Analysis of the proteome of Mycobacterium tuberculosis in silico

Tubercle and Lung Disease

Volumn 79, Issue 6, 1999, Pages 329-342

  Tekaia, F ^a   Gordon, S V ^a   Garnier, T ^a   Brosch, R ^a   Barrell, B G ^b   Cole, S T ^a  

^a INSTITUT PASTEUR   (France)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CARRIER PROTEIN; GLYCINE; MEMBRANE PROTEIN; POLYPEPTIDE; PROTEIN; PROTEOME; UNCLASSIFIED DRUG;

ARTICLE; FATTY ACID METABOLISM; GENE DUPLICATION; GENE EXPRESSION REGULATION; GENETIC LINKAGE; HOST CELL; LIFESTYLE; LIPID TRANSPORT; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; OPERON; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN SECRETION;

MYCOBACTERIUM TUBERCULOSIS;

EID: 0032708648     PISSN: 09628479     EISSN: None     Source Type: Journal    
DOI: 10.1054/tuld.1999.0220     Document Type: Article

References (52)

1. Goffeau A. Genes in search of functions. Nature (London). 369:1994;101-102.
2. Cole S T, Brosch R, Parkhill J. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature (London). 393:1998;537-544.
3. Cole S T, Barrel B G. Analysis of the genome of Mycobacterium tuberculosis H37Rv. Chadwick D J, Cardew G. Genetics and tuberculosis (Novartis Foundation Symposium 217). 1998;160-172 J Wiley, Chichester.
4. Altschul S, Gish W, Miller W, Myers E, Lipman D. A basic local alignment search tool. J Mol Biol. 215:1990;403-410.
5. Wootton J C. Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput & Chem. 18:1994;269-285.
6. Tekaia F, Dujon B. Pervasiveness of gene conservation and persistence of duplicatges in cullular genomes. J Mol Evol. 49:1999.
7. Greenacre M. Theory and application of correspondence analysis. 1984;Academic Press, London.
8. Benzecri J-P. L'Analyse des Données. 1973;2 Dunod, Paris.
9. Bailey, T, L, Elkan, C, Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, 1994, 28, 36.
10. Bailey T L, Gribskov M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics. 14:1998;48-45.
11. Devereux J, Haeberli P, Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucl Acids Res. 12:1984;387-395.
12. Pearson W, Lipman D. Improved tools for biological sequence comparisons. Proc Natl Acad USA. 85:1988;2444-2448.
13. Nielsen H, Engelbrecht J, Drunak S, von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Prot Eng. 10:1997;1-6.
14. Sonnhammer, E, L L, von Heijne, G, Krogh, A, A hidden Markov model for predicting transmembrane helices in protein sequences. Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology, 1998, 175, 182.
15. Thompson J D, Higgin D G, Gibson T J, Clustal W. Improving the sensitivity of progressive multiple alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680.
16. Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics. 5:1989;164-166.
17. Poulet S, Cole S T. Characterisation of the polymorphic GC-rich repetitive sequence (PGRS) present in Mycobacterium tuberculosis. Arch Microbiol. 163:1995;87-95.
18. Ross B C, Raios K, Jackson K, Dwyer B. Molecular cloning of a highly repeated DNA element from Mycobacterium tuberculosis and its use as an epidemiological tool. J Clin Microbiol. 30:1992;942-946.
19. van Soolingen D, de Haas P E W, Hermans P W M, Groenen P M A, van Embden J D A. Comparison of various repetitive DNA elements as genetic markers for strain differentiation and epidemiology ofMycobacterium tuberculosis. J Clin Microbiol. 31:1993;1987-1995.
20. Grosset J. Bacteriology of tuberculosis. Reichmann L B, Hershfield E S. Tuberculosis: A comprehensive international approach. 1993;49-74 Marcel Dekker.
21. Gordon S V, Heym B, Parkhill J, Barrell B, Cole S T. New insertion sequences and a novel repeated sequence in the genome of Mycobacterium tuberculosis H37Rv. Microbiology. 145:1999;881-892.
22. 70family; Sequence conservation and evolutionary relationships. J Bacteriol. 174:1992;3843-3849.
23. Gomez J E, Chen J-M, Bishai W R. The sigma factors of Mycobacterium tuberculosis. Tubercle Lung Dis. 78:1998;175-183.
24. Barry C E III, Lee R E, Mdluli K, Sampson A E, Schroder B G, Slayden R A, Yuan Y. Mycolic acids: Structure, biosynthesis, and physiological functions. Prog Lipid Res. 37:1998;143-157.
25. Munro A W, Lindsay J G. Bacterial cytochromes P-450. Mol Microbiol. 20:1996;1115-1125.
26. Arand M, Grant D F, Beetham J K, Friedberg T, Hammock B D O F. Sequence similarity of mammalian epoxide hydrolases to the bacterial haloalkane dehalogenase and other related proteins. FEBS Lett. 338:1994;251-256.
27. Hofmann B, Tolzer S, Pelletier I, Altenbuchner J, van P K, Hecht H J. Structural investigation of the cofactor-free chloroperoxidases. J Mol Biol. 279:1998;889-900.
28. Pelletier I, Altenbuchner J, Mattes R. A catalytic triad is required by the non-heme haloperoxidases to perform halogenation. Biochim Biophys Acta. 1250:1995;149-157.
29. Pelletier I, Altenbuchner J. A bacterial esterase is homologous with non-haem haloperoxidases and displays brominating activity. Microbiology. 1995.
30. Saier J M H, Tam R, Reizer A, Reizer J. Two novel families of bacterial membrane proteins concerned with nodulation, cell division and transport. Mol Microbiol. 11:1994;841-847.
31. Paulsen I T, Brown M H, Skurray R A. Proton-dependent multidrug efflux systems. Microbiol Rev. 60:1996;575-608.
32. Kunst F, Ogasawara N, Moszer I. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature (London). 390:1997;249-256.
33. Pao S S, Paulsen I T, Saier M J. Major facilitator superfamily. Microbiology and Molecular Biology Reviews. 62:1998;1-34.
34. Paulsen I T, Sliwinski M K, Saier M J. Microbial genome analyses: global comparisons of transport capabilities based on phylogenies, bioenergetics and substrate specificities. J Mol Biol. 277:1998;573-592.
35. Ainsa J A, Blokpoel M C J, Otal I, Young D B, de Smet K A L, Martin C. Molecular cloning and characterization of Tap, a putative multidrug efflux pump present in Mycobacterium fortuitum and Mycobacterium tuberculosis. J Bacteriol. 180:1998;5836-5843.
36. Kanamaru K, Kashiwagi S, Mizuno T. A copper-transporting P-type ATPase found in the thylakoid membrane of the cyanobacterium Synechococcus species PCC7942. Mol Microbiol. 13:1994;369-377.
37. Arruda S, Bomfim G, Knight R, Huima-Byron T, Riley L W. Cloning of an M. tuberculosis DNA fragment associated with entry and survival inside cells. Science. 261:1993;1454-1457.
38. Elhay M J, Oettinger T, Andersen P. Delayed-type hypersensitivity responses to ESAT-6 and MPT64 from Mycobacterium tuberculosis in the guinea pig. Infect Immun. 66:1998;3454-3456.
39. Lalvani A, Brookes R, Wilkinson R J. Human cytolytic and interferon gamma-secreting CD8+ T lymphocytes specific for Mycobacterium tuberculosis. Proceedings of the National Academy of Sciences of the United States of America. 95:1998;270-275.
40. Harboe M, Oettinger T, Wiker H G, Rosenkrands I, Andersen P. Evidence for occurrence of the ESAT-6 protein in Mycobacterium tuberculosis and virulent Mycobacterium bovis and for its absence in Mycobacterium bovis BCG. Infect Immun. 64:1996;16-22.
41. Mahairas G G, Sabo P J, Hickey M J, Singh D C, Stover C K. Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis. J Bacteriol. 178:1996;1274-1282.
42. Gordon S V, Brosch R, Billault A, Garnier T, Eiglmeier K, Cole S T. Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays. Mol Microbiol. 32:1999;643-656.
43. Chubb A J, Woodman Z L, da Silva Tatley F M P R, Hoffman H J, Scholle R R, Ehlers M R W. Identification of Mycobacterium tuberculosis signal sequences that direct the export of a leaderless beta-lactamase gene product in Escherichia coli. Microbiology. 144:1998;1619-1629.
44. Pugsley A P. The complete general secretory pathway in gram-negative bacteria. Microbiol Rev. 57:1993;50-108.
45. Brennan P J. Proteins and antigens of Mycobacterium tuberculosis. Bloom B R. Tuberculosis: pathogenesis, protection, and control. 1994;307-336 American Society for Microbiology.
46. Berthet F X, Rasmussen P B, Rosenkrandt I, Andersen P, Gicquel B. A Mycobacterium tuberculosis operon encoding ESAT-6 and a novel low-molecular-mass culture filtrate protein (CFP-10). Microbiology. 144:1998;3195-3203.
47. Finlay B B, Falkow S. Common themes in microbial pathogenicity revisited. Microbiol Mol Biol Rev. 61:1997;136-169.
48. Nissen M J, Nes I F. Ribosomally synthesized antimicrobial peptides: their function, structure, biogenesis, and mechanism of action. Arch Microbiol. 167:1997;67-77.
49. Havarstein L S, Diep D B, Nes I F. A family of bacteriocin ABC transporters carry out proteolytic processing of their substrates concomitant with export. Mol Microbiol. 16:1995;229-240.
50. Menard R, Sansonetti P, Parsot C. The secretion of the Shigella flexneri Ipa invasins is activated by epithelial cells and controlled by IpaB and IpaD. Embo Journal. 13:1994;5293-5302.
51. Menozzi F D, Bischoff R, Fort E, Brennan M J, Locha C. Molecular characterization of the mycobacterial heparin-binding hemagglutinin, a mycobacterial adhesin. Proc Natl Acad Sci USA. 95:1998;12625-12630.
52. Weldingh K, Rosenkrands I, Jacobsen S, Rasmussen P B, Elhay M J, Andersen P. Two-dimensional electrophoresis for analysis of Mycobacterium tuberculosis culture filtrate and purification and characterization of six novel proteins. Infect Immun. 66:1998;349-500.