Structural proteomics and computational analysis of a deadly pathogen: Combating mycobacterium tuberculosis from multiple fronts

Methods of Biochemical Analysis

Volumn 49, Issue , 2006, Pages 245-269

  Strong, Michael ^a   Goulding, Celia W ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ANTIGEN; TUBERCULOSTATIC AGENT;

ANTIBIOTIC RESISTANCE; BIOLOGY; CHEMICAL STRUCTURE; CHROMOSOME MAP; COMPUTER PROGRAM; DNA SEQUENCE; GENOME; METABOLISM; METHODOLOGY; MICROBIOLOGY; MYCOBACTERIUM TUBERCULOSIS; PATHOGENICITY; PHYLOGENY; PROTEOMICS; REVIEW; TUBERCULOSIS;

ANTIGENS, BACTERIAL; ANTITUBERCULAR AGENTS; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DRUG RESISTANCE, BACTERIAL; GENOME; MODELS, MOLECULAR; MYCOBACTERIUM TUBERCULOSIS; PHYLOGENY; PROTEOMICS; SEQUENCE ANALYSIS, DNA; SOFTWARE; TUBERCULOSIS;

EID: 33749066325     PISSN: 00766941     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Review

References (116)

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Anderson, D. H., Harth, G., Horwitz, M. A., and Eisenberg, D. (2001). An interfacial mechanism and a class of inhibitors inferred from two crystal structures of the Mycobacterium tuberculosis 30 kDa major secretory protein (antigen 85B), a mycolyl transferase. J. Mol. Biol. 307:671-681.
3. Armitige, L. Y., Jagannath, C., Wanger, A. R., and Norris, S. J. (2000). Disruption of the genes encoding antigen 85A and antigen 85B of Mycobacterium tuberculosis H37Rv: Effect on growth in culture and in macrophages. Infect. Immun. 68:767-778.
4. Av-Gay, Y., and Everett, M. (2000). The eukaryotic-like Ser/Thr protein kinases of Mycobacterium tuberculosis. Trends Microbiol 8:238-244.
5. Bader, G. D., Betel, D., and Hogue, C. W. (2003). BIND: The Biomolecular Interaction Network Database. Nucleic Acids Res. 31:248-250.
6. Banerjee, A., Dubnau, E., Quemard, A., Balasubramanian, V., Um, K. S., Wilson, T., Collins, D., de Lisle, G., and Jacobs, W. R. Jr. (1994). InhA, a gene encoding a target for isoniazid and ethionamide in Mycobacterium tuberculosis. Science 263:227-230.
7. Belanger, A. E., Besra, G. S., Ford, M. E., Mikusova, K., Belisle, J. T., Brennan, P. J., and Inamine, J. M. (1996). The embAB genes of Mycobacterium avium encode an arabinosyl transferase involved in cell wall arabinan biosynthesis that is the target for the antimycobacterial drug ethambutol. Proc. Natl. Acad. Sci. USA 93:11919-11924.
8. Billings, P. C., Whitbeck, J. C., Adams, C. S., Abrams, W. R., Cohen, A. J., Engelsberg, B. N., Howard, P. S., and Rosenbloom, J. (2002). The transforming growth factor-beta-inducible matrix protein (beta)ig-h3 interacts with fibronectin. J. Biol. Chem. 277:28003-28009.
9. Bossi, R. T., Aliverti, A., Raimondi, D., Fischer, F., Zanetti, G., Ferrari, D., Tahallah, N., Maier, C. S., Heck, A. J., Rizzi, M., and Mattevi, A. (2002). A covalent modification of NADP + revealed by the atomic resolution structure of FprA, a Mycobacterium tuberculosis oxidoreductase. Biochemistry 41:8807-8818.
10. Bowers, P. M., Pellegrini, M., Thompson, M. J., Fierro, J., Yeates, T. O., and Eisenberg, D. (2004). Prolinks: A database of protein functional linkages derived from coevolution. Genome Biol. 5:R35.
11. Braunstein, M., Brown, A. M., Kurtz, S., and Jacobs, W. R. Jr. (2001). Two nonredundant SecA homologues function in mycobacteria. J. Bacteriol. 183:6979-6790.
12. Braunstein, M., Espinosa, B. J., Chan, J., Belisle, J. T., and Jacobs, W. R. Jr. (2003). SecA2 functions in the secretion of superoxide dismutase A and in the virulence of Mycobacterium tuberculosis. Mol Microbiol. 48:453-464.
13. Brown, P. O., and Botstein, D. (1999). Exploring the new world of the genome with DNA microarrays. Nat. Genet. 21:33-37.
14. Carr, M. D., Bloemink, M. J., Dentten, E., Whelan, A. O., Gordon, S. V., Kelly, G., Frenkiel, T. A., Hewinson, R. G., and Williamson, R. A. (2003). Solution Structure of the Mycobacterium tuberculosis complex protein MPB70: From Tuberculosis Pathogenesis to Inherited Human Corneal Disease. J. Biol. Chem. 278:43736-43743.
15. Chang, G., Spencer, R. H., Lee, A. T., Barclay, M. T., and Rees, D. C. (1998). Structure of the MscL homolog from Mycobacterium tuberculosis: A gated mechanosensitive ion channel. Science 282:2220-2226.
16. Clout, N. J., Tisi, D., and Hohenester, E. (2003). Novel fold revealed by the structure of a FAS1 domain pair from the insect cell adhesion molecule fasciclin I. Structure (Camb.) 11:197-203.
17. 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., Krogh, A., McLean, J., Moule, S., Murphy, L., Oliver, K., Osborne, J., Quail, M. A., Rajandream, M. A., Rogers, J., Rutter, S., Seeger, K., Skelton, J., Squares, R., Squares, S., Sulston, J. E., Taylor, K., Whitehead, S., and Barrell, B. G. (1998). Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393:537-544.
18. Cooper, J. B., McIntyre, K., Badasso, M. O., Wood, S. P., Zhang, Y., Garbe, T. R., and Young, D. (1995). X-ray structure analysis of the iron-dependent superoxide dismutase from Mycobacterium tuberculosis at 2.0 Angstroms resolution reveals novel dimer-dimer interactions. J. Mol. Biol. 246:531-544.
19. Cowley, S., Ko, M., Pick, N., Chow, R., Downing, K. J., Gordhan, B. G., Betts, J. C., Mizrahi, V., Smith, D. A., Stokes, R. W., and Av-Gay, Y. (2004). The Mycobacterium tuberculosis protein serine/threonine kinase PknG is linked to cellular glutamate/glutamine levels and is important for growth in vivo. Mol. Microbiol. 52:1691-1702.
20. Daffe, M. (2000). The mycobacterial antigens 85 complex-from structure to function and beyond. Trends Microbiol. 8:438-440.
21. Dandekar, T., Schuster, S., Snel, B., Huynen, M., and Bork, P. (1999). Pathway alignment: Application to the comparative analysis of glycolytic enzymes. Biochem. J. 343 (Pt 1): 115-124.
22. Dessen, A., Quemard, A., Blanchard, J. S., Jacobs, W. R. Jr., and Sacchettini, J. C. (1995). Crystal structure and function of the isoniazid target of Mycobacterium tuberculosis. Science 267:1638-1641.
23. Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 95:14863-14868.
24. Eisenberg, D., Gill, H. S., Pfluegl, G. M., and Rotstein, S. H. (2000a). Structure-function relationships of glutamine synthetases. Biochim. Biophys. Acta 1477:122-145.
25. Eisenberg, D., Marcotte, E. M., Xenarios, I., and Yeates, T. O. (2000b). Protein function in the post-genomic era. Nature 405:823-826.
26. Ermolarva, M. D., White, O., and Salzbaerg, S. L. (2001). Prediction of operons in microbial genomes. Nucleic Acids Res. 29:1216-1221.
27. Faller, M., Niederweis, M., and Schulz, G. E. (2004). The structure of a mycobacterial outer-membrane channel. Science 303:1189-1192.
28. Fultz, P. N., and Kemper, J. (1981). Wild-type isopropylmalate isomerase in Salmonella typhimurium is composed of two different subunits. J. Bacteriol. 148:210-219.
29. George, K. M., Yuan, Y., Sherman, D. R., and Barry, C. E., 3rd (1995). The biosynthesis of cyclopropanated mycolic acids in Mycobacterium tuberculosis. Identification and functional analysis of CMAS-2. J. Biol. Chem. 270:27292-27298.
30. Gill, H. S., Pfluegl, G. M., and Eisenberg, D. (2002). Multicopy crystallographic refinement of a relaxed glutamine synthetase from Mycobacterium tuberculosis highlights flexible loops in the enzymatic mechanism and its regulation. Biochemistry 41:9863-9872.
31. Glickman, M. S., Cox, J. S., and Jacobs, W. R. Jr. (2000). A novel mycolic acid cyclopropane synthetase is required for cording, persistence, and virulence of Mycobacterium tuberculosis. Mol. Cell. 5:717-727.
32. Goldstone, D., Baker, E. N., and Metcalf, P. (2005). Crystallization and preliminary diffraction studies of the C-terminal domain of the DipZ homologue from Mycobacterium tuberculosis. Acta Crystallograph Sect F Struct Biol Cryst Commun., 61:243-245.
33. Gomez, M., Johnson, S., and Gennaro, M. L. (2000). Identification of secreted proteins of Mycobacterium tuberculosis by a bioinformatic approach. Infect. Immun. 68:2323-2327.
34. Good, M. C., Greenstein, A. E., Young, T. A., Ng, H. L., and Alber, T. (2004). Sensor domain of the Mycobacterium tuberculosis receptor Ser/Thr protein kinase, PknD, forms a highly symmetric beta propeller. J. Mol. Biol. 339:459-469.
35. Goulding, C. W., Apostol, M., Anderson, D. H., Gill, H. S., Smith, C. V., Kuo, M. R., Yang, J. K., Waldo, G. S., Suh, S. W., Chauhan, R., Kale, A., Bachhawat, N., Mande, S. C., Johnston, J. M., Lott, J. S., Baker, E. N., Arcus, V. L., Leys, D., McLean, K. J., Munro, A. W., Berendzen, J., Sharma, V., Park, M. S., Eisenberg, D., Sacchettini, J., Alber, T., Rupp, B., Jacobs, W. Jr., and Terwilliger, T. C. (2002a). The, T. B. structural genomics consortium: Providing a structural foundation for drug discovery. Curr. Drug Targets Infect. Disord. 2:121-141.
36. Goulding, C. W., Gleiter, S., Apostol, M. I., Parseghian, A., Bardwell, J., Gennaro, M. L., and Eisenberg, D. (2004). Gram-positive DsbE proteins function differently from gram-negative DsbE homologs: A structure to function analysis of DsbE from Mycobacterium tuberculosis. J. Biol. Chem. 279:3516-3524.
37. Goulding, C. W., Parseghian, A., Sawaya, M. R., Cascio, D., Apostol, M. I., Gennaro, M. L., and Eisenberg, D. (2002b). Crystal structure of a major secreted protein of Mycobacterium tuberculosis-MFT63 at 1.5-A resolution. Protein Sci. 11:2887-2893.
38. Grigoriev, A. (2001). A relationship between gene expression and protein interactions on the proteome scale: Analysis of the bacteriophage T7 and the yeast Saccharomyces cerevisiae. Nucleic Acids Res. 29:3513-3519.
39. Hanks, S. K., and Hunter, T. (1995). Protein kinases 6. The eukaryotic protein kinase superfamily: Kinase (catalytic) domain structure and classification. FASEB J. 9:576-596.
40. Harth, G., Clemens, D. L., and Horwitz, M. A. (1994). Glutamine synthetase of Mycobacterium tuberculosis: Extracellular release and characterization of its enzymatic activity. Proc. Natl. Acad. Sci. USA 91:9342-9346.
41. Harth, G., and Horwitz, M. A. (1999). An inhibitor of exported Mycobacterium tuberculosis glutamine synthetase selectively blocks the growth of pathogenic mycobacteria in axenic culture and in human monocytes: Extracellular proteins as potential novel drug targets. J. Exp. Med. 189:1425-1436.
42. Harth, G., and Horwitz, M. A. (2003). Inhibition of Mycobacterium tuberculosis glutamine synthetase as a novel antibiotic strategy against tuberculosis: Demonstration of efficacy in vivo. Infect. Immun. 71:456-464.
43. Hewinson, R. G., Michell, S. L., Russell, W. P., McAdam, R. A., and Jacobs, W. R. Jr. (1996). Molecular characterization of MPT83: A seroreactive antigen of Mycobacterium tuberculosis with homology to MPT70. Scand. J. Immunol. 43:490-499.
44. Hirschfield, G. R., McNeil, M., and Brennan, P. J. (1990). Peptidoglycan-associated polypeptides of Mycobacterium tuberculosis. J. Bacteriol. 172:1005-1013.
45. Horswill, A. R., and Escalante-Semerena, J. C. (2001). In vitro conversion of propionate to pyruvate by Salmonella enterica enzymes: 2-Methylcitrate dehydratase (PrpD) and aconitase enzymes catalyze the conversion of 2-methylcitrate to 2-methylisocitrate. Biochemistry 40:4703-4713.
46. Huse, M., and Kuriyan, J. (2002). The conformational plasticity of protein kinases. Cell 109:275-282.
47. Kantardjieff, K. A., Kim, C. Y., Naranjo, C., Waldo, G. S., Lekin, T., Segelke, B. W., Zemla, A., Park, M. S., Terwilliger, T. C., and Rupp, B. (2004). Mycobacterium tuberculosis RmIC epimerase (Rv3465): A promising drug-target structure in the rhamnose pathway. Acta Crystallogr. D Biol. Crystallogr. 60:895-902.
48. Leys, D., Mowat, C. G., McLean, K. J., Richmond, A., Chapman, S. K., Walkinshaw, M. D., and Munro, A. W. (2003). Atomic structure of Mycobacterium tuberculosis CYP121 to 1.06 A reveals novel features of cytochrome P450. J. Biol. Chem. 278:5141-5147.
49. Lodish, H., Baltimore, D., MBerk, A., Szipursky, S., Matsudaira, P., and Ndarnell, J. (1995). Molecular Cell Biology. New York: Scientific American Books.
50. Madigan, M., Martinko, J., and Parker, J. (2000). Brock Biology of Microorganisms. Englewood cliffs, NJ: Prentice-Hall.
51. Manca, C., Lyashchenko, K., Wiker, H. G., Usai, D., Colangeli, R., and Gennaro, M. L. (1997). Molecular cloning, purification, and serological characterization of MPT63, a novel antigen secreted by Mycobacterium tuberculosis. Infect. Immun. 65:16-23.
52. Marcotte, C. J., and Marcotte, E. M. (2002). Predicting functional linkages from gene fusions with confidence. Appl Bioinformatics 1:93-100.
53. Marcotte, E. M., Pellegrini, M., Ng, H. L., Rice, D. W., Yeates, T. O., and Eisenberg, D. (1999a). Detecting protein function and protein-protein interactions from genome sequences. Science 285:751-753.
54. Marcotte, E. M., Pellegrini, M., Thompson, M. J., Yeates, T. O., and Eisenberg, D. (1999b). A combined algorithm for genome-wide prediction of protein function. Nature 402:83-86.
55. Mariani, F., Cappelli, G., Riccardi, G., and Colizzi, V. (2000). Mycobacterium tuberculosis H37Rv comparative gene-expression analysis in synthetic medium and human macrophage. Gene 253:281-291.
56. Maynes, J. T., Garen, C., Cherney, M. M., Newton, G., Arad, D., Av-Gay, Y., Fahey, R. C., and James, M. N. (2003). The crystal structure of 1-D-myo-inosityl 2-acetamido-2-deoxy-{alpha}-D-glucopyranoside deacetylase (MshB) from Mycobacterium tuberculosis reveals a zinc hydrolase with a lactate dehydrogenase fold. J. Biol. Chem. 278:47166-47170.
57. McCarthy, A. A., Peterson, N. A., Knijff, R., and Baker, E. N. (2004). Crystal structure of MshB from Mycobacterium tuberculosis, a deacetylase involved in mycothiol biosynthesis. J. Mol. Biol. 335:1131-1141.
58. McKinney, J. D., Honer zu Bentrup, K., Munoz-Elias, E. J., Miczak, A., Chen, B., Chan, W. T., Swenson, D., Sacchettini, J. C., Jacobs, W. R., Jr., and Russell, D. G. (2000). Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase. Nature 406:735-738.
59. Mellor, J. C., Yanai, I., Clodfelter, K. H., Mintseris, J., and DeLisi, C. (2002). Predictome: A database of putative functional links between proteins. Nucleic Acids Res. 30:306-309.
60. Mewes, H. W., Frishman, D., Guldener, U., Mannhaupt, G., Mayer, K., Mokrejs, M., Morgenstern, B., Munsterkotter, M., Rudd, S., and Weil, B. (2002). MIPS: A database for genomes and protein sequences. Nucleic Acids Res. 30:31-34.
61. Milani, M., Pesce, A., Quellet, Y., Ascenzi, P., Guertin, M., and Bolognesi, M. (2001). Mycobacterium tuberculosis hemoglobin N displays a protein tunnel suited for O2 diffusion to the heme. EMBO J. 20:3902-3909.
62. Milani, M., Savard, P. Y., Ouellet, H., Ascenzi, P., Guertin, M., and Bolognesi, M. (2003). ATyrCD1/TrpG8 hydrogen bond network and a TyrB10TyrCD1 covalent link shape the heme distal site of Mycobacterium tuberculosis hemoglobin O. Proc. Natl. Acad. Sci. USA 100:5766-5771.
63. Moreno-Hagelsieb, G., and Collado-Vides, J. (2002a): Operon conservation from the point of view of Escherichia coli, and inference of functional interdependence of gene products from genome context. In Silica Biol. 2:87-95.
64. Moreno-Hagelsieb, G., and Collado-Vides, J. (2002b). A powerful non-homology method for the prediction of operons in prokaryotes. Bioinformatics 18 (Suppl. 1):S329-S336.
65. Moreno-Hagelsieb, G., Trevino, V., Perez-Rueda, E., Smith, T. F., and Collado-Vides, J. (2001). Transcription unit conservation in the three domains of life: A perspective from Escherichia coli. Trends Genet. 17:175-177.
66. Mori, H., and Ito, K. (2001). The Sec protein-translocation pathway. Trends Microbiol. 9:494-500.
67. Moskovitz, J., Bar-Noy, S., Williams, W. M., Requena, J., Berlett, B. S., and Stadtman, E. R. (2001). Methionine sulfoxide reductase (MsrA) is a regulator of antioxidant defense and lifespan in mammals. Proc. Natl. Acad. Sci. USA 98:12920-12925.
68. Munoz, S., Hernandez-Pando, R., Abraham, S. N., and Enciso, J. A. (2003). Mast cell activation by Mycobacterium tuberculosis: Mediator release and role of CD48. J. Immunol. 170:5590-5596.
69. Munro, A. W., McLean, K. J., Marshall, K. R., Warman, A. J., Lewis, G., Roitel, O., Sutcliffe, M. J., Kemp, C. A., Modi, S., Scrutton, N. S., and Leys, D. (2003). Cytochromes P450: Novel drug targets in the war against multidrug-resistant Mycobacterium tuberculosis. Biochem. Soc. Trans. 31:625-630.
70. Norman, R. A., McAlister, M. S., Murray-Rust, J., Movahedzadeh, F., Stoker, N. G., and McDonald, N. Q. (2002). Crystal structure of inositol 1-phosphate synthase from Mycobacterium tuberculosis, a key enzyme in phosphatidylinositol synthesis. Structure (Camb.) 10:393-402.
71. Ortiz-Lombardia, M., Pompeo, F., Boitel, B., and Alzari, P. M. (2003). Crystal structure of the catalytic domain of the PknB serine/threonine kinase from Mycobacterium tuberculosis. J. Biol. Chem. 278:13094-13100.
72. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G. D., and Maltsev, N. (1999). Use of contiguity on the chromosome to predict functional coupling. In Silica Biol. 1:93-108.
73. Pallen, M., Chaudhuri, R., and Khan, A. (2002): Bacterial, FHA domains: Neglected players in the phospho-threonine signalling game? Trends Microbiol. 10:556-563.
74. Pellegrini, M., Marcotte, E. M., Thompson, M. J., Eisenberg, D., and Yeates, T. O. (1999). Assigning protein functions by comparative genome analysis: Protein phylogenetic profiles. Proc. Natl. Acad. Sci. USA 96:4285-4288.
75. Pellegrini, M., Thompson, M., Fierro, J., and Bowers, P. (2001). Computational method to assign microbial genes to pathways. J. Cell. Biochem. Suppl. 37:106-109.
76. Podust, L. M., Poulos, T. L., and Waterman, M. R. (2001). Crystal structure of cytochrome P450 14alpha -sterol demethylase (CYP51) from Mycobacterium tuberculosis in complex with azole inhibitors. Proc. Natl. Acad. Sci. USA 98:3068-3073.
77. Pullen, K. E., Ng, H. L., Sung, P. Y., Good, M. C., Smith, S. M., and Alber, T. (2004). An alternate conformation and a third metal in PstP/Ppp, the M. tuberculosis PP2C-Family Ser/Thr protein phosphatase. Structure 12:1947-1954.
78. Ravasz, E., Somera, A. L., Mongru, D. A., Oltvai, Z. N., and Barabasi, A. L. (2002). Hierarchical organization of modularity in metabolic networks. Science 297:1551-1555.
79. Rives, A. W., and Galitski, T. (2003). Modular organization of cellular networks. Proc. Natl. Acad. Sci. USA 100:1128-1133.
80. Ronning, D. R., Klabunde, T., Besra, G. S., Vissa, V. D., Belisle, J. T., and Sacchettini, J. C. (2000). Crystal structure of the secreted form of antigen 85C reveals potential targets for mycobacterial drugs and vaccines. Nat. Struct. Biol. 7:141-146.
81. Ronning, D. R., Vissa, V., Besra, G. S., Belisle, J. T., and Sacchettini, J. C. (2004). Mycobacterium tuberculosis antigen 85 A and 85C structures confirm binding orientation and conserved substrate specificity. J. Biol. Chem. 23:2972-2981.
82. Rozwarski, D. A., Grant, G. A., Barton, D. H., Jacobs, W. R., Jr., and Sacchettini, J. C. (1998). Modification of the NADH of the isoniazid target (InhA) from Mycobacterium tuberculosis. Science 279:98-102.
83. Rozwarski, D. A., Vilcheze, C., Sugantino, M., Bittman, R., and Sacchettini, J. C. (1999). Crystal structure of the Mycobacterium tuberculosis enoyl-ACP reductase, InhA, in complex with NAD + and a C16 fatty acyl substrate. J. Biol. Chem. 274:15582-15589.
84. Salgado, H., Moreno-Hagelsieb, G., Smith, T. F., and Collado-Vides, J. (2000). Operons in Escherichia coli: Genomic analyses and predictions. Proc. Natl. Acad. Sci. USA 97:6652-6657.
85. Salgado, H., Santos-Zavaleta, A., Gama-Castro, S., Millan-Zarate, D., Diaz-Peredo, E., Sanchez-Solano, F., Perez-Rueda, E., Bonavides-Martinez, C., and Collado-Vides, J. (2001). RegulonDB (version 3.2): Transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res. 29:72-74.
86. Sharma, V., Arockiasamy, A., Ronning, D. R., Savva, C. G., Holzenburg, A., Braunstein, M., Jacobs, W. R., Jr., and Sacchettini, J. C. (2003). Crystal structure of Mycobacterium tuberculosis SecA, a preprotein translocating ATPase. Proc. Natl. Acad. Sci. USA 100:2243-2248.
87. Sharma, V., Grubmeyer, C., and Sacchettini, J. C. (1998). Crystal structure of quinolinic acid phosphoribosyltransferase from Mycobacterium tuberculosis: A potential TB drug target. Structure 6:1587-1599.
88. Sharma, V., Sharma, S., Hoener zu Bentrup, K., McKinney, J. D., Russell, D. G., Jacobs, W. R., Jr., and Sacchettini, J. C. (2000). Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis. Nat. Struct. Biol. 7:663-668.
89. Skaar, E. P., Gaspar, A. H., and Schneewind, O. (2004). IsdG and IsdI, heme-degrading enzymes in the cytoplasm of Staphylococcus aureus. J. Biol. Chem. 279:436-443.
90. Snel, B., Bork, P., and Huynen, M. A. (2002). The identification of functional modules from the genomic association of genes. Proc. Natl. Acad. Sci. USA 99:5890-5895.
91. Stewart, G., Robertson, B., and Young, D. (2003): Tuberculosis: A problem with persistence. Nat. Rev. Microbiol. 1:97-105.
92. Strong, M., Graeber, T. G., Beeby, M., Pellegrini, M., Thompson, M. J., Yeates, T. O., and Eisenberg, D. (2003a). Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Res. 31:7099-7109.
93. Strong, M., Mallick, P., Pellegrini, M., Thompson, M. J., and Eisenberg, D. (2003b). Inference of protein function and protein linkages in Mycobacterium tuberculosis based on prokaryotic genome organization: A combined computational approach. Genome Biol. 4:R59.
94. Tamakoshi, M., Yamagishi, A., and Oshima, T. (1998). The organization of the leuC, leuD and leuB genes of the extreme thermophile Thermus thermophilus. Gene 222:125-132.
95. Taylor, A. B., Benglis, D. M. Jr., Dhandayuthapani, S., and Hart, P. J. (2003). Structure of Mycobacterium tuberculosis methionine sulfoxide reductase A in complex with protein-bound methionine. J. Bacteriol. 185:4119-4126.
96. Terwilliger, T. C., Park, M. S., Waldo, G. S., Berendzen, J., Hung, L. W., Kim, C. Y., Smith, C. V., Sacchettini, J. C., Bellinzoni, M., Bossi, R., De Rossi, E., Mattevi, A., Milano, A., Riccardi, G., Rizzi, M., Roberts, M. M., Coker, A. R., Fossati, G., Mascagni, P., Coates, A. R., Wood, S. P., Goulding, C. W., Apostol, M. I., Anderson, D. H., Gill, H. S., Eisenberg, D. S., Taneja, B., Mande, S., Pohl, E., Lamzin, V., Tucker, P., Wilmanns, M., Colovos, C., Meyer-Klaucke, W., Munro, A. W., McLean, K. J., Marshall, K. R., Leys, D., Yang, J. K., Yoon, H. J., Lee, B. I., Lee, M. G., Kwak, J. E., Han, B. W., Lee, J. Y., Baek, S. H., Sun, S. W., Komen, M. M., Arcus, V. L., Baker, E. N., Lott, J. S., Jacobs, W. Jr., Alber, T., and Rupp, B. (2003). The, T. B. structural genomics consortium: A resource for Mycobacterium tuberculosis biology. Tuberculosis (Edinb.) 83:223-249.
97. Tullius, M. V., Harth, G., and Horwitz, M. A. (2003). Glutamine synthetase GlnA1 is essential for growth of Mycobacterium tuberculosis in human THP-1 macrophages and guinea pigs. Infect. Immun. 71:3927-3936.
98. Uetz, P., Giot, L., Cagney, G., Mansfield, T. A., Judson, R. S., Knight, J. R., Lockshon, D., Narayan, V., Srinivasan, M., Pochart, P., Qureshi-Emili, A., Li, Y., Godwin, B., Conover, D., Kalbfleisch, T., Vijayadamodar, G., Yang, M., Johnston, M., Fields, S., and Rothberg, J. M. (2000). A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403:623-627.
99. Vetting, M. W., Roderick, S. L., Yu, M., and Blanchard, J. S. (2003). Crystal structure of mycothiol synthase (Rv0819) from Mycobacterium tuberculosis shows structural homology to the GNAT family of N-acetyltransferases. Protein Sci. 12:1954-1959.
100. Vilcheze, C., Morbidoni, H. R., Weisbrod, T. R., Iwamoto, H., Kuo, M., Sacchettini, J. C., and Jacobs, W. R., Jr. (2000). Inactivation of the inhA-encoded fatty acid synthase II (FASII) enoyl-acyl carrier protein reductase induces accumulation of the FASI end products and cell lysis of Mycobacterium smegmatis. J. Bacteriol. 182:4059-4067.
101. von Mering, C., Huynen, M., Jaeggi, D., Schmidt, S., Bork, P., and Snel, B. (2003). STRING: A database of predicted functional associations between proteins. Nucleic Acids Res. 31:258-261.
102. Vyas, N. K., Vyas, M. N., and Quiocho, F. A. (2003). Crystal structure of M tuberculosis ABC phosphate transport receptor: Specificity and charge compensation dominated by ion-dipole interactions. Structure (Camb.) 11:765-774.
103. Walburger, A., Koul, A., Ferrari, G., Nguyen, L., Prescianotto-Baschong, C., Huygen, K., Klebl, B., Thompson, C., Bacher, G., and Pieters, J. (2004). Protein kinase G from pathogenic mycobacteria promotes survival within macrophages. Science 304:1800-1804.
104. Wiker, H. G., and Harboe, M. (1992). The antigen 85 complex: A major secretion product of Mycobacterium tuberculosis. Microbiol. Rev. 56:648-661.
105. Wiker, H. G., Harboe, M., and Nagai, S. (1991). A localization index for distinction between extracellular and intracellular antigens of Mycobacterium tuberculosis. J. Gen. Microbiol. 137(Pt. 4):875-884.
106. Wilson, R. A., Rai, S., Maughan, W. N., Kremer, L., Kariuki, B. M., Harris, K. D., Wagner, T., Besra, G. S., and Futterer, K. (2003). Crystallization and preliminary X-ray diffraction data of Mycobacterium tuberculosis FbpC1 (Rv3803c). Acta Crystallogr. D Biol. Crystallogr. 59:2303-2305.
107. Wolf, Y. I., Rogozin, I. B., Kondrashov, A. S., and Koonin, E. V. (2001). Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context. Genome Res. 11:356-372.
108. World Health Organization (2002). Tuberculosis Fact Sheet. Geneva, Switzerland: WHO.
109. Xenarios, I., Salwinski, L., Duan, X. J., Higney, P., Kim, S. M., and Eisenberg, D. (2002). DIP, the Database of Interacting Proteins: A research tool for studying cellular networks of protein interactions. Nucleic Acids Res. 30:303-305.
110. Yanai, I., Wolf, Y. I., and Koonin, E. V. (2002). Evolution of gene fusions: Horizontal transfer versus independent events. Genome Biol. 3:1-13.
111. Yeats, C., Finn, R. D., and Bateman, A. (2002). The, PASTA domain: A beta-lactam-binding domain. Trends Biochem. Sci. 27:438.
112. Young, D., Garbe, T., Lathigra, R., Abou-Zeid, C., and Zhang, Y. (1991). Characterization of prominent protein antigens from mycobacteria. Bull Int. Union Tuberc Lung Dis. 66:47-51.
113. Young, T. A., Delagoutte, B., Endrizzi, J. A., Falick, A. M., Alber, T. (2003). Structure of Mycobacterium tuberculosis PknB supports a universal activation mechanism for Ser/Thr protein kinases. Nat. Struct. Biol. 10:168-174.
114. Yuan, Y., Lee, R. E., Besra, G. S., Belisle, J. T., and Barry, C. E., 3rd (1995). Identification of a gene involved in the biosynthesis of cyclopropanated mycolic acids in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 92:6630-6634.
115. Zhang, Y., Lathigra, R., Garbe, T., Catty, D., and Young, D. (1991). Genetic analysis of superoxide dismutase, the 23 kilodalton antigen of Mycobacterium tuberculosis. Mol. Microbiol. 5:381-391.
116. Zheng, Y., Roberts, R. J., and Kasif, S. (2002). Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biol. 3:1-9.