A β-(1,2)-glycosynthase and an attempted selection method for the directed evolution of glycosynthases

Biochemistry

Volumn 50, Issue 47, 2011, Pages 10359-10366

  Jakeman, David L ^a   Sadeghi Khomami, Ali ^a  

^a DALHOUSIE UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL CHARACTERIZATION; BIOINFORMATICS ANALYSIS; BIOTECHNOLOGICAL APPLICATIONS; DIRECTED EVOLUTION; GLYCOSIDASES; GLYCOSIDIC LINKAGES; GLYCOSYNTHASE; IN-VIVO; MACROLIDE ANTIBIOTICS; SELECTION METHODS;

BIOCHEMISTRY; BIOINFORMATICS; CLONING; ESCHERICHIA COLI; SUGARS;

ANTIBIOTICS;

BACTERIAL PROTEIN; BETA (1,2) GLYCOSYNTHASE; ERYBI PROTEIN; ERYTHROMYCIN; FLUORIDE; GLYCOSIDASE; GLYCOSIDE; MACROLIDE; NUCLEOPHILE; RECOMBINANT PROTEIN; SYNTHETASE; UNCLASSIFIED DRUG;

ANTIBIOTIC RESISTANCE; ARTICLE; BIOCHEMISTRY; BIOINFORMATICS; BIOSYNTHESIS; ESCHERICHIA COLI; EVOLUTION; GLYCOSYLATION; HYDROLYSIS; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PURIFICATION;

AMINO SUGARS; BACTERIAL PROTEINS; CATALYSIS; DIRECTED MOLECULAR EVOLUTION; ERYTHROMYCIN; GLYCOSIDE HYDROLASES; GLYCOSYLATION; KINETICS; MUTATION; SACCHAROPOLYSPORA; SUBSTRATE SPECIFICITY;

ESCHERICHIA COLI;

EID: 81855199904     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi201438q     Document Type: Article

References (41)

1. Boltje, T. J., Buskas, T., and Boons, G. J. (2009) Opportunities and Challenges in Synthetic Oligosaccharide and Glycoconjugate Research Nat. Chem. 1, 611-622
2. Addington, T., Calisto, B., Alfonso-Prieto, M., Rovira, C., Fita, I., and Planas, A. (2011) Re-Engineering Specificity in 1,3-1,4-β-Glucanase to Accept Branched Xyloglucan Substrates Proteins: Struct., Funct., Bioinf. 79, 365-375
3. Cobucci-Ponzano, B., Perugino, G., Rossi, M., and Moracci, M. (2011) Engineering the Stability and the Activity of a Glycoside Hydrolase Protein Eng., Des. Sel. 24, 21-26
4. Cobucci-Ponzano, B., Zorzetti, C., Strazzulli, A., Carillo, S., Bedini, E., Corsaro, M. M., Comfort, D. A., Kelly, R. M., Rossi, M., and Moracci, M. (2011) A Novel α- d -Galactosynthase from Thermotoga maritima Converts β- d -Galactopyranosyl Azide to α-Galacto-Oligosaccharides Glycobiology 21, 448-456
5. Goddard-Borger, E. D., Fiege, B., Kwan, E. M., and Withers, S. G. (2011) Glycosynthase-Mediated Assembly of Xylanase Substrates and Inhibitors ChemBioChem 12, 1703-1711
6. Perez, X., Faijes, M., and Planes, A. (2011) Artificial Mixed-Linked β-Glucans Produced by Glycosynthase-Catalyzed Polymerization: Tuning Morphology and Degree of Polymerization Biomacromolecules 12, 494-501
7. Spadiut, O., Ibatullin, F. M., Peart, J., Gullfot, F., Martinez-Fleites, C., Ruda, M., Xu, C., Sundqvist, G., Davies, G. J., and Brumer, H. (2011) Building Custom Polysaccharides in Vitro with an Efficient, Broad-Specificity Xyloglucan Glycosynthase and a Fucosyltransferase J. Am. Chem. Soc. 133, 10892-10900
8. Hidaka, M., Fushinobu, S., Honda, Y., Wakagi, T., Shoun, H., and Kitaoka, M. (2010) Structural Explanation for the Acquisition of Glycosynthase Activity J. Biochem. 147, 237-244
9. Umekawa, M., Li, C., Higashiyama, T., Huang, W., Ashida, H., Yamamoto, K., and Wang, L. (2010) Efficient Glycosynthase Mutant Derived from Mucor hiemalis Endo-β- N -Acetylglucosaminidase Capable of Transferring Oligosaccharide from both Sugar Oxazoline and Natural N -Glycan J. Biol. Chem. 285, 511-521
10. Vasur, J., Kawai, R., Jonsson, K. H. M., Widmalm, G., Engstrom, A., Frank, M., Andersson, E., Hansson, H., Forsberg, Z., Igarashi, K., Samejima, M., Sandgren, M., and Stahlberg, J. (2010) Synthesis of Cyclic β-Glucan using Laminarinase 16A Glycosynthase Mutant from the Basidiomycete Phanerochaete chrysosporium J. Am. Chem. Soc. 132, 1724-1730
11. Mackenzie, L. F., Wang, Q. P., Warren, R. A. J., and Withers, S. G. (1998) Glycosynthases: Mutant Glycosidases for Oligosaccharide Synthesis J. Am. Chem. Soc. 120, 5583-5584
12. Wang, L. and Huang, W. (2009) Enzymatic Transglycosylation for Glycoconjugate Synthesis Curr. Opin. Chem. Biol. 13, 592-600
13. Mayer, C., Jakeman, D. L., Mah, M., Karjala, G., Gal, L., Warren, R. A., and Withers, S. G. (2001) Directed Evolution of New Glycosynthases from Agrobacterium β-Glucosidase: A General Screen to Detect Enzymes for Oligosaccharide Synthesis Chem. Biol. 8, 437-443 (Pubitemid 32455898)
14. Kim, Y. W., Lee, S. S., Warren, R. A., and Withers, S. G. (2004) Directed Evolution of a Glycosynthase from Agrobacterium sp. Increases its Catalytic Activity Dramatically and Expands its Substrate Repertoire J. Biol. Chem. 279, 42787-42793 (Pubitemid 39372166)
15. Lin, H., Tao, H., and Cornish, V. W. (2004) Directed Evolution of a Glycosynthase via Chemical Complementation J. Am. Chem. Soc. 126, 15051-15059 (Pubitemid 39557264)
16. Ben-David, A., Shoham, G., and Shoham, Y. (2008) A Universal Screening Assay for Glycosynthases: Directed Evolution of Glycosynthase XynB2(E335G) Suggests a General Path to Enhance Activity Chem. Biol. 15, 546-551 (Pubitemid 351815055)
17. Hancock, S. M., Rich, J. R., Caines, M. E. C., Strynadka, N. C. J., and Withers, S. G. (2009) Designer Enzymes for Glycosphingolipid Synthesis by Directed Evolution Nat. Chem. Biol. 5, 508-514
18. Quiros, L. M., Aguirrezabalaga, I., Olano, C., Mendez, C., and Salas, J. A. (1998) Two Glycosyltransferases and a Glycosidase are Involved in Oleandomycin Modification during its Biosynthesis by Streptomyces antibioticus Mol. Microbiol. 28, 1177-1185 (Pubitemid 28293541)
19. Reeves, A. R., Seshadri, R., Brikun, I. A., Cernota, W. H., Gonzalez, M. C., and Weber, J. M. (2008) Knockout of the Erythromycin Biosynthetic Cluster Gene, eryBI, Blocks Isoflavone Glucoside Bioconversion during Erythromycin Fermentations in Aeromicrobium erythreum but Not in Saccharopolyspora erythraea Appl. Environ. Microbiol. 74, 7383-7390 (Pubitemid 352773584)
20. Stubbs, K. A., Scaffidi, A., Debowski, A. W., Mark, B. L., Stick, R. V., and Vocadlo, D. J. (2008) Synthesis and use of Mechanism-Based Protein-Profiling Probes for Retaining β- d -Glucosaminidases Facilitate Identification of Pseudomonas aeruginosa NagZ J. Am. Chem. Soc. 130, 327-335
21. Sadeghi-Khomami, A., Lumsden, M. D., and Jakeman, D. L. (2008) Glycosidase Inhibition by Macrolide Antibiotics Elucidated by STD-NMR Spectroscopy Chem. Biol. 15, 739-749 (Pubitemid 351957908)
22. Junneman, J., Lundt, I., and Thiem, J. (1991) Preparation of some 2-Deoxy-Glycosyl Fluorides and 2,6-Dideoxy-Glycosyl Fluorides Acta Chem. Scand. 45, 494-498
23. Yoon, J. H. and Rhee, J. S. (2000) The Efficient Enzymatic Synthesis of N-Acetyllactosamine in an Organic Co-Solvent Carbohydr. Res. 327, 377-383 (Pubitemid 30456327)
24. Yang, M., Proctor, M. R., Bolam, D. N., Errey, J. C., Field, R. A., Gilbert, H. J., and Davis, B. G. (2005) Probing the Breadth of Macrolide Glycosyltransferases: In Vitro Remodeling of a Polyketide Antibiotic Creates Active Bacterial Uptake and Enhances Potency J. Am. Chem. Soc. 127, 9336-9337 (Pubitemid 40934725)
25. Zhao, L., Beyer, N. J., Borisova, S. A., and Liu, H. W. (2003) β-Glucosylation as a Part of Self-Resistance Mechanism in methymycin/pikromycin Producing Strain Streptomyces venezuelae Biochemistry 42, 14794-14804 (Pubitemid 37553507)
26. Juncker, A. S., Willenbrock, H., Von Heijne, G., Brunak, S., Nielsen, H., and Krogh, A. (2003) Prediction of Lipoprotein Signal Peptides in Gram-Negative Bacteria Protein Sci. 12, 1652-1662 (Pubitemid 36910046)
27. Gaisser, S., Bohm, G. A., Doumith, M., Raynal, M. C., Dhillon, N., Cortes, J., and Leadlay, P. F. (1998) Analysis of eryBI eryBIII and eryBVII from the Erythromycin Biosynthetic Gene Cluster in Saccharopolyspora erythraea Mol. Gen. Genet. 258, 78-88
28. Bennett-Lovsey, R. M., Herbert, A. D., Sternberg, M. J. E., and Kelley, L. A. (2008) Exploring the Extremes of Sequence/Structure Space with Ensemble Fold Recognition in the Program Phyre Proteins 70, 611-625 (Pubitemid 351161924)
29. Kelley, L. A. and Sternberg, M. J. E. (2009) Protein Structure Prediction on the Web: A Case Study using the Phyre Server Nat. Protoc. 4, 363-371
30. Hrmova, M., Varghese, J. N., De Gori, R., Smith, B. J., Driguez, H., and Fincher, G. B. (2001) Catalytic Mechanisms and Reaction Intermediates along the Hydrolytic Pathway of a Plant β- d -Glucan Glucohydrolase Structure 9, 1005-1016 (Pubitemid 33092104)
31. Stubbs, K. A., Balcewich, M., Mark, B. L., and Vocadlo, D. J. (2007) Small Molecule Inhibitors of a Glycoside Hydrolase Attenuate Inducible AmpC-Mediated β-Lactam Resistance J. Biol. Chem. 282, 21382-21391 (Pubitemid 47099917)
32. Litzinger, S., Fischer, S., Polzer, P., Diederichs, K., Welte, W., and Mayer, C. (2010) Structural and Kinetic Analysis of Bacillus subtilis N-Acetylglucosaminidase Reveals a Unique Asp-His Dyad Mechanism J. Biol. Chem. 285, 35675-35684
33. Wilkinson, S. M., Liew, C. W., Mackay, J. P., Salleh, H. M., Withers, S. G., and McLeod, M. D. (2008) Escherichia coli glucuronylsynthase: An Engineered Enzyme for the Synthesis of β-Glucuronides Org. Lett. 10, 1585-1588
34. Ruiz, N., Falcone, B., Kahne, D., and Silhavy, T. J. (2005) Chemical Conditionality: A Genetic Strategy to Probe Organelle Assembly Cell 121, 307-317 (Pubitemid 40546397)
35. Goldman, R. C., Fesik, S. W., and Doran, C. C. (1990) Role of Protonated and Neutral Forms of Macrolides in Binding to Ribosomes from Gram-Positive and Gram-Negative Bacteria Antimicrob. Agents Chemother. 34, 426-431 (Pubitemid 20068665)
36. Angulo, J., Langpap, B., Blume, A., Biet, T., Meyer, B., Krishna, N. R., Peters, H., Palcic, M. M., and Peters, T. (2006) Blood Group B Galactosyltransferase: Insights into Substrate Binding from NMR Experiments J. Am. Chem. Soc. 128, 13529-13538 (Pubitemid 44583038)
37. Angulo, J., Rademacher, C., Biet, T., Benie, A. J., Blume, A., Peters, H., Palcic, M., Parra, F., and Peters, T. (2006) NMR Analysis of Carbohydrate-Protein Interactions Methods Enzymol. 416, 12-30 (Pubitemid 44750102)
38. Fielding, L. (2007) NMR Methods for the Determination of Protein-Ligand Dissociation Constants Prog. Nucl. Magn. Reson. Spectrosc. 51, 219-242 (Pubitemid 350064300)
39. Middleton, D. A. (2007) NMR Methods for Characterising Ligand-Receptor and Drug-Membrane Interactions in Pharmaceutical Research Annu. Rep. NMR Spectrosc. 60, 39-75
40. Novak, P., Tatic, I., Tepes, P., Kostrun, S., and Barber, J. (2006) Systematic Approach to Understanding Macrolide-Ribosome Interactions: NMR and Modeling Studies of Oleandomycin and its Derivatives J. Phys. Chem. A 110, 572-579 (Pubitemid 43164647)
41. Novak, P., Barber, J., Cikos, A., Arsic, B., Plavec, J., Lazarevski, G., Tepes, P., and Kosutic-Hulita, N. (2009) Free and Bound State Structures of 6-O-Methyl Homoerythromycins and Epitope Mapping of Their Interactions with Ribosomes Bioorg. Med. Chem. 17, 5857-5867