1251–1255.
   PubMed Web of Science ®Google Scholar
• Nestl BM, Nebel BA, Hauer B. 2011. Recent progress in industrial biocatalysis. Curr Opin Chem Biol 15: 187–193.
   PubMed Web of Science ®Google Scholar
• Neylon C. 2004. Chemical and biochemical strategies for the randomization of protein encoding DNA sequences: Library construction methods for directed evolution. Nucleic Acids Res 32: 1448–1459.
   PubMed Web of Science ®Google Scholar
• O’Maille PE, Bakhtina M, Tsai MD. 2002. Structure-based combinatorial protein engineering (SCOPE). J Mol Biol 321: 677–691.
   PubMed Web of Science ®Google Scholar
• Oh KH, Nam SH, Kim HS. 2002. Directed evolution of N-carbamyl-D-amino acid amidohydrolase for simultaneous improvement of oxidative and thermal stability. Biotechnol Prog 18: 413–417.
   Google Scholar
• Ostermeier M. 2003. Synthetic gene libraries: In search of the optimal diversity. Trends Biotechnol 21: 244–247.
   PubMed Web of Science ®Google Scholar
• Ostermeier M, Shim JH, Benkovic SJ. 1999. A combinatorial approach to hybrid enzymes independent of DNA homology. Nat Biotechnol 17: 1205–1209.
   PubMed Web of Science ®Google Scholar
• Otten LG, Quax WJ. 2005. Directed evolution: Selecting today’s biocatalysts. Biomol Eng 22: 1–9.
   PubMedGoogle Scholar
• Park HS, Nam SH, Lee JK, Yoon CN, Mannervik B, Benkovic SJ, Kim HS. 2006. Design and evolution of new catalytic activity with an existing protein scaffold. Science 311: 535–538.
   PubMed Web of Science ®Google Scholar
• Parikh MR, Matsumura I. 2005. Site-saturation mutagenesis is more efficient than DNA shuffling for the directed evolution of β-fucosidase from β-galactosidase. J Mol Biol 352: 621–628.
   PubMed Web of Science ®Google Scholar
• Pire C, Esclapez J, Diaz S, Perez-Pomares F, Ferrer J, Bonete MJ. 2009. Alteration of coenzyme specificity in halophilic NAD(P)+glucose dehydrogenase by site-directed mutagenesis. J Mol Catal B Enzyme 59, 261–265.
   Google Scholar
• Powell KA, Sandra WR, Stephen BDC, Willem PCS, Matthew BT, Pascal FL, Gjalt WH. 2001. Directed Evolution and Biocatalysis. Angewandte Chemie International Edition. 40: 3948–3959.
   PubMedGoogle Scholar
• Pritcharda L, Corne D, Kell D, Rowland J, Winson M.. 2005. A general model of error-prone PCR. J Theor Biol 234: 497–509.
   Google Scholar
• Reetz MT. 2004. Controlling the enantioselectivity of enzymes by directed evolution: Practical and theoretical ramifications. Proc Natl Acad Sci USA 101: 5716–5722.
   PubMed Web of Science ®Google Scholar
• Reetz MT, Bocola M, Carballeira JD, Zha D, Vogel A. 2005. Expanding the range of substrate acceptance of enzymes: Combinatorial active-site saturation test. Angew Chem Int Ed Engl 44: 4192–4196.
   PubMed Web of Science ®Google Scholar
• Reetz MT, Carballeira JD, Vogel A. 2006. Iterative saturation mutagenesis on the basis of B factors as a strategy for increasing protein thermostability. Angew Chem Int Ed Engl 45: 7745–7751.
   PubMed Web of Science ®Google Scholar
• Reetz MT, Carballeira JD. 2007. Iterative saturation mutagenesis (ISM) for rapid directed evolution of functional enzymes. Nat Protoc 2: 891–903.
   PubMed Web of Science ®Google Scholar
• Reymond JL, Wahler D. 2002. Substrate arrays as enzyme fingerprinting tools. Chembiochem 3: 701–708.
   Google Scholar
• Robertson DE, Steer BA. 2004. Recent progress in biocatalyst discovery and optimization. Curr Opin Chem Biol 8: 141–149.
   PubMedGoogle Scholar
• Romero PA, Arnold FH. 2009. Exploring protein fitness landscapes by directed evolution. Nat Rev Mol Cell Biol 10: 866–876.
   PubMed Web of Science ®Google Scholar
• Röthlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, Betker J, Gallaher JL, Althoff EA, Zanghellini A, Dym O, Albeck S, Houk KN, Tawfik DS, Baker D. 2008. Kemp elimination catalysts by computational enzyme design. Nature 453: 190–195.
   PubMed Web of Science ®Google Scholar
• Rothman SC, Voorhies M, Kirsch JF. 2004. Directed evolution relieves product inhibition and confers in vivo function to a rationally designed tyrosine aminotransferase. Protein Sci 13: 763–772.
   PubMed Web of Science ®Google Scholar
• Rubin-Pitel SB, Zhao H. 2006. Recent advances in biocatalysis by directed enzyme evolution. Comb Chem High Throughput Screen 9: 247–257.
   PubMed Web of Science ®Google Scholar
• Salamone PR, Kavakli IH, Slattery CJ, Okita TW. 2002. Directed molecular evolution of ADP-glucose pyrophosphorylase. Proc Natl Acad Sci USA 99: 1070–1075.
   Google Scholar
• Saraf MC, Horswill AR, Benkovic SJ, Maranas CD. 2004. FamClash: A method for ranking the activity of engineered enzymes. Proc Natl Acad Sci USA 101: 4142–4147.
   PubMed Web of Science ®Google Scholar
• Savile CK, Janey JM, Mundorff EC, Moore JC, Tam S, Jarvis WR, Colbeck JC, Krebber A, Fleitz FJ, Brands J, Devine PN, Huisman GW, Hughes GJ. 2010. Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufacture. Science 329: 305–309.
   PubMed Web of Science ®Google Scholar
• Schmidt M, Hasenpusch D, Kähler M, Kirchner U, Wiggenhorn K, Langel W, Bornscheuer UT. 2006. Directed evolution of an esterase from Pseudomonas fluorescens yields a mutant with excellent enantioselectivity and activity for the kinetic resolution of a chiral building block. Chembiochem 7: 805–809.
   Google Scholar
• Schmidt-Dannert C. 2001. Directed evolution of single proteins, metabolic pathways, and viruses. Biochemistry 40: 13125–13136.
   PubMed Web of Science ®Google Scholar
• Seelig B. 2011. mRNA display for the selection and evolution of enzymes from in vitro-translated protein libraries. Nat Protoc 6: 540–552.
   Google Scholar
• Shim JH, Kim YW, Kim TJ, Chae HY, Park JH, Cha H, Kim JW, Kim YR, Schaefer T, Spendler T, Moon TW, Park KH. 2004. Improvement of cyclodextrin glucanotransferase as an antistaling enzyme by error-prone PCR. Protein Eng Des Sel 17: 205–211.
   PubMed Web of Science ®Google Scholar
• Shu Z-Y, Jiang H, Lin R-F, Jiang Y-M, Lin L, Huang J-Z. 2010. Technical methods to improve yield, activity and stability in the development of microbial lipases. J Mol Catal B Enzym 62: 1–8.
   Web of Science ®Google Scholar
• Sieber V, Martinez CA, Arnold FH. 2001. Libraries of hybrid proteins from distantly related sequences. Nat Biotechnol 19: 456–460.
   PubMed Web of Science ®Google Scholar
• Song JK, Chung B, Oh YH, Rhee JS. 2002. Construction of DNA-shuffled and incrementally truncated libraries by a mutagenic and unidirectional reassembly method: Changing from a substrate specificity of phospholipase to that of lipase. Appl Environ Microbiol 68: 6146–6151.
   Google Scholar
• Stefan A, Radeghieri A, Gonzalez Vara y Rodriguez A, Hochkoeppler A. 2001. Directed evolution of β-galactosidase from Escherichia coli by mutator strains defective in the 3′–>5′ exonuclease activity of DNA polymerase III. FEBS Lett 493: 139–143.
   PubMed Web of Science ®Google Scholar
• Stemmer WP. 1994a. Rapid evolution of a protein in vitro by DNA shuffling. Nature 370: 389–391.
   PubMed Web of Science ®Google Scholar
• Stemmer WP. 1994b. DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution. Proc Natl Acad Sci USA 91: 10747–10751.
   PubMed Web of Science ®Google Scholar
• Stephens DE, Permaul K, Prior BA, Singh S. 2004. Protein engineering of xylanases. In: Saha Hayashi, ed. Lignocellulosic Biodegradation. Washington, DC: ACS publication, 227–240.
   Google Scholar
• Stephens DE, Rumbold K, Permaul K, Prior BA, Singh S. 2007. Directed evolution of the thermostable xylanase from Thermomyces lanuginosus. J Biotechnol 127: 348–354.
   PubMed Web of Science ®Google Scholar
• Stephens DE, Singh S, Permaul K. 2009. Error-prone PCR of a fungal xylanase for improvement of its alkaline and thermal stability. FEMS Microbiol Lett 293: 42–47.
   PubMed Web of Science ®Google Scholar
• Suen WC, Zhang N, Xiao L, Madison V, Zaks A. 2004. Improved activity and thermostability of Candida antarctica lipase B by DNA family shuffling. Protein Eng Des Sel 17: 133–140.
   PubMed Web of Science ®Google Scholar
• Taly V, Kelly BT, Griffiths AD. 2007. Droplets as microreactors for high-throughput biology. Chembiochem 8: 263–272.
   Google Scholar
• Tong Z, Zhenfang W, Chen H, Wu Q, Tang Z, Gou JWH, Hao W, Wang C, Li C. 2010. Progress in strategies for sequence diversity library creation for directed evolution. Afri J Biotechnol 54: 9277–9285.
   Google Scholar
• Tracewell CA, Arnold FH. 2009. Directed enzyme evolution: Climbing fitness peaks one amino acid at a time. Curr Opin Chem Biol 13: 3–9.
   PubMed Web of Science ®Google Scholar
• Udit AK, Silberg JJ, Sieber V. 2003. Sequence homology-independent protein recombination (SHIPREC). Methods Mol Biol 231: 153–163.
   Google Scholar
• van Beilen JB, Li Z. 2002. Enzyme technology: An overview. Curr Opin Biotechnol 13: 338–344.
   PubMed Web of Science ®Google Scholar
• van der Veen BA, Potocki-Véronèse G, Albenne C, Joucla G, Monsan P, Remaud-Simeon M. 2004. Combinatorial engineering to enhance amylosucrase performance: Construction, selection, and screening of variant libraries for increased activity. FEBS Lett 560: 91–97.
   PubMed Web of Science ®Google Scholar
• van der Veen BA, Skov LK, Potocki-Véronèse G, Gajhede M, Monsan P, Remaud-Simeon M. 2006. Increased amylosucrase activity and specificity, and identification of regions important for activity, specificity and stability through molecular evolution. FEBS J 273: 673–681.
   PubMed Web of Science ®Google Scholar
• Volkov AA, Shao Z, Arnold FH. 1999. Recombination and chimeragenesis by in vitro heteroduplex formation and in vivo repair. Nucleic Acids Res 27: e18.
   Google Scholar
• Williams GJ, Domann S, Nelson A, Berry A. 2003. Modifying the stereochemistry of an enzyme-catalyzed reaction by directed evolution. Proc Natl Acad Sci USA 100: 3143–3148.
   PubMed Web of Science ®Google Scholar
• Williams GJ, Nelson AS, Berry A. 2004. Directed evolution of enzymes for biocatalysis and the life sciences. Cell Mol Life Sci 61: 3034–3046.
   Google Scholar
• Wong TS, Tee KL, Hauer B, Schwaneberg U. 2004. Sequence saturation mutagenesis (SeSaM): A novel method for directed evolution. Nucleic Acids Res 32: e26.
   PubMed Web of Science ®Google Scholar
• Wong TS, Tee KL, Hauer B, Schwaneberg U. 2005. Sequence saturation mutagenesis with tunable mutation frequencies. Anal Biochem 341: 187–189.
   PubMedGoogle Scholar
• Wong TS, Roccatano D, Zacharias M, Schwaneberg U. 2006. A statistical analysis of random mutagenesis methods used for directed protein evolution. J Mol Biol 355: 858–871.
   Google Scholar
• Yu H, Li J, Zhang D, Yang Y, Jiang W, Yang S. 2009. Improving the thermostability of N-carbamyl-D-amino acid amidohydrolase by error-prone PCR. Appl Microbiol Biotechnol 82: 279–285.
   PubMed Web of Science ®Google Scholar
• Zha D, Eipper A, Reetz MT. 2003. Assembly of designed oligonucleotides as an efficient method for gene recombination: A new tool in directed evolution. Chembiochem 4: 34–39.
   Google Scholar
• Zhang YX, Perry K, Vinci VA, Powell K, Stemmer WP, del Cardayré SB. 2002. Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature 415: 644–646.
   PubMed Web of Science ®Google Scholar
• Zhang S, Xing K, Hu Y, Xie C, Liu D, Yao D. 2011. Directed evolution of aflatoxin detoxifzyme in vitro by error-prone PCR. Sheng Wu Gong Cheng Xue Bao 27: 1100–1108.
   Google Scholar
• Zhao H. 2004. Staggered extension process in vitro DNA recombination. Meth Enzymol 388: 42–49.
   Google Scholar
• Zhao H, Zha W. 2004. Evolutionary methods for protein engineering. In: Svendsen A, ed. Enzyme Functionality: Design, Engineering and Screening. New York, NY: Marcel Dekker, Inc, 353–373.
   Google Scholar
• Zhao H, Giver L, Shao Z, Affholter JA, Arnold FH. 1998. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat Biotechnol 16: 258–261.
   PubMed Web of Science ®Google Scholar
• Zheng L, Baumann U, Reymond JL. 2004. An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res 32: e115.
   PubMed Web of Science ®Google Scholar