Selection strategies for improved biocatalysts

Enzymes have become an attractive alternative to conventional catalysts in numerous industrial processes. However, their properties do not always meet the criteria of the application of interest. Directed evolution is a powerful tool for adapting the characteristics of an enzyme. However, selection of the evolved variants is a critical step, and therefore new strategies to enable selection of the desired enzymatic activity have been developed. This review focuses on these novel strategies for selecting enzymes from large libraries, in particular those that are used in the synthesis of pharmaceutical intermediates and pharmaceuticals.

[1]  B. Kay,et al.  Filamentous phage display in the new millennium. , 2005, Chemical reviews.

[2]  T. S. Wong,et al.  The diversity challenge in directed protein evolution. , 2006, Combinatorial chemistry & high throughput screening.

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

[4]  G. Robillard,et al.  Novel Surface Display System for Proteins on Non-Genetically Modified Gram-Positive Bacteria , 2006, Applied and Environmental Microbiology.

[5]  D. Ladant,et al.  In vitro selection for enzymatic activity: a model study using adenylate cyclase. , 2003, Journal of molecular biology.

[6]  Wim J. Quax,et al.  Altering the Substrate Specificity of Cephalosporin Acylase by Directed Evolution of the β-Subunit* , 2002, The Journal of Biological Chemistry.

[7]  P Soumillion,et al.  Selection of Metalloenzymes by Catalytic Activity Using Phage Display and Catalytic Elution , 2001, Chembiochem : a European journal of chemical biology.

[8]  J. van Duin,et al.  Phage display selects for amylases with improved low pH starch-binding. , 2002, Journal of biotechnology.

[9]  D. Hilvert,et al.  Deciphering enzymes. Genetic selection as a probe of structure and mechanism. , 2004, European journal of biochemistry.

[10]  B. Witholt,et al.  Selection of biocatalysts for chemical synthesis. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[11]  V. Cornish,et al.  Chemical complementation: A reaction-independent genetic assay for enzyme catalysis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[12]  F. Romesberg,et al.  Directed evolution of novel polymerases. , 2005, Biomolecular engineering.

[13]  Laura Cipolla.  Combinatorial libraries of biocatalysts: application and screening. , 2004, Combinatorial chemistry & high throughput screening.

[14]  T. Meyer,et al.  Autodisplay: one-component system for efficient surface display and release of soluble recombinant proteins from Escherichia coli , 1997, Journal of bacteriology.

[15]  S. Fukuyama,et al.  Evolving catalytic antibodies in a phage-displayed combinatorial library , 1998, Nature Biotechnology.

[16]  Stephen J Benkovic,et al.  Using an AraC-based three-hybrid system to detect biocatalysts in vivo , 2000, Nature Biotechnology.

[17]  Sang Yup Lee,et al.  Microbial cell-surface display. , 2003, Trends in biotechnology.

[18]  Ichiro Matsumura,et al.  Directed evolution of RuBisCO hypermorphs through genetic selection in engineered E.coli. , 2006, Protein engineering, design & selection : PEDS.

[19]  S. Walker,et al.  Enabling Glycosyltransferase Evolution: A Facile Substrate‐Attachment Strategy for Phage‐Display Enzyme Evolution , 2006, Chembiochem : a European journal of chemical biology.

[20]  A. Plückthun,et al.  In vitro selection for catalytic activity with ribosome display. , 2002, Journal of the American Chemical Society.

[21]  B. Dijkstra,et al.  Directed Evolution of Bacillus subtilis Lipase A by Use of Enantiomeric Phosphonate Inhibitors: Crystal Structures and Phage Display Selection , 2006, Chembiochem : a European journal of chemical biology.

[22]  Yawen Bai,et al.  Selection of stably folded proteins by phage-display with proteolysis. , 2004, European journal of biochemistry.

[23]  K. Jaeger,et al.  Select the best: novel biocatalysts for industrial applications. , 2006, Trends in biotechnology.

[24]  Joachim Jose,et al.  Autodisplay: efficient bacterial surface display of recombinant proteins , 2006, Applied Microbiology and Biotechnology.

[25]  Rohit Sharma,et al.  Directed Evolution: An Approach to Engineer Enzymes , 2006, Critical reviews in biotechnology.

[26]  W. Quax,et al.  Binding of phage displayed Bacillus subtilis lipase A to a phosphonate suicide inhibitor. , 2003, Journal of biotechnology.

[27]  A. Jäschke,et al.  Nucleic acid enzymes. , 2005, Current opinion in biotechnology.

[28]  Selection of an Active Enzyme by Phage Display on the Basis of the Enzyme's Catalytic Activity in vivo , 2005, Chembiochem : a European journal of chemical biology.

[29]  Hu Zhu,et al.  Mutant library construction in directed molecular evolution , 2006, Molecular biotechnology.

[30]  Donald Hilvert,et al.  Investigating and Engineering Enzymes by Genetic Selection. , 2001, Angewandte Chemie.

[31]  Ling Yuan,et al.  Laboratory-Directed Protein Evolution , 2005, Microbiology and Molecular Biology Reviews.

[32]  T. Eggert,et al.  Identification of Novel Benzoylformate Decarboxylases by Growth Selection , 2006, Applied and Environmental Microbiology.

[33]  Andreas Plückthun,et al.  Signal sequences directing cotranslational translocation expand the range of proteins amenable to phage display , 2006, Nature Biotechnology.

[34]  Matthias Paschke,et al.  Phage display systems and their applications , 2006, Applied Microbiology and Biotechnology.

[35]  A. Kondo,et al.  Display of active enzymes on the cell surface of Escherichia coli using PgsA anchor protein and their application to bioconversion , 2006, Applied Microbiology and Biotechnology.

[36]  S. Atwell,et al.  Selection for improved subtiligases by phage display. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[37]  E. Kobatake,et al.  Ribosome display for selection of active dihydrofolate reductase mutants using immobilized methotrexate on agarose beads , 2002, FEBS letters.

[38]  H. Kolmar,et al.  Functional Cell‐Surface Display of a Lipase‐Specific Chaperone , 2007, Chembiochem : a European journal of chemical biology.

[39]  S. Delagrave,et al.  In vitro evolution of proteins for drug development. , 2003, Assay and drug development technologies.

[40]  E. Toone,et al.  A bacterial selection for the directed evolution of pyruvate aldolases. , 2004, Bioorganic & medicinal chemistry.

[41]  C. Craik,et al.  Substrate specificity of trypsin investigated by using a genetic selection. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

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

[43]  W. Dower,et al.  In vitro selection as a powerful tool for the applied evolution of proteins and peptides. , 2002, Current opinion in chemical biology.

[44]  D. Neri,et al.  Selections for enzymatic catalysts , 2005 .

[45]  G. Volckaert,et al.  Functional display of family 11 endoxylanases on the surface of phage M13. , 2005, Journal of biotechnology.

[46]  Dan S. Tawfik,et al.  In vitro compartmentalization by double emulsions: sorting and gene enrichment by fluorescence activated cell sorting. , 2004, Analytical biochemistry.

[47]  Andreas Schwienhorst,et al.  Evolutionary methods in biotechnology : clever tricks for directed evolution , 2004 .

[48]  Dan S. Tawfik,et al.  Altering the sequence specificity of HaeIII methyltransferase by directed evolution using in vitro compartmentalization. , 2004, Protein engineering, design & selection : PEDS.

[49]  Mattijs K. Julsing,et al.  Phage Display of an Intracellular Carboxylesterase of Bacillus subtilis: Comparison of Sec and Tat Pathway Export Capabilities , 2006, Applied and Environmental Microbiology.

[50]  E. Farinas.  Fluorescence activated cell sorting for enzymatic activity. , 2006, Combinatorial chemistry & high throughput screening.

[51]  Hening Lin,et al.  Directed evolution of a glycosynthase via chemical complementation. , 2004, Journal of the American Chemical Society.

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

[53]  Karl-Erich Jaeger,et al.  A generic system for the Escherichia coli cell‐surface display of lipolytic enzymes , 2005, FEBS letters.

[54]  B. A. van der Veen,et al.  Combinatorial engineering to enhance amylosucrase performance: construction, selection, and screening of variant libraries for increased activity , 2004, FEBS letters.

[55]  J. Fastrez,et al.  Selection of the most active enzymes from a mixture of phage-displayed β-lactamase mutants , 1996 .

[56]  H. Wernérus,et al.  Biotechnological applications for surface‐engineered bacteria , 2004, Biotechnology and applied biochemistry.

[57]  Joachim Jose,et al.  Functional esterase surface display by the autotransporter pathway in Escherichia coli , 2002 .

[58]  Juhan Kim,et al.  Pro-antibiotic Substrates for the Identification of Enantioselective Hydrolases , 2006, Biotechnology Letters.

[59]  L. Hansson,et al.  Mechanism-based phage display selection of active-site mutants of human glutathione transferase A1-1 catalyzing SNAr reactions. , 1997, Biochemistry.

[60]  Paul A Dalby,et al.  Optimising enzyme function by directed evolution. , 2003, Current opinion in structural biology.

[61]  L. Otten,et al.  Directed evolution: selecting today's biocatalysts. , 2005, Biomolecular engineering.

[62]  J. Jestin,et al.  A population of thermostable reverse transcriptases evolved from Thermus aquaticus DNA polymerase I by phage display. , 2006, Angewandte Chemie.

[63]  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.

[64]  Chi-Huey Wong,et al.  Observation of Covalent Intermediates in an Enzyme Mechanism at Atomic Resolution , 2001, Science.

[65]  M. Taussig,et al.  Ribosome display: cell-free protein display technology. , 2002, Briefings in functional genomics & proteomics.

[66]  Susanne Wilhelm,et al.  Ultra-high-throughput screening based on cell-surface display and fluorescence-activated cell sorting for the identification of novel biocatalysts. , 2004, Current opinion in biotechnology.

[67]  B. Park,et al.  Display of Bacterial Lipase on the Escherichia coli Cell Surface by Using FadL as an Anchoring Motif and Use of the Enzyme in Enantioselective Biocatalysis , 2004, Applied and Environmental Microbiology.

[68]  Patrik Samuelson,et al.  Display of proteins on bacteria. , 2002, Journal of biotechnology.

[69]  H. Kagamiyama,et al.  Directed evolution of an aspartate aminotransferase with new substrate specificities. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[70]  Chi‐Huey Wong,et al.  Directed evolution of aldolases. , 2004, Methods in enzymology.

[71]  L. Loeb,et al.  Genetic complementation protocols. , 2003, Methods in molecular biology.

[72]  A. Plückthun,et al.  In vitro display technologies: novel developments and applications. , 2001, Current opinion in biotechnology.

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

[74]  F. Arnold,et al.  Directed evolution of biocatalysts. , 1999, Current opinion in chemical biology.

[75]  U. Bornscheuer.  Trends and challenges in enzyme technology. , 2005, Advances in biochemical engineering/biotechnology.

[76]  W. Höhne,et al.  A twin-arginine translocation (Tat)-mediated phage display system. , 2005, Gene.

[77]  Viktor Stein,et al.  New genotype-phenotype linkages for directed evolution of functional proteins. , 2005, Current opinion in structural biology.

[78]  A. Radeghieri,et al.  Expanding the substrate repertoire of a DNA polymerase by directed evolution. , 2004, Journal of the American Chemical Society.

[79]  Luis Echegoyen,et al.  Cover Picture: Retro-Cycloaddition Reaction of Pyrrolidinofullerenes (Angew. Chem. Int. Ed. 1/2006) , 2006 .

[80]  G. P. Smith,et al.  Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. , 1985, Science.

[81]  Andrew D Griffiths,et al.  High-throughput screens and selections of enzyme-encoding genes. , 2005, Current opinion in chemical biology.

[82]  D. Ollis,et al.  and Sole Phosphorus Source Phosphodiesterase , Using Paraoxon as the Glycerophosphodiester Phosphotriesterase and Coexpressing Escherichia coli Growth of , 2003 .

[83]  I. Benhar.  Biotechnological applications of phage and cell display. , 2001, Biotechnology advances.

[84]  P G Schultz,et al.  A method for directed evolution and functional cloning of enzymes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[85]  E. Kobatake,et al.  Activity-based in vitro selection of T4 DNA ligase. , 2005, Biochemical and biophysical research communications.

[86]  Jong Hyun Choi,et al.  Enantioselective resolution of racemic compounds by cell surface displayed lipase , 2004 .

[87]  Dan S. Tawfik,et al.  Man-made cell-like compartments for molecular evolution , 1998, Nature Biotechnology.

[88]  Kouhei Ohnishi,et al.  Directed evolution of bacterial alanine racemases with higher expression level. , 2005, Journal of bioscience and bioengineering.

[89]  Chi-Huey Wong,et al.  Structure-based mutagenesis approaches toward expanding the substrate specificity of D-2-deoxyribose-5-phosphate aldolase. , 2003, Bioorganic & medicinal chemistry.

[90]  Gavin J. Williams,et al.  Directed evolution of enzymes for biocatalysis and the life sciences , 2004, Cellular and Molecular Life Sciences CMLS.

[91]  Dan S. Tawfik,et al.  Investigating the target recognition of DNA cytosine-5 methyltransferase HhaI by library selection using in vitro compartmentalisation. , 2002, Nucleic acids research.

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

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

[94]  R. Hosse,et al.  In vitro display technologies reveal novel biopharmaceutics , 2006, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[95]  J. Reymond,et al.  High-throughput screening for biocatalysts. , 2001, Current opinion in biotechnology.

[96]  Dan S. Tawfik,et al.  High-throughput screening of enzyme libraries: thiolactonases evolved by fluorescence-activated sorting of single cells in emulsion compartments. , 2005, Chemistry & biology.

[97]  Hening Lin,et al.  Screening and selection methods for large-scale analysis of protein function. , 2002, Angewandte Chemie.