In vivo versus in vitro screening or selection for catalytic activity in enzymes and abzymes

The recent development of catalytic antibodies and the introduction of new techniques to generate huge libraries of random mutants of existing enzymes have created the need for powerful tools for finding in large populations of cells those producing the catalytically most active proteins. Several approaches have been developed and used to reach this goal. The screening techniques aim at easily detecting the clones producing active enzymes or abzymes; the selection techniques are designed to extract these clones from mixtures. These techniques have been applied both in vivo and in vitro. This review describes the advantages and limitations of the various methods in terms of ease of use, sensitivity, and convenience for handling large libraries. Examples are analyzed and tentative rules proposed. These techniques prove to be quite powerful to study the relationship between structure and function and to alter the properties of enzymes.

[1]  Daniel Thomas,et al.  Abzyme generation using an anti-idiotypic antibody as the “internal image” of an enzyme active site , 1994, Applied biochemistry and biotechnology.

[2]  J. McCafferty,et al.  Phage-enzymes: expression and affinity chromatography of functional alkaline phosphatase on the surface of bacteriophage. , 1991, Protein engineering.

[3]  Kevin Burgess,et al.  New Catalysts and Conditions for a CH Insertion Reaction Identified by High Throughput Catalyst Screening , 1996 .

[4]  J. Fastrez,et al.  Overexpression of the phage lambda lysozyme cloned in Escherichia coli: use of a degenerative mixture of synthetic ribosome binding sites and increase of the protein stability in vivo. , 1991, Protein Engineering.

[5]  S. P. Fodor,et al.  Applications of combinatorial technologies to drug discovery. 2. Combinatorial organic synthesis, library screening strategies, and future directions. , 1994, Journal of medicinal chemistry.

[6]  W. E. Fahl,et al.  Forced evolution of glutathione S-transferase to create a more efficient drug detoxication enzyme. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[7]  S. Brenner,et al.  Lambda foo: a lambda phage vector for the expression of foreign proteins. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[8]  G. Mulder Forced evolution of glutathione S-transferase to create a more efficient drug detoxication enzyme. , 1996, Human & experimental toxicology.

[9]  C. Craik,et al.  Isolation of a High Affinity Inhibitor of Urokinase-type Plasminogen Activator by Phage Display of Ecotin (*) , 1995, The Journal of Biological Chemistry.

[10]  C. Hutchison,et al.  Complete mutagenesis of protein coding domains. , 1991, Methods in enzymology.

[11]  L. Loeb,et al.  Herpes thymidine kinase mutants with altered catalytic efficiencies obtained by random sequence selection. , 1994, Protein engineering.

[12]  O. Uhlenbeck,et al.  In vitro selection of RNAs that undergo autolytic cleavage with Pb2+. , 1992, Biochemistry.

[13]  J. Devlin,et al.  Random peptide libraries: a source of specific protein binding molecules. , 1990, Science.

[14]  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.

[15]  S. Akanuma,et al.  Further stabilization of 3-isopropylmalate dehydrogenase of an extreme thermophile, Thermus thermophilus, by a suppressor mutation method , 1996, Journal of bacteriology.

[16]  J. Link,et al.  Selection and rapid purification of murine antibody fragments that bind a transition-state analog by phage display , 1994, Applied biochemistry and biotechnology.

[17]  C. Gorman,et al.  A survey of furin substrate specificity using substrate phage display , 1994, Protein science : a publication of the Protein Society.

[18]  A. Schwienhorst,et al.  Combinatorial libraries by cassette mutagenesis. , 1995, Nucleic acids research.

[19]  A. Fink,et al.  Substitution of Asp for Asn at position 132 in the active site of TEM beta-lactamase. Activity toward different substrates and effects of neighboring residues. , 1995, The Journal of biological chemistry.

[20]  R. W. Davis,et al.  Functional genetic expression of eukaryotic DNA in Escherichia coli. , 1976, Proceedings of the National Academy of Sciences of the United States of America.

[21]  J. Knowles,et al.  Directed selective pressure on a β-lactamase to analyse molecular changes involved in development of enzyme function , 1976, Nature.

[22]  R. Hoffmann,et al.  Enzyme evolution in Rhodobacter sphaeroides: selection of a mutant expressing a new galactitol dehydrogenase and biochemical characterization of the enzyme. , 1995, Microbiology.

[23]  K. O'Neil,et al.  Phage display: protein engineering by directed evolution. , 1995, Current opinion in structural biology.

[24]  D. Hilvert,et al.  Monitoring Catalytic Activity by Immunoassay: Implications for Screening , 1994 .

[25]  D. White,et al.  Directed evolution of a protein: selection of potent neutrophil elastase inhibitors displayed on M13 fusion phage. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[26]  A. Fink,et al.  A New TEM -Lactamase Double Mutant with Broadened Specificity Reveals Substrate-dependent Functional Interactions (*) , 1995, The Journal of Biological Chemistry.

[27]  J. Knowles,et al.  Searching sequence space by definably random mutagenesis: improving the catalytic potency of an enzyme. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[28]  J. Wells,et al.  Hormone phage: An enrichment method for variant proteins with altered binding properties , 1990, Proteins.

[29]  D. Danley,et al.  Experimental evolution of penicillin G acylases from Escherichia coli and Proteus rettgeri , 1985, Journal of bacteriology.

[30]  L. Gold,et al.  Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. , 1990, Science.

[31]  S. Benkovic,et al.  Catalytic antibodies: perusing combinatorial libraries. , 1994, Trends in biochemical sciences.

[32]  R. Burgess,et al.  An RNA polymerase mutant with reduced accuracy of chain elongation. , 1986, Biochemistry.

[33]  L. Forney,et al.  Selection of amidases with novel substrate specificities from penicillin amidase of Escherichia coli , 1989, Applied and environmental microbiology.

[34]  C. Kautzer,et al.  Increased antibody expression from Escherichia coli through wobble-base library mutagenesis by enzymatic inverse PCR. , 1993, Gene.

[35]  J. Frère,et al.  Bacterial DD-transpeptidases and penicillin. , 1995, Essays in biochemistry.

[36]  B. Cunningham,et al.  Improvement in the alkaline stability of subtilisin using an efficient random mutagenesis and screening procedure. , 1987, Protein engineering.

[37]  M. Larocco,et al.  Evolution of antibiotic resistance: several different amino acid substitutions in an active site loop alter the substrate profile of β‐lactamase , 1994, Molecular microbiology.

[38]  J. Richards,et al.  Site-saturation studies of beta-lactamase: production and characterization of mutant beta-lactamases with all possible amino acid substitutions at residue 71. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[39]  G. Winter,et al.  Phage antibodies: filamentous phage displaying antibody variable domains , 1990, Nature.

[40]  N. Declerck,et al.  Hyperthermostable Variants of a Highly Thermostable Alpha-Amylase , 1992, Bio/Technology.

[41]  C R Cantor,et al.  Immuno-PCR: very sensitive antigen detection by means of specific antibody-DNA conjugates. , 1992, Science.

[42]  C. O. Fágáin,et al.  Understanding and increasing protein stability. , 1995, Biochimica et biophysica acta.

[43]  In vitro selection for catalytic turnover from a library of β-lactamase mutants and penicillin-binding proteins , 1997 .

[44]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[45]  T. Mckenzie,et al.  Isolation of a thermostable enzyme variant by cloning and selection in a thermophile. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[46]  Dan S. Tawfik,et al.  catELISA: a facile general route to catalytic antibodies. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[47]  C. Wills Controlling protein evolution. , 1976, Federation proceedings.

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

[49]  J. Fastrez,et al.  Phage display of enzymes and in vitro selection for catalytic activity , 1994, Applied biochemistry and biotechnology.

[50]  F. Arnold,et al.  Directed evolution of subtilisin E in Bacillus subtilis to enhance total activity in aqueous dimethylformamide. , 1996, Protein engineering.

[51]  J. Scott,et al.  Searching for peptide ligands with an epitope library. , 1990, Science.

[52]  K. Struhl,et al.  An efficient method for generating proteins with altered enzymatic properties: application to beta-lactamase. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[53]  M. Black,et al.  Identification of important residues within the putative nucleoside binding site of HSV-1 thymidine kinase by random sequence selection: analysis of selected mutants in vitro. , 1993, Biochemistry.

[54]  L. Simmons,et al.  Translational level is a critical factor for the secretion of heterologous proteins in Escherichia coli , 1996, Nature Biotechnology.

[55]  T. McCutchan,et al.  Immunogenicity and epitope mapping of foreign sequences via genetically engineered filamentous phage. , 1988, The Journal of biological chemistry.

[56]  George Georgiou,et al.  Construction and Characterization of a Set of E. coli Strains Deficient in All Known Loci Affecting the Proteolytic Stability of Secreted Recombinant Proteins , 1994, Bio/Technology.

[57]  L. Loeb,et al.  Mutants generated by the insertion of random oligonucleotides into the active site of the beta-lactamase gene. , 1989, Biochemistry.

[58]  R. Mortlock Metabolic acquisitions through laboratory selection. , 1982, Annual review of microbiology.

[59]  M. Matsumura,et al.  Screening for thermostable mutant of kanamycin nucleotidyltransferase by the use of a transformation system for a thermophile, Bacillus stearothermophilus. , 1985, The Journal of biological chemistry.

[60]  P Soumillion,et al.  Selection of beta-lactamase on filamentous bacteriophage by catalytic activity. , 1994, Journal of molecular biology.

[61]  C. Barbas,et al.  Direct selection for a catalytic mechanism from combinatorial antibody libraries. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[62]  L. Loeb,et al.  Artificial mutants generated by the insertion of random oligonucleotides into the putative nucleoside binding site of the HSV-1 thymidine kinase gene. , 1991, Biochemistry.

[63]  P. Schultz,et al.  Stereospecific Hydrolysis of Alkyl Esters by Antibodies , 1989 .

[64]  J. Szostak,et al.  A DNA metalloenzyme with DNA ligase activity , 1995, Nature.

[65]  Jack W. Szostak,et al.  In vitro evolution of a self-alkylatlng ribozyme , 1995, Nature.

[66]  G. F. Joyce,et al.  Directed evolution of an RNA enzyme. , 1992, Science.

[67]  D. Goeddel,et al.  A method for random mutagenesis of a defined DNA segment using a modified polymerase chain reaction , 1989 .

[68]  P. Schultz,et al.  A chromogenic assay for screening large antibody libraries , 1992 .

[69]  B. Mannervik,et al.  Glutathione transferases with novel active sites isolated by phage display from a library of random mutants. , 1995, Journal of molecular biology.

[70]  G. F. Joyce,et al.  Evolutionary optimization of the catalytic properties of a DNA-cleaving ribozyme. , 1994, Biochemistry.

[71]  J. Pyati,et al.  A revised strategy for cloning antibody gene fragments in bacteria. , 1993, Gene.

[72]  Dan S. Tawfik,et al.  Detection of catalytic monoclonal antibodies. , 1992, Analytical biochemistry.

[73]  D. Bartel,et al.  Isolation of new ribozymes from a large pool of random sequences [see comment]. , 1993, Science.

[74]  R. Lerner,et al.  From molecular diversity to catalysis: lessons from the immune system. , 1995, Science.

[75]  John M. Burke,et al.  Optimization of an anti-HIV hairpin ribozyme by in vitro selection. , 1993, The Journal of biological chemistry.

[76]  R. Lerner,et al.  Encoded reaction cassette for the highly sensitive detection of the making and breaking of chemical bonds. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[77]  A rapid and effective procedure for screening protease mutants. , 1996, Protein engineering.

[78]  J. A. Wozniak,et al.  A genetic screen for mutations that increase the thermal stability of phage T4 lysozyme. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[79]  C. Craik,et al.  A genetic selection elucidates structural determinants of arginine versus lysine specificity in trypsin. , 1993, Gene.

[80]  S. Benkovic,et al.  Selection of catalytic antibodies for a biosynthetic reaction from a combinatorial cDNA library by complementation of an auxotrophic Escherichia coli: antibodies for orotate decarboxylation. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[81]  A D Ellington,et al.  Artificial evolution and natural ribozymes , 1995, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[82]  D. Hilvert,et al.  In vivo catalysis of a metabolically essential reaction by an antibody. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[83]  A. Schwabacher,et al.  Sensitive detection of catalytic species without chromophoric substrates , 1993 .

[84]  P. Jennings,et al.  Improved peptide function from random mutagenesis over short 'windows'. , 1988, Protein engineering.

[85]  C. Milstein,et al.  Continuous cultures of fused cells secreting antibody of predefined specificity , 1975, Nature.

[86]  L. Dorner,et al.  Direct selection of binding proficient/catalytic deficient variants of BamHI endonuclease. , 1994, Nucleic acids research.

[87]  H. Lilja,et al.  Expression of prostate specific antigen on the surface of a filamentous phage. , 1994, Biochemical and biophysical research communications.

[88]  R. Barrett,et al.  Peptides on phage: a vast library of peptides for identifying ligands. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[89]  F. Arnold,et al.  Protein engineering for unusual environments. , 1993, Current opinion in biotechnology.

[90]  C. Barbas,et al.  Direct selection of antibodies that coordinate metals from semisynthetic combinatorial libraries. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[91]  Jon R. Lorsch,et al.  In vitro evolution of new ribozymes with polynucleotide kinase activity , 1994, Nature.

[92]  C. Craik,et al.  Development of an Efficient Method for Generating and Screening Active Trypsin and Trypsin Variants , 1988, Annals of the New York Academy of Sciences.

[93]  J. Wells,et al.  Substrate phage: selection of protease substrates by monovalent phage display. , 1993, Science.

[94]  J. Kraut,et al.  A second-site mutation at phenylalanine-137 that increases catalytic efficiency in the mutant aspartate-27----serine Escherichia coli dihydrofolate reductase. , 1990, Biochemistry.

[95]  B. Matthews,et al.  Structural and genetic analysis of protein stability. , 1993, Annual review of biochemistry.

[96]  L. Gold,et al.  Posttranscriptional regulatory mechanisms in Escherichia coli. , 1988, Annual review of biochemistry.

[97]  P. Schultz,et al.  Expanding the scope of RNA catalysis. , 1994, Science.

[98]  G. P. Smith,et al.  Antibody-selectable filamentous fd phage vectors: affinity purification of target genes. , 1988, Gene.

[99]  A. Friboulet,et al.  Monoclonal anti-idiotypic antibodies as functional internal images of enzyme active sites: production of a catalytic antibody with a cholinesterase activity. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[100]  J. Szostak,et al.  In vitro selection of RNA molecules that bind specific ligands , 1990, Nature.

[101]  Frances H. Arnold,et al.  Enzyme Engineering for Nonaqueous Solvents: Random Mutagenesis to Enhance Activity of Subtilisin E in Polar Organic Media , 1991, Bio/Technology.

[102]  R. Lerner,et al.  Random mutagenesis of staphylococcal nuclease and phage display selection. , 1995, Bioorganic & medicinal chemistry.

[103]  C. Barbas,et al.  Linkage of recognition and replication functions by assembling combinatorial antibody Fab libraries along phage surfaces. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[104]  C. Barbas,et al.  Assembly of combinatorial antibody libraries on phage surfaces: the gene III site. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[105]  D. Corey,et al.  Trypsin display on the surface of bacteriophage. , 1993, Gene.

[106]  N. Welker,et al.  Isolation of a Bacillus stearothermophilus mutant exhibiting increased thermostability in its restriction endonuclease , 1985, Journal of bacteriology.

[107]  D. Botstein,et al.  Probing β‐lactamase structure and function using random replacement mutagenesis , 1992 .

[108]  Gerald F. Joyce,et al.  Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA , 1990, Nature.

[109]  John M. Burke,et al.  In vitro selection and evolution of RNA: applications for catalytic RNA, molecular recognition, and drug discovery , 1993, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[110]  S. Bouvier,et al.  Systematic mutation of bacteriophage T4 lysozyme. , 1991, Journal of molecular biology.

[111]  L. Everitt,et al.  Selection of multiple human immunodeficiency virus type 1 variants that encode viral proteases with decreased sensitivity to an inhibitor of the viral protease. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[112]  Dan S. Tawfik,et al.  Simple method for selecting catalytic monoclonal antibodies that exhibit turnover and specificity. , 1990, Biochemistry.

[113]  L. Forney,et al.  Alteration of the catalytic efficiency of penicillin amidase from Escherichia coli , 1989, Applied and environmental microbiology.

[114]  I. Urabe,et al.  Stability-increasing mutants of glucose dehydrogenase from Bacillus megaterium IWG3. , 1989, The Journal of biological chemistry.

[115]  J. Lengyel,et al.  Evolution of a Second Gene for β-Galactosidase in Escherichia coli , 1973 .

[116]  P G Schultz,et al.  At the crossroads of chemistry and immunology: catalytic antibodies. , 1991, Science.

[117]  L. Loeb,et al.  Permissible amino acid substitutions within the putative nucleoside binding site of herpes simplex virus type 1 encoded thymidine kinase established by random sequence mutagenesis [corrected]. , 1992, The Journal of biological chemistry.

[118]  P. Brown,et al.  Evolution in Action , 1974, Nature.

[119]  Philip Pjura,et al.  Development of an in vivo method to identify mutants of phage T4 lysozyme of enhanced thermostability , 1993, Protein science : a publication of the Protein Society.

[120]  R. Hoess,et al.  Display of peptides and proteins on the surface of bacteriophage lambda. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[121]  S. Altman,et al.  Selection of guide sequences that direct efficient cleavage of mRNA by human ribonuclease P. , 1994, Science.

[122]  D. Botstein,et al.  Selection of functional signal peptide cleavage sites from a library of random sequences , 1994, Journal of bacteriology.

[123]  J W Szostak,et al.  In vitro selection of catalytic RNAs. , 1994, Current opinion in structural biology.

[124]  L. Loeb,et al.  Thymidine kinase mutants obtained by random sequence selection. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[125]  P. Schultz,et al.  A genetic approach to the generation of antibodies with enhanced catalytic activities. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[126]  H. Liao Thermostable mutants of kanamycin nucleotidyltransferase are also more stable to proteinase K, urea, detergents, and water-miscible organic solvents. , 1993, Enzyme and microbial technology.

[127]  D. Hilvert,et al.  Catalysis of concerted reactions by antibodies: the Claisen rearrangement. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[128]  P. Jennings,et al.  Random mutagenesis of the substrate-binding site of a serine protease can generate enzymes with increased activities and altered primary specificities. , 1993, Biochemistry.

[129]  D R Burton,et al.  Generation of a large combinatorial library of the immunoglobulin repertoire in phage lambda. , 1989, Science.

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

[131]  S. P. Fodor,et al.  Applications of combinatorial technologies to drug discovery. 1. Background and peptide combinatorial libraries. , 1994, Journal of medicinal chemistry.

[132]  T. Poulos,et al.  Proteases of enhanced stability: Characteization of a thermostable variant of subtilisin , 1986, Proteins.

[133]  W. Sommergruber,et al.  Proteinase trapping: screening for viral proteinase mutants by alpha complementation. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[134]  P. Schultz,et al.  Phage display of catalytically active staphylococcal nuclease. , 1994, Bioorganic & medicinal chemistry.