Analysis of the proteome of Mycobacterium tuberculosis in silico

Tubercle and Lung Disease - Tập 79 - Trang 329-342 - 1999
F. Tekaia1, S.V. Gordon2, T. Garnier2, R. Brosch2, B.G. Barrell3, S.T. Cole2
1Unité de Génétique Moléculaire des Levures, Institut Pasteur, 25 rue du Docteur Roux, 75724, Paris, Cedex 15, France
2Unité de Génétique Moléculaire Bactérienne, Institut Pasteur, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
3Sanger Centre, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, U.K.

Tài liệu tham khảo

Goffeau, 1994, Genes in search of functions, Nature (London), 369, 101, 10.1038/369101a0 Cole, 1998, Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence, Nature (London), 393, 537, 10.1038/31159 Cole, 1998, Analysis of the genome of Mycobacterium tuberculosis H37Rv, 160 Altschul, 1990, A basic local alignment search tool, J Mol Biol, 215, 403, 10.1016/S0022-2836(05)80360-2 Wootton, 1994, Non-globular domains in protein sequences: automated segmentation using complexity measures, Comput & Chem, 18, 269, 10.1016/0097-8485(94)85023-2 Tekaia, 1999, Pervasiveness of gene conservation and persistence of duplicatges in cullular genomes, J Mol Evol, 49, 10.1007/PL00006580 Greenacre, 1984 Benzecri, 1973 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 Bailey, 1998, Combining evidence using p-values: application to sequence homology searches, Bioinformatics, 14, 45, 10.1093/bioinformatics/14.1.48 Devereux, 1984, A comprehensive set of sequence analysis programs for the VAX, Nucl Acids Res, 12, 387, 10.1093/nar/12.1Part1.387 Pearson, 1988, Improved tools for biological sequence comparisons, Proc Natl Acad USA, 85, 2444, 10.1073/pnas.85.8.2444 Nielsen, 1997, Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites, Prot Eng, 10, 1, 10.1093/protein/10.1.1 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 Thompson, 1994, Improving the sensitivity of progressive multiple alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res, 22, 4673, 10.1093/nar/22.22.4673 Felsenstein, 1989, PHYLIP – Phylogeny Inference Package (Version 3.2), Cladistics, 5, 164 Poulet, 1995, Characterisation of the polymorphic GC-rich repetitive sequence (PGRS) present in Mycobacterium tuberculosis, Arch Microbiol, 163, 87, 10.1007/BF00381781 Ross, 1992, Molecular cloning of a highly repeated DNA element from Mycobacterium tuberculosis and its use as an epidemiological tool, J Clin Microbiol, 30, 942, 10.1128/JCM.30.4.942-946.1992 van Soolingen, 1993, Comparison of various repetitive DNA elements as genetic markers for strain differentiation and epidemiology ofMycobacterium tuberculosis, J Clin Microbiol, 31, 1987, 10.1128/JCM.31.8.1987-1995.1993 Grosset, 1993, Bacteriology of tuberculosis, 49 Gordon, 1999, New insertion sequences and a novel repeated sequence in the genome of Mycobacterium tuberculosis H37Rv, Microbiology, 145, 881, 10.1099/13500872-145-4-881 Lonetto, 1992, The σ70family; Sequence conservation and evolutionary relationships, J Bacteriol, 174, 3843, 10.1128/jb.174.12.3843-3849.1992 Gomez, 1998, The sigma factors of Mycobacterium tuberculosis, Tubercle Lung Dis, 78, 175, 10.1016/S0962-8479(97)90024-1 Barry, 1998, Mycolic acids: Structure, biosynthesis, and physiological functions, Prog Lipid Res, 37, 143, 10.1016/S0163-7827(98)00008-3 Munro, 1996, Bacterial cytochromes P-450, Mol Microbiol, 20, 1115, 10.1111/j.1365-2958.1996.tb02632.x Arand, 1994, Sequence similarity of mammalian epoxide hydrolases to the bacterial haloalkane dehalogenase and other related proteins, FEBS Lett, 338, 251, 10.1016/0014-5793(94)80278-5 Hofmann, 1998, Structural investigation of the cofactor-free chloroperoxidases, J Mol Biol, 279, 889, 10.1006/jmbi.1998.1802 Pelletier, 1995, A catalytic triad is required by the non-heme haloperoxidases to perform halogenation, Biochim Biophys Acta, 1250, 149, 10.1016/0167-4838(95)00055-Y Pelletier, 1995, A bacterial esterase is homologous with non-haem haloperoxidases and displays brominating activity, Microbiology, 10.1099/13500872-141-2-459 Saier, 1994, Two novel families of bacterial membrane proteins concerned with nodulation, cell division and transport, Mol Microbiol, 11, 841, 10.1111/j.1365-2958.1994.tb00362.x Paulsen, 1996, Proton-dependent multidrug efflux systems, Microbiol Rev, 60, 575, 10.1128/MR.60.4.575-608.1996 Kunst, 1997, The complete genome sequence of the gram-positive bacterium Bacillus subtilis, Nature (London), 390, 249, 10.1038/36786 Pao, 1998, Major facilitator superfamily, Microbiology and Molecular Biology Reviews, 62, 1, 10.1128/MMBR.62.1.1-34.1998 Paulsen, 1998, Microbial genome analyses: global comparisons of transport capabilities based on phylogenies, bioenergetics and substrate specificities, J Mol Biol, 277, 573, 10.1006/jmbi.1998.1609 Ainsa, 1998, Molecular cloning and characterization of Tap, a putative multidrug efflux pump present in Mycobacterium fortuitum and Mycobacterium tuberculosis, J Bacteriol, 180, 5836, 10.1128/JB.180.22.5836-5843.1998 Kanamaru, 1994, A copper-transporting P-type ATPase found in the thylakoid membrane of the cyanobacterium Synechococcus species PCC7942, Mol Microbiol, 13, 369, 10.1111/j.1365-2958.1994.tb00430.x Arruda, 1993, Cloning of an M. tuberculosis DNA fragment associated with entry and survival inside cells, Science, 261, 1454, 10.1126/science.8367727 Elhay, 1998, Delayed-type hypersensitivity responses to ESAT-6 and MPT64 from Mycobacterium tuberculosis in the guinea pig, Infect Immun, 66, 3454, 10.1128/IAI.66.7.3454-3456.1998 Lalvani, 1998, 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, 270, 10.1073/pnas.95.1.270 Harboe, 1996, 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, 16, 10.1128/IAI.64.1.16-22.1996 Mahairas, 1996, Molecular analysis of genetic differences between Mycobacterium bovis BCG and virulent M. bovis, J Bacteriol, 178, 1274, 10.1128/jb.178.5.1274-1282.1996 Gordon, 1999, Identification of variable regions in the genomes of tubercle bacilli using bacterial artificial chromosome arrays, Mol Microbiol, 32, 643, 10.1046/j.1365-2958.1999.01383.x Chubb, 1998, Identification of Mycobacterium tuberculosis signal sequences that direct the export of a leaderless beta-lactamase gene product in Escherichia coli, Microbiology, 144, 1619, 10.1099/00221287-144-6-1619 Pugsley, 1993, The complete general secretory pathway in gram-negative bacteria, Microbiol Rev, 57, 50, 10.1128/MR.57.1.50-108.1993 Brennan, 1994, Proteins and antigens of Mycobacterium tuberculosis, 307 Berthet, 1998, A Mycobacterium tuberculosis operon encoding ESAT-6 and a novel low-molecular-mass culture filtrate protein (CFP-10), Microbiology, 144, 3195, 10.1099/00221287-144-11-3195 Finlay, 1997, Common themes in microbial pathogenicity revisited, Microbiol Mol Biol Rev, 61, 136, 10.1128/.61.2.136-169.1997 Nissen, 1997, Ribosomally synthesized antimicrobial peptides: their function, structure, biogenesis, and mechanism of action, Arch Microbiol, 167, 67, 10.1007/s002030050418 Havarstein, 1995, A family of bacteriocin ABC transporters carry out proteolytic processing of their substrates concomitant with export, Mol Microbiol, 16, 229, 10.1111/j.1365-2958.1995.tb02295.x Menard, 1994, The secretion of the Shigella flexneri Ipa invasins is activated by epithelial cells and controlled by IpaB and IpaD, Embo Journal, 13, 5293, 10.1002/j.1460-2075.1994.tb06863.x Menozzi, 1998, Molecular characterization of the mycobacterial heparin-binding hemagglutinin, a mycobacterial adhesin, Proc Natl Acad Sci USA, 95, 12625, 10.1073/pnas.95.21.12625 Weldingh, 1998, Two-dimensional electrophoresis for analysis of Mycobacterium tuberculosis culture filtrate and purification and characterization of six novel proteins, Infect Immun, 66, 349, 10.1128/IAI.66.8.3492-3500.1998