High-throughput screening of enzyme libraries

Current Opinion in Biotechnology

Volumn 11, Issue 4, 2000, Pages 331-337

  Olsen, Mark ^a   Iverson, Brent ^a   Georgiou, George ^b  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b The University of Texas at Austin   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME;

ENZYME SPECIFICITY; ENZYME STRUCTURE; EVOLUTION; GENETIC ENGINEERING; LIBRARY; MUTAGENESIS; MUTANT; PHAGE DISPLAY; PRIORITY JOURNAL; REVIEW; STRUCTURE ACTIVITY RELATION;

EID: 0033904795     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(00)00108-7     Document Type: Review

References (42)

1. Gordon D.B., Marshall S.A., Mayo S.L. Energy functions for protein design. Curr Opin Struct Biol. 9:1999;509-513.
2. Schlichting I., Berendzen J., Chu K., Stock A.M., Maves S.A., Benson D.E., Sweet R.M., Ringe D., Petsko G.A., Sligar S.G. The catalytic pathway of cytochrome p450cam at atomic resolution. Science. 287:2000;1615-1622.
3. Quemeneur E., Moutiez M., Charbonnier J.B., Menez A. Engineering cyclophilin into a proline-specific endopeptidase. Nature. 391:1998;301-304.
4. Nixon A.E., Firestine S.M., Salinas F.G., Benkovic S.J. Rational design of a scytalone dehydratase-like enzyme using a structurally homologous protein scaffold. Proc Natl Acad Sci USA. 96:1999;3568-3571.
5. Altamirano M.M., Blackburn J.M., Aguayo C., Fersht A.R. Directed evolution of new catalytic activity using the α/β-barrel scaffold. Nature. 403:2000;617-622. A combination of rational engineering of key structural elements and directed evolution was used to evolve a new substrate specificity of an α/β barrel scaffold protein. Significant phosphoribosylanthranilate activity was demonstrated from an indole-3-glycerol-phosphate synthase framework. This strategy has potential for engineering a wide range of novel catalytic activities from the common α/β barrel fold family of proteins.
6. Chartrain M., Salmon P.M., Robinson D.K., Buckland B.C. Metabolic engineering and directed evolution for the production of pharmaceuticals. Curr Opin Biotechnol. 11:2000;209-214.
7. Protein Design by Directed Evolution/Biocatalysis on World Wide Web URL http://www.che.caltech.edu/groups/fha/Enzyme/Enzyme.html .
8. Zhong G., Lerner R.A., Barbas C.F. Jr. Broadening the aldolase catalytic antibody repertoire by combining reactive immunization and transition state theory: new enantio- and diastereoselectivities. Angew Chem Int Ed. 38:1999;3738-3741.
9. Karlstrom A., Zhong G., Rader C., Larsen N.A., Heine A., Fuller R., List B., Tanaka F., Wilson I.A., Barbas C.F. Jr., Lerner R.A. Using antibody catalysis to study the outcome of multiple evolutionary trials of a chemical task. Proc Natl Acad Sci USA. 97:2000;3878-3883. Reactive immunization of aldolase activity was characterized for two different β-diketone haptens. Catalytic antibodies were isolated and analyzed with respect to kinetics and sequence, and a model for catalytic activity was tested using site-directed mutagensis.
10. Arnold F.H., Volkov A.A. Directed evolution of biocatalysts. Curr Opin Chem Biol. 3:1999;54-59.
11. Chen L., Sigler P.B. The crystal structure of a GroEL/peptide complex: plasticity as a basis for substrate diversity. Cell. 99:1999;757-768.
12. Stemmer W.P. Rapid evolution of a protein in vitro by DNA shuffling. Nature. 370:1994;389-391.
13. Zhao H., Giver L., Shao Z., Affholter J.A., Arnold F.H. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat Biotechnol. 16:1998;258-261.
14. Ostermeier M., Shim J.H., Benkovic S.J. A combinatorial approach to hybrid enzymes independent of DNA homology. Nat Biotechnol. 17:1999;1205-1209.
15. Hopfner K.P., Kopetzki E., Kresse G.B., Bode W., Huber R., Engh R.A. New enzyme lineages by subdomain shuffling. Proc Natl Acad Sci USA. 95:1998;9813-9818.
16. Yano T., Oue S., Kagamiyama H. Directed evolution of an aspartate aminotransferase with new substrate specificities. Proc Natl Acad Sci USA. 95:1998;5511-5515.
17. Oue S., Okamoto A., Yano T., Kagamiyama H. Redesigning the substrate specificity of an enzyme by cumulative effects of the mutations of non-active site residues. J Biol Chem. 274:1999;2344-2349. A combination of rational and directed evolution approaches, including random mutagenesis and DNA shuffling, was used to alter the substrate specificity of aspartate aminotransferase using amino acid auxotrophies for selection of mutants with increased catalytic activity with branched amino acids. A three dimensional structure of the best evolved mutant shows how the active site of the enzyme was remodeled to accommodate the new substrate specificity observed.
18. MacBeath G., Kast P., Hilvert D. Redesigning enzyme topology by directed evolution. Science. 279:1998;1958-1961. Chorismate mutase was redesigned to fold as a monomeric four-bundle helix using a combination of protein design and directed evolution approaches. A thermostable enzyme was used as a starting point, and point mutations destabilizing the native dimeric structure were used as a starting point for a stringent catalytic selection.
19. Encell L.P., Loeb L.A. Redesigning the substrate specificity of human O(6)-alkylguanine-DNA alkyltransferase. Mutants with enhanced repair of O(4)-methylthymine. Biochemistry. 38:1999;12 097-12 103.
20. Landis D.M., Loeb L.A. Random sequence mutagenesis and resistance to 5-fluorouridine in human thymidylate synthases. J Biol Chem. 273:1998;25 809-25 817.
21. Joo H., Arisawa A., Lin Z., Arnold F.H. A high-throughput digital imaging screen for the discovery and directed evolution of oxygenases. Chem Biol. 6:1999;699-706. Digital imaging screening technology was used to select for chlorobenzene hydroxylation by P450cam activity using a coupled system with functional horseradish peroxidase. The coupled assay resulted in a range of fluorescent products, each based upon the substrate specificity of the expressed P450cam mutant.
22. Matsumura I., Wallingford J.B., Surana N.K., Vize P.D., Ellington A.D. Directed evolution of the surface chemistry of the reporter enzyme beta-glucuronidase. Nat Biotechnol. 17:1999;696-701.
23. Joo H., Lin Z., Arnold F.H. Laboratory evolution of peroxide-mediated cytochrome P450 hydroxylation. Nature. 399:1999;670-673.
24. Bylina E.J., Coleman W.J., Tanner M.A., Young M.M., Youvan D.C. Solid-phase enzyme screening. ASM News. 66:2000;211-217.
25. Cherry J.R., Lamsa M.H., Schneider P., Vind J., Svendsen A., Jones A., Pedersen A.H. Directed evolution of a fungal peroxidase. Nat Biotechnol. 17:1999;379-384.
26. Evotec at World Wide Web URL http://www.evotec.de .
27. Forrer P., Jung S., Pluckthun A. Beyond binding: using phage display to select for structure, folding and enzymatic activity in proteins. Curr Opin Struct Biol. 9:1999;514-520. A recent review of phage display for isolating molecules with superior folding and/or catalytic activities. The authors describe methods for recovering proteins with improved thermostability and folding properties, including selectively infective phage. Recent strategies for phage-based isolation for catalytic activity are also discussed.
28. Sidhu S.S., Weiss G.A., Wells J.A. High copy display of large proteins on phage for functional selections. J Mol Biol. 296:2000;487-495.
29. Janda K.D., Lo L.C., Lo C.H.L., Sim M.M., Wang R., Wong C.H., Lerner R.A. Chemical selection for catalysis in combinatorial antibody libraries. Science. 275:1997;945-948.
30. Hansson L.O., Widersten M., Mannervik B. An approach to optimizing the active site in a glutathione transferase by evolution in vitro. Biochem J. 344:1999;93-100.
31. Vanwetswinkel S., Avalle B., Fastrez J. Selection of beta-lactamases and penicillin binding mutants from a library of phage displayed TEM-1 beta-lactamase randomly mutated in the active site omega-loop. J Mol Biol. 295:2000;527-540.
32. Legendre D., Laraki N., Graslund T., Bjornvad M.E., Bouchet M., Nygren P.A., Borchert T.V., Fastrez J. Display of active subtilisin 309 on phage: analysis of parameters influencing the selection of subtilisin variants with changed substrate specificity from libraries using phosphonylating inhibitors. J Mol Biol. 296:2000;87-102. A method for phage display of subtilisin 309 (savinase) was devised using co-expression of proteic inhibitor CI2. Phage are released from the inhibitor complex, and are exposed to a biotinylated phosphonylating inhibitor for recovery with streptavidin beads. Site-directed libraries of savinase were prepared and enriched using inhibitors requiring altered substrate specificity.
33. Jestin J.L., Kristensen P., Winter G. A method for the selection of catalytic activity using phage display and proximity coupling. Angew Chem Int Ed. 38:1999;1124-1127. Phage displaying Stoffel fragment from Thermus aquaticus DNA polymerase were enriched using substrate proximity coupling. Substrate was displayed using a covalent alkylation of gpVIII, and catalysts for DNA synthesis were enriched 123-fold from catalytically inactive phage.
34. Pedersen H., Holder S., Sutherlin D.P., Schwitter U., King D.S., Schultz P.G. A method for directed evolution and functional cloning of enzymes. Proc Natl Acad Sci USA. 95:1998;10 523-10 528. Phage expressing both a substrate display fusion protein and a catalyst were enriched using staphylococcal nuclease. Substrate was displayed using a combination of gpIII fusion proteins and a synthetic peptide. Enzymatic hydrolysis of the DNA substrate releases the catalytically competent phage from the streptavidin surface.
35. Demartis S., Huber A., Viti F., Lozzi L., Giovannoni L., Neri P., Winter G., Neri D. A strategy for the isolation of catalytic activities from repertoires of enzymes displayed on phage. J Mol Biol. 286:1999;617-633. Substrate display using calmodulin was used to enrich for enzymes expressing glutathione-S-transferase and an endopeptidase. A gpIII fusion consisting of calmodulin followed by the enzyme of interest is used, and substrate is attached through a calmodulin-binding peptide.
36. Atwell S., Wells J.A. Selection for improved subtiligases by phage display. Proc Natl Acad Sci USA. 96:1999;9497-9502. Phage display of subtiligase was used to improve catalytic activity using site-directed library construction followed by phage enrichment. Catalysts form an amide bond with a biotinylated substrate, providing for enrichment using a biotin binding surface.
37. Tawfik D.S., Griffiths A.D. Man-made cell-like compartments for molecular evolution. Nat Biotechnol. 16:1998;652-656.
38. Firestine S.M., Salinas F., Nixon A.E., Baker S.J., Benkovic S.J. Using an AraC-based three-hybrid system to detect biocatalysts in vivo. Nat Biotechnol. 18:2000;544-547. The authors developed and implemented a trihybrid strategy using AraC and scytalone dehydratase as the model system. A synthetic chemical inducer of dimerization is used to dimerize a chimeric transcriptional activator. The substrate inhibits transciption, but catalytic depletion of substrate results in activation of the chromosomal araBAD genes, and can be screened using fluorescent pH-sensitive probes. This system was used to enrich a library for cells expressing active scytalone dehydratase.
39. Daugherty P.S., Chen G., Iverson B.L., Georgiou G. Quantitative analysis of the effect of the mutation frequency on the affinity maturation of single chain Fv antibodies. Proc Natl Acad Sci USA. 97:2000;2029-2034. Flow cytometery was used to evaluate the effect of random mutagenesis on a high affinity anti-digoxin antibody. At low error rates, the number of functional clones dropped exponentially, but at high error rates a small but unexpectedly high number of clones retained strong binding activity. Improved clones isolated from libraries with high error rates displayed the greatest affinity for the target hapten.
40. Daugherty, P.S., Iverson, B.L., Georgiou, G. Flow cytometric screening of cellular combinatorial libraries. J Immunol Methods 2000, in press.
41. Holler P.D., Holman P.O., Shusta E.V., O'Herrin S., Wittrup K.D., Kranz D.M. In vitro evolution of a T cell receptor with high affinity for peptide/MHC. Proc Natl Acad Sci USA. 97:2000;5387-5392.
42. Watson J.V., Dive C. Enzyme kinetics. Methods Cell Biol. 41:1994;469-507.