Use of bioinformatics to predict a function for the GS element in Mycobacterium avium subspecies paratuberculosis

Journal of Molecular Microbiology and Biotechnology

Volumn 5, Issue 1, 2003, Pages 57-66

  Sheridan, Joe M ^a,b   Bull, Tim J ^a   Hermon Taylor, John ^a  

^a ST GEORGE'S UNIVERSITY OF LONDON   (United Kingdom)

^b Proteom Ltd   (United Kingdom)

Author keywords

Crohn's disease; Glycopeptidolipid; GS; Mycobacterium; Paratuberculosis; Virulence

Indexed keywords

ARTICLE; BACTERIAL CELL WALL; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BIOINFORMATICS; COMPUTER PREDICTION; DRUG TARGETING; ENZYME SYNTHESIS; IMMUNOMODULATION; MYCOBACTERIUM AVIUM; MYCOBACTERIUM PARATUBERCULOSIS; NUCLEOTIDE SEQUENCE; PROTEIN MODIFICATION; PROTEIN MOTIF; PROTEIN SYNTHESIS; STRUCTURAL HOMOLOGY; AMINO ACID SEQUENCE; ANIMAL; BIOLOGY; CROHN DISEASE; DNA SEQUENCE; ENZYMOLOGY; GENETICS; HUMAN; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; PARATUBERCULOSIS; PATHOGENICITY; PATHOPHYSIOLOGY; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; TRANSPOSON; VIRULENCE;

MYCOBACTERIUM; MYCOBACTERIUM AVIUM; MYCOBACTERIUM AVIUM COMPLEX; MYCOBACTERIUM AVIUM COMPLEX (MAC); MYCOBACTERIUM AVIUM SUBSP. AVIUM; MYCOBACTERIUM AVIUM SUBSP. PARATUBERCULOSIS;

BACTERIAL PROTEIN; GLYCOLIPID; PEPTIDE;

AMINO ACID SEQUENCE; ANIMALS; BACTERIAL PROTEINS; COMPUTATIONAL BIOLOGY; CROHN DISEASE; DNA TRANSPOSABLE ELEMENTS; GLYCOLIPIDS; HUMANS; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM PARATUBERCULOSIS; PARATUBERCULOSIS; PEPTIDES; POLYMERASE CHAIN REACTION; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; VIRULENCE;

EID: 0037636356     PISSN: 14641801     EISSN: None     Source Type: Journal    
DOI: 10.1159/000068723     Document Type: Article

References (49)

1. Allison, G.E. and Verma, N.K. 2000. Serotype-converting bacteriophages and O-antigen modification in Shigella flexneri. Trends Microbiol. 8: 17-23.
2. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang Z., Miller, W. and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
3. Andrianopoulos, K., Wang, L. and Reeves, P.R. 1998. Identification of the fucose synthetase gene in the colanic acid gene cluster of Escherichia coli K-12. J. Bacteriol. 180:998-1001.
4. Aspinall, G.O., Chatterjee, D. and Brennan, P.J. 1995. The variable surface glycolipids of mycobacteria: structures, synthesis of epitopes, and biological properties. Adv. Carbohydr. Chem. Biochem. 51:169-242.
5. Belisle, J.T., Klaczkiewicz, K., Brennan, P.J., Jacobs, W.R. and Inamine, J.M. 1993. Rough morphological variants of Mycobacterium avium. Characterization of genomic deletions resulting in the loss of glycopeptidolipid expression. J. Biol. Chem. 268:10517-10523.
6. Berck, S., Perret, X., Quesada-Vincens, D., Prome, J., Broughton, W.J. and Jabbouri, S. 1999. NolL of Rhizobium sp. strain NGR234 is required for O-acetyltransferase activity. J Bacteriol. 181:957-964.
7. Breton, C., Oriol, R. and Imberty, A. 1998. Conserved structural features in eukaryotic and prokaryotic fucosyltransferases. Glycobiology 8:87-94.
8. Brownback, P.E. and Barrow, W.W. 1988. Modified lymphocyte response to mitogens after intraperitoneal injection of glycopeptidolipid antigens from Mycobacterium avium complex. Infect Immun. 56:1044-1050.
9. Bujnicki, J.M., Elofsson, A., Fischer, D., Rychlewski, L. 2001. Structure prediction meta server. Bioinformatics 17:750-751.
10. Bull, T., Sheridan, J.M., Martin, H., Sumar, N., Tizard, M. and Hermon-Taylor, J. 2000. Further studies on the GS Element: A novel mycobacterial insertion sequence (IS1612), inserted into an acetylase gene (mpa) in Mycobacterium avium subsp. silvaticum but not in Mycobacterium avium subsp. paratuberculosis. Vet Microbiol. 77:453-63.
11. Campbell, J.A., Davies, G.J., Bulone, V. and Henrissat, B. 1997. A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Biochem. J. 326:929-942.
12. Charnock, S.J. and Davies, G.J. 1999. Structure of the nucleotide-diphospho-sugar transferase, SpsA from Bacillus subtilis, in native and nucleotide-complexed forms. Biochemistry 38:6380-6385.
13. Cheng, X. and Roberts, R.J. 2001. AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res. 29:3784-3795.
14. Cole, S.T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S.V., Eiglmeier, K., Gas, S., Barry, C.E. 3rd, Tekaia, F., Badcock, K., Basham, D., Brown, D., Chillingworth, T., Connor, R., Davies, R., Devlin, K., Feltwell, T., Gentles, S., Hamlin, N., Holroyd, S., Hornsby, T., Jagels, K., Barrell, B.G., et al. 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537-544.
15. Corvera, A., Prome, D., Prome, J.C., Martinez-Romero, E. and Romero, D. 1999. ThenolL gene from Rhizobium etli determines nodulation efficiency by mediating the acetylation of the fucosyl residue in the nodulation factor. Mol. Plant-Microbe Interact. 12:236-246.
16. DeShazer, D., Brett, P.J. and Woods, D.E. 1998. The type II O-antigenic polysaccharide moiety of Burkholderia pseudomallei lipopolysaccharide is required for serum resistance and virulence. Mol. Microbiol. 30:1081-1100.
17. Eckstein, T.M., Silbaq, F.S., Chatterjee, D., Kelly, N.J., Brennan, P.J. and Belisle, J.T. 1998. Identification and recombinant expression of a Mycobacterium avium Rhamnosyl-transferase gene (rtfA) involved in glycopeptidolipid biosynthesis. J. Bacteriol. 180:5567-5573.
18. Ellingson, J.L., Bolin, C.A. and Stabel, J.R. 1998. Identification of a gene unique to Mycobacterium avium subspecies paratuberculosis and application to diagnosis of paratuberculosis. Mol. Cell. Probes 12:133-142.
19. Green, E.P., Tizard, M.L.V, Moss, M.T., Thompson, J., Winterbourne, D.J., McFadden, J.J. and Hermon-Taylor, J. 1989. Sequence and characteristics of IS900, an insertion element identified in a human Crohn's disease isolate of Mycobacterium paratuberculosis. Nucleic Acids Res. 17:9063-9073.
20. Guex, N. and Peitsch, M.C. 1997. SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modelling. Electrophoresis 18:2714-2723.
21. Gunawardena, S., Fiore, C.R., Johnson, J.A. and Bush, C.A. 1999. Conformation of a rigid tetrasaccharide epitope in the capsular polysaccharide of Vibrio cholerae O139. Biochemistry 38:12062-12071.
22. Hacker, J., Blum-Oehler, G., Mühldorfer, I. and Tschäpe, H. 1997. Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol. Microbiol. 23:1089-1097.
23. Hermon-Taylor, J., Bull, T.J., Sheridan, J.M., Cheng, J., Stellakis, M.L. and Sumar, N. 2000. Causation of Crohn's Disease by Mycobacterium avium subsp. Paratuberculosis. Can. J. Gastroenterol. 14:521-539.
24. Hines, I.I., Jaynes, M.E., Barker, J. M., Newton, S. A., Enright, J. C. F. M. and Snider, T. G. III 1993. Isolation and partial characterization of glycolipid fractions from Mycobacterium avium serovar 2 (Mycobacterium paratuberculosis 18) that inhibit activated macrophages. Infect. Immun. 61:1-7.
25. Hofmann, K., Bucher, P., Falquet, L. and Bairoch, A. 1999. The PROSITE database, its status in 1999. Nucleic Acids Res. 27:215-219.
26. Horgen, L., Barrow, E.L., Barrow, W.W. and Rastogi, N. 2000. Exposure of human peripheral blood mononuclear cells to total lipids and serovar-specific glycopeptidolipids from Mycobacterium avium serovars 4 and 8 results in inhibition of TH1-type responses. Microb. Pathog. 29:9-16.
27. Jabbouri, S., Relic, B., Hanin, M., Kamalaprija, P., Burger, U., Prome, D., Prome, J.C. and Broughton, W.J. 1998. nolO and noeI (HsnIII) of Rhizobium sp. NGR234 are involved in 3-O-carbamoylation and 2-O-methylation of Nod factors. J. Biol. Chem. 273:12047-12055.
28. Jones, D.T., Taylor, W.R. and Thornton, J.M. 1994. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry 33:3038-3048.
29. Kelley, L.A., MacCallum, R.M. and Sternberg, M.J. 2000. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299:499-520.
30. McNeil, M., Chatterjee, D., Hunter, S.W. and Brennan, P.J. 1989. Mycobacterial glycolipids: Isolation, structures, antigenicity, and synthesis of neoantigens. Methods Enzymol. 179:215-242.
31. Mills, J.A., McNeil, M.R., Belisle, J.T., Jacobs, W.R. and Brennan, P.J. 1994. Loci of Mycobactrium avium ser2 gene cluster and their functions. J. Bacteriol. 176:4803-4808.
32. Nakai, K. and Kanehisa, M. 1991. Expert system for predicting protein localization sites in gram-negative bacteria. Proteins 11:95-110.
33. Nielsen, H., Engelbrecht, J., Brunak, S. and von Heijne, G. 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10:1-6.
34. Oriol, R., Mollicone, R., Cailleau, A., Balanzino, L. and Breton, C. 1999. Divergent evolution of fucosyltransferase genes from vertebrates, invertebrates, and bacteria. Glycobiology 9:323-334.
35. Pedrosa, J., Florido, M., Kunze, Z.M., Castro, A.G., Portaels, F., McFadden, J., Silva, M.T. and Appelberg, R. 1994. Characterization of the virulence of Mycobacterium avium complex (MAC) isolates in mice. Clin. Exp. Immunol. 98:210-216.
36. Pourshafie, M.R., Sonnenfeld, G. and Barrow, W.W. 1999. Immunological and ultrastructural disruptions of T lymphocytes following exposure to the glycopeptidolipid isolated from the Mycobacterium avium complex. Scand. J. Immunol. 49:405-410.
37. Rizzi, M., Tonetti, M., Vigevani, P., Sturla, L., Bisso, A., Flora, A.D., Bordo, D. and Bolognesi, M. 1998. GDP-4-keto-6-deoxy-D-mannose epimerase/reductase from Escherichia coli, a key enzyme in the biosynthesis of GDP-L-fucose, displays the structural characteristics of the RED protein homology superfamily. Structure 6:1453-1465.
38. Rodriguez, R., Chinea, G., Lopez, N., Pons, T. and Vriend, G. 1998. Homology modelling, model and software evaluation: three related resources. Bioinformatics 14:523-528.
39. Skurnik, M., Peippo, A. and Ervelä, E. 2000. Characterization of the O-antigen gene clusters of Yersinia pseudotuberculosis and the cryptic O-antigen gene cluster of Y. pestis shows that the plague bacillus is most closely related to and has evolved from Y. pseudotuberculosis serotype O:1b. Mol. Microbiol. 37:316-330.
40. Slauch, J.M., Lee, A.A., Mahan, M.J. and Mekalanos, J.J. 1996. Molecular characterization of the oafA locus responsible for acetylation of Salmonella typhimurium O-antigen: oafA is a member of a family of integral membrane trans-acylases. J. Bacteriol. 178:5904-5909.
41. Somoza, J.R., Menon, S., Schmidt, H., Joseph-McCarthy, D., Dessen, A., Stahl, M.L., Somers, W.S. and Sullivan, F.X. 2000. Structural and kinetic analysis of Escherichia coli GDP-mannose 4,6 dehydratase provides insights into the enzyme's catalytic mechanism and regulation by GDP-fucose. Structure Fold Des. 8:123-135.
42. Sonnhammer, E.L.L., von Heijne, G. and Krogh, A. 1998. A hidden Markov model for predicting transmembrane helices in protein sequences. In: Proc. of Sixth Int. Conf. on Intelligent Systems for Molecular Biology. J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff and C. Sensen, eds. AAAI Press, Menlo Park, pp. 175-182.
43. Stroeher, U.H., Karageorgos, L.E., Morona, R. and Manning, P.A. 1992. Serotype conversion in Vibrio cholerae O1. Proc. Natl. Acad. Sci. USA. 89:2566-2570.
44. Strohmeier, G.R. and Fenton, M.J. 1999. Roles of lipoarabinomannan in the pathogenesis of tuberculosis. Microbes Infect. 1:709-717.
45. Sturla, L., Bisso, A., Zanardi, D., Benatti, U., De Flora, A. and Tonetti, M. 1997. Expression, purification and characterization of GDP-D-mannose 4,6-dehydratase from Escherichia coli. FEBS Lett. 412:126-130.
46. Thorel, M.-F., Krichevsky, M. and Levy-Frebault, V.V. 1990. Numerical taxonomy of mycobactin-dependent mycobacteria, amended description of Mycobacterium avium, and description of Mycobacterium avium subsp. avium subsp. nov., Mycobacterium avium subsp. paratuberculosis subsp. nov., and Mycobacterium avium subsp. silvaticum subsp. nov. Int. J. Syst. Bacteriol. 40:254-260.
47. Tizard, M., Bull, T., Millar, D., Doran, T., Martin, H., Sumar, N., Ford, J. and Hermon-Taylor, J. 1998. A low G+C content genetic island in Mycobacterium avium subsp. paratuberculosis and M. avium subsp. silvaticum with homologous genes in Mycobacterium tuberculosis. Microbiology 144:3413-3423.
48. Tusnády, G.E. and Simon, I. 1998. Principles Governing Amino Acid Composition of Integral Membrane Proteins: Applications to Topology Prediction. J. Mol. Biol. 283:489-506.
49. Wang, L., Curd, H., Qu, W. and Reeves P.R. 1998. Sequencing of Escherichia coli O111 O-antigen gene cluster and identification of O111-specific genes. J. Clin. Microbiol. 36:3182-3187.