Computer-based analyses of the protein constituents of transport systems catalysing export of complex carbohydrates in bacteria

Microbiology

Volumn 143, Issue 8, 1997, Pages 2685-2699

  Paulsen, Ian T ^a   Beness, Alison M ^a   Saier Jr , Milton H ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Capsular polysaccharides; Exopolysaccharides; Lipo oligosaccharides; Lipopolysaccharides; Teichoic acids; Transport

Indexed keywords

ABC TRANSPORTER; BACTERIAL POLYSACCHARIDE; CARBOHYDRATE; LIPOPOLYSACCHARIDE; MEMBRANE PROTEIN; POLYSACCHARIDE; TEICHOIC ACID;

ARTICLE; BACTERIAL MEMBRANE; BACTERIUM; CARBOHYDRATE SYNTHESIS; CARBOHYDRATE TRANSPORT; CARBOXY TERMINAL SEQUENCE; COMPUTER ANALYSIS; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; HYDROPHOBICITY; MEMBRANE TRANSPORT; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; PROTEIN FAMILY;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; POSIBACTERIA;

EID: 0030843523     PISSN: 13500872     EISSN: None     Source Type: Journal    
DOI: 10.1099/00221287-143-8-2685     Document Type: Article

References (76)

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). Basic local alignment search tool. J Mol Biol 215, 403-410.
2. Bailey, T. L. & Elkan, C. (1994). Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36. Menlo Park, CA: AAAI Press.
3. Bairoch, A. (1992). PROSITE: a dictionary of sites and patterns in proteins. Nucleic Acids Res 20, 2013-2018.
4. Bartlett, D. H., Wright, M. E. & Silverman, M. (1988). Variable expression of extracellular polysaccharide in the marine bacterium Pseudomonas atlantica is controlled by genome rearrangement. Proc Natl Acad Sci USA 85, 3923-3927.
5. Bayer, M. E. (1968). Areas of adhesion between wall and membrane of Escherichia coli. J Gen Microbiol 53, 395-404.
6. Berger, E. A. & Heppel, L. A. (1974). Different mechanisms of energy coupling for the shock-sensitive and shock-resistant amino acid permeases of Escherichia coli. J Biol Chem 249, 7747-7755.
7. Betlach, M. R., Capage, M. A., Doherty, D. H., Hassler, R. A., Henderson, N. M., van der Slice, R. W., Marrelli, J. D. & Ward, M. B. (1987). Genetically engineered polymers: manipulation of xanthan biosynthesis. In Industrial Polysaccharides: Genetic Engineering, Structure/Property Relations and Applications, pp. 35-50. Edited by M. Yalpani. Amsterdam: Elsevier Science Publishers.
8. Bik, E. M., Bunschoten, A. E., Gouw, R. D. & Mooi, F. R. (1995). Genesis of the novel epidemic Vibrio cholerae O139 strain: evidence for horizontal transfer of genes involved in polysaccharide synthesis. EMBO J 14, 209-216.
9. Boulnois, G. J. & Jann, K. (1989). Bacterial polysaccharide capsule synthesis, export and evolution of structural diversity. Mol Microbiol 3, 1819-1823.
10. Boulnois, G. J. & Roberts, I. S. (1990). Genetics of capsular polysaccharide production in bacteria. Curr Top Microbiol Immunol 150, 1-20.
11. Bronner, D., Sieberth, V., Pazzani, C., Roberts, I. S., Boulnois, G. J., Jann, B. & Jann, K. (1993a). Expression of the capsular K5 polysaccharide of Escherichia coli: biochemical and electron microscopic analyses of mutants with defects in region 1 of the K5 gene cluster. J Bacteriol 175, 5984-5992.
12. Bronner, D., Sieberth, V., Pazzani, C., Smith, A., Boulnois, G., Roberts, I., Jann, B. & Jann, K. (1993b). Synthesis of the K5 (group II) capsular polysaccharide in transport-deficient recombinant Escherichia coli. FEMS Microbiol Lett 113, 279-284.
13. Bugert, P. & Geider, K. (1995). Molecular analysis of the ams operon required for exopolysaccharide synthesis of Erwinia amylovora. Mol Microbiol 15, 917-933.
14. Capage, M. A., Doherty, D. H., Betlach, M. R. & van der Slice, R. (1987). Recombinant-DNA mediated production of xanthan gum. Patent International Publication No. WO87/05938.
15. Chou, P. Y. & Fasman, G. D. (1978). Empirical prediction of protein conformation. Annu Rev Biochem 47, 251-276.
16. Dayhoff, M. O., Barker, W. C. & Hunt, L. T. (1983). Establishing homologies in protein sequences. Methods Enzymol 91, 524-545.
17. Devereux, J., Haeberli, P. & Smithies, O. (1984). A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12, 387-395.
18. Dey, S. & Rosen, B. P. (1995). Dual mode of energy coupling by the oxyanion-translocating ArsB protein. J Bacteriol 177, 385-389.
19. Dinh, T., Paulsen, I. T. & Saier, M. H., Jr (1994). A family of extracytoplasmic proteins that allow transport of large molecules across the outer membranes of Gram-negative bacteria. J Bacteriol 176, 3825-3831.
20. Dong, Q. & Mergeay, M. (1994). Czc/Cnr efflux: a three-component chemiosmotic antiport pathway with a 12-transmembrane-helix protein. Mol Microbiol 14, 185-187.
21. Dorman, C. J. (1995). DNA topology and the global control of bacterial gene expression: implications for the regulation of virulence gene expression. Microbiology 141, 1271-1280.
22. Dybvig, K. (1993). DNA rearrangements and phenotypic switching in prokaryotes. Mol Microbiol 10, 465-471.
23. Fath, M. J. & Kolter, R. (1993). ABC transporters: bacterial exporters. Microbiol Rev 57, 995-1017.
24. Feng, D.-F. & Doolittle, R. F. (1990). Progressive alignment and phylogenetic tree construction of protein sequences. Methods Enzymol 183, 375-387.
25. Frosch, M., Weisgerber, C. & Meyer, T. F. (1989). Molecular characterization and expression in Escherichia coli of the gene complex encoding the polysaccharide capsule of Neisseria meningitidis group B. Proc Natl Acad Sci USA 86, 1669-1673.
26. Frosch, M., Edwards, U., Bousset, K., Krauße, B. & Weisgerber, C. (1991). Evidence for a common molecular origin of the capsule gene loci in Gram-negative bacteria expressing group II capsular polysaccharides. Mol Microbiol 5, 1251-1263.
27. Frosch, M., Müller, D., Bousset, K. & Müller, A. (1992). Conserved outer membrane protein of Neisseria meningitidis involved in capsule expression. Infect Immun 60, 798-803.
28. Gamier, J., Osguthorpe, D. J. & Robson, B. (1978). Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. J Mol Biol 120, 97-120.
29. Glucksmann, M. A., Reuber, T. L. & Walker, G. C. (1993). Genes needed for the modification, polymerization, export, and processing of succinoglycan by Rhizobium meliloti: a model for succinoglycan biosynthesis. J Bacteriol 175, 7045-7055.
30. Guidolin, A., Morona, J. K., Morona, R., Hansman, D. & Paton, J. C. (1994). Nucleotide sequence analysis of genes essential for capsular polysaccharide biosynthesis in Streptococcus pneumoniae Type 19F. Infect Immun 62, 5384-5396.
31. Hashimoto, Y., Li, N., Yokoyama, H. & Ezaki, T. (1993). Complete nucleotide sequence and molecular characterization of ViaB region encoding Vi antigen in Salmonella typhi. J Bacteriol 175, 4456-4465.
32. von Heijne, G. (1992). Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J Mol Biol 225, 487-194.
33. Higgins, C. F. (1992). ABC transporters: from microorganisms to man. Annu Rev Cell Biol 8, 67-113.
34. Hoischen, C., Pitaknarongphorn, S., Reizer, J., Levin, J., Tomich, J. M. & Saier, M. H., Jr (1996). Involvement of the central loop of the lactose permease of Escherichia coli in its allosteric regulation by the glucose-specific Enzyme IIA of the phosphoenolpyruvate-dependent phosphotransferase system. J Bacteriol 178, 6082-6086.
35. Hornick, R. B., Greisman, S. E., Woodward, T. E., DuPont, H. L., Dawkins, A. T. & Snyder, M. J. (1970). Typhoid fever: pathogenesis and immunologic control. N Engl J Med 283, 739-746.
36. Huang, J. & Schell, M. (1995). Molecular characterization of the eps gene cluster of Pseudomonas solanacearum and its transcriptional regulation at a single promoter. Mol Microbiol 16, 977-989.
37. Jann, B. & Jann, K. (1990). Structure and biosynthesis of the capsular antigens of Escherichia coli. Curr Top Microbiol Immunol 150, 19-42.
38. Jann, K. & Jann, B. (1984). Structure and biosynthesis of O-antigens. In Handbook of Endotoxin, Vol. 1. Chemistry of Endotoxin, pp. 138-186. Edited by E. T. Rietsche. Amsterdam: Elsevier Science Publishers.
39. Jann, K., Pillat, M., Weisgerber, C., Shibaev, V. N. & Torgov, V. I. (1985). Biosynthesis of the O9 antigen of Escherichia coli. Synthetic glycosyldiphosphomoraprenols as probes for requirement of mannose acceptors. Eur J Biochem 151, 393-397.
40. Kido, N., Torgov, V. I., Sugiyama, T., Uchiya, K., Sugihara, H., Komatsu, T., Kato, N. & Jann, K. (1995). Expression of the O9 polysaccharide of Escherichia coli: sequencing of the E. coli O9 rfb gene cluster, characterization of mannosyl transferases, and evidence for an ATP-binding cassette transport system. J Bacteriol 177, 2178-2187.
41. Klena, J. D. & Schnaitman, C. A. (1993). Function of the rfb gene cluster and the rfe gene in the synthesis of O antigen by Shigella dysenteriae 1. Mol Microbiol 9, 393-402.
42. Kroll, J. S., Loynds, B., Brophy, L. M. & Moxon, E. R. (1990). The bex locus in encapsulated Haemophilus influenzae: a chromosomal region involved in capsule polysaccharide export. Mol Microbiol 4, 1853-1862.
43. Kröncke, K.-D., Boulnois, G., Roberts, I., Bitter-Suermann, D., Golecki, J. R., Jann, B. & Jann, K. (1990). Expression of the Escherichia coli K5 capsular antigen: immunoelectron microscopic and biochemical studies with recombinant E. coli. J Bacteriol 172, 1085-1091.
44. Kuan, G., Dassa, E., Saurin, W., Hofnung, M. & Saier, M. H., Jr (1995). Phylogenetic analyses of the ATP-binding constituents of bacterial extracytoplasmic receptor-dependent ABC-type nutrient uptake permeases. Res Microbiol 146, 271-278.
45. Kyte, J. & Doolittle, R. F. (1982). A simple method for displaying the hydropathic character of a protein. J Mol Biol 157, 105-132.
46. Lazarevic, V. & Karamata, D. (1995). The tagGH operon of Bacillus subtilis 168 encodes a two-component ABC transporter involved in the metabolism of two wall teichoic acids. Mol Microbiol 16, 345-355.
47. Lin, W. S., Cunneen, T. & Lee, C. Y. (1994). Sequence analysis and molecular characterization of genes required for the biosynthesis of type 1 capsular polysaccharide in Staphylococcus aureus. J Bacteriol 176, 7005-7016.
48. Liu, D., Cole, R. A. & Reeves, P. R. (1996). An O-antigen function for Wzx (RfbX): a promising candidate for O-unit flippase. J Bacteriol 178, 2102-2107.
49. Long, S., Reed, J. W., Himawan, J. & Walker, G. C. (1988). Genetic analysis of a cluster of genes required for synthesis of the calcofluor-binding exopolysaccharide of Rhizobium meliloti. J Bacteriol 170, 4239-1248.
50. McGrath, B. C. & Osborn, M. J. (1991). Evidence for energy-dependent transposition of core lipopolysaccharide across the inner membrane of Salmonella typhimurium. J Bacteriol 173, 3134-3137.
51. Macpherson, D. F., Manning, P. A. & Morona, R. (1995). Genetic analysis of the rfbX gene of Shigella flexneri. Gene 155, 9-17.
52. Manning, P. A., Stroeher, U. H., Karageorgos, L. E. & Morona, R. (1995). Putative O-antigen transport genes within the rfb region of Vibrio cholerae O1 are homologous to those for capsule transport. Gene 158, 1-7.
53. Morona, R., Macpherson, D. F., van den Bosch, L., Carlin, N. I. A. & Manning, P. A. (1995). Lipopolysaccharide with an altered O-antigen produced in Escherichia coli K-12 harbouring mutated, cloned Shigella flexneri rfb genes. Mol Microbiol 18, 209-223.
54. Mulford, C. A. & Osborn, M. J. (1983). An intermediate step in translocation of lipopolysaccharide to the outer membrane of Salmonella typhimurium. Proc Natl Acad Sci USA 80, 1159-1163.
55. Pavelka, M. S., Jr, Wright, L. F. & Silver, R. P. (1991). Identification of two genes, kpsM and kpsT, in region 3 of the polysialic acid gene cluster of Escherichia coli K12. J Bacteriol 173, 4603-1610.
56. Pearce, R. & Roberts, I. S. (1995). Cloning and analysis of gene clusters for production of the Escherichia coli K10 and K54 antigens: identification of a new group of serA-linked capsule gene clusters. J Bacteriol 177, 3992-3997.
57. Pearson, W. R. & Lipman, D. J. (1988). Improved tools for biological sequence comparison. Proc Natl Acad Sci USA 85, 2444-2448.
58. Reeves, P. R. (1992). Variation in O-antigens, niche-specific selection and bacterial populations. FEMS Microbiol Lett 100, 509-516.
59. Reeves, P. (1993). Evolution of Salmonella O antigen variation by interspecific gene transfer on a large scale. Trends Genet 9, 17-22.
60. Reizer, J., Reizer, A. & Saier, M. H., Jr (1992). A new subfamily of bacterial ABC-type transport systems catalyzing export of drugs and carbohydrates. Protein Sci 1, 1326-1332.
61. Reuber, T. L. & Walker, G. C. (1993). Biosynthesis of succinoglycan, a symbiotically important exopolysaccharide of Rhizobium meliloti. Cell 74, 269-280.
62. Reuber, T. L., Long, S. & Walker, G. C. (1991). Regulation of Rhizobium meliloti exo genes in free-living cells and in planta examined by using TnphoA fusions. J Bacteriol 173, 426-434.
63. Robbins, J. D. & Robbins, J. B. (1984). Re-examination of the protective role of the capsular polysaccharide (Vi antigen) of Salmonella typhi. J Infect Dis 150, 436-149.
64. Roberts, I. S. (1995). Bacterial polysaccharides in sickness and in health. Microbiology 141, 2023-2031.
65. Rosenow, C., Esumeh, F., Roberts, I. S. & Jann, K. (1995). Characterization and localization of the KpsE protein of Escherichia coli K5, which is involved in polysaccharide export. J Bacteriol 177, 1137-1143.
66. Saier, M. H., Jr (1994). Computer-aided analyses of transport protein sequences: gleaning evidence concerning function, structure, biogenesis, and evolution. Microbiol Rev 58, 71-93.
67. Saier, M. H., Jr (1996). Phylogenetic approaches to the identification and characterization of protein families and superfamihes. Microb Comp Genomics 1, 129-150.
68. Saier, M. H., Jr & Jacobson, G. R. (1984). The Molecular Basis of Sex and Differentiation: a Comparative Study of Evolution, Mechanism and Control in Microorganisms. New York: Springer.
69. Saier, M. H., Jr, Tam, R., Reizer, A. & Reizer, J. (1994). Two novel families of bacterial membrane proteins concerned with nodulation, cell division and transport. Mol Microbiol 11, 841-847.
70. Schnaitman, C. A. & Klena, J. D. (1993). Genetics of lipopolysaccharide biosynthesis in enteric bacteria. Microbiol Rev 57, 655-682.
71. Seifert, H. S. & So, M. (1988). Genetic mechanisms of bacterial antigenic variation. Microbiol Rev 52, 327-336.
72. Silver, R. P., Aaronson, W. & Vann, W. F. (1987). Translocation of capsular polysaccharides in pathogenic strains of Escherichia coli requires a 60-kilodalton periplasmic protein. J Bacteriol 169, 5489-5495.
73. Smith, A. N., Boulnois, G. J. & Roberts, I. S. (1990). Molecular analysis of the Escherichia coli K5 kps locus: identification and characterization of an inner-membrane capsular polysaccharide transport system. Mol Microbiol 4, 1863-1869.
74. Tam, R. & Saier, M. H., Jr (1993). Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. Microbiol Rev 57, 320-346.
75. Walker, J. E., Saraste, M., Runswick, M. J. & Gay, N. J. (1982). Distantly related sequences in the α- and β-subunits of ATP synthase myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1, 945-951.
76. Wilson, T. H., Yunker, P. L. & Hansen, C. L. (1990). Lactose transport of Escherichia coli resistant to inhibition by the phosphotransferase system. Biochim Biophys Acta 1029, 113-116.