UDP-glucuronic acid decarboxylases of Bacteroides fragilis and their prevalence in bacteria

Journal of Bacteriology

Volumn 193, Issue 19, 2011, Pages 5252-5259

  Coyne, Michael J ^a   Fletcher, C Mark ^a   Reinap, Barbara ^a   Comstock, Laurie E ^a  

^a CHANNING LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GLUCURONIC ACID; POLYSACCHARIDE; URIDINE DIPHOSPHATE; XYLOSE;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; BACTEROIDES FRAGILIS; CONTROLLED STUDY; DECARBOXYLATION; ENZYME ACTIVITY; GENE DELETION; GENE LOCUS; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; PREVALENCE; PRIORITY JOURNAL;

BACTEROIDES FRAGILIS; BLOTTING, WESTERN; CARBOXY-LYASES; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; COMPUTATIONAL BIOLOGY; ELECTROPHORESIS, POLYACRYLAMIDE GEL; GENOME, BACTERIAL; POLYSACCHARIDES, BACTERIAL; XYLOSE;

BACTERIA (MICROORGANISMS); BACTEROIDES; BACTEROIDES FRAGILIS; BACTEROIDES FRAGILIS NCTC 9343; PROTEOBACTERIA;

EID: 80053614489     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.05337-11     Document Type: Article

References (44)

1. Adamczak, R., A. Porollo, and J. Meller. 2005. Combining prediction of secondary structure and solvent accessibility in proteins. Proteins 59:467-475.
2. Allard, S. T., et al. 2002. Toward a structural understanding of the dehydratase mechanism. Structure 10:81-92.
3. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
4. Altschul, S. F., et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
5. Ankel, H., and D. S. Feingold. 1966. Biosynthesis of UDP D-xylose. II. UDP D-glucuronate carboxy-lyase of Cryptococcus laurentii. Biochemistry 5:182- 189.
6. Bar-Peled, M., C. L. Griffith, and T. L. Doering. 2001. Functional cloning and characterization of a UDP-glucuronic acid decarboxylase: the pathogenic fungus Cryptococcus neoformans elucidates UDP-xylose synthesis. Proc. Natl. Acad. Sci. U. S. A. 98:12003-12008.
7. Breazeale, S. D., A. A. Ribeiro, and C. R. Raetz. 2002. Oxidative decarboxylation of UDP-glucuronic acid in extracts of polymyxin-resistant Escherichia coli. Origin of lipid A species modified with 4-amino-4-deoxy-L-arabinose. J. Biol. Chem. 277:2886-2896.
8. Burget, E. G., R. Verma, M. Molhoj, and W. D. Reiter. 2003. The biosynthesis of L-arabinose in plants: molecular cloning and characterization of a Golgi-localized UDP-D-xylose 4-epimerase encoded by the MUR4 gene of Arabidopsis. Plant Cell 15:523-531.
9. Burrows, L. L., D. F. Charter, and J. S. Lam. 1996. Molecular characterization of the Pseudomonas aeruginosa serotype O5 (PAO1) B-band lipopolysaccharide gene cluster. Mol. Microbiol. 22:481-495.
10. Bystrova, O. V., et al. 2006. Structures of the core oligosaccharide and O-units in the R- and SR-type lipopolysaccharides of reference strains of Pseudomonas aeruginosa O-serogroups. FEMS Immunol. Med. Microbiol. 46:85-99.
11. Chatzidaki-Livanis, M., M. J. Coyne, H. Roche-Hakansson, and L. E. Comstock. 2008. Expression of a uniquely regulated extracellular polysaccharide confers a large-capsule phenotype to Bacteroides fragilis. J. Bacteriol. 190: 1020-1026.
12. Coyne, M. J., M. Chatzidaki-Livanis, L. C. Paoletti, and L. E. Comstock. 2008. Role of glycan synthesis in colonization of the mammalian gut by the bacterial symbiont Bacteroides fragilis. Proc. Natl. Acad. Sci. U. S. A. 105: 13099-13104.
13. Coyne, M. J., B. Reinap, M. M. Lee, and L. E. Comstock. 2005. Human symbionts use a host-like pathway for surface fucosylation. Science 307: 1778-1781.
14. Filling, C., et al. 2002. Critical residues for structure and catalysis in shortchain dehydrogenases/reductases. J. Biol. Chem. 277:25677-25684.
15. Fletcher, C. M., M. J. Coyne, D. L. Bentley, O. F. Villa, and L. E. Comstock. 2007. Phase-variable expression of a family of glycoproteins imparts a dynamic surface to a symbiont in its human intestinal ecosystem. Proc. Natl. Acad. Sci. U. S. A. 104:2413-2418.
16. Fletcher, C. M., M. J. Coyne, and L. E. Comstock. 2011. Theoretical and experimental characterization of the scope of protein O-glycosylation in Bacteroides fragilis. J. Biol. Chem. 286:3219-3226.
17. Fletcher, C. M., M. J. Coyne, O. F. Villa, M. Chatzidaki-Livanis, and L. E. Comstock. 2009. A general O-glycosylation system important to the physiology of a major human intestinal symbiont. Cell 137:321-331.
18. Gatzeva-Topalova, P. Z., A. P. May, and M. C. Sousa. 2004. Crystal structure of Escherichia coli ArnA (PmrI) decarboxylase domain. A key enzyme for lipid A modification with 4-amino-4-deoxy-L-arabinose and polymyxin resistance. Biochemistry 43:13370-13379.
19. Gu, X., et al. 2010. Identification of a bifunctional UDP-4-keto-pentose/UDP-xylose synthase in the plant pathogenic bacterium Ralstonia solanacearum strain GMI1000, a distinct member of the 4,6-dehydratase and decarboxylase family. J. Biol. Chem. 285:9030-9040.
20. Gu, X., S. G. Lee, and M. Bar-Peled. 2011. Biosynthesis of UDP-xylose and UDP-arabinose in Sinorhizobium meliloti 1021: first characterization of a bacterial UDP-xylose synthase, and UDP-xylose 4-epimerase. Microbiology 157:260-269.
21. Guyett, P., J. Glushka, X. Gu, and M. Bar-Peled. 2009. Real-time NMR monitoring of intermediates and labile products of the bifunctional enzyme UDP-apiose/UDP-xylose synthase. Carbohydr. Res. 344:1072-1078.
22. Harper, A. D., and M. Bar-Peled. 2002. Biosynthesis of UDP-xylose. Cloning and characterization of a novel Arabidopsis gene family, UXS, encoding soluble and putative membrane-bound UDP-glucuronic acid decarboxylase isoforms. Plant Physiol. 130:2188-2198.
23. Isogai, E., H. Isogai, Y. Kurebayashi, and N. Ito. 1986. Biological activities of leptospiral lipopolysaccharide. Zentralbl. Bakteriol. Mikrobiol. Hyg. A 261:53-64.
24. Kavanagh, K. L., H. Jornvall, B. Persson, and U. Oppermann. 2008. The SDR superfamily: functional and structural diversity within a family of metabolic and regulatory enzymes. Cell. Mol. Life Sci. 65:3895-3906.
25. Knirel, Y. A. 1990. Polysaccharide antigens of Pseudomonas aeruginosa. Crit. Rev. Microbiol. 17:273-304.
26. Kornfeld, R., and S. Kornfeld. 1976. Comparative aspects of glycoprotein structure. Annu. Rev. Biochem. 45:217-237.
27. Krinos, C. M., et al. 2001. Extensive surface diversity of a commensal microorganism by multiple DNA inversions. Nature 414:555-558.
28. Larkin, M. A., et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948.
29. Lesk, A. M. 1995. NAD-binding domains of dehydrogenases. Curr. Opin. Struct. Biol. 5:775-783.
30. Mazmanian, S. K., J. L. Round, and D. L. Kasper. 2008. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 453:620- 625.
31. Moriarity, J. L., et al. 2002. UDP-glucuronate decarboxylase, a key enzyme in proteoglycan synthesis: cloning, characterization, and localization. J. Biol. Chem. 277:16968-16975.
32. Pantosti, A., A. O. Tzianabos, A. B. Onderdonk, and D. L. Kasper. 1991. Immunochemical characterization of two surface polysaccharides of Bacteroides fragilis. Infect. Immun. 59:2075-2082.
33. Reiss, E., M. Huppert, and R. Cherniak. 1985. Characterization of protein and mannan polysaccharide antigens of yeasts, moulds, and actinomycetes. Curr. Top. Med. Mycol. 1:172-207.
34. Rose, P. W., et al. 2011. The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res. 39:D392-D401.
35. Shimizu, T., et al. 1987. Chemical properties of lipopolysaccharide-like substance (LLS) extracted from Leptospira interrogans serovar canicola strain Moulton. Microbiol. Immunol. 31:717-725.
36. Sonnenburg, J. L., et al. 2005. Glycan foraging in vivo by an intestineadapted bacterial symbiont. Science 307:1955-1959.
37. Studier, F. W., and B. A. Moffatt. 1986. Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J. Mol. Biol. 189:113-130.
38. Thoden, J. B., J. M. Henderson, J. L. Fridovich-Keil, and H. M. Holden. 2002. Structural analysis of the Y299C mutant of Escherichia coli UDPgalactose 4-epimerase. Teaching an old dog new tricks. J. Biol. Chem. 277: 27528-27534.
39. Thompson, J. S., and M. H. Malamy. 1990. Sequencing the gene for an imipenem-cefoxitin-hydrolyzing enzyme (CfiA) from Bacteroides fragilis TAL2480 reveals strong similarity between CfiA and Bacillus cereus betalactamase II. J. Bacteriol. 172:2584-2593.
40. Tzianabos, A. O., A. B. Onderdonk, B. Rosner, R. L. Cisneros, and D. L. Kasper. 1993. Structural features of polysaccharides that induce intraabdominal abscesses. Science 262:416-419.
41. Williams, G. J., S. D. Breazeale, C. R. Raetz, and J. H. Naismith. 2005. Structure and function of both domains of ArnA, a dual function decarboxylase and a formyltransferase, involved in 4-amino-4-deoxy-L-arabinose biosynthesis. J. Biol. Chem. 280:23000--23008.
42. Xu, J., et al. 2003. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science 299:2074-2076.
43. York, W. S., and M. A. O'Neill. 2008. Biochemical control of xylan biosynthesis- which end is up? Curr. Opin. Plant Biol. 11:258-265.
44. Zitomersky, N., M. J. Coyne, and L. E. Comstock. 2011. Longitudinal analysis of the prevalence, maintenance, and IgA response to species of the order Bacteroidales in the human gut. Infect. Immun. 79:2012-2020.