Origin and Diversity of Alginate Lyases of Families PL-5 and -7 in Sphingomonas sp. Strain A1

Journal of Bacteriology

Volumn 186, Issue 9, 2004, Pages 2891-2896

  Miyake, Osamu ^a   Ochiai, Akihito ^a   Hashimoto, Wataru ^a   Murata, Kousaku ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ALGINATE LYASE A1 I; ALGINATE LYASE A1 II; ALGINATE LYASE A1 III; ALGINIC ACID; LYASE; POLYSACCHARIDE LYASE; POLYSACCHARIDE LYASE 5; POLYSACCHARIDE LYASE 7; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CONTROLLED STUDY; DNA MODIFICATION; ENZYME SPECIFICITY; ENZYME SUBSTRATE; GENE DUPLICATION; GENE STRUCTURE; GENE TRANSLOCATION; GENETIC CODE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FAMILY; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; SPHINGOMONAS;

AMINO ACID SEQUENCE; BASE SEQUENCE; ESCHERICHIA COLI; HYDROGEN-ION CONCENTRATION; MOLECULAR SEQUENCE DATA; MOLECULAR WEIGHT; POLYSACCHARIDE-LYASES; RECOMBINANT PROTEINS; SPHINGOMONAS; SUBSTRATE SPECIFICITY;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; PROKARYOTA; SPHINGOMONAS; SPHINGOMONAS SP.;

EID: 1942443159     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.186.9.2891-2896.2004     Document Type: Article

References (36)

1. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl. 1987. Current protocols in molecular biology. Greene Publishing Associates, New York, N.Y.
2. Baron, A. J., T. Y. Wong, S. J. Hicks, P. Gacesa, D. Willcock, and M. J. McPherson. 1994. Alginate lyase from Klebsiella pneumoniae, subsp. aerogenes: gene cloning, sequence analysis and high-level production in Escherichia coli. Gene 27:61-66.
3. Batten, J. C., and D. J. Matthew. 1983. The respiratory system, p. 105-131. In M. E. Hodson, A. P. Norman, and J. C. Batten, (ed.), Cystic fibrosis. Bailliere Tindall, London, United Kingdom.
4. Boat, T. F., A. L. Beadet, and M. J. Welsh. 1989. The metabolic basis of inheritated disease, p. 2649-2680. In C. R. Seriver, (ed.), Cystic fibrosis. McGraw-Hill, New York, N.Y.
5. Bradford, M. M. 1976. A rapid and sensitive method for the quantification of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248-254.
6. Buell, C. R., V. Joardar, M. Lindeberg, J. Selengut, I. T. Paulsen, M. L. Gwinn, R. J. Dodson, R. T. Deboy, A. S. Durkin, J. F. Kolonay, R. Madupu, S. Daugherty, L. Brinkac, M. J. Beanan, D. H. Haft, W. C. Nelson, T. Davidsen, N. Zafar, L. Zhou, J. Liu, Q. Yuan, H. Khouri, N. Fedorova, B. Tran, D. Russell, K. Berry, T. Utterback, S. E. Van Aken, T. V. Feldblyum, M. D'Ascenzo, W. L. Deng, A. R. Ramos, J. R. Alfano, S. Cartinhour, A. K. Chatterjee, T. P. Delaney, S. G. Lazarowitz, G. B. Martin, D. J. Schneider, X. Tang, C. L. Bender, O. White, C. M. Fraser, and A. Collmer. 2003. The complete genome sequence of the Arabidopsis and tomato pathogen Pseudomonas syringae pv. tomato DC3000. Proc. Natl. Acad. Sci. USA 100: 10181-10186.
7. Gacesa, P. 1988. Alginates. Carbohydr. Polym. 8:161-182.
8. Hashimoto, W., O. Miyake, K. Momma, S. Kawai, and K. Murata. 2000. Molecular identification of oligoalginate lyase of Sphingomonas sp. strain A1 as one of the enzymes required for complete depolymerization of alginate. J. Bacteriol. 182:4572-4577.
9. Hashimoto, W., H. Nankai, B. Mikami, and K. Murata. 2003. Crystal structure of Bacillus sp. GL1 xanthan lyase, which acts on the side chains of xanthan. J. Biol. Chem. 278:7663-7673.
10. Hashimoto, W., M. Okamoto, T. Hisano, K. Momma, and K. Murata. 1998. Sphingomonas sp. A1 lyase active on both poly-β-D-mannuronate and heteropolymeric regions in alginate. J. Ferment. Bioeng. 86:236-238.
11. Hashimoto, W., H. Suzuki, K. Yamamoto, and H. Kumagai. 1995. Effect of site-directed mutations on processing and activity of γ -glutamyltranspeptidase of Escherichia coli K-12. J. Biochem. 118:75-80.
12. Hawley, D. K., and W. R. McClure. 1983. Comparison and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 11:2237-2255.
13. Hisano, T., N. Kimura, W. Hashimoto, and K. Murata. 1996. Pit structure on bacterial cell surface. Biochem. Biophys. Res. Commun. 220:979-982.
14. Hisano, T., M. Nishimura, T. Yamashita, K. Sakaguchi, and K. Murata. 1994. On the self-processing of bacterial alginate lyase. J. Ferment. Bioeng. 78:109-110.
15. Huang, W., L. Boju, L. Tkalec, H. Su, H. O. Yang, N. S. Gunay, R. J. Linhardt, Y. S. Kim, A. Matte, and M. Cygler. 2001. Active site of chondroitin AC lyase revealed by the structure of enzyme-oligosaccharide complexes and mutagenesis. Biochemistry 40:2359-2372.
16. Iwamoto, Y., K. Iriyama, K. Osatomi, T. Oda., and T. Muramatsu. 2002, Primary structure and chemical modification of some amino acid residues of bifunctional alginate lyase from marine bacterium Pseudoalteromonas sp. strain no. 272. J. Protein Chem. 21:455-463.
17. Jedrzejas, M. J., L. V. Mello, B. L. de Groot, and S. Li. 2002. Mechanism of hyaluronan degradation by Streptococcus pneumoniae hyaluronate lyase. Structures of complexes with the substrate. J. Biol. Chem. 277:28287-28297.
18. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
19. Malissard, M., C. Duez, M. Guinand, M. J. Vacheron, G. Michel, N. Marty, B. Joris, I. Thamm, and J. M. Ghuysen. 1993. Sequence of a gene encoding a (poly ManA) alginate lyase active on Pseudomonas aeruginosa alginate. FEMS Microbiol. Lett. 110:101-106.
20. Matsubara, Y., R. Kawada, K. Iwasaki, Y. Kimura, T. Oda, and T. Muramatsu. 2000. Cloning and sequence analysis of a gene (aly PG) encoding poly(α-L-guluronate)lyase from Corynebacterium sp. strain ALY-1. J. Biosci. Bioeng. 89:199-202.
21. Mishima, Y., K. Momma, O. Miyake, W. Hashimoto, B. Mikami, and K. Murata. 2002. Super-channel in bacteria: macromolecule uptake and depolymerization systems of Sphingomonas sp. A1 with special cell surface structure. Biotechnol. Genet. Eng. Rev. 19:1015-1019.
22. Momma, K., M. Okamoto, Y. Mishima, S. Mori, W. Hashimoto, and K. Murata. 2000. A novel bacterial ATP-binding cassette (ABC) transporter system that allows uptake of macromolecules. J. Bacteriol. 182:3998-4004.
23. Onsøyen, E. 1996. Commercial applications of alginates. Carbohydr. Eur. 14:26-31.
24. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
25. Sanger, F., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad, Sci. USA 74:5463-5467.
26. Sawabe, T., M. Otsuka, and Y. Ezura. 1997. Novel alginate lyases from marine bacterium Alteromonas sp. strain H-4. Carbohydr. Res. 304:69-76.
27. Schnier, J., M. Kimura, K. Foulaki, A. R. Subramanian, K. KIsono, and B. Wittmann-Liebold. 1982. Primary structure of Escherichia coli ribosomal protein S1 and of its gene rpsA. Proc. Natl. Acad. Sci. USA 79:1008-1011.
28. Shine, J., and L. Dalgarno. 1974. The 3′ terminal sequence of E. coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosomal binding sites. Proc. Natl. Acad. Sci. USA 71:1342-1346.
29. Stover, C. K., X. Q. Pham, A. L. Erwin, S. D. Mizoguchi, P. Warrener, M. J. Hickey, F. S. L. Brinkman, W. O. Hufnagle, D. J. Kowalik, M. Lagrou, R. L. Garber, L. Goltry, E. Tolentino, S. Westbrock-Wadman, Y. Yuan, L. L. Brody, S. N. Coulter, K. R. Folger, A. Kas, K. Larbig, R. Lim, K. Smith, D. Spencer, G. K.-S. Wong, Z. Wu, I. T. Paulsen, J. Reizer, M. H. Saier, R. E. W. Hancock, S. Lory, and M. V. Olson. 2000. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406:959-964.
30. Tettelin, H., N. J. Saunders, J. Heidelberg, A. C. Jeffries, K. E. Nelson, J. A. Eisen, K. A. Ketchum, D. W. Hood, J. F. Peden, R. J. Dodson, W. C. Nelson, M. L. Gwinn, R. DeBoy, J. D. Peterson, E. K. Hickey, D. H. Haft, S. L. Salzberg, O. White, R. D. Fleischmann, B. A. Dougherty, T. Mason, A. Ciecko, D. S. Parksey, E. Blair, H. Cittone, E. B. Clark, M. D. Cotton, T. R. Utterback, H. Khouri, H. Qin, J. Vamathevan, J. Gill, V. Scarlato, V. Masignani, M. Pizza, G. Grandi, L. Sun, H. O. Smith, C. M. Fraser, E. R. Moxon, R. Rappuoli, and J. C. Venter. 2000. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 287:1809-1815.
31. Warren, L. 1960. Thiobarbituric acid spray reagent for deoxy sugars and sialic acids. Nature 186:237.
32. Wong, T. Y., L. A. Preston, and N. L. Schiller. 2000. Alginate lyase: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications. Annu. Rev. Microbiol. 54:289-340.
33. Yamasaki, M., S. Moriwaki, W. Hashimoto, B. Mikami, and K. Murata. 2003. Crystallization and preliminary X-ray analysis of alginate lyase, a member of polysaccharide lyase family PL-7, from Pseudomonas aeruginosa. Acta Crystallogr. Sect. D 59:1499-1501.
34. Yoon, H.-J., W. Hashimoto, Y. Katsuya, Y. Mezaki, K. Murata, and B. Mikami. 2000. Crystallization and preliminary X-ray crystallographic analysis of alginate lyase A1-II from Sphingomonas species A1. Biochim. Biophys. Acta 1476:382-385.
35. Yoon, H.-J., W. Hashimoto, O. Miyake, K. Murata, and B. Mikami. 2001. Crystal structure of alginate lyase A1-III complexed with trisaccharide product at 2.0Å resolution. J. Mol. Biol, 307:9-16.
36. Yoon, H.-J., W. Hashimoto, O. Miyake, M. Okamoto, B. Mikami, and K. Murata. 2000. Overexpression in Escherichia coli, purification, and characterization of Sphingomonas sp. A1 alginate lyases, Protein Expr. Purif, 19: 84-90.