Disease Markers

Copyright © 2014 Conrad C. Swanepoel and Du Toit Loots. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

1. R. Koch, “Classics in infectious diseases. The etiology of tuberculosis: Robert Koch. Berlin, Germany 1882,” Reviews of Infectious Diseases, vol. 4, no. 6, pp. 1270–1274, 1982. View at Google Scholar · View at Scopus
2. B. Mathema, N. E. Kurepina, P. J. Bifani, and B. N. Kreiswirth, “Molecular epidemiology of tuberculosis: current insights,” Clinical Microbiology Reviews, vol. 19, no. 4, pp. 658–685, 2006. View at Publisher · View at Google Scholar · View at Scopus
3. World Health Organization, Global Tuberculosis Control: WHO Report, Global Tuberculosis Programme, World Health Organization, 2010.
4. World Health Organization, Global Tuberculosis Control 2011: WHO Report, WHO, Geneva, Switzerland, 2011.
5. N. R. Gandhi, A. Moll, A. W. Sturm et al., “Extensively drug-resistant tuberculosis as a cause of death in patients co-infected with tuberculosis and HIV in a rural area of South Africa,” The Lancet, vol. 368, no. 9547, pp. 1575–1580, 2006. View at Publisher · View at Google Scholar · View at Scopus
6. J. A. Caminero, G. Sotgiu, A. Zumla, and G. B. Migliori, “Best drug treatment for multidrug-resistant and extensively drug-resistant tuberculosis,” The Lancet Infectious Diseases, vol. 10, no. 9, pp. 621–629, 2010. View at Publisher · View at Google Scholar · View at Scopus
7. N. A. Knechel, “Tuberculosis: pathophysiology, clinical features, and diagnosis,” Critical Care Nurse, vol. 29, no. 2, pp. 34–43, 2009. View at Publisher · View at Google Scholar · View at Scopus
8. D. G. Russell, “Mycobacterium tuberculosis and the intimate discourse of a chronic infection,” Immunological Reviews, vol. 240, no. 1, pp. 252–268, 2011. View at Publisher · View at Google Scholar · View at Scopus
9. I. Olivier and D. Loots, “An overview of tuberculosis treatments and diagnostics. What role could metabolomics play,” Journal of Cell and Tissue Research, vol. 11, pp. 2655–2671, 2011. View at Google Scholar
10. A. Aderem, J. N. Adkins, C. Ansong et al., “A systems biology approach to infectious disease research: innovating the pathogen-host research paradigm,” mBio, vol. 2, no. 1, pp. 1–4, 2011. View at Publisher · View at Google Scholar · View at Scopus
11. T. Sakata and E. A. Winzeler, “Genomics, systems biology and drug development for infectious diseases,” Molecular BioSystems, vol. 3, no. 12, pp. 841–848, 2007. View at Publisher · View at Google Scholar · View at Scopus
12. W. B. Dunn and D. I. Ellis, “Metabolomics: current analytical platforms and methodologies,” Trends in Analytical Chemistry, vol. 24, no. 4, pp. 285–294, 2005. View at Publisher · View at Google Scholar · View at Scopus
13. J. C. Schoeman, I. du Preez, and D. T. Loots, “A comparison of four sputum pre-extraction preparation methods for identifying and characterising M. tuberculosis using GCxGC-TOFMS metabolomics,” Journal of Microbiological Methods, vol. 91, pp. 301–311, 2012. View at Google Scholar
14. J. M. Halket, D. Waterman, A. M. Przyborowska, R. K. P. Patel, P. D. Fraser, and P. M. Bramley, “Chemical derivatization and mass spectral libraries in metabolic profiling by GC/MS and LC/MS/MS,” Journal of Experimental Botany, vol. 56, no. 410, pp. 219–243, 2005. View at Publisher · View at Google Scholar · View at Scopus
15. J. K. Nicholson, J. C. Lindon, and E. Holmes, “‘Metabonomics’: understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data,” Xenobiotica, vol. 29, no. 11, pp. 1181–1189, 1999. View at Google Scholar · View at Scopus
16. L. M. Raamsdonk, B. Teusink, D. Broadhurst et al., “A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations,” Nature Biotechnology, vol. 19, no. 1, pp. 45–50, 2001. View at Publisher · View at Google Scholar · View at Scopus
17. L. Wu, W. A. Van Winden, W. M. Van Gulik, and J. J. Heijnen, “Application of metabolome data in functional genomics: a conceptual strategy,” Metabolic Engineering, vol. 7, no. 4, pp. 302–310, 2005. View at Publisher · View at Google Scholar · View at Scopus
18. S. G. Oliver, M. K. Winson, D. B. Kell, and F. Baganz, “Systematic functional analysis of the yeast genome,” Trends in Biotechnology, vol. 16, no. 9, pp. 373–378, 1998. View at Publisher · View at Google Scholar · View at Scopus
19. L. P. S. de Carvalho, S. M. Fischer, J. Marrero, C. Nathan, S. Ehrt, and K. Y. Rhee, “Metabolomics of Mycobacterium tuberculosis reveals compartmentalized co-catabolism of carbon substrates,” Chemistry and Biology, vol. 17, no. 10, pp. 1122–1131, 2010. View at Publisher · View at Google Scholar · View at Scopus
20. W. Weckwerth, “Metabolomics in systems biology,” Annual Review of Plant Biology, vol. 54, pp. 669–689, 2003. View at Google Scholar · View at Scopus
21. T. Nanda, M. Das, K. Tripathy et al., “Metabolomics: the future of systems biology,” Journal Computer Science Systems Biology, vol. 1, pp. 2–6, 2011. View at Google Scholar
22. Q.-Z. Wang, C.-Y. Wu, T. Chen, X. Chen, and X.-M. Zhao, “Integrating metabolomics into systems biology framework to exploit metabolic complexity: strategies and applications in microorganisms,” Applied Microbiology and Biotechnology, vol. 70, no. 2, pp. 151–161, 2006. View at Publisher · View at Google Scholar · View at Scopus
23. S. G. Villas-Bôas, S. Mas, M. Åkesson, J. Smedsgaard, and J. Nielsen, “Mass spectrometry in metabolome analysis,” Mass Spectrometry Reviews, vol. 24, no. 5, pp. 613–646, 2005. View at Publisher · View at Google Scholar · View at Scopus
24. T. J. Phelps, A. V. Palumbo, and A. S. Beliaev, “Metabolomics and microarrays for improved understanding of phenotypic characteristics controlled by both genomics and environmental constraints,” Current Opinion in Biotechnology, vol. 13, no. 1, pp. 20–24, 2002. View at Publisher · View at Google Scholar · View at Scopus
25. S. Halouska, O. Chacon, R. J. Fenton, D. K. Zinniel, R. G. Barletta, and R. Powers, “Use of NMR metabolomics to analyze the targets of D-cycloserine in mycobacteria: role of D-alanine racemase,” Journal of Proteome Research, vol. 6, no. 12, pp. 4608–4614, 2007. View at Publisher · View at Google Scholar · View at Scopus
26. H. K. Kim, Y. H. Choi, and R. Verpoorte, “NMR-based plant metabolomics: where do we stand, where do we go?” Trends in Biotechnology, vol. 29, no. 6, pp. 267–275, 2011. View at Publisher · View at Google Scholar · View at Scopus
27. N. Glassbrook, C. Beecher, and J. Ryals, “Metabolic profiling on the right path,” Nature Biotechnology, vol. 18, no. 11, pp. 1142–1143, 2000. View at Publisher · View at Google Scholar · View at Scopus
28. H. Kitano, “Systems biology: a brief overview,” Science, vol. 295, no. 5560, pp. 1662–1664, 2002. View at Publisher · View at Google Scholar · View at Scopus
29. R. M. Warren, N. C. Gey van Pittius, M. Barnard et al., “Differentiation of Mycobacterium tuberculosis complex by PCR amplification of genomic regions of difference,” International Journal of Tuberculosis and Lung Disease, vol. 10, no. 7, pp. 818–822, 2006. View at Google Scholar · View at Scopus
30. R. Brosch, S. V. Gordon, A. Pym, K. Eiglmeier, T. Garnier, and S. T. Cole, “Comparative genomics of the mycobacteria,” International Journal of Medical Microbiology, vol. 290, no. 2, pp. 143–152, 2000. View at Google Scholar · View at Scopus
31. K. N. Lewis, R. Liao, K. M. Guinn et al., “Deletion of RD1 from Mycobacterium tuberculosis mimics bacille Calmette-Guérin attenuation,” Journal of Infectious Diseases, vol. 187, no. 1, pp. 117–123, 2003. View at Publisher · View at Google Scholar · View at Scopus
32. A. S. Pym, P. Brodin, R. Brosch, M. Huerre, and S. T. Cole, “Loss of RD1 contributed to the attenuation of the live tuberculosis vaccines Mycobacterium bovis BCG and Mycobacterium microti,” Molecular Microbiology, vol. 46, no. 3, pp. 709–717, 2002. View at Publisher · View at Google Scholar · View at Scopus
33. S. Cole, R. Brosch, J. Parkhill et al., “Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence,” Nature, vol. 393, pp. 537–544, 1998. View at Google Scholar
34. J.-C. Camus, M. J. Pryor, C. Médigue, and S. T. Cole, “Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv,” Microbiology, vol. 148, no. 10, pp. 2967–2973, 2002. View at Google Scholar · View at Scopus
35. I. Olivier and D. T. Loots, “A metabolomics approach to characterise and identify various Mycobacterium species,” Journal of Microbiological Methods, vol. 88, no. 3, pp. 419–426, 2012. View at Publisher · View at Google Scholar · View at Scopus
36. D. T. Loots, R. J. Meissner-Roloff, M. Newton-Foot et al., “A metabolomics approach exploring the function of the ESX-3 type VII secretion system of M. smegmatis,” Metabolomics, vol. 9, pp. 631–641, 2013. View at Google Scholar
37. I. du Preez and D. T. Loots, “Altered fatty acid metabolism due to rifampicin-resistance conferring mutations in the rpoB gene of Mycobacterium tuberculosis: mapping the potential of pharmaco-metabolomics for global health and personalized medicine,” OMICS, vol. 16, pp. 596–603, 2012. View at Google Scholar
38. R. J. Meissner-Roloff, G. Koekemoer, R. M. Warren, and D. T. Loots, “A metabolomics investigation of a hyper- and hypo-virulent phenotype of Beijing lineage M. tuberculosis,” Metabolomics, vol. 8, pp. 1194–1203, 2012. View at Publisher · View at Google Scholar · View at Scopus
39. I. du Preez and D. Loots, “New sputum metabolite markers implicating adaptations of the host to Mycobacterium tuberculosis, and vice versa,” Tuberculosis, vol. 93, pp. 330–337, 2013. View at Google Scholar
40. P. R. Wheeler and C. Ratledge, “Metabolism of Mycobacterium tuberculosis,” in Tuberculosis: Pathogenesis, Protection, and Control, B. R. Bloom, Ed., pp. 353–385, American Soceity for Microbiology Press, Washington, DC, USA, 1994. View at Google Scholar
41. J. Tian, R. Bryk, M. Itoh, M. Suematsu, and C. Nathan, “Variant tricarboxylic acid cycle in Mycobacterium tuberculosis: identification of α-ketoglutarate decarboxylase,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 30, pp. 10670–10675, 2005. View at Publisher · View at Google Scholar · View at Scopus
42. M. Suematsu, T. Hishiki, T. Iwabuchi et al., “Biomedical application of metabolomics,” Cell, vol. 25, pp. 1427–1431, 2006. View at Google Scholar
43. K. Y. Rhee, L. P. S. D. Carvalho, R. Bryk et al., “Central carbon metabolism in Mycobacterium tuberculosis: an unexpected frontier,” Trends in Microbiology, vol. 19, no. 7, pp. 307–314, 2011. View at Publisher · View at Google Scholar · View at Scopus
44. L. P. S. de Carvalho, H. Zhao, C. E. Dickinson et al., “Activity-based metabolomic profiling of enzymatic function: identification of Rv1248c as a mycobacterial 2-hydroxy-3-oxoadipate synthase,” Chemistry and Biology, vol. 17, no. 4, pp. 323–332, 2010. View at Publisher · View at Google Scholar · View at Scopus
45. D. J. V. Beste and J. McFadden, “Metabolism of Mycobacterium tuberculosis,” Systems Biology of Tuberculosis, vol. 10, pp. 55–78, 2013. View at Google Scholar
46. E. J. Muñoz-Elías and J. D. McKinney, “Mycobacterium tuberculosis isocitrate lyases 1 and 2 are jointly required for in vivo growth and virulence,” Nature Medicine, vol. 11, no. 6, pp. 638–644, 2005. View at Publisher · View at Google Scholar · View at Scopus
47. K. Liu, J. Yu, and D. G. Russell, “pckA-deficient Mycobacterium bovis BCG shows attenuated virulence in mice and in macrophages,” Microbiology, vol. 149, no. 7, pp. 1829–1835, 2003. View at Google Scholar · View at Scopus
48. J. Marrero, K. Y. Rhee, D. Schnappinger, K. Pethe, and S. Ehrt, “Gluconeogenic carbon flow of tricarboxylic acid cycle intermediates is critical for Mycobacterium tuberculosis to establish and maintain infection,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 21, pp. 9819–9824, 2010. View at Publisher · View at Google Scholar · View at Scopus
49. T. Ramakrishnan, P. S. Murthy, and K. P. Gopinathan, “Intermediary metabolism of mycobacteria,” Bacteriological Reviews, vol. 36, no. 1, pp. 65–108, 1972. View at Google Scholar · View at Scopus
50. K. L. Olszewski, M. W. Mather, J. M. Morrisey et al., “Branched tricarboxylic acid metabolism in Plasmodium falciparum,” Nature, vol. 466, pp. 774–778, 2010. View at Google Scholar
51. M. J. Gardner, N. Hall, E. Fung et al., “Genome sequence of the human malaria parasite Plasmodium falciparum,” Nature, vol. 419, no. 6906, pp. 498–511, 2002. View at Publisher · View at Google Scholar · View at Scopus
52. D. Kaur, M. E. Guerin, H. Škovierová, P. J. Brennan, and M. Jackson, “Biogenesis of the cell wall and other glycoconjugates of Mycobacterium tuberculosis,” Advances in Applied Microbiology, vol. 69, pp. 23–78, 2009. View at Publisher · View at Google Scholar · View at Scopus
53. O. Neyrolles and C. Guilhot, “Recent advances in deciphering the contribution of Mycobacterium tuberculosis lipids to pathogenesis,” Tuberculosis, vol. 91, no. 3, pp. 187–195, 2011. View at Publisher · View at Google Scholar · View at Scopus
54. D. J. Murphy and J. R. Brown, “Identification of gene targets against dormant phase Mycobacterium tuberculosis infections,” BMC Infectious Diseases, vol. 7, article 84, 2007. View at Publisher · View at Google Scholar · View at Scopus
55. P. J. Brennan, “Structure, function, and biogenesis of the cell wall of Mycobacterium tuberculosis,” Tuberculosis, vol. 83, no. 1-3, pp. 91–97, 2003. View at Publisher · View at Google Scholar · View at Scopus
56. J. K. Tang, L. You, R. E. Blankenship et al., “Recent advances in mapping environmental microbial metabolisms through 13C isotopic fingerprints,” Journal of the Royal Society Interface, vol. 9, pp. 2767–2780, 2012. View at Google Scholar
57. W. Salaemae, A. Azhar, G. W. Booker, and S. W. Polyak, “Biotin biosynthesis in Mycobacterium tuberculosis: physiology, biochemistry and molecular intervention,” Protein and Cell, vol. 2, no. 9, pp. 691–695, 2011. View at Publisher · View at Google Scholar · View at Scopus
58. J. Rabinowitz, J. Purdy, L. Vastag et al., “Metabolomics in drug target discovery,” Cold Spring Harbor Symposia on Quantitative Biology, vol. 76, pp. 235–246, 2011. View at Google Scholar
59. H. C. Wong, G. Liu, Y.-M. Zhang, C. O. Rock, and J. Zheng, “The solution structure of acyl carrier protein from Mycobacterium tuberculosis,” Journal of Biological Chemistry, vol. 277, no. 18, pp. 15874–15880, 2002. View at Publisher · View at Google Scholar · View at Scopus
60. P. Domenech, C. E. Barry III, and S. T. Cole, “Mycobacterium tuberculosis in the post-genomic age,” Current Opinion in Microbiology, vol. 4, no. 1, pp. 28–34, 2001. View at Publisher · View at Google Scholar · View at Scopus
61. C. Vilchèze, H. R. Morbidoni, T. R. Weisbrod et al., “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,” Journal of Bacteriology, vol. 182, no. 14, pp. 4059–4067, 2000. View at Publisher · View at Google Scholar · View at Scopus
62. O. Zimhony, C. Vilchèze, and W. R. Jacobs Jr., “Characterization of Mycobacterium smegmatis expressing the Mycobacterium tuberculosis fatty acid synthase I (fas1) gene,” Journal of Bacteriology, vol. 186, no. 13, pp. 4051–4055, 2004. View at Publisher · View at Google Scholar · View at Scopus
63. E. Sacco, A. S. Covarrubias, H. M. O'Hare et al., “The missing piece of the type II fatty acid synthase system from Mycobacterium tuberculosis,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 37, pp. 14628–14633, 2007. View at Publisher · View at Google Scholar · View at Scopus
64. L. Kremer, L. G. Dover, S. Carrère et al., “Mycolic acid biosynthesis and enzymic characterization of the β-ketoacyl-ACP synthase A-condensing enzyme from Mycobacterium tuberculosis,” Biochemical Journal, vol. 364, no. 2, pp. 423–430, 2002. View at Publisher · View at Google Scholar · View at Scopus
65. C.-J. Zheng, M.-J. Sohn, and W.-G. Kim, “Atromentin and leucomelone, the first inhibitors specific to enoyl-ACP reductase (FabK) of Streptococcus pneumoniae,” Journal of Antibiotics, vol. 59, no. 12, pp. 808–812, 2006. View at Publisher · View at Google Scholar · View at Scopus
66. G. Lamichhane, “Novel targets in M. tuberculosis: search for new drugs,” Trends in Molecular Medicine, vol. 17, no. 1, pp. 25–33, 2011. View at Publisher · View at Google Scholar · View at Scopus
67. N. A. Kruh, J. Troudt, A. Izzo, J. Prenni, and K. M. Dobos, “Portrait of a pathogen: the Mycobacterium tuberculosis proteome In vivo,” PLoS ONE, vol. 5, no. 11, Article ID e13938, 2010. View at Publisher · View at Google Scholar · View at Scopus
68. R. Van Crevel, J. Kleinnijenhuis, M. Oosting, L. A. B. Joosten, and M. G. Netea, “Innate immune recognition of Mycobacterium tuberculosis,” Clinical and Developmental Immunology, vol. 2011, Article ID 405310, 12 pages, 2011. View at Publisher · View at Google Scholar · View at Scopus
69. G. P. Bisson, C. Mehaffy, C. Broeckling et al., “Upregulation of the phthiocerol dimycocerosate biosynthetic pathway by rifampin-resistant, rpoB mutant Mycobacterium tuberculosis,” Journal of Bacteriology, vol. 194, pp. 6441–6452, 2012. View at Google Scholar
70. N. C. Gey Van Pittius, J. Gamieldien, W. Hide, G. D. Brown, R. J. Siezen, and A. D. Beyers, “The ESAT-6 gene cluster of Mycobacterium tuberculosis and other high G+C Gram-positive bacteria,” Genome Biology, vol. 2, no. 10, 2001. View at Google Scholar · View at Scopus
71. A. M. Abdallah, N. C. Gey van Pittius, P. A. DiGiuseppe Champion et al., “Type VII secretion—mycobacteria show the way,” Nature Reviews Microbiology, vol. 5, no. 11, pp. 883–891, 2007. View at Publisher · View at Google Scholar · View at Scopus
72. A. Serafini, F. Boldrin, G. Palù, and R. Manganelli, “Characterization of a Mycobacterium tuberculosis ESX-3 conditional mutant: essentiality and rescue by iron and zinc,” Journal of Bacteriology, vol. 191, no. 20, pp. 6340–6344, 2009. View at Publisher · View at Google Scholar · View at Scopus
73. M. S. Siegrist, M. Unnikrishnan, M. J. McConnell et al., “Mycobacterial Esx-3 is required for mycobactin-mediated iron acquisition,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 44, pp. 18792–18797, 2009. View at Publisher · View at Google Scholar · View at Scopus
74. G. M. Rodriguez, M. I. Voskuil, B. Gold, G. K. Schoolnik, and I. Smith, “ideR, an essential gene in Mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response,” Infection and Immunity, vol. 70, no. 7, pp. 3371–3381, 2002. View at Publisher · View at Google Scholar · View at Scopus
75. C. M. Sassetti and E. J. Rubin, “Genetic requirements for mycobacterial survival during infection,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 22, pp. 12989–12994, 2003. View at Publisher · View at Google Scholar · View at Scopus
76. J. J. De Voss, K. Rutter, B. G. Schroeder, and C. E. Barry III, “Iron acquisition and metabolism by mycobacteria,” Journal of Bacteriology, vol. 181, no. 15, pp. 4443–4451, 1999. View at Google Scholar · View at Scopus
77. A. Torosantucci, P. Chiani, F. De Bernardis, A. Cassone, J. A. Calera, and R. Calderone, “Deletion of the two-component histidine kinase gene (CHK1) of Candida albicans contributes to enhanced growth inhibition and killing by human neutrophils in vitro,” Infection and Immunity, vol. 70, no. 2, pp. 985–987, 2002. View at Publisher · View at Google Scholar · View at Scopus
78. C.-M. Kang, D. W. Abbott, T. P. Sang, C. C. Dascher, L. C. Cantley, and R. N. Husson, “The Mycobacterium tuberculosis serine/threonine kinases PknA and PknB: substrate identification and regulation of cell shape,” Genes and Development, vol. 19, no. 14, pp. 1692–1704, 2005. View at Publisher · View at Google Scholar · View at Scopus
79. Y. Av-Gay and M. Everett, “The eukaryotic-like Ser/Thr protein kinases of Mycobacterium tuberculosis,” Trends in Microbiology, vol. 8, no. 5, pp. 238–244, 2000. View at Publisher · View at Google Scholar · View at Scopus
80. A. Narayan, P. Sachdeva, K. Sharma, A. K. Saini, A. K. Tyagi, and Y. Singh, “Serine threonine protein kinases of mycobacterial genus: phylogeny to function,” Physiological Genomics, vol. 29, no. 1, pp. 66–75, 2007. View at Publisher · View at Google Scholar · View at Scopus
81. A. Koul, A. Choidas, A. K. Tyagi, K. Drlica, Y. Singh, and A. Ullrich, “Serine/threonine protein kinases PknF and PknG of Mycobacterium tuberculosis: characterization and localization,” Microbiology, vol. 147, no. 8, pp. 2307–2314, 2001. View at Google Scholar · View at Scopus
82. N. C. Gey van Pittius, S. L. Sampson, H. Lee, Y. Kim, P. D. van Helden, and R. M. Warren, “Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions,” BMC Evolutionary Biology, vol. 6, article 95, 2006. View at Publisher · View at Google Scholar · View at Scopus
83. D. Bottai and R. Brosch, “Mycobacterial PE, PPE and ESX clusters: novel insights into the secretion of these most unusual protein families,” Molecular Microbiology, vol. 73, no. 3, pp. 325–328, 2009. View at Publisher · View at Google Scholar · View at Scopus
84. A. M. Abdallah, T. Verboom, E. M. Weerdenburg et al., “PPE and PE-PGRS proteins of Mycobacterium marinum are transported via the type VII secretion system ESX-5,” Molecular Microbiology, vol. 73, no. 3, pp. 329–340, 2009. View at Publisher · View at Google Scholar · View at Scopus
85. R. Simeone, D. Bottai, and R. Brosch, “ESX/type VII secretion systems and their role in host-pathogen interaction,” Current Opinion in Microbiology, vol. 12, no. 1, pp. 4–10, 2009. View at Publisher · View at Google Scholar · View at Scopus
86. S. E. Converse and J. S. Cox, “A protein secretion pathway critical for Mycobacterium tuberculosis virulence is conserved and functional in Mycobacterium smegmatis,” Journal of Bacteriology, vol. 187, no. 4, pp. 1238–1245, 2005. View at Publisher · View at Google Scholar · View at Scopus
87. D. Chatterjee and K.-H. Khoo, “Mycobacterial lipoarabinomannan: an extraordinary lipoheteroglycan with profound physiological effects,” Glycobiology, vol. 8, no. 2, pp. 113–120, 1998. View at Publisher · View at Google Scholar · View at Scopus
88. I. W. Chen and C. F. Charalampous, “Biochemical studies on inositol. IX. D-Inositol 1-phosphate as intermediate in the biosynthesis of inositol from glucose 6-phosphate, and characteristics of two reactions in this biosynthesis,” Journal of Biological Chemistry, vol. 241, no. 10, pp. 2194–2199, 1966. View at Google Scholar · View at Scopus
89. M. B. Reed, S. Gagneux, K. DeRiemer, P. M. Small, and C. E. Barry III, “The W-Beijing lineage of Mycobacterium tuberculosis overproduces triglycerides and has the DosR dormancy regulon constitutively upregulated,” Journal of Bacteriology, vol. 189, no. 7, pp. 2583–2589, 2007. View at Publisher · View at Google Scholar · View at Scopus
90. A. Vercellone, J. Nigou, and G. Puzo, “Relationships between the structure and the roles of lipoarabinomannans and related glycoconjugates in tuberculosis pathogenesis,” Frontiers in Bioscience, vol. 3, pp. e149–e163, 1998. View at Google Scholar · View at Scopus
91. M. Viveiros and L. Amaral, “Enhancement of antibiotic activity against poly-drug resistant Mycobacterium tuberculosis by phenothiazines,” International Journal of Antimicrobial Agents, vol. 17, no. 3, pp. 225–228, 2001. View at Publisher · View at Google Scholar · View at Scopus
92. Y. Zhang, “The magic bullets and tuberculosis drug targets,” Annual Review of Pharmacology and Toxicology, vol. 45, pp. 529–564, 2005. View at Publisher · View at Google Scholar · View at Scopus
93. G. D. Wright, “Bacterial resistance to antibiotics: enzymatic degradation and modification,” Advanced Drug Delivery Reviews, vol. 57, no. 10, pp. 1451–1470, 2005. View at Publisher · View at Google Scholar · View at Scopus
94. N. Zhang, J. B. Torrelles, M. R. McNeil et al., “The Emb proteins of mycobacteria direct arabinosylation of lipoarabinomannan and arabinogalactan via an N-terminal recognition region and a C-terminal synthetic region,” Molecular Microbiology, vol. 50, no. 1, pp. 69–76, 2003. View at Publisher · View at Google Scholar · View at Scopus
95. A. Telenti, D. Lowrie, L. Matter et al., “Detection of rifampicin-resistance mutation in Mycobacterium tuberculosis,” The Lancet, vol. 341, no. 8846, pp. 647–650, 1993. View at Publisher · View at Google Scholar · View at Scopus
96. Y. Zhang, B. Heym, B. Allen, D. Young, and S. Cole, “The catalase-peroxidase gene and isoniazid resistance of Mycobacterium tuberculosis,” Nature, vol. 358, no. 6387, pp. 591–593, 1992. View at Publisher · View at Google Scholar · View at Scopus
97. A. Somoskovi, L. M. Parsons, and M. Salfinger, “The molecular basis of resistance to isoniazid, rifampin, and pyrazinamide in Mycobacterium tuberculosis,” Respiratory Research, vol. 2, no. 3, pp. 164–168, 2001. View at Publisher · View at Google Scholar · View at Scopus
98. H. Rinder, K. T. Mieskes, E. Tortoli et al., “Detection of embB codon 306 mutations in ethambutol resistant Mycobacterium tuberculosis directly from sputum samples: a low-cost, rapid approach,” Molecular and Cellular Probes, vol. 15, no. 1, pp. 37–42, 2001. View at Publisher · View at Google Scholar · View at Scopus
99. P. Sheen, P. Ferrer, R. H. Gilman et al., “Effect of pyrazinamidase activity on pyrazinamide resistance in Mycobacterium tuberculosis,” Tuberculosis, vol. 89, no. 2, pp. 109–113, 2009. View at Publisher · View at Google Scholar · View at Scopus
100. C. Raynaud, M.-A. Lanéelle, R. H. Senaratne, P. Draper, G. Lanéelle, and M. Daffé, “Mechanisms of pyrazinamide resistance in mycobacteria: importance of lack of uptake in addition to lack of pyrazinamidase activity,” Microbiology, vol. 145, no. 6, pp. 1359–1367, 1999. View at Google Scholar · View at Scopus
101. R. M. Anthony, A. R. J. Schuitema, I. L. Bergval, T. J. Brown, L. Oskam, and P. R. Klatser, “Acquisition of rifabutin resistance by a rifampicin resistant mutant of Mycobacterium tuberculosis involves an unusual spectrum of mutations and elevated frequency,” Annals of Clinical Microbiology and Antimicrobials, vol. 4, article 9, 2005. View at Publisher · View at Google Scholar · View at Scopus
102. R. Garrett and C. Grisham, “Biochemistry,” in The Synthesis and Degradation of Nucleotides, pp. 853–878, Thomson Brooks/Cole, Belmont, Calif, USA, 2005. View at Google Scholar
103. J. Nigou, M. Gilleron, and G. Puzo, “Lipoarabinomannans: from structure to biosynthesis,” Biochimie, vol. 85, no. 1-2, pp. 153–166, 2003. View at Publisher · View at Google Scholar · View at Scopus
104. M. S. Glickman and W. R. Jacobs Jr., “Microbial pathogenesis of Mycobacterium tuberculosis: dawn of a discipline,” Cell, vol. 104, no. 4, pp. 477–485, 2001. View at Publisher · View at Google Scholar · View at Scopus
105. L. Shi, C. D. Sohaskey, C. Pfeiffer et al., “Carbon flux rerouting during Mycobacterium tuberculosis growth arrest,” Molecular Microbiology, vol. 78, no. 5, pp. 1199–1215, 2010. View at Publisher · View at Google Scholar · View at Scopus
106. E. J. Muñoz-Elías, A. M. Upton, J. Cherian, and J. D. McKinney, “Role of the methylcitrate cycle in Mycobacterium tuberculosis metabolism, intracellular growth, and virulence,” Molecular Microbiology, vol. 60, no. 5, pp. 1109–1122, 2006. View at Publisher · View at Google Scholar · View at Scopus
107. D. T. Loots, “An altered M. tuberculosis metabolome induced by katG mutations resulting in isoniazid-resistance,” Antimicrobial Agents and Chemotherapy, 2014. View at Publisher · View at Google Scholar
108. M. I. Voskuil, D. Schnappinger, K. C. Visconti et al., “Inhibition of respiration by nitric oxide induces a Mycobacterium tuberculosis dormancy program,” Journal of Experimental Medicine, vol. 198, no. 5, pp. 705–713, 2003. View at Publisher · View at Google Scholar · View at Scopus
109. S. Watanabe, M. Zimmermann, M. B. Goodwin, U. Sauer, C. E. Barry, and H. I. Boshoff, “Fumarate reductase activity maintains an energized membrane in anaerobic Mycobacterium tuberculosis,” PLoS Pathogens, vol. 7, no. 10, Article ID e1002287, 2011. View at Publisher · View at Google Scholar · View at Scopus
110. S. Malm, Y. Tiffert, J. Micklinghoff et al., “The roles of the nitrate reductase NarGHJI, the nitrite reductase NirBD and the response regulator GlnR in nitrate assimilation of Mycobacterium tuberculosis,” Microbiology, vol. 155, no. 4, pp. 1332–1339, 2009. View at Publisher · View at Google Scholar · View at Scopus
111. R. W. Honaker, A. Stewart, S. Schittone, A. Izzo, M. R. Klein, and M. I. Voskuil, “Mycobacterium bovis BCG vaccine strains lack narK2 and narX induction and exhibit altered phenotypes during dormancy,” Infection and Immunity, vol. 76, no. 6, pp. 2587–2593, 2008. View at Publisher · View at Google Scholar · View at Scopus
112. M. Y. Hirai, M. Yano, D. B. Goodenowe et al., “Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 27, pp. 10205–10210, 2004. View at Publisher · View at Google Scholar · View at Scopus
113. M. Stitt and A. R. Fernie, “From measurements of metabolites to metabolomics: an “on the fly” perspective illustrated by recent studies of carbon-nitrogen interactions,” Current Opinion in Biotechnology, vol. 14, no. 2, pp. 136–144, 2003. View at Publisher · View at Google Scholar · View at Scopus
114. S. Hemaiswarya, A. K. Kruthiventi, and M. Doble, “Synergism between natural products and antibiotics against infectious diseases,” Phytomedicine, vol. 15, no. 8, pp. 639–652, 2008. View at Publisher · View at Google Scholar · View at Scopus
115. K. L. Seib, G. Dougan, and R. Rappuoli, “The key role of genomics in modern vaccine and drug design for emerging infectious diseases,” PLoS Genetics, vol. 5, no. 10, Article ID e1000612, 2009. View at Publisher · View at Google Scholar · View at Scopus