A novel and comprehensive meta-analysis of the M. tuberculosis gene expression and …

• Abstract
• Background
• Results
• Discussion
• Conclusion
• Methods
• References
• Figures
• Tables

Biology Articles » Microbiology » Microbial Genetics » Identification of gene targets against dormant phase Mycobacterium tuberculosis infections » References

References

- Identification of gene targets against dormant phase Mycobacterium tuberculosis infections

1.   Dye C, Watt CJ, Bleed DM, Hosseini SM, Raviglione MC: Evolution of tuberculosis control and prospects for reducing tuberculosis incidence, prevalence, and deaths globally.JAMA 2005, 293:2767-2775.       2.   Wayne LG, Sohaskey CD: Nonreplicating persistence of mycobacterium tuberculosis.Annu Rev Microbiol 2001, 55:139-163.       3.   Lillebaek T, Dirksen A, Vynnycky E, Baess I, Thomsen VO, Andersen AB: Stability of DNA patterns and evidence of Mycobacterium tuberculosis reactivation occurring decades after the initial infection.J Infect Dis 2003, 188:1032-1039.       4.   Mitchison DA: Antimicrobial therapy of tuberculosis: justification for currently recommended treatment regimens.Semin Respir Crit Care Med 2004, 25:307-315.       5.   Mitchison DA: The diagnosis and therapy of tuberculosis during the past 100 years.Am J Respir Crit Care Med 2005, 171:699-706.       6.   Zhang Y: The magic bullets and tuberculosis drug targets.Annu Rev Pharmacol Toxicol 2005, 45:529-564.       7.   van Helden PD, Donald PR, Victor TC, Schaaf HS, Hoal EG, Walzl G, Warren RM: Antimicrobial resistance in tuberculosis: an international perspective.Expert Review of Anti-infective Therapy 2006, 4:759-766.       8.   Wayne LG, Hayes LG: An in vitro model for sequential study of shiftdown of Mycobacterium tuberculosis through two stages of nonreplicating persistence.Infect Immun 1996, 64:2062-2069.       9.   Boshoff HI, Barry CE III: Tuberculosis - metabolism and respiration in the absence of growth.Nat Rev Microbiol 2005, 3:70-80.       10.   Rhoades ER, Frank AA, Orme IM: Progression of chronic pulmonary tuberculosis in mice aerogenically infected with virulent Mycobacterium tuberculosis.Tuber Lung Dis 1997, 78:57-66.       11.   Lamichhane G, Tyagi S, Bishai WR: Designer arrays for defined mutant analysis to detect genes essential for survival of Mycobacterium tuberculosis in mouse lungs.Infect Immun 2005, 73:2533-2540.       12.   Rengarajan J, Bloom BR, Rubin EJ: Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages.Proc Natl Acad Sci U S A 2005, 102:8327-8332.       13.   Sassetti CM, Boyd DH, Rubin EJ: Genes required for mycobacterial growth defined by high density mutagenesis.Mol Microbiol 2003, 48:77-84.       14.   Sassetti CM, Rubin EJ: Genetic requirements for mycobacterial survival during infection.Proc Natl Acad Sci U S A 2003, 100:12989-12994.       15.   Hasan S, Daugelat S, Rao PS, Schreiber M: Prioritizing genomic drug targets in pathogens: application to Mycobacterium tuberculosis.PLoS Comput Biol 2006, 2:e61.       16.   Payne DJ, Gwynn MN, Holmes DJ, Pompliano DL: Drugs for bad bugs: confronting the challenges of antibacterial discovery.Nat Rev Drug Discov 2007, 6:29-40.       17.   Cole ST, Brosch R, Parkhill J, Garnier T, Churcher C, Harris D, Gordon SV, Eiglmeier K, Gas S, Barry CE III, 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 MA, Rajandream MA, Rogers J, Rutter S, Seeger K, Skelton J, Squares R, Squares S, Sulston JE, Taylor K, Whitehead S, Barrell BG: Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.Nature 1998, 393:537-544.       18.   Voskuil MI, Schnappinger D, Visconti KC, Harrell MI, Dolganov GM, Sherman DR, Schoolnik GK: Inhibition of respiration by nitric oxide induces a Mycobacterium tuberculosis dormancy program.J Exp Med 2003, 198:705-713.       19.   Park HD, Guinn KM, Harrell MI, Liao R, Voskuil MI, Tompa M, Schoolnik GK, Sherman DR: Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis.Mol Microbiol 2003, 48:833-843.       20.   Kendall SL, Movahedzadeh F, Rison SC, Wernisch L, Parish T, Duncan K, Betts JC, Stoker NG: The Mycobacterium tuberculosis dosRS two-component system is induced by multiple stresses.Tuberculosis (Edinb ) 2004, 84:247-255.       21.   Ohno H, Zhu G, Mohan VP, Chu D, Kohno S, Jacobs WR Jr., Chan J: The effects of reactive nitrogen intermediates on gene expression in Mycobacterium tuberculosis.Cell Microbiol 2003, 5:637-648.       22.   Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, Koonin E, Krylov D, Mazumder R, Mekhedov S, Nikolskaya A, Rao BS, Smirnov S, Sverdlov A, Vasudevan S, Wolf Y, Yin J, Natale D: The COG database: an updated version includes eukaryotes.BMC Bioinformatics 2003, 4:41.       23.   Tatusov RL, Koonin EV, Lipman DJ: A Genomic Perspective on Protein Families.Science 1997, 278:631-637.       24.   Marchler-Bauer A, Bryant SH: CD-Search: protein domain annotations on the fly.Nucl Acids Res 2004, 32:W327-W331.       25.   Wayne LG: Synchronized replication of Mycobacterium tuberculosis.Infect Immun 1977, 17:528-530.       26.   Warner DF, Mizrahi V: Tuberculosis Chemotherapy: the Influence of Bacillary Stress and Damage Response Pathways on Drug Efficacy.Clin Microbiol Rev 2006, 19:558-570.       27.   Shi L, Sohaskey CD, Kana BD, Dawes S, North RJ, Mizrahi V, Gennaro ML: Changes in energy metabolism of Mycobacterium tuberculosis in mouse lung and under in vitro conditions affecting aerobic respiration.Proc Natl Acad Sci U S A 2005, 102:15629-15634.       28.   Hu YM, Butcher PD, Sole K, Mitchison DA, Coates AR: Protein synthesis is shutdown in dormant Mycobacterium tuberculosis and is reversed by oxygen or heat shock.FEMS Microbiol Lett 1998, 158:139-145.       29.   Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, Monahan IM, Dolganov G, Efron B, Butcher PD, Nathan C, Schoolnik GK: Transcriptional Adaptation of Mycobacterium tuberculosis within Macrophages: Insights into the Phagosomal Environment.J Exp Med 2003, 198:693-704.       30.   Hampshire T, Soneji S, Bacon J, James BW, Hinds J, Laing K, Stabler RA, Marsh PD, Butcher PD: Stationary phase gene expression of Mycobacterium tuberculosis following a progressive nutrient depletion: a model for persistent organisms?Tuberculosis (Edinb ) 2004, 84:228-238.       31.   Voskuil MI, Visconti KC, Schoolnik GK: Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy.Tuberculosis (Edinb ) 2004, 84:218-227.       32.   HURFORD JV, VALENTINE WH: Viable tubercle bacilli in closed lesions.Tubercle 1957, 38:194-198.       33.   SALKIN D, Wayne LG: The bacteriology of resected tuberculous pulmonary lesions. I. The effect of interval between reversal of infectiousness and subsequent surgery.Am Rev Tuberc 1956, 74:376-387.       34.   Kaplan G, Post FA, Moreira AL, Wainwright H, Kreiswirth BN, Tanverdi M, Mathema B, Ramaswamy SV, Walther G, Steyn LM, Barry CE III, Bekker LG: Mycobacterium tuberculosis growth at the cavity surface: a microenvironment with failed immunity.Infect Immun 2003, 71:7099-7108.       35.   Mitchison DA: The search for new sterilizing anti-tuberculosis drugs.Front Biosci 2004, 9:1059-1072.       36.   Sherman DR, Voskuil M, Schnappinger D, Liao R, Harrell MI, Schoolnik GK: Regulation of the Mycobacterium tuberculosis hypoxic response gene encoding alpha -crystallin.Proc Natl Acad Sci U S A 2001, 98:7534-7539.       37.   Cho SH, Goodlett D, Franzblau S: ICAT-based comparative proteomic analysis of non-replicating persistent Mycobacterium tuberculosis.Tuberculosis (Edinb ) 2006, 86:445-460.       38.   Malhotra V, Sharma D, Ramanathan VD, Shakila H, Saini DK, Chakravorty S, Das TK, Li Q, Silver RF, Narayanan PR, Tyagi JS: Disruption of response regulator gene, devR, leads to attenuation in virulence of Mycobacterium tuberculosis.FEMS Microbiol Lett 2004, 231:237-245.       39.   Boon C, Dick T: Mycobacterium bovis BCG response regulator essential for hypoxic dormancy.J Bacteriol 2002, 184:6760-6767.       40.   MacMicking JD, North RJ, LaCourse R, Mudgett JS, Shah SK, Nathan CF: Identification of nitric oxide synthase as a protective locus against tuberculosis.Proc Natl Acad Sci U S A 1997, 94:5243-5248.        41.   Darwin KH, Nathan CF: Role for nucleotide excision repair in virulence of Mycobacterium tuberculosis.Infect Immun 2005, 73:4581-4587.       42.   Stock AM, Robinson VL, Goudreau PN: Two-component signal transduction.Annu Rev Biochem 2000, 69:183-215.       43.   Parkinson JS, Kofoid EC: Communication modules in bacterial signaling proteins.Annu Rev Genet 1992, 26:71-112.       44.   Barrett JF, Hoch JA: Two-component signal transduction as a target for microbial anti-infective therapy.Antimicrob Agents Chemother 1998, 42:1529-1536.       45.   Macielag MJ, Goldschmidt R: Inhibitors of bacterial two-component signalling systems.Expert Opin Investig Drugs 2000, 9:2351-2369.       46.   Roberts DM, Liao RP, Wisedchaisri G, Hol WG, Sherman DR: Two sensor kinases contribute to the hypoxic response of Mycobacterium tuberculosis.J Biol Chem 2004, 279:23082-23087.       47.   Saini DK, Malhotra V, Dey D, Pant N, Das TK, Tyagi JS: DevR-DevS is a bona fide two-component system of Mycobacterium tuberculosis that is hypoxia-responsive in the absence of the DNA-binding domain of DevR.Microbiology 2004, 150:865-875.       48.   Saini DK, Malhotra V, Tyagi JS: Cross talk between DevS sensor kinase homologue, Rv2027c, and DevR response regulator of Mycobacterium tuberculosis.FEBS Lett 2004, 565:75-80.       49.   Saini DK, Tyagi JS: High-throughput microplate phosphorylation assays based on DevR-DevS/Rv2027c 2-component signal transduction pathway to screen for novel antitubercular compounds.J Biomol Screen 2005, 10:215-224.       50.   Wisedchaisri G, Wu M, Rice AE, Roberts DM, Sherman DR, Hol WG: Structures of Mycobacterium tuberculosis DosR and DosR-DNA complex involved in gene activation during adaptation to hypoxic latency.J Mol Biol 2005, 354:630-641.       51.   Zhang Y: Persistent and dormant tubercle bacilli and latent tuberculosis.Front Biosci 2004, 9:1136-1156.       52.   Zhang Y, Post-Martens K, Denkin S: New drug candidates and therapeutic targets for tuberculosis therapy.Drug Discov Today 2006, 11:21-27.       53.   Erickson MG, Ulijasz AT, Weisblum B: Bacterial 2-Component Signal Transduction Systems: A Fluorescence Polarization Screen for Response Regulator-Protein Binding.J Biomol Screen 2005, 10:270-274.       54.   Fabian MA, Biggs WH III, Treiber DK, Atteridge CE, Azimioara MD, Benedetti MG, Carter TA, Ciceri P, Edeen PT, Floyd M, Ford JM, Galvin M, Gerlach JL, Grotzfeld RM, Herrgard S, Insko DE, Insko MA, Lai AG, Lelias JM, Mehta SA, Milanov ZV, Velasco AM, Wodicka LM, Patel HK, Zarrinkar PP, Lockhart DJ: A small molecule-kinase interaction map for clinical kinase inhibitors.Nat Biotechnol 2005, 23:329-336.       55.   Kvint K, Nachin L, Diez A, Nystrom T: The bacterial universal stress protein: function and regulation.Current Opinion in Microbiology 2003, 6:140-145.       56.   Nystrom T, Neidhardt FC: Effects of overproducing the universal stress protein, UspA, in Escherichia coli K-12.Journal Of Bacteriology 1996, 178:927-930.       57.   Nystrom T, Neidhardt FC: Isolation and properties of a mutant of Escherichia coli with an insertional inactivation of the uspA gene, which encodes a universal stress protein.Journal Of Bacteriology 1993, 175:3949-3956.       58.   Freestone P, Nystrom T, Trinei M, Norris V: The universal stress protein, UspA, of Escherichia coli is phosphorylated in response to stasis.Journal of Molecular Biology 1997, 274:318-324.       59.   Freestone P, Trinei M, Clarke SC, Nystrom T, Norris V: Tyrosine phosphorylation in Escherichia coli.Journal of Molecular Biology 1998, 279:1045-1051.       60.   O'Toole R, Williams HD: Universal stress proteins and Mycobacterium tuberculosis.Res Microbiol 2003, 154:387-392.       61.   Zarembinski TI, Hung LW, Mueller-Dieckmann HJ, Kim KK, Yokota H, Kim R, Kim SH: Structure-based assignment of the biochemical function of a hypothetical protein: A test case of structural genomics.PNAS 1998, 95:15189-15193.       62.   Zahrt TC, Wozniak C, Jones D, Trevett A: Functional Analysis of the Mycobacterium tuberculosis MprAB Two-Component Signal Transduction System.Infect Immun 2003, 71:6962-6970.       63.   Zahrt TC, Deretic V: Mycobacterium tuberculosis signal transduction system required for persistent infections.Proc Natl Acad Sci U S A 2001, 98:12706-12711.       64.   Rodrigue S, Provvedi R, Jacques PE, Gaudreau L, Manganelli R: The sigma factors of Mycobacterium tuberculosis.FEMS Microbiology Reviews 2006, 30:926-941.       65.   DeMaio J, Zhang Y, Ko C, Bishai WR: Mycobacterium tuberculosis sigF is part of a gene cluster with similarities to the Bacillus subtilis sigF and sigB operons.Tuber Lung Dis 1997, 78:3-12.       66.   DeMaio J, Zhang Y, Ko C, Young DB, Bishai WR: A stationary-phase stress-response sigma factor from Mycobacterium tuberculosis.Proc Natl Acad Sci U S A 1996, 93:2790-2794.       67.   Cappelli G, Volpe E, Grassi M, Liseo B, Colizzi V, Mariani F: Profiling of Mycobacterium tuberculosis gene expression during human macrophage infection: Upregulation of the alternative sigma factor G, a group of transcriptional regulators, and proteins with unknown function.Res Microbiol 2006       68.   He H, Hovey R, Kane J, Singh V, Zahrt TC: MprAB Is a Stress-Responsive Two-Component System That Directly Regulates Expression of Sigma Factors SigB and SigE in Mycobacterium tuberculosis.J Bacteriol 2006, 188:2134-2143.       69.   Dahl JL, Kraus CN, Boshoff HI, Doan B, Foley K, Avarbock D, Kaplan G, Mizrahi V, Rubin H, Barry CE III: 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 2003, 100:10026-10031.       70.   Avarbock D, Salem J, Li L, Wang Z, Rubin H: Cloning and characterization of a bifunctional RelA/SpoT homologue from Mycobacterium tuberculosis.Gene 1999, 233:261-269.       71.   Primm TP, Andersen SJ, Mizrahi V, Avarbock D, Rubin H, Barry CE III: The stringent response of Mycobacterium tuberculosis is required for long-term survival.J Bacteriol 2000, 182:4889-4898.       72.   Jain V, Saleem-Batcha R, China A, Chatterji D: Molecular dissection of the mycobacterial stringent response protein Rel.Protein Sci 2006, 15:1449-1464.       73.   Rachman H, Strong M, Schaible U, Schuchhardt J, Hagens K, Mollenkopf H, Eisenberg D, Kaufmann SH: Mycobacterium tuberculosis gene expression profiling within the context of protein networks.Microbes Infect 2006.       74.   McKinney JD, Honer Zu BK, Munoz-Elias EJ, Miczak A, Chen B, Chan WT, Swenson D, Sacchettini JC, Jacobs WR Jr., Russell DG: Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase.Nature 2000, 406:735-738.       75.   Daniel J, Deb C, Dubey VS, Sirakova TD, Abomoelak B, Morbidoni HR, Kolattukudy PE: Induction of a Novel Class of Diacylglycerol Acyltransferases and Triacylglycerol Accumulation in Mycobacterium tuberculosis as It Goes into a Dormancy-Like State in Culture.J Bacteriol 2004, 186:5017-5030.       76.   Crick DC, Mahapatra S, Brennan PJ: Biosynthesis of the arabinogalactan-peptidoglycan complex of Mycobacterium tuberculosis.Glycobiology 2001, 11:107R-118R.       77.   Brennan PJ: Structure, function, and biogenesis of the cell wall of Mycobacterium tuberculosis.Tuberculosis (Edinb ) 2003, 83:91-97.       78.   Choudhry AE, Mandichak TL, Broskey JP, Egolf RW, Kinsland C, Begley TP, Seefeld MA, Ku TW, Brown JR, Zalacain M, Ratnam K: Inhibitors of Pantothenate Kinase: Novel Antibiotics for Staphylococcal Infections.Antimicrob Agents Chemother 2003, 47:2051-2055.       79.   Sambandamurthy VK, Wang X, Chen B, Russell RG, Derrick S, Collins FM, Morris SL, Jacobs WR Jr.: A pantothenate auxotroph of Mycobacterium tuberculosis is highly attenuated and protects mice against tuberculosis.Nat Med 2002, 8:1171-1174.       80.   Munoz-Elias EJ, McKinney JD: Mycobacterium tuberculosis isocitrate lyases 1 and 2 are jointly required for in vivo growth and virulence.Nat Med 2005, 11:638-644.       81.   Li J, Zhu D, Yi Z, He Y, Chun Y, Liu Y, Li N: DNAzymes targeting the icl gene inhibit ICL expression and decrease Mycobacterium tuberculosis survival in macrophages.Oligonucleotides 2005, 15:215-222.       82.   Munoz-Elias EJ, McKinney JD: Carbon metabolism of intracellular bacteria.Cell Microbiol 2006, 8:10-22.       83.   Sharma V, Sharma S, Hoener zu BK, McKinney JD, Russell DG, Jacobs WR Jr., Sacchettini JC: Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis.Nat Struct Biol 2000, 7:663-668.       84.   Hutter B, Dick T: Increased alanine dehydrogenase activity during dormancy in Mycobacterium smegmatis.FEMS Microbiol Lett 1998, 167:7-11.       85.   Hutter B, Singh M: Properties of the 40 kDa antigen of Mycobacterium tuberculosis, a functional L-alanine dehydrogenase.Biochem J 1999, 343 Pt 3:669-672.       86.   Usha V, Jayaraman R, Toro JC, Hoffner SE, Das KS: Glycine and alanine dehydrogenase activities are catalyzed by the same protein in Mycobacterium smegmatis: upregulation of both activities under microaerophilic adaptation.Can J Microbiol 2002, 48:7-13.       87.   Starck J, Kallenius G, Marklund BI, Andersson DI, Akerlund T: Comparative proteome analysis of Mycobacterium tuberculosis grown under aerobic and anaerobic conditions.Microbiology 2004, 150:3821-3829.       88.   Weber I, Fritz C, Ruttkowski S, Kreft A, Bange FC: Anaerobic nitrate reductase (narGHJI) activity of Mycobacterium bovis BCG in vitro and its contribution to virulence in immunodeficient mice.Mol Microbiol 2000, 35:1017-1025.       89.   Sohaskey CD: Regulation of nitrate reductase activity in Mycobacterium tuberculosis by oxygen and nitric oxide.Microbiology 2005, 151:3803-3810.       90.   Sohaskey CD, Wayne LG: Role of narK2X and narGHJI in hypoxic upregulation of nitrate reduction by Mycobacterium tuberculosis.J Bacteriol 2003, 185:7247-7256.       91.   Xie Z, Siddiqi N, Rubin EJ: Differential antibiotic susceptibilities of starved Mycobacterium tuberculosis isolates.Antimicrob Agents Chemother 2005, 49:4778-4780.       92.   Weinstein EA, Yano T, Li LS, Avarbock D, Avarbock A, Helm D, McColm AA, Duncan K, Lonsdale JT, Rubin H: Inhibitors of type II NADH:menaquinone oxidoreductase represent a class of antitubercular drugs.Proc Natl Acad Sci U S A 2005, 102:4548-4553.       93.   Andries K, Verhasselt P, Guillemont J, Gohlmann HW, Neefs JM, Winkler H, Van Gestel J, Timmerman P, Zhu M, Lee E, Williams P, de Chaffoy D, Huitric E, Hoffner S, Cambau E, Truffot-Pernot C, Lounis N, Jarlier V: A diarylquinoline drug active on the ATP synthase of Mycobacterium tuberculosis.Science 2005, 307:223-227.       94.   Maragos WF, Korde AS: Mitochondrial uncoupling as a potential therapeutic target in acute central nervous system injury.J Neurochem 2004, 91:257-262       95.   Loomis WF, Lipmann F: Reversible inhibition of the coupling between phosphorylation and oxidation.J Biol Chem 1948, 173:807-808.       96.   Wooff E, Michell SL, Gordon SV, Chambers MA, Bardarov S, Jacobs WR Jr., Hewinson RG, Wheeler PR: Functional genomics reveals the sole sulphate transporter of the Mycobacterium tuberculosis complex and its relevance to the acquisition of sulphur in vivo.Mol Microbiol 2002, 43:653-663.       97.   Wheeler PR, Coldham NG, Keating L, Gordon SV, Wooff EE, Parish T, Hewinson RG: Functional demonstration of reverse transsulfuration in the Mycobacterium tuberculosis complex reveals that methionine is the preferred sulfur source for pathogenic Mycobacteria.J Biol Chem 2005, 280:8069-8078.       98.   Pinto R, Tang QX, Britton WJ, Leyh TS, Triccas JA: The Mycobacterium tuberculosis cysD and cysNC genes form a stress-induced operon that encodes a tri-functional sulfate-activating complex.Microbiology 2004, 150:1681-1686.       99.   Sun M, Andreassi JL, Liu S, Pinto R, Triccas JA, Leyh TS: The trifunctional sulfate-activating complex (SAC) of Mycobacterium tuberculosis.J Biol Chem 2005, 280:7861-7866.       100.   Williams SJ, Senaratne RH, Mougous JD, Riley LW, Bertozzi CR: 5'-adenosinephosphosulfate lies at a       101.   Schelle MW, Bertozzi CR: Sulfate metabolism in mycobacteria.Chembiochem 2006, 7:1516-1524.       102.   Pabst MJ, Gross JM, Brozna JP, Goren MB: Inhibition of macrophage priming by sulfatide from Mycobacterium tuberculosis.J Immunol 1988, 140:634-640.       103.   Grosset J, Truffot C, Fermanian J, Lecoeur H: [Sterilizing activity of the main drugs on the mouse experimental tuberculosis (author's transl)].Pathol Biol (Paris) 1982, 30:444-448.       104.   Jindani A, Dore CJ, Mitchison DA: Bactericidal and sterilizing activities of antituberculosis drugs during the first 14 days.Am J Respir Crit Care Med 2003, 167:1348-1354.       105.   Dawes SS, Warner DF, Tsenova L, Timm J, McKinney JD, Kaplan G, Rubin H, Mizrahi V: Ribonucleotide reduction in Mycobacterium tuberculosis: function and expression of genes encoding class Ib and class II ribonucleotide reductases.Infect Immun 2003, 71:6124-6131.       106.   Boshoff HI, Barry III CE: Is the mycobacterial cell wall a hopeless drug target for latent tuberculosis?Drug Discovery Today: Disease Mechanisms 2006, 3:237-245.       107.   Mani Tripathi S, Ramachandran R: Direct Evidence for a Glutamate Switch Necessary for Substrate Recognition: Crystal Structures of Lysine [epsilon]-Aminotransferase (Rv3290c) from Mycobacterium tuberculosis H37Rv.Journal of Molecular Biology 2006, 362:877-886.       108.   Makinoshima H, Glickman MS: Regulation of Mycobacterium tuberculosis cell envelope composition and virulence by intramembrane proteolysis.Nature 2005, 436:406-409.       109.   Hu Y, Movahedzadeh F, Stoker NG, Coates AR: Deletion of the Mycobacterium tuberculosis alpha-crystallin-like hspX gene causes increased bacterial growth in vivo.Infect Immun 2006, 74:861-868.       110.   Stewart JN, Rivera HN, Karls R, Quinn FD, Roman J, Rivera-Marrero CA: Increased pathology in lungs of mice after infection with an alpha-crystallin mutant of Mycobacterium tuberculosis: changes in cathepsin proteases and certain cytokines.Microbiology 2006, 152:233-244.       111.   Stewart GR, Newton SM, Wilkinson KA, Humphreys IR, Murphy HN, Robertson BD, Wilkinson RJ, Young DB: The stress-responsive chaperone alpha-crystallin 2 is required for pathogenesis of Mycobacterium tuberculosis.Mol Microbiol 2005, 55:1127-1137.       112.   Qamra R, Mande SC: Crystal structure of the 65-kilodalton heat shock protein, chaperonin 60.2, of Mycobacterium tuberculosis.J Bacteriol 2004, 186:8105-8113.       113.   Rachman H, Strong M, Ulrichs T, Grode L, Schuchhardt J, Mollenkopf H, Kosmiadi GA, Eisenberg D, Kaufmann SH: Unique transcriptome signature of Mycobacterium tuberculosis in pulmonary tuberculosis.Infect Immun 2006, 74:1233-1242.       114.   Wayne LG, Sramek HA: Metronidazole is bactericidal to dormant cells of Mycobacterium tuberculosis.Antimicrob Agents Chemother 1994, 38:2054-2058.       115.   Muttucumaru DG, Roberts G, Hinds J, Stabler RA, Parish T: Gene expression profile of Mycobacterium tuberculosis in a non-replicating state.Tuberculosis (Edinb ) 2004, 84:239-246.       116.   Betts JC, Lukey PT, Robb LC, McAdam RA, Duncan K: Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling.Mol Microbiol 2002, 43:717-731.       117.   Karakousis PC, Yoshimatsu T, Lamichhane G, Woolwine SC, Nuermberger EL, Grosset J, Bishai WR: Dormancy phenotype displayed by extracellular Mycobacterium tuberculosis within artificial granulomas in mice.J Exp Med 2004, 200:647-657.       118.   Talaat AM, Lyons R, Howard ST, Johnston SA: The temporal expression profile of Mycobacterium tuberculosis infection in mice.Proc Natl Acad Sci U S A 2004, 101:4602-4607.       119.   Kanehisa M, Goto S, Kawashima S, Nakaya A: The KEGG databases at GenomeNet.Nucl Acids Res 2002, 30:42-46.