Systems biology approaches to understanding mycobacterial survival mechanisms

Drug Discovery Today: Disease Mechanisms

Volumn 7, Issue 1, 2010, Pages

  Boshoff, Helena I M ^a   Lun, Desmond S ^b  

^a Building 33   (United States)

^b UNIVERSITY OF SOUTH AUSTRALIA   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL METABOLISM; BACTERIAL SURVIVAL; GENOME ANALYSIS; HOST PARASITE INTERACTION; HUMAN; METABOLOMICS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PROTEOMICS; REVIEW; SYSTEMS BIOLOGY; TRANSCRIPTOMICS; TUBERCULOSIS;

EID: 78049306942     PISSN: 17406765     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ddmec.2010.09.008     Document Type: Review

References (83)

1. L. Rizzetto, and D. Cavalieri A systems biology approach to the mutual interaction between yeast and the immune system Immunobiology 215 9-10 2010 762 769
2. G. Napolitani Selected Toll-like receptor agonist combinations synergistically trigger a T helper type 1-polarizing program in dendritic cells Nat. Immunol. 6 2005 769 776
3. D.E. Kirschner Tuberculosis: global approaches to a global disease Curr. Opin. Biotechnol. 21 4 2010 524 531
4. D.E. Sullivan Data integration for dynamic and sustainable systems biology resources: challenges and lessons learned Chem. Biodivers. 7 5 2010 1124 1141
5. A. Wang A systemic network for Chlamydia pneumoniae entry into human cells J. Bacteriol. 192 11 2010 2809 2815
6. Y.C. Wang Global screening of potential Candida albicans biofilmrelated transcription factors via network comparison BMC Bioinformat. 11 2010 53
7. S.M. Hingley-Wilson Survival perspectives from the world's most successful pathogen, Mycobacterium tuberculosis Nat. Immunol. 4 2003 949 955
8. D.E. Sturdevant Host-microbe interaction systems biology: lifecycle transcriptomics and comparative genomics Future Microbiol. 5 2 2010 205 219
9. J. Bacon Lipid composition and transcriptional response of Mycobacterium tuberculosis grown under iron-limitation in continuous culture: identification of a novel wax ester Microbiology 153 Pt 5 2007 1435 1444
10. J.C. Betts Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling Mol. Microbiol. 43 2002 717 731
11. J.L. Dahl The role of RelMtb-mediated adaptation to stationary phase in long-term persistence of Mycobacterium tuberculosis in mice Proc. Natl. Acad. Sci. U. S. A. 100 2003 10026 10031
12. C. Deb A novel in vitro multiple-stress dormancy model for Mycobacterium tuberculosis generates a lipid-loaded, drug-tolerant, dormant pathogen PLoS One 4 2009 e6077
13. M.A. Fisher Microarray analysis of the Mycobacterium tuberculosis transcriptional response to the acidic conditions found in phagosomes J. Bacteriol. 184 2002 4025 4032
14. T.R. Rustad The enduring hypoxic response of Mycobacterium tuberculosis PLoS One 3 2008 e1502
15. U. Schwab Transcriptional responses of Mycobacterium tuberculosis to lung surfactant Microb. Pathog. 46 2009 185 193
16. A.M. Talaat The temporal expression profile of Mycobacterium tuberculosis infection in mice Proc. Natl. Acad. Sci. U. S. A. 101 2004 4602 4607
17. A.M. Talaat Mycobacterial bacilli are metabolically active during chronic tuberculosis in murine lungs: insights from genome-wide transcriptional profiling J. Bacteriol. 189 2007 4265 4274
18. M.I. Voskuil Inhibition of respiration by nitric oxide induces a Mycobacterium tuberculosis dormancy program J. Exp. Med. 198 2003 705 713
19. H.I.M. Boshoff The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism J. Biol. Chem. 279 2004 40174 40184
20. K.H. Rohde Mycobacterium tuberculosis invasion of macrophages: linking bacterial gene expression to environmental cues Cell Host Microbe 2 2007 352 364
21. D. Schnappinger Transcriptional adaptation of Mycobacterium tuberculosis within macrophages: insights into the phagosomal environment J. Exp. Med. 198 2003 693 704
22. R.L. Leistikow The Mycobacterium tuberculosis DosR regulon assists in metabolic homeostasis and enables rapid recovery from nonrespiring dormancy J. Bacteriol. 192 6 2010 1662 1670
23. H.D. Park Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis Mol. Microbiol. 48 2003 833 843
24. A. Singh Mycobacterium tuberculosis WhiB3 maintains redox homeostasis by regulating virulence lipid anabolism to modulate macrophage response PLoS Pathog. 5 2009 e1000545
25. N. Banaiee Regulation of Mycobacterium tuberculosis whiB3 in the mouse lung and macrophages Infect. Immun. 74 2006 6449 6457
26. S.L. Kendall A highly conserved transcriptional repressor controls a large regulon involved in lipid degradation in Mycobacterium smegmatis and Mycobacterium tuberculosis Mol. Microbiol. 65 2007 684 699
27. S.T. Park Regulation of the SigH stress response regulon by an essential protein kinase in Mycobacterium tuberculosis Proc. Natl. Acad. Sci. U. S. A. 105 2008 13105 13110
28. G.M. Rodriguez Control of iron metabolism in Mycobacterium tuberculosis Trends Microbiol. 14 2006 320 327
29. J. Gonzalo-Asensio PhoP: a missing piece in the intricate puzzle of Mycobacterium tuberculosis virulence PLoS One 3 2008 e3496
30. N.J. Garton Cytological and transcript analyses reveal fat and lazy persister-like bacilli in tuberculous sputum PLoS Med. 5 2008 e75
31. H. Rachman Unique transcriptome signature of Mycobacterium tuberculosis in pulmonary tuberculosis Infect. Immun. 74 2006 1233 1242
32. G.J. Ryan Multiple M. tuberculosis phenotypes in mouse and guinea pig lung tissue revealed by a dual-staining approach PLoS One 5 6 2010 e11108
33. J. Timm Differential expression of iron-, carbon-, and oxygen-responsive mycobacterial genes in the lungs of chronically infected mice and tuberculosis patients Proc. Natl. Acad. Sci. U. S. A. 100 2003 14321 14326
34. J. Baumbach CoryneRegNet 4.0 - a reference database for corynebacterial gene regulatory networks BMC Bioinformat. 8 2007 429
35. J. Krawczyk From Corynebacterium glutamicum to Mycobacterium tuberculosis - towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet Nucleic Acids Res. 37 2009 e97
36. G. Balazsi The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest Mol. Syst. Biol. 4 2008 225
37. T.B. Reddy TB database: an integrated platform for tuberculosis research Nucleic Acids Res. 37 Database issue 2009 D499 508
38. M. Caws The influence of host and bacterial genotype on the development of disseminated disease with Mycobacterium tuberculosis PLoS Pathog. 4 2008 e1000034
39. A.G. Tsolaki Genomic deletions classify the Beijing/W strains as a distinct genetic lineage of Mycobacterium tuberculosis J. Clin. Microbiol. 43 2005 3185 3191
40. A.G. Tsolaki Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains Proc. Natl. Acad. Sci. U. S. A. 101 2004 4865 4870
41. S. Homolka Functional genetic diversity among Mycobacterium tuberculosis complex clinical isolates: delineation of conserved core and lineage-specific transcriptomes during intracellular survival PLoS Pathog. 6 7 2010 e1000988
42. R. Hershberg High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography PLoS Biol. 6 2008 e311
43. A. Toledo-Arana The Listeria transcriptional landscape from saprophytism to virulence Nature 459 2009 950 956
44. K.B. Arnvig, and D.B. Young Identification of small RNAs in Mycobacterium tuberculosis Mol. Microbiol. 73 2009 397 408
45. A.L. Goodman Identifying genetic determinants needed to establish a human gut symbiont in its habitat Cell Host Microbe 6 2009 279 289
46. G.C. Langridge Simultaneous assay of every Salmonella typhi gene using one million transposon mutants Genome Res. 19 2009 2308 2316
47. J.D. Gawronski Tracking insertion mutants within libraries by deep sequencing and a genome-wide screen for Haemophilus genes required in the lung Proc. Natl. Acad. Sci. U. S. A. 106 2009 16422 16427
48. T. van Opijnen Tn-seq: high-throughput parallel sequencing for fitness and genetic interaction studies in microorganisms Nat. Methods 6 2009 767 772
49. G. Lamichhane A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: application to Mycobacterium tuberculosis Proc. Natl. Acad. Sci. U. S. A. 100 2003 7213 7218
50. C.M. Sassetti Genes required for mycobacterial growth defined by high density mutagenesis Mol. Microbiol. 48 2003 77 84
51. G. Lamichhane Designer arrays for defined mutant analysis to detect genes essential for survival of Mycobacterium tuberculosis in mouse lungs Infect. Immun. 73 2005 2533 2540
52. C.M. Sassetti, and E.J. Rubin Genetic requirements for mycobacterial survival during infection Proc. Natl. Acad. Sci. U. S. A. 100 2003 12989 12994
53. A.K. Pandey, and C.M. Sassetti Mycobacterial persistence requires the utilization of host cholesterol Proc. Natl. Acad. Sci. U. S. A. 105 2008 4376 4380
54. A.P. Bhavsar Proteomics as a probe of microbial pathogenesis and its molecular boundaries Future Microbiol. 5 2 2010 253 265
55. S. Chavadi Global effects of inactivation of the pyruvate kinase gene in the Mycobacterium tuberculosis complex J. Bacteriol. 191 2009 7545 7553
56. S. Sinha Proteome analysis of the plasma membrane of Mycobacterium tuberculosis Comp. Funct. Genom. 3 2002 470 483
57. J. Watrous Expansion of the mycobacterial 'PUPylome' Mol. Biosyst. 6 2 2010 376 385
58. K.Y. Rhee S-nitroso proteome of Mycobacterium tuberculosis: enzymes of intermediary metabolism and antioxidant defense Proc. Natl. Acad. Sci. U. S. A. 102 2005 467 472
59. P.K. Rao, and Q. Li Principal component analysis of proteome dynamics in iron-starved Mycobacterium tuberculosis J. Proteomics Bioinform. 2 2009 19 31
60. P.K. Rao Protein dynamics in iron-starved Mycobacterium tuberculosis revealed by turnover and abundance measurement using hybrid-linear ion trap-Fourier transform mass spectrometry Anal. Chem. 80 2008 6860 6869
61. S.M. Chowdhury A method for investigating protein-protein interactions related to Salmonella typhimurium pathogenesis J. Proteome Res. 8 2009 1504 1514
62. T. Cui Uncovering new signaling proteins and potential drug targets through the interactome analysis of Mycobacterium tuberculosis BMC Genomics 10 2009 118
63. K. Raman targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome, and genome-scale structural analysis BMC Syst. Biol. 2 2008 109
64. S. Rodrigue Identification of mycobacterial σ binding sites by chromatin immunoprecipitation assays J. Bacteriol. 189 2007 1505 1513
65. D.S. Lun A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data Genome Biol. 10 2009 R142
66. E.R. Mardis ChIP-seq: welcome to the new frontier Nat. Methods 4 2007 613 614
67. L.P. de Carvalho Activity-based metabolomic profiling of enzymatic function: identification of Rv1248c as a mycobacterial 2-hydroxy-3-oxoadipate synthase Chem. Biol. 17 4 2010 323 332
68. J. Marrero Gluconeogenic carbon flow of tricarboxylic acid cycle intermediates is critical for Mycobacterium tuberculosis to establish and maintain infection Proc. Natl. Acad. Sci. U. S. A. 107 21 2010 9819 9824
69. M. Jain Lipidomics reveals control of Mycobacterium tuberculosis virulence lipids via metabolic coupling Proc. Natl. Acad. Sci. U. S. A. 104 2007 5133 5138
70. V.K. Singh, and I. Ghosh Kinetic modeling of tricarboxylic acid cycle and glyoxylate bypass in Mycobacterium tuberculosis, and its application to assessment of drug targets Theor. Biol. Med. Model. 3 2006 27
71. C.B. Milne Accomplishments in genome-scale in silico modeling for industrial and medical biotechnology Biotechnol. J. 4 2009 1653 1670
72. A.M. Feist A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information Mol. Syst. Biol. 3 2007 121
73. J.D. Orth What is flux balance analysis? Nat. Biotechnol. 28 2010 245 248
74. K. Raman, and N. Chandra Flux balance analysis of biological systems: applications and challenges Briefings Bioinformat. 10 2009 435 449
75. R. Mahadevan Dynamic flux balance analysis of diauxic growth in Escherichia coli Biophys. J. 83 2002 1331 1340
76. J.S. Edwards In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data Nat. Biotechnol. 19 2001 125 130
77. K. Raman Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs PLoS Comput. Biol. 1 2005 e46
78. D.J. Beste GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism Genome Biol. 8 2007 R89
79. N. Jamshidi, and B.O. Palsson Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets BMC Syst. Biol. 1 2007 26
80. C. Colijn Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production PLoS Comput. Biol. 5 2009 e1000489
81. P.C. Karakousis Altered expression of isoniazid-regulated genes in drug-treated dormant Mycobacterium tuberculosis J. Antimicrob. Chemoth. 61 2008 323 331
82. X. Fang A systems biology framework for modeling metabolic enzyme inhibition of Mycobacterium tuberculosis BMC Syst. Biol. 3 2009 92
83. L.E. Via Tuberculous granulomas are hypoxic in guinea pigs, rabbits, and nonhuman primates Infect. Immun. 76 2008 2333 2340