Ultra-high-throughput screening based on cell-surface display and fluorescence-activated cell sorting for the identification of novel biocatalysts

Current Opinion in Biotechnology

Volumn 15, Issue 4, 2004, Pages 323-329

  Becker, Stefan ^a   Schmoldt, Hans Ulrich ^a   Adams, Thorsten Michael ^a   Wilhelm, Susanne ^b   Kolmar, Harald ^a  

^a UNIVERSITY OF GÖTTINGEN   (Germany)

^b HEINRICH HEINE UNIVERSITY   (Germany)

Author keywords

FACS; fluorescence resonance energy transfer; fluorescence activated cell sorting; FRET; GFP; green fluorescent protein; horseradish peroxidase; HRP; TSA; tyramide signal amplification

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; CRE RECOMBINASE; GREEN FLUORESCENT PROTEIN; PHOSPHOTRIESTERASE;

BIOCATALYST; BIOTECHNOLOGY; CATALYSIS; CELL GROWTH; CELL SURFACE; CELL SURVIVAL; COVALENT BOND; ENZYME ACTIVITY; ENZYME IMMOBILIZATION; ENZYME INHIBITION; ENZYME MECHANISM; ENZYME PURIFICATION; ENZYME RELEASE; ENZYME SPECIFICITY; ENZYME SUBSTRATE; ENZYME SYNTHESIS; ESCHERICHIA COLI; FLOW CYTOMETRY; FLUORESCENCE ACTIVATED CELL SORTING; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENE EXPRESSION; HIGH THROUGHPUT SCREENING; METHANOCOCCUS JANNASCHII; MICROBIAL POPULATION DYNAMICS; MOLECULAR EVOLUTION; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN VARIANT; REPORTER GENE; REVIEW;

BACTERIA; BIOLOGICAL ASSAY; CATALYSIS; ENZYME ACTIVATION; ENZYMES; FLOW CYTOMETRY; FLUORESCENCE RESONANCE ENERGY TRANSFER; MEMBRANE PROTEINS; PEPTIDE LIBRARY; PROTEIN ENGINEERING; PROTEIN INTERACTION MAPPING;

ARMORACIA RUSTICANA; ESCHERICHIA COLI; METHANOCALDOCOCCUS JANNASCHII; METHANOCOCCUS;

EID: 3543063987     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2004.06.001     Document Type: Review

References (44)

1. Smith G.P. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science. 228:1985;1315-1317
2. Fernandez-Gacio A., Uguen M., Fastrez J. Phage display as a tool for the directed evolution of enzymes. Trends Biotechnol. 21:2003;408-414
3. Forrer P., Jung S., Plückthun A. Beyond binding: using phage display to select for structure, folding and enzymatic activity in proteins. Curr Opin Struct Biol. 9:1999;514-520
4. Adams TM, Kolmar H: Enzyme engineering by microbial cell surface display. In Enzyme Functionality Design, Engineering, and Screening, vol 1. Edited by Svendsen A. New York, USA: Marcel Dekker, Inc.; 2004:599-616.
5. Wittrup K.D. Protein engineering by cell-surface display. Curr Opin Biotechnol. 12:2001;395-399
6. Boder E.T., Wittrup K.D. Yeast surface display for screening combinatorial polypeptide libraries. Nat Biotechnol. 15:1997;553-557
7. Amstutz P., Forrer P., Zahnd C., Plückthun A. In vitro display technologies: novel developments and applications. Curr Opin Biotechnol. 12:2001;400-405
8. Jaeger K.E., Eggert T. Lipases for biotechnology. Curr Opin Biotechnol. 13:2002;390-397
9. Reetz M.T. Select protocols of high-throughput ee-screening systems for assaying enantioselective enzymes. Methods Mol Biol. 230:2003;283-290 The author reviews current methods for high-throughput screening of enzyme libraries for determining enantioselectivity. The select protocols include mass spectrometry, assays based on NMR and gas chromatography.
10. Glieder A., Farinas E.T., Arnold F.H. Laboratory evolution of a soluble, self-sufficient, highly active alkane hydroxylase. Nat Biotechnol. 20:2002;1135-1139
11. Dalby P.A. Optimising enzyme function by directed evolution. Curr Opin Struct Biol. 13:2003;500-505
12. Liebeton K., Zonta A., Schimossek K., Nardini M., Lang D., Dijkstra B.W., Reetz M.T., Jaeger K.E. Directed evolution of an enantioselective lipase. Chem Biol. 7:2000;709-718 A P. aeruginosa PAL lipase mutant with enhanced enantioselectivity against the chiral model substrate 2-methyldecanoic acid p-nitrophenyl ester was evolved by successive rounds of random and saturation mutagenesis.
13. Arnold F.H. Combinatorial and computational challenges for biocatalyst design. Nature. 409:2001;253-257
14. Georgiou G. Analysis of large libraries of protein mutants using flow cytometry. Adv Protein Chem. 55:2000;293-315
15. Daugherty P.S., Iverson B.L., Georgiou G. Flow cytometric screening of cell-based libraries. J Immunol Methods. 243:2000;211-227
16. Boder E.T., Wittrup K.D. Optimal screening of surface-displayed polypeptide libraries. Biotechnol Prog. 14:1998;55-62
17. Ashcroft R.G., Lopez P.A. Commercial high speed machines open new opportunities in high throughput flow cytometry (HTFC). J Immunol Methods. 243:2000;13-24
18. Wahler D., Reymond J.L. Novel methods for biocatalyst screening. Curr Opin Chem Biol. 5:2001;152-158
19. Long-McGie J., Liu A.D., Schellenberger V. Rapid in vivo evolution of a β-lactamase using phagemids. Biotechnol Bioeng. 68:2000;121-125
20. Stemmer W.P. Rapid evolution of a protein in vitro by DNA shuffling. Nature. 370:1994;389-391
21. 8-barrel enzyme to catalyze related reactions in two different metabolic pathways. Proc Natl Acad Sci USA. 97:2000;9925-9930
22. Smiley J.A., Benkovic S.J. Selection of catalytic antibodies for a biosynthetic reaction from a combinatorial cDNA library by complementation of an auxotrophic Escherichia coli: antibodies for orotate decarboxylation. Proc Natl Acad Sci USA. 91:1994;8319-8323
23. D of 48 fM has been isolated from a randomly mutagenized library using yeast cell-surface display and FACS. This constitutes the highest monovalent ligand-binding affinity reported so far for an engineered protein.
24. Olsen M.J., Stephens D., Griffiths D., Daugherty P., Georgiou G., Iverson B.L. Function-based isolation of novel enzymes from a large library. Nat Biotechnol. 18:2000;1071-1074 The first reported system for isolation of enzyme variants with enhanced catalytic activities out of a large library applying E. coli cell-surface display and FACS. OmpT protease was chosen as a model enzyme. Active variants were able to cleave a FRET peptide substrate, which resulted in release of the FRET quenching partner while the fluorescent product was retained on the cell surface.
25. Santoro S.W., Wang L., Herberich B., King D.S., Schultz P.G. An efficient system for the evolution of aminoacyl-tRNA synthetase specificity. Nat Biotechnol. 20:2002;1044-1048 A combined genetic selection and high-throughput screen for the rapid evolution of aminoacyl-tRNA synthetase substrate specifity. The system uses a chloramphenicol-resistance reporter to select highly active synthetase variants and an amplifiable fluorescence reporter together with FACS to screen for variants with the desired change in amino acid specificity.
26. Santoro S.W., Schultz P.G. Directed evolution of the site specificity of Cre recombinase. Proc Natl Acad Sci USA. 99:2002;4185-4190 A directed evolution strategy to isolate variants of the bacteriophage P1 Cre recombinase with altered recognition site specificities using a reporter plasmid with variant recognition (loxP) sites. Recombination results in an altered pattern of fluorescent protein expression that can be identified by FACS.
27. Griffiths A.D., Tawfik D.S. Directed evolution of an extremely fast phosphotriesterase by in vitro compartmentalization. EMBO J. 22:2003;24-35 The authors describe the selection of a phosphotriesterase with an enzyme activity 63 times higher than the wild-type enzyme. The variant was selected using a novel strategy based on in vitro compartmentalization using water-in-oil emulsions.
28. Olsen M.J., Gam J., Iverson B.L., Georgiou G. High-throughput FACS method for directed evolution of substrate specificity. Methods Mol Biol. 230:2003;329-342
29. Olsen M., Iverson B., Georgiou G. High-throughput screening of enzyme libraries. Curr Opin Biotechnol. 11:2000;331-337
30. Cohen N., Abramov S., Dror Y., Freeman A. In vitro enzyme evolution: the screening challenge of isolating the one in a million. Trends Biotechnol. 19:2001;507-510
31. Cesaro-Tadic S., Lagos D., Honegger A., Rickard J.H., Partridge L.J., Blackburn G.M., Plückthun A. Turnover-based in vitro selection and evolution of biocatalysts from a fully synthetic antibody library. Nat Biotechnol. 21:2003;679-685
32. 7-fold excess of genes encoding for another enzyme (folA).
33. Bernath K., Hai M., Mastrobattista E., Griffiths A.D., Magdassi S., Tawfik D.S. In vitro compartmentalization by double emulsions: sorting and gene enrichment by fluorescence activated cell sorting. Anal Biochem. 325:2004;151-157
34. Francisco J.A., Earhart C.F., Georgiou G. Transport and anchoring of β-lactamase to the external surface of Escherichia coli. Proc Natl Acad Sci USA. 89:1992;2713-2717
35. Lattemann C.T., Maurer J., Gerland E., Meyer T.F. Autodisplay: functional display of active β-lactamase on the surface of Escherichia coli by the AIDA-I autotransporter. J Bacteriol. 182:2000;3726-3733
36. Jung H.C., Lebeault J.M., Pan J.G. Surface display of Zymomonas mobilis levansucrase by using the ice-nucleation protein of Pseudomonas syringae. Nat Biotechnol. 16:1998;576-580
37. Washida M., Takahashi S., Ueda M., Tanaka A. Spacer-mediated display of active lipase on the yeast cell surface. Appl Microbiol Biotechnol. 56:2001;681-686
38. Murai T., Ueda M., Yamamura M., Atomi H., Shibasaki Y., Kamasawa N., Osumi M., Amachi T., Tanaka A. Construction of a starch-utilizing yeast by cell-surface engineering. Appl Environ Microbiol. 63:1997;1362-1366
39. Murai T., Ueda M., Kawaguchi T., Arai M., Tanaka A. Assimilation of cellooligosaccharides by a cell surface-engineered yeast expressing β-glucosidase and carboxymethylcellulase from Aspergillus aculeatus. Appl Environ Microbiol. 64:1998;4857-4861
40. Kim Y.S., Jung H.C., Pan J.G. Bacterial cell surface display of an enzyme library for selective screening of improved cellulase variants. Appl Environ Microbiol. 66:2000;788-793
41. Bobrow L.G., Hirsch F.R., Hay F.G., Happerfield L., Skov B.G., Law K., Leonard R.C., Souhami R.L. An immunohistochemical investigation of diagnostic biopsy material taken from short- and long-term survivors with small cell lung cancer. Br J Cancer. 66:1992;547-551
42. Hunyady B., Krempels K., Harta G., Mezey E. Immunohistochemical signal amplification by catalyzed reporter deposition and its application in double immunostaining. J Histochem Cytochem. 44:1996;1353-1362
43. Chao J., DeBiasio R., Zhu Z., Giuliano K.A., Schmidt B.F. Immunofluorescence signal amplification by the enzyme-catalyzed deposition of a fluorescent reporter substrate (CARD). Cytometry. 23:1996;48-53
44. Wilhelm S., Tommassen J., Jaeger K.E. A novel lipolytic enzyme located in the outer membrane of Pseudomonas aeruginosa. J Bacteriol. 181:1999;6977-6986