Singh AK, Reyrat JM: Laboratory maintenance of Mycobacterium smegmatis. Curr Protoc Microbiol. 2009, Chapter 10: Unit10C 11-
Google Scholar
Zhang J, Biswas I: A phenotypic microarray analysis of a Streptococcus mutans liaS mutant. Microbiology. 2009, 155 (Pt 1): 61-68. 10.1099/mic.0.023077-0.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bhatt A, Molle V, Besra GS, Jacobs WR, Kremer L: The Mycobacterium tuberculosis FAS-II condensing enzymes: their role in mycolic acid biosynthesis, acid-fastness, pathogenesis and in future drug development. Mol Microbiol. 2007, 64 (6): 1442-1454. 10.1111/j.1365-2958.2007.05761.x.
Article
CAS
PubMed
Google Scholar
Smeulders MJ, Keer J, Speight RA, Williams HD: Adaptation of Mycobacterium smegmatis to stationary phase. J Bacteriol. 1999, 181 (1): 270-283.
PubMed Central
CAS
PubMed
Google Scholar
McGuire AM, Weiner B, Park ST, Wapinski I, Raman S, Dolganov G, Peterson M, Riley R, Zucker J, Abeel T, White J, Sisk P, Stolte C, Koehrsen M, Yamamoto RT, Iacobelli-Martinez M, Kidd MJ, Maer AM, Schoolnik GK, Regev A, Galagan J: Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis. BMC Genomics. 2013, 13: 120-10.1186/1471-2164-13-120.
Article
Google Scholar
Prasanna AN, Mehra S: Comparative phylogenomics of pathogenic and non-pathogenic mycobacterium. PLoS One. 2013, 8 (8): e71248-10.1371/journal.pone.0071248.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gupta A, Bhakta S: An integrated surrogate model for screening of drugs against Mycobacterium tuberculosis. J Antimicrob Chemother. 2013, 67 (6): 1380-1391. 10.1093/jac/dks056.
Article
Google Scholar
Mishra MN, Daniels L: Characterization of the MSMEG_2631 gene (mmp) encoding a multidrug and toxic compound extrusion (MATE) family protein in Mycobacterium smegmatis and exploration of its polyspecific nature using biolog phenotype microarray. J Bacteriol. 2013, 195 (7): 1610-1621. 10.1128/JB.01724-12.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wang R, Prince JT, Marcotte EM: Mass spectrometry of the M. smegmatis proteome: protein expression levels correlate with function, operons, and codon bias. Genome Res. 2005, 15 (8): 1118-1126. 10.1101/gr.3994105.
Article
PubMed Central
CAS
PubMed
Google Scholar
Reddy TB, Riley R, Wymore F, Montgomery P, DeCaprio D, Engels R, Gellesch M, Hubble J, Jen D, Jin H, Koehrsen M, Larson L, Mao M, Nitzberg M, Sisk P, Stolte C, Weiner B, White J, Zachariah ZK, Sherlock G, Galagan JE, Ball CA, Schoolnik GK: TB database: an integrated platform for tuberculosis research. Nucleic Acids Res. 2009, 37 (Database issue): D499-D508. 10.1093/nar/gkn652.
Article
PubMed Central
CAS
PubMed
Google Scholar
Titgemeyer F, Amon J, Parche S, Mahfoud M, Bail J, Schlicht M, Rehm N, Hillmann D, Stephan J, Walter B, Burkovski A, Niederweis M: A genomic view of sugar transport in Mycobacterium smegmatis and Mycobacterium tuberculosis. J Bacteriol. 2007, 189 (16): 5903-5915. 10.1128/JB.00257-07.
Article
PubMed Central
CAS
PubMed
Google Scholar
Price MN, Deutschbauer AM, Skerker JM, Wetmore KM, Ruths T, Mar JS, Kuehl JV, Shao W, Arkin AP: Indirect and suboptimal control of gene expression is widespread in bacteria. Mol Syst Biol. 2013, 9: 660-10.1038/msb.2013.16.
Article
PubMed Central
PubMed
Google Scholar
Zhu X, Gerstein M, Snyder M: Getting connected: analysis and principles of biological networks. Genes Dev. 2007, 21 (9): 1010-1024. 10.1101/gad.1528707.
Article
CAS
PubMed
Google Scholar
Ideker T, Galitski T, Hood L: A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet. 2001, 2: 343-372. 10.1146/annurev.genom.2.1.343.
Article
CAS
PubMed
Google Scholar
Karsch-Mizrachi I, Nakamura Y, Cochrane G: The International Nucleotide Sequence Database Collaboration. Nucleic Acids Res. 2011, 40 (Database issue): D33-D37.
PubMed Central
PubMed
Google Scholar
Soo VW, Hanson-Manful P, Patrick WM: Artificial gene amplification reveals an abundance of promiscuous resistance determinants in Escherichia coli. Proc Natl Acad Sci U S A. 2010, 108 (4): 1484-1489. 10.1073/pnas.1012108108.
Article
PubMed Central
PubMed
Google Scholar
Bochner BR, Gadzinski P, Panomitros E: Phenotype microarrays for high-throughput phenotypic testing and assay of gene function. Genome Res. 2001, 11 (7): 1246-1255. 10.1101/gr.186501.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chang WE, Sarver K, Higgs BW, Read TD, Nolan NM, Chapman CE, Bishop-Lilly KA, Sozhamannan S: PheMaDB: a solution for storage, retrieval, and analysis of high throughput phenotype data. BMC Bioinformatics. 2011, 12: 109-10.1186/1471-2105-12-109.
Article
PubMed Central
PubMed
Google Scholar
Yoon SH, Han MJ, Jeong H, Lee CH, Xia XX, Lee DH, Shim JH, Lee SY, Oh TK, Kim JF: Comparative multi-omics systems analysis of Escherichia coli strains B and K-12. Genome Biol. 2012, 13 (5): R37-10.1186/gb-2012-13-5-r37.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chen JW, Scaria J, Chang YF: Phenotypic and transcriptomic response of auxotrophic Mycobacterium avium subsp. paratuberculosis leuD mutant under environmental stress. PLoS One. 2012, 7 (6): e37884-10.1371/journal.pone.0037884.
Article
PubMed Central
CAS
PubMed
Google Scholar
Gopalaswamy R, Narayanan S, Jacobs WR, Av-Gay Y: Mycobacterium smegmatis biofilm formation and sliding motility are affected by the serine/threonine protein kinase PknF. FEMS Microbiol Lett. 2008, 278 (1): 121-127. 10.1111/j.1574-6968.2007.00989.x.
Article
CAS
PubMed
Google Scholar
Sweeney KA, Dao DN, Goldberg MF, Hsu T, Venkataswamy MM, Henao-Tamayo M, Ordway D, Sellers RS, Jain P, Chen B, Chen M, Kim J, Lukose R, Chan J, Orme IM, Porcelli SA, Jacobs WR: A recombinant Mycobacterium smegmatis induces potent bactericidal immunity against Mycobacterium tuberculosis. Nat Med. 2011, 17 (10): 1261-1268. 10.1038/nm.2420.
Article
PubMed Central
CAS
PubMed
Google Scholar
Raghunand TR, Bishai WR: Mapping essential domains of Mycobacterium smegmatis WhmD: insights into WhiB structure and function. J Bacteriol. 2006, 188 (19): 6966-6976. 10.1128/JB.00384-06.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lew JM, Kapopoulou A, Jones LM, Cole ST: TubercuList10years after. Tuberculosis (Edinb). 2011, 91 (1): 1-7. 10.1016/j.tube.2010.09.008.
Article
Google Scholar
Sidders B, Withers M, Kendall SL, Bacon J, Waddell SJ, Hinds J, Golby P, Movahedzadeh F, Cox RA, Frita R, Ten Bokum AM, Wernisch L, Stoker NG: Quantification of global transcription patterns in prokaryotes using spotted microarrays. Genome Biol. 2007, 8 (12): R265-10.1186/gb-2007-8-12-r265.
Article
PubMed Central
PubMed
Google Scholar
Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M: Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 2014, 42 (Database issue): D199-D205. 10.1093/nar/gkt1076.
Article
PubMed Central
CAS
PubMed
Google Scholar
Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD: The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 2014, 42 (Database issue): D459-D471. 10.1093/nar/gkt1103.
Article
PubMed Central
CAS
PubMed
Google Scholar
Vogel C, Marcotte EM: Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat Rev Genet. 2012, 13 (4): 227-232.
PubMed Central
CAS
PubMed
Google Scholar
Gouet P, Robert X, Courcelle E: ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res. 2003, 31 (13): 3320-3323. 10.1093/nar/gkg556.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mackie AM, Hassan KA, Paulsen IT, Tetu SG: Biolog phenotype microarrays for phenotypic characterization of microbial cells. Methods Mol Biol. 2014, 1096: 123-130. 10.1007/978-1-62703-712-9_10.
Article
CAS
PubMed
Google Scholar
Lofthouse EK, Wheeler PR, Beste DJ, Khatri BL, Wu H, Mendum TA, Kierzek AM, McFadden J: Systems-based approaches to probing metabolic variation within the Mycobacterium tuberculosis complex. PLoS One. 2013, 8 (9): e75913-10.1371/journal.pone.0075913.
Article
PubMed Central
CAS
PubMed
Google Scholar
Khatri B, Fielder M, Jones G, Newell W, Abu-Oun M, Wheeler PR: High throughput phenotypic analysis of Mycobacterium tuberculosis and Mycobacterium bovis strains metabolism using biolog phenotype microarrays. PLoS One. 2013, 8 (1): e52673-10.1371/journal.pone.0052673.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bochner BR: Global phenotypic characterization of bacteria. FEMS Microbiol Rev. 2009, 33 (1): 191-205. 10.1111/j.1574-6976.2008.00149.x.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tang YJ, Shui W, Myers S, Feng X, Bertozzi C, Keasling JD: Central metabolism in Mycobacterium smegmatis during the transition from O2-rich to O2-poor conditions as studied by isotopomer-assisted metabolite analysis. Biotechnol Lett. 2009, 31 (8): 1233-1240. 10.1007/s10529-009-9991-7.
Article
PubMed Central
CAS
PubMed
Google Scholar
Alfoldi L, Rasko I, Kerekes E: L-serine deaminase of Escherichia coli. J Bacteriol. 1968, 96 (5): 1512-1518.
PubMed Central
CAS
PubMed
Google Scholar
Singhal N, Sharma P, Kumar M, Joshi B, Bisht D: Analysis of intracellular expressed proteins of Mycobacterium tuberculosis clinical isolates. Proteome Sci. 2012, 10 (1): 14-10.1186/1477-5956-10-14.
Article
PubMed Central
CAS
PubMed
Google Scholar
Feng Z, Barletta RG: Roles of Mycobacterium smegmatis D-alanine:D-alanine ligase and D-alanine racemase in the mechanisms of action of and resistance to the peptidoglycan inhibitor D-cycloserine. Antimicrob Agents Chemother. 2003, 47 (1): 283-291. 10.1128/AAC.47.1.283-291.2003.
Article
PubMed Central
CAS
PubMed
Google Scholar
Greendyke R, Rajagopalan M, Parish T, Madiraju MV: Conditional expression of Mycobacterium smegmatis dnaA, an essential DNA replication gene. Microbiology. 2002, 148 (Pt 12): 3887-3900.
Article
CAS
PubMed
Google Scholar
Klutts JS, Hatanaka K, Pan YT, Elbein AD: Biosynthesis of d-arabinose in Mycobacterium smegmatis: specific labeling from d-glucose. Arch Biochem Biophys. 2002, 398 (2): 229-239. 10.1006/abbi.2001.2723.
Article
CAS
PubMed
Google Scholar
Izumori K, Yamanaka K, Elbein D: Pentose metabolism in Mycobacterium smegmatis: specificity of induction of pentose isomerases. J Bacteriol. 1976, 128 (2): 587-591.
PubMed Central
CAS
PubMed
Google Scholar
Izumori K, Ueda Y, Yamanaka K: Pentose metabolism in Mycobacterium smegmatis: comparison of L-arabinose isomerases induced by L-arabinose and D-galactose. J Bacteriol. 1978, 133 (1): 413-414.
PubMed Central
CAS
PubMed
Google Scholar
Mehta RJ, Fare LR, Shearer ME, Nash CH: Mannitol oxidation in two Micromonospora isolates and in representative species of other actinomycetes. Appl Environ Microbiol. 1977, 33 (4): 1013-1015.
PubMed Central
CAS
PubMed
Google Scholar
Zhang R, Pan YT, He S, Lam M, Brayer GD, Elbein AD, Withers SG: Mechanistic analysis of trehalose synthase from Mycobacterium smegmatis. J Biol Chem. 2011, 286 (41): 35601-35609. 10.1074/jbc.M111.280362.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yang Y, Kulka K, Montelaro RC, Reinhart TA, Sissons J, Aderem A, Ojha AK: A hydrolase of trehalose dimycolate induces nutrient influx and stress sensitivity to balance intracellular growth of Mycobacterium tuberculosis. Cell Host Microbe. 2014, 15 (2): 153-163. 10.1016/j.chom.2014.01.008.
Article
PubMed Central
CAS
PubMed
Google Scholar
Woodruff PJ, Carlson BL, Siridechadilok B, Pratt MR, Senaratne RH, Mougous JD, Riley LW, Williams SJ, Bertozzi CR: Trehalose is required for growth of Mycobacterium smegmatis. J Biol Chem. 2004, 279 (28): 28835-28843. 10.1074/jbc.M313103200.
Article
CAS
PubMed
Google Scholar
Tahlan K, Wilson R, Kastrinsky DB, Arora K, Nair V, Fischer E, Barnes SW, Walker JR, Alland D, Barry CE, Boshoff HI: SQ109 targets MmpL3, a membrane transporter of trehalose monomycolate involved in mycolic acid donation to the cell wall core of Mycobacterium tuberculosis. Antimicrob Agents Chemother. 2012, 56 (4): 1797-1809. 10.1128/AAC.05708-11.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lopez-Marin LM, Segura E, Hermida-Escobedo C, Lemassu A, Salinas-Carmona MC: 6,6?-Dimycoloyl trehalose from a rapidly growing Mycobacterium: an alternative antigen for tuberculosis serodiagnosis. FEMS Immunol Med Microbiol. 2003, 36 (12): 47-54. 10.1016/S0928-8244(03)00036-1.
Article
CAS
PubMed
Google Scholar
Harland CW, Rabuka D, Bertozzi CR, Parthasarathy R: The Mycobacterium tuberculosis virulence factor trehalose dimycolate imparts desiccation resistance to model mycobacterial membranes. Biophys J. 2008, 94 (12): 4718-4724. 10.1529/biophysj.107.125542.
Article
PubMed Central
CAS
PubMed
Google Scholar
Milligan DL, Tran SL, Strych U, Cook GM, Krause KL: The alanine racemase of Mycobacterium smegmatis is essential for growth in the absence of D-alanine. J Bacteriol. 2007, 189 (22): 8381-8386. 10.1128/JB.01201-07.
Article
PubMed Central
CAS
PubMed
Google Scholar
Chacon O, Feng Z, Harris NB, Caceres NE, Adams LG, Barletta RG: Mycobacterium smegmatis D-alanine racemase mutants are not dependent on D-alanine for growth. Antimicrob Agents Chemother. 2002, 46 (1): 47-54. 10.1128/AAC.46.2.47-54.2002.
Article
PubMed Central
CAS
PubMed
Google Scholar
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 (1): 7-13. 10.1139/w01-126.
Article
CAS
PubMed
Google Scholar
Buckoreelall K, Wilson L, Parker WB: Identification and characterization of two adenosine phosphorylase activities in Mycobacterium smegmatis. J Bacteriol. 2011, 193 (20): 5668-5674. 10.1128/JB.05394-11.
Article
PubMed Central
CAS
PubMed
Google Scholar
Parker WB, Barrow EW, Allan PW, Shaddix SC, Long MC, Barrow WW, Bansal N, Maddry JA: Metabolism of 2-methyladenosine in Mycobacterium tuberculosis. Tuberculosis (Edinb). 2004, 84 (5): 327-336. 10.1016/j.tube.2004.02.004.
Article
Google Scholar
Chen CK, Barrow EW, Allan PW, Bansal N, Maddry JA, Suling WJ, Barrow WW, Parker WB: The metabolism of 2-methyladenosine in Mycobacterium smegmatis. Microbiology. 2002, 148 (Pt 1): 289-295.
Article
CAS
PubMed
Google Scholar
Buckoreelall K, Sun Y, Hobrath JV, Wilson L, Parker WB: Identification of Rv0535 as methylthioadenosine phosphorylase from Mycobacterium tuberculosis. Tuberculosis (Edinb). 2012, 92 (2): 139-147. 10.1016/j.tube.2011.11.010.
Article
CAS
Google Scholar
Raman K, Yeturu K, Chandra N: targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis. BMC Syst Biol. 2008, 2: 109-10.1186/1752-0509-2-109.
Article
PubMed Central
PubMed
Google Scholar
Boshoff HI, Myers TG, Copp BR, McNeil MR, Wilson MA, Barry CE: The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action. J Biol Chem. 2004, 279 (38): 40174-40184. 10.1074/jbc.M406796200.
Article
CAS
PubMed
Google Scholar
Cook GM, Berney M, Gebhard S, Heinemann M, Cox RA, Danilchanka O, Niederweis M: Physiology of mycobacteria. Adv Microb Physiol. 2009, 55: 81-182. 10.1016/S0065-2911(09)05502-7. 318189
Article
PubMed Central
CAS
PubMed
Google Scholar
Vaas LA, Sikorski J, Michael V, Goker M, Klenk HP: Visualization and curve-parameter estimation strategies for efficient exploration of phenotype microarray kinetics. PLoS One. 2012, 7 (4): e34846-10.1371/journal.pone.0034846.
Article
PubMed Central
CAS
PubMed
Google Scholar
Vaas LA, Sikorski J, Hofner B, Fiebig A, Buddruhs N, Klenk HP, Goker M: opm: an R package for analysing OmniLog(R) phenotype microarray data. Bioinformatics. 2013, 29 (14): 1823-1824. 10.1093/bioinformatics/btt291.
Article
CAS
PubMed
Google Scholar
Griffin JE, Pandey AK, Gilmore SA, Mizrahi V, McKinney JD, Bertozzi CR, Sassetti CM: Cholesterol catabolism by Mycobacterium tuberculosis requires transcriptional and metabolic adaptations. Chem Biol. 2012, 19 (2): 218-227. 10.1016/j.chembiol.2011.12.016.
Article
PubMed Central
CAS
PubMed
Google Scholar
Eoh H, Rhee KY: Multifunctional essentiality of succinate metabolism in adaptation to hypoxia in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2013, 110 (16): 6554-6559. 10.1073/pnas.1219375110.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dick T, Lee BH, Murugasu-Oei B: Oxygen depletion induced dormancy in Mycobacterium smegmatis. FEMS Microbiol Lett. 1998, 163 (2): 159-164. 10.1111/j.1574-6968.1998.tb13040.x.
Article
CAS
PubMed
Google Scholar
Chaudhuri RR, Pallen MJ: xBASE, a collection of online databases for bacterial comparative genomics. Nucleic Acids Res. 2006, 34 (Database issue): D335-D337. 10.1093/nar/gkj140.
Article
PubMed Central
CAS
PubMed
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215 (3): 403-410. 10.1016/S0022-2836(05)80360-2.
Article
CAS
PubMed
Google Scholar