Characterization of a thermoacidophilic L-arabinose isomerase from Alicyclobacillus acidocaldarius: Role of Lys-269 in pH optimum

Applied and Environmental Microbiology

Volumn 71, Issue 12, 2005, Pages 7888-7896

  Lee, Sang Jae ^a   Lee, Dong Woo ^b   Choe, Eun Ah ^c   Hong, Young Ho ^a   Kim, Seong Bo ^d   Kim, Byoung Chan ^e   Pyun, Yu Ryang ^a  

^a Yonsei University   (South Korea)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d CJ Corporation   (South Korea)

^e UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; CHROMATOGRAPHIC ANALYSIS; ESCHERICHIA COLI; FILTRATION; GELS; GENES; ION EXCHANGE; PH EFFECTS; POSITIVE IONS;

GEL FILTRATION; GENE ENCODING; ION-EXCHANGE CHROMATOGRAPHY; L-ARABINOSE ISOMERASE;

ENZYMES;

ARABINOSE; BACTERIAL ENZYME; GENOMIC DNA; ISOMERASE; LYSINE; METAL ION;

ENZYME; MOLECULAR ANALYSIS; PH;

ALICYCLOBACILLUS ACIDOCALDARIUS; AMINO ACID SEQUENCE; ARTICLE; BACTERIUM CULTURE; CHROMATOGRAPHY; ENZYME ASSAY; ENZYME PURIFICATION; GENE EXPRESSION; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PH; POLYMERASE CHAIN REACTION; STRAIN DIFFERENCE; THERMOPHILIC BACTERIUM;

ALDOSE-KETOSE ISOMERASES; AMINO ACID SEQUENCE; BACILLUS; BASE SEQUENCE; DNA PRIMERS; HYDROGEN-ION CONCENTRATION; KINETICS; LYSINE; MOLECULAR SEQUENCE DATA; MUTAGENESIS, SITE-DIRECTED; POLYMERASE CHAIN REACTION; PROTEIN STRUCTURE, SECONDARY; RECOMBINANT PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; THERMODYNAMICS;

ALICYCLOBACILLUS ACIDOCALDARIUS; BACILLUS HALODURANS; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; GEOBACILLUS STEAROTHERMOPHILUS;

EID: 29144453887     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.71.12.7888-7896.2005     Document Type: Article

References (42)

1. Bornscheuer, U. T., and M. Pohl. 2001. Improved biocatalysts by directed evolution and rational protein design. Curr. Opin. Chem. Biol. 5:137-143.
2. Burley, S. K., and J. B. Bonanno. 2002. Structural genomics of proteins from conserved biochemical pathways and processes. Curr. Opin. Struct. Biol. 12:383-391.
3. Burley, S. K., and J. B. Bonanno. 2002. Structuring the universe of proteins. Annu. Rev. Genom. Hum. Genet. 3:243-262.
4. Cheetham, P. S. J., and A. N. Wootton. 1993. Bioconversion of D-galactose to D-tagatose. Enzyme Microb. Technol. 15:105-108.
5. Cuff, J. A., M. E. Clamp, A. S. Siddiqui, M. Finlay, and G. J. Barton. 1998. Jpred: a consensus secondary structure prediction server. Bioinformatics 14:892-893.
6. Dalby, P. A. 2003. Optimizing enzyme function by directed evolution. Curr. Opin. Struct. Biol. 13:500-505.
7. Darland, G., and T. G. Brock. 1971. Bacillus acidocaldarius sp. nov. An acidophilic thermophilie spore-forming bacteria. J. Gen. Microbiol. 67:9-15.
8. Dische, Z., and E. Borefreund. 1951. A new spectrophotometric method for the detection and determination of keto sugars and trioses. J. Biol. Chem. 192:583-587.
9. Eckert, K., F. Zielinski, L. L. Leggio, and E. Schneider. 2002. Gene cloning, sequencing, and characterization of a family 9 endoglucanase (Ce1A) with an unusual pattern of activity from the thermoacidophile Alicyclobacillus acidocaldarius ATCC27009. Appl. Microbiol. Biotechnol. 60:428-436.
10. Eckert, K., and E. Schneider. 2003. A thermoacidophilic endoglucanase (Ce1B) from Alicyclobacillus acidocaldarius displays high sequence similarity to arabinofuranosidases belonging to family 51 of glycoside hydrolases. Eur. J. Biochem. 270:3593-3602.
11. Felsenstein, J. 1996. Inferring phylogenies from protein sequences by parsimony, distance and likelihood methods. Methods Enzymol. 266:418-427.
12. Izumori, K., Y. Ueda, and K. Yamanaka. 1978. Pentose metabolism in Mycobacterium smegmatis: comparison of L-arabinose isomerases induced by L-arabinose and D-galactose. J. Bacteriol. 133:413-414.
13. Jones, D. T. 1999. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292:195-202.
14. Jørgensen, F., O. C. Hansen, and P. Stougaard. 2004. Enzymatic conversion of D-galactose to D-tagatose: heterologous expression and characterisation of a thermostable L-arabinose isomerase from Thermoanaerobacter mathranii. Appl. Microbiol. Biotechnol. 64:816-822.
15. Karimäki, J., T. Parkkinen, H. Santa, O. Pastinen, M. Leisola, J. Rouvinen, and O. Turunen. 2004. Engineering the substrate specificity of xylose isomerase. Protein Eng. Des. Sel. 17:861-869.
16. Kim, B. C., Y. H. Lee, H. S. Lee, D. W. Lee, E. A. Choe, and Y. R. Pyun. 2002. Cloning, expression and characterization of L-arabinose isomerase from Thermotoga neapolitana: bioconversion of D-galactose to D-tagatose using the enzyme. FEMS Microbiol. Lett. 212:121-126.
17. Kim, J. W., Y. W. Kim, H. J. Roh, H. Y. Kim, J. H. Cha, K. H. Park, and C. S. Park. 2003. Production of tagatose by a recombinant thermostable L-arabinose isomerase from Thermus sp. IM6501. Biotechnol. Lett. 25:963-967.
18. Kim, P. 2004. Current studies on biological tagatose production using L-arabinose isomerase: a review and future perspective. Appl. Microbiol. Biotechnol. 65:243-249.
19. 95 with Gly or Asn. J. Biol. Chem. 267:22014-22017.
20. Kirk, O., T. V. Borchert, and C. C. Fuglsang. 2003. Industrial enzyme applications. Curr. Opin. Biotechnol. 13:345-351.
21. Kumar, S., K. Tamura, and M. Nei. 2004. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5:150-163.
22. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 277:680-685.
23. Lee, D. W., E. A. Choe, S. B. Kim, S. H. Eom, Y. H. Hong, S. J. Lee, H. S. Lee, D. Y. Lee, and Y. R. Pyun. 2005. Distinct metal dependence for catalytic and structural functions in the L-arabinose isomerases from the mesophilic Bacillus halodurans and the thermophilic Geobacillus stearothermophilus. Arch. Biochem. Biophys. 434:333-343.
24. Lee, D. W., Y. H. Hong, E. A. Choe, S. J. Lee, S. B. Kim, H. S. Lee, J. W. Oh, H. H. Shin, and Y. R. Pyun. 2005. A thermodynamic study of mesophilic, thermophilic, and hyperthermophilic L-arabinose isomerases: the effects of divalent metal ions on protein stability at elevated temperatures. FEBS Lett. 579:1261-1266.
25. Lee, D.-W., H.-J. Jang, E.-A. Choe, B.-C. Kim, S.-J. Lee, S.-B. Kim, Y.-H. Hong, and Y.-R. Pyun. 2004. Characterization of a thermostable L-arabinose (D-galactose) isomerase from the hyperthermophilic eubacterium Thermotoga maritima. Appl. Environ. Microbiol. 70:1397-1404.
26. Lehmann, M., C. Loch, A. Middendorf, D. Studer, S. F. Lassen, L. Pasamontes, A. P. G. M. van Loon, and, M. Wyss. 2002. The consensus concept for thermostability engineering of proteins: further proof of concept. Protein Eng. 15:403-411.
27. Lehmann, M., and M. Wyss. 2001. Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolution. Curr. Opin. Biotechnol. 12:371-375.
28. Levin, G. V., and L. R. Zehner. 1995. Sugar substitutes: their energy values, bulk characteristics, and potential health benefits. Am. J. Clin. Nutr. 62:1161-1168.
29. Liu, S. Y., J. Wiegel, and F. C. Gherardini. 1996. Purification and cloning of a thermostable xylose (glucose) isomerase with an acidic pH optimum from Thermoanaerobacterium strain JW/SL-YS 489. J. Bacteriol. 178:5938-5945.
30. Patrick, J. W., and N. Lee. 1968. Purification and properties of an L-arabinose isomerase from Escherichia coli. J. Biol. Chem. 243:4312-4318.
31. Rzhetsky, A., and M. Nei. 1993. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol. Biol. Evol. 10:1073-1095.
32. Saitou, N., and M. Nei. 1987. The neighbor-joining method - a new method for reconstructing phylogenetic tress. Mol. Biol. Evol. 4:406-425.
33. Sato, T., M. Kouda, and T. Hoshino. 2004. Site-directed mutagenesis experiments on the putative deprotonation site of squalene-hopene cyclase from Alicyclobacillus acidocaldarius. Biosci. Biotechnol. Biochem. 68:728-738.
34. Schäfer, K., U. Magnusson, F. Scheffel, A. Schiefner, M. O. Sandgren, K. Diederichs, W. Welte, A. Hulsmann, E. Schneider, and S. L. Mowbray. 2004. X-ray structures of the maltose-maltodextrin-binding protein of the thermoacidophilic bacterium Alicyclobacillus acidocaldarius provide insight into acid stability of proteins. J. Mol. Biol. 335:261-274.
35. Shaw, A., B. Richard, and A. G. Day. 1999. Protein engineering of α-amylase for low pH performance. Curr. Opin. Biotechnol. 10:349-352.
36. Smith, P. K., G. T. Krohn, and D. C. Klenk. 1985. Measurement of protein using bicinchoninic acid. Anal. Biochem. 150:76-85.
37. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25:4876-4882.
38. Tobin, M. B., C. Gustafsson, and G. W. Huisman. 2000. Directed evolution: the 'rational' basis for 'irrational' design. Curr. Opin. Struct. Biol. 10:421-427.
39. Tomschy, A., R. Brugger, M. Lehmann, A. Svendsen, K. Vogel, D. Kostrewa, S. F. Lassen, D. Burger, A. Kronenberger, A. P. G. M. van Loon, L. Pasamontes, and M. Wyss. 2002. Engineering of phytase for improved activity at low pH. Appl. Environ. Microbiol. 68:1907-1913.
40. Triglia, T., M. G. Peterson, and D. J. Kemp. 1988. A procedure for in vitro amplification of DNA segments that lie outside the boundaries of known sequences. Nucleic Acid Res. 16:8186.
41. Tsuruoka, N., T. Nakayama, M. Ashida, H. Hemmi, M. Nakao, H. Minakata, H. Oyama, K. Oda, and T. Nishino. 2003. Collagenolytic serine-carboxyl proteinase from Alicyclobacillus sendaiensis strain NTAP-1: purification, characterization, gene cloning, and heterologous expression. Appl. Environ. Microbiol. 69:162-169.
42. Wisotzkey, J. D., P. Jurtshuk, Jr., G. E. Fox, G. Deinhard, and K. Poralla. 1992. Comparative sequence analyses on the 16S rRNA (rDNA) of Bacillus acidocaldarius, Bacillus acidoterrestris, and Bacillus cyclohepranicus and proposal for creation of new genus, Alicyclobacillus gen. nov. Int. J. Syst. Bacteriol. 42:263-269.