Improvement of the thermostability and activity of a pectate lyase by single amino acid substitutions, using a strategy based on melting-temperature- guided sequence alignment

Applied and Environmental Microbiology

Volumn 74, Issue 4, 2008, Pages 1183-1189

  Xiao, Zhizhuang ^a   Bergeron, Hélène ^a   Grosse, Stephan ^a   Beauchemin, Manon ^a   Garron, Marie Line ^a   Shaya, David ^a   Sulea, Traian ^a   Cygler, Miroslaw ^a   Lau, Peter C K ^a  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; GENES; MELTING POINT; SUBSTITUTION REACTIONS; THERMODYNAMIC STABILITY;

AMINO ACID SUBSTITUTIONS; MUTATED GENES; PECTATE LYASE;

ENZYME KINETICS;

AMINO ACID; PECTATE LYASE;

AMINO ACID; BACTERIUM; CATALYSIS; ENZYME ACTIVITY; MELTING; MUTATION; PROTEIN;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; CATALYSIS; ENZYME ACTIVITY; GENE LIBRARY; MUTATION; NONHUMAN; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT; STRUCTURE ANALYSIS; TEMPERATURE; THERMOSTABILITY; XANTHOMONAS CAMPESTRIS;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; BASE SEQUENCE; CATALYSIS; CRYSTALLIZATION; ENZYME STABILITY; KINETICS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; POLYSACCHARIDE-LYASES; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TRANSITION TEMPERATURE; XANTHOMONAS CAMPESTRIS;

CANNABIS SATIVA; XANTHOMONAS CAMPESTRIS;

EID: 39649114576     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.02220-07     Document Type: Article

References (44)

1. Akin, D. E., G. Henriksson, J. D. Evans, A. P. S. Adamsen, J. A. Foulk, and R. B. Dodd. 2004. Progress in enzyme-retting of flax. J. Natural Fibers 1:21-47.
2. Antonov, V., J. Msarek, M. Bjelkova, P. Smirous, and H. Fischer. 2007. Easily available enzymes as natural retting agents. Biotechnol. J. 2:342-346.
3. Berensmeier, S., S. A. Singh, J. Meens, and K. Buchholz. 2004. Cloning of the pelA gene from Bacillus licheniformis 14A and biochemical characterization of recombinant, thermostable, high-alkaline pectate lyase. Appl. Microbiol. Biotechnol. 64:560-567.
4. Bjørk, A., B. Dalhus, D. Mantzilas, R. Sirevag, and V. G. H. Eijsink. 2004. Large improvement in the thermal stability of a tetrameric malate dehydrogenase by single point mutations at the dimer-dimer interface. J. Mol. Biol. 341:1215-1226.
5. Bradford, M. 1976. A rapid and sensitive method for quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248-254.
6. Chaparro-Riggers, J. F., K. M. Polizzi, and A. S. Bommarius. 2007. Better library design: data-driven protein engineering. Biotechnol. J. 2:180-191.
7. Chinea, G., G. Padron, R. W. Hooft, C. Sander, and G. Vriend. 1995. The use of position-specific rotamers in model building by homology. Proteins 23: 415-421.
8. Collmer, A., J. L. Ried, and M. S. Mount. 1988. Assay methods for pectic enzymes. Methods Enzymol. 161:329-335.
9. da Silva, A. C. R., et al. 2002. Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417:459-463.
10. Dehdashti, S. J., C. N. Doan, K. L. Chao, and M. D. Yoder. 2003. Effect of mutations in the T1.5 loop of pectate lyase A from Erwinia chrysanthemi EC16. Acta Crystallogr. D 59:1339-1342.
11. Eijsink, V. G. H., S. Gaseidnes, T. V. Borchert, and T. van den Burg. 2005. Directed evolution of enzyme stability. Biomol. Eng. 22:21-30.
12. Emsley, P., and K. Cowtan. 2004. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60:2126-2132.
13. Guerois, R., J. E. Nielsen, and L. Serrano. 2002. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J. Mol. Biol. 320:369-387.
14. Hatada, Y., T. Kobayashi, and S. Ito. 2001. Enzymatic properties of the highly thermophilic and alkaline pectate lyase Pel-4B from alkaliphilic Bacillus sp. strain P-4-N and the entire nucleotide and amino acid sequences. Extremophiles 5:127-133.
15. Herron, S. R., J. A. E. Benen, R. D. Scavetta, J. Visser, and F. Jurnak. 2000. Structure and function of pectic enzymes: virulence factors of plant pathogens. Proc. Natl. Acad. Sci. USA 97:8762-8769.
16. Hooft, R. W., C. Sander, and G. Vriend. 1996. Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins 26:363-376.
17. Jaenicke, R. 2000. Stability and stabilization of globular proteins in solution. J. Biotechnol. 79:193-203.
18. Kluskens, L. D., G. van Alebeek, A. Voragen, W. M. de Vos, and J. van der Oost. 2003. Molecular and biochemical characterization of the thermoactive family 1 pectate lyase from the hyperthermophilic bacterium Thermotoga maritima. Biochem. J. 370:651-659.
19. Kuchner, O., and F. H. Arnold. 1997. Directed evolution of enzyme catalysts. Trends Biotechnol. 15:523-530.
20. Laskowski, R. A., M. W. MacArthur, D. S. Moss, and J. M. Thornton. 1993. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallogr. 26:283-291.
21. Lehmann, M., et al. 2002. The consensus concept for thermostability engineering of proteins: further proof of concept. Protein Eng. 15:403-411.
22. Lietzke, S. E., R. D. Scavetta, M. D. Yoder, and F. Jurnak. 1996. The refined three-dimensional structure of pectate lyase E from Erwinia chrysanthemi at 2.2 Å resolution. Plant Physiol. 111:73-92.
23. Matthews, B. W. 1968. Solvent content of protein crystals. J. Mol. Biol. 33:491-497.
24. Mok, Y., E. L. Elisseeva, A. R. Davidson, and J. D. Forman-Kay. 2001. Dramatic stabilization of an SH3 domain by a single substitution: roles of the folded and unfolded states. J. Mol. Biol. 307:913-928.
25. Morley, K., and R. Kazlauskas. 2005. Improving enzyme properties: when are closer mutations better? Trends Biotechnol. 23:231-237.
26. Murshudov, G. N., A. A. Vagin, and E. J. Dodson. 1997. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53:240-255.
27. Otwinowski, Z., and W. Minor. 1997. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:307-326.
28. Ouajai, S., and R. A. Shanks. 2005. Morphology and structure of hemp fibre after bioscouring. Macromol. Biosci. 5:124-134.
29. Perrakis, A., M. Harkiolaki, K. S. Wilson, and V. S. Lamzin. 2001. ARP/ wARP and molecular replacement. Acta Crystallogr. D 57:1445-1450.
30. Polizzi, K. M., A. S. Bommarius, J. M. Broering, and J. F. Chaparro-Riggers. 2007. Stability of biocatalysts. Curr. Opin. Chem. Biol. 11:220-225.
31. Riesenberg, D. 1991. High-cell-density cultivation of Escherichia coli. Curr. Opin. Biotechnol. 2:380-384.
32. Robinson-Rechavi, M., and A. Godzik. 2005. Structural genomics of Thermotoga maritima proteins shows that contact order is a major determinant of protein thermostability. Structure 13:857-860.
33. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
34. Smith, S. P., K. R. Barber, S. D. Dunn, and G. S. Shaw. 1996. Structural influence of cation binding to recombinant human brain S100b: evidence for calcium-induced exposure of a hydrophobic surface. Biochemistry 35:8805-8814.
35. Solbak, A., et al. 2005. Discovery of pectin-degrading enzymes and directed evolution of a novel pectate lyase for processing cotton fabric. J. Biol. Chem. 280:9431-9438.
36. Sterner, R., and W. Liebl. 2001. Thermophilic adaptation of proteins. Crit. Rev. Biochem. Mol. Biol. 36:39-106.
37. Takao, M., T. Nakaniwa, K. Yoshikawa, T. Terashita, and T. Sakai. 2001. Molecular cloning, DNA sequence, and expression of the gene encoding for thermostable pectate lyase of thermophilic Bacillus sp. TS 47. Biosci. Biotechnol. Biochem. 65:322-329.
38. Vagin, A., and A. Teplyakov. 1997. MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30:1022-1025.
39. van den Burg, B., H. G. Enequist, M. E. van der Haar, V. G. Eijsink, B. K. Stulp, and G. Venema. 1991. A highly thermostable neutral protease from Bacillus caldolyticus: cloning and expression of the gene in Bacillus subtilis and characterization of the gene product. J. Bacteriol. 173:4107-4135.
40. van den Burg, B., B. W. Dijkstra, G. Vriend, B. Van Dar Vinne, G. Venema, and V. G. Eijsink. 1994. Protein stabilization by hydrophobic interactions at the surface. Eur. J. Biochem. 220:981-985.
41. Vieille, B. R., and G. J. Zeikus. 2001. Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol. Mol. Biol. Rev. 65:1-43.
42. Vriend, G. 1990. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8:52-56.
43. Yoder, M. D., N. T. Keen, and F. Jurnak. 1993. New domain motif: the structure of pectate lyase C, a secreted plant virulence factor. Science 260: 1503-1507.
44. Zhao, H. 2007. Directed evolution of novel protein functions. Biotechnol. Bioeng. 98:313-317.