A comparison of directed evolution approaches using the β-glucuronidase model system

Journal of Molecular Biology

Volumn 332, Issue 4, 2003, Pages 851-860

  Rowe, Lori A ^a   Geddie, Melissa L ^a   Alexander, Omar B ^a   Matsumura, Ichiro ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Clonal interference; Directed evolution; DNA shuffling; High throughput screening; glucuronidase

Indexed keywords

BETA GLUCURONIDASE;

ALLELE; ARTICLE; ASSAY; EVOLUTIONARY ADAPTATION; MODEL; MUTAGENESIS; MUTATION; PRIORITY JOURNAL; TECHNIQUE;

ESCHERICHIA COLI;

EID: 0041324888     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00972-0     Document Type: Article

References (58)

1. Ballinger M.D., Tom J., Wells J.A. Furilisin: a variant of subtilisin BPN′ engineered for cleaving tribasic substrates. Biochemistry. 35:1996;13579-13585.
2. Chen R., Greer A., Dean A.M. Redesigning secondary structure to invert coenzyme specificity in isopropylmalate dehydrogenase. Proc. Natl Acad. Sci. USA. 93:1996;12171-12176.
3. Harris J.L., Craik C.S. Engineering enzyme specificity. Curr. Opin. Chem. Biol. 2:1998;127-132.
4. Hedstrom L., Szilagyi L., Rutter W.J. Converting trypsin to chymotrypsin: the role of surface loops. Science. 255:1992;1249-1253.
5. Onuffer J.J., Kirsch J.F. Redesign of the substrate specificity of Escherichia coli aspartate aminotransferase to that of Escherichia coli tyrosine aminotransferase by homology modeling and site-directed mutagenesis. Protein Sci. 4:1995;1750-1757.
6. Wilks H.M., Hart K.W., Feeney R., Dunn C.R., Muirhead H., Chia W.N., et al. A specific, highly active malate dehydrogenase by redesign of a lactate dehydrogenase framework. Science. 242:1988;1541-1544.
7. Kang C., Sun N., Honzatko R.B., Fromm H.J. Replacement of Asp333 with Asn by site-directed mutagenesis changes the substrate specificity of Escherichia coli adenylosuccinate synthetase from guanosine 5′ -triphosphate to xanthosine 5′-triphosphate. J. Biol. Chem. 269:1994;24046-24049.
8. Nilsson L.O., Gustafsson A., Mannervik B. Redesign of substrate-selectivity determining modules of glutathione transferase A1-1 installs high catalytic efficiency with toxic alkenal products of lipid peroxidation. Proc. Natl Acad. Sci. USA. 97:2000;9408-9412.
9. Galzi J.L., Devillers-Thiery A., Hussy N., Bertrand S., Changeux J.P., Bertrand D. Mutations in the channel domain of a neuronal nicotinic receptor convert ion selectivity from cationic to anionic. Nature. 359:1992;500-505.
10. Zhu Z., Sun D., Davidson V.L. Conversion of methylamine dehydrogenase to a long-chain amine dehydrogenase by mutagenesis of a single residue. Biochemistry. 39:2000;11184-11186.
11. Yokoyama S. Molecular genetic basis of adaptive selection: examples from color vision in vertebrates. Annu. Rev. Genet. 31:1997;315-336.
12. Broun P., Shanklin J., Whittle E., Somerville C. Catalytic plasticity of fatty acid modification enzymes underlying chemical diversity of plant lipids. Science. 282:1998;1315-1317.
13. el Hawrani A.S., Sessions R.B., Moreton K.M., Holbrook J.J. Guided evolution of enzymes with new substrate specificities. J. Mol. Biol. 264:1996;97-110.
14. Forney L.J., Wong D.C., Ferber D.M. Selection of amidases with novel substrate specificities from penicillin amidase of Escherichia coli. Appl. Environ. Microbiol. 55:1989;2550-2555.
15. Joo H., Lin Z., Arnold F.H. Laboratory evolution of peroxide-mediated cytochrome P450 hydroxylation. Nature. 399:1999;670-673.
16. Jurgens C., Strom A., Wegener D., Hettwer S., Wilmanns M., Sterner R. Directed evolution of a (beta alpha)8-barrel enzyme to catalyze related reactions in two different metabolic pathways. Proc. Natl Acad. Sci. USA. 97:2000;9925-9930.
17. May O., Nguyen P.T., Arnold F.H. Inverting enantioselectivity by directed evolution of hydantoinase for improved production of l-methionine. Nature Biotechnol. 18:2000;317-320.
18. Stemmer W.P. Rapid evolution of a protein in vitro by DNA shuffling. Nature. 370:1994;389-391.
19. 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.
20. Zaccolo M., Gherardi E. The effect of high-frequency random mutagenesis on in vitro protein evolution: a study on TEM-1 beta-lactamase. J. Mol. Biol. 285:1999;775-783.
21. Zhang J.H., Dawes G., Stemmer W.P. Directed evolution of a fucosidase from a galactosidase by DNA shuffling and screening. Proc. Natl Acad. Sci. USA. 94:1997;4504-4509.
22. Moore J.C., Arnold F.H. Directed evolution of a para-nitrobenzyl esterase for aqueous-organic solvents. Nature Biotechnol. 14:1996;458-467.
23. Cadwell R.C., Joyce G.F. Randomization of genes by PCR mutagenesis. PCR Methods Appl. 2:1992;28-33.
24. Matsumura I., Ellington A.D. Mutagenic PCR of protein-coding genes for in vitro evolution. Braman J. In Vitro Mutagenesis Protocols. 2002;Humana Press, Totowa, NJ. pp. 259-267.
25. Sieber V., Martinez C.A., Arnold F.H. Libraries of hybrid proteins from distantly related sequences. Nature Biotechnol. 19:2001;456-460.
26. Lutz S., Ostermeier M., Moore G.L., Maranas C.D., Benkovic S.J. Creating multiple-crossover DNA libraries independent of sequence identity. Proc. Natl Acad. Sci. USA. 98:2001;11248-11253.
27. Crameri A., Raillard S.A., Bermudez E., Stemmer W.P. DNA shuffling of a family of genes from diverse species accelerates directed evolution. Nature. 391:1998;288-291.
28. Matsumura I., Ellington A.D. In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates. J. Mol. Biol. 305:2001;331-339.
29. Stemmer W.P. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc. Natl Acad. Sci. USA. 91:1994;10747-10751.
30. Zhao H., Arnold F.H. Optimization of DNA shuffling for high fidelity recombination. Nucl. Acids Res. 25:1997;1307-1308.
31. Patten P.A., Sonoda T., Davis M.M. Directed evolution studies with combinatorial libraries of T4 lysozyme mutants. Mol. Divers. 1:1996;97-108.
32. Ness J.E., Welch M., Giver L., Bueno M., Cherry J.R., Borchert T.V., et al. DNA shuffling of subgenomic sequences of subtilisin. Nature Biotechnol. 17:1999;893-896.
33. Olsen M., Iverson B., Georgiou G. High-throughput screening of enzyme libraries. Curr. Opin. Biotechnol. 11:2000;331-337.
34. Matsumura I., Olsen M.J., Ellington A.D. Optimization of heterologous gene expression for in vitro evolution. Biotechniques. 30:2001;474-476.
35. Schwaneberg U., Otey C., Cirino P.C., Farinas E., Arnold F.H. Cost-effective whole-cell assay for laboratory evolution of hydroxylases in Escherichia coli. J. Biomol. Screen. 6:2001;111-117.
36. Judo M.S., Wedel A.B., Wilson C. Stimulation and suppression of PCR-mediated recombination. Nucl. Acids Res. 26:1998;1819-1825.
37. Gerrish P.J., Lenski R.E. The fate of competing beneficial mutations in an asexual population. Genetica. 103:1998;127-144.
38. Wells J.A., Vasser M., Powers D.B. Cassette mutagenesis: an efficient method for generation of multiple mutations at defined sites. Gene. 34:1985;315-323.
39. Bartel D.P., Szostak J.W. Isolation of new ribozymes from a large pool of random sequences. Science. 261:1993;1411-1418.
40. Imhof M., Schlotterer C. Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc. Natl Acad. Sci. USA. 98:2001;1113-1117.
41. Gillespie J. Population Genetics: A Concise Guide. 1998;The Johns Hopkins University Press, Baltimore, MD.
42. Rice W.R., Chippindale A.K. Sexual recombination and the power of natural selection. Science. 294:2001;555-559.
43. Jain S., Drendel W.B., Chen Z.W., Mathews F.S., Sly W.S., Grubb J.H. Structure of human beta-glucuronidase reveals candidate lysosomal targeting and active-site motifs. Nature Struct. Biol. 3:1996;375-381.
44. Naleway J.J. Histochemical, spectrophotometric, and fluorometric GUS substrates. Gallagher S.R. GUS Protocols: Using the GUS Gene as a Reporter of Gene Expression. 1992;61-76 Academic Press, New York.
45. Graham L.D., Haggett K.D., Jennings P.A., Le Brocque D.S., Whittaker R.G., Schober P.A. Random mutagenesis of the substrate-binding site of a serine protease can generate enzymes with increased activities and altered primary specificities. Biochemistry. 32:1993;6250-6258.
46. Rufer A.W., Sauer B. Non-contact positions impose site selectivity on Cre recombinase. Nucl. Acids Res. 30:2002;2764-2771.
47. Stefan A., Radeghieri A., Gonzalez Vara y Rodriguez A., Hochkoeppler A. Directed evolution of beta-galactosidase from Escherichia coli by mutator strains defective in the 3′→5′ exonuclease activity of DNA polymerase III. FEBS Letters. 493:2001;139-143.
48. Fong S., Machajewski T.D., Mak C.C., Wong C. 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. 7:2000;873-883.
49. Lazcano A., Diaz-Villagomez E., Mills T., Oro J. On the levels of enzymatic substrate specificity: implications for the early evolution of metabolic pathways. Advan. Space Res. 15:1995;345-356.
50. Kacser H., Beeby R. Evolution of catalytic proteins or on the origin of enzyme species by means of natural selection. J. Mol. Evol. 20:1984;38-51.
51. Jensen R.A. Enzyme recruitment in evolution of new function. Annu. Rev. Microbiol. 30:1976;409-425.
52. Ycas M. On earlier states of the biochemical system. J. Theor. Biol. 44:1974;145-160.
53. Waley S.G. Some aspects of the evolution of metabolic pathways. Comput. Biochem. Physiol. 30:1969;1-11.
54. 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. Nature Biotechnol. 17:1999;696-701.
55. Eisinger D.P., Trumpower B.L. Long-inverse PCR to generate regional peptide libraries by codon mutagenesis. Biotechniques. 22:1997;250-252.
56. Wybranietz W.A., Lauer U. Distinct combination of purification methods dramatically improves cohesive-end subcloning of PCR products. Biotechniques. 24:1998;578-580.
57. Islam M.R., Tomatsu S., Shah G.N., Grubb J.H., Jain S., Sly W.S. Active site residues of human beta-glucuronidase. Evidence for Glu(540) as the nucleophile and Glu(451) as the acid-base residue. J. Biol. Chem. 274:1999;23451-23455.
58. Emlen J.M. Population Biology: The Co-Evolution of Population Dynamics and Behavior. 1984;MacMillan Publishing Co. New York.