REMap: Operon map of M. tuberculosis based on RNA sequence data

Zumla, 2013, WHO's 2013 global report on tuberculosis: successes, threats, and opportunities, Lancet, 382, 1765, 10.1016/S0140-6736(13)62078-4 Via, 2008, Tuberculous granulomas are hypoxic in guinea pigs, rabbits, and nonhuman primates, Infect Immun, 76, 2333, 10.1128/IAI.01515-07 Dannenberg, 1993, Immunopathogenesis of pulmonary tuberculosis, Hosp Pract Off Ed, 28, 51, 10.1080/21548331.1993.11442738 Voskuil, 2003, Inhibition of respiration by nitric oxide induces a Mycobacterium tuberculosis dormancy program, J Exp Med, 198, 705, 10.1084/jem.20030205 Manabe, 2008, The aerosol rabbit model of TB latency, reactivation and immune reconstitution inflammatory syndrome, Tuberculosis (Edinb), 88, 187, 10.1016/j.tube.2007.10.006 Newton-Foot, 2013, The complex architecture of mycobacterial promoters, Tuberculosis (Edinb), 93, 60, 10.1016/j.tube.2012.08.003 Mao, 2009, DOOR: a database for prokaryotic operons, Nucleic Acids Res, 37, D459, 10.1093/nar/gkn757 Bashyam, 1996, A study of mycobacterial transcriptional apparatus: identification of novel features in promoter elements, J Bacteriol, 178, 4847, 10.1128/JB.178.16.4847-4853.1996 Cole, 2002, Comparative and functional genomics of the Mycobacterium tuberculosis complex, Microbiology, 148, 2919, 10.1099/00221287-148-10-2919 Cortes, 2013, Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis, Cell Rep, 5, 1121, 10.1016/j.celrep.2013.10.031 Romero, 2004, Using functional and organizational information to improve genome-wide computational prediction of transcription units on pathway-genome databases, Bioinformatics, 20, 709, 10.1093/bioinformatics/btg471 Ermolaeva, 2001, Prediction of operons in microbial genomes, Nucleic Acids Res, 29, 1216, 10.1093/nar/29.5.1216 Roback, 2007, A predicted operon map for Mycobacterium tuberculosis, Nucleic Acids Res, 35, 5085, 10.1093/nar/gkm518 Ranjan, 2006, MycoperonDB: a database of computationally identified operons and transcriptional units in mycobacteria, BMC Bioinforma, 7, S9, 10.1186/1471-2105-7-S5-S9 Haller, 2010, The transcriptome of Mycobacterium tuberculosis, Appl Microbiol Biotechnol, 86, 1, 10.1007/s00253-009-2399-4 Lynch, 2001, Genetic organization of the region encoding regulation, biosynthesis, and transport of rhizobactin 1021, a siderophore produced by Sinorhizobium meliloti, J Bacteriol, 183, 2576, 10.1128/JB.183.8.2576-2585.2001 Lew, 2013, Database resources for the tuberculosis community, Tuberculosis (Edinb), 93, 12, 10.1016/j.tube.2012.11.003 Sharma, 2010, The primary transcriptome of the major human pathogen Helicobacter pylori, Nature, 464, 250, 10.1038/nature08756 McClure, 2013, Computational analysis of bacterial RNA-Seq data, Nucleic Acids Res, 41, e140, 10.1093/nar/gkt444 Wang, 2013, Revealing of Mycobacterium marinum transcriptome by RNA-seq, PLoS One, 8, e75828, 10.1371/journal.pone.0075828 Valway, 1998, An outbreak involving extensive transmission of a virulent strain of Mycobacterium tuberculosis, N Engl J Med, 338, 633, 10.1056/NEJM199803053381001 Lee, 1991, Site-specific integration of mycobacteriophage L5: integration-proficient vectors for Mycobacterium smegmatis, Mycobacterium tuberculosis, and bacille Calmette–Guerin, Proc Natl Acad Sci U S A, 88, 3111, 10.1073/pnas.88.8.3111 Hatfull, 2000, Some common methods in mycobacterial genetics, 313 Wickham, 2009 Fleischmann, 2002, Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains, J Bacteriol, 184, 5479, 10.1128/JB.184.19.5479-5490.2002 Camacho, 2001, Analysis of the phthiocerol dimycocerosate locus of Mycobacterium tuberculosis. Evidence that this lipid is involved in the cell wall permeability barrier, J Biol Chem, 276, 19845, 10.1074/jbc.M100662200 Salgado, 2000, Operons in Escherichia coli: genomic analyses and predictions, Proc Natl Acad Sci U S A, 97, 6652, 10.1073/pnas.110147297 Voskuil, 2004, Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy, Tuberculosis (Edinb), 84, 218, 10.1016/j.tube.2004.02.003 Goh, 2005, Molecular evolutionary history of tubercle bacilli assessed by study of the polymorphic nucleotide within the nitrate reductase (narGHJI) operon promoter, J Clin Microbiol, 43, 4010, 10.1128/JCM.43.8.4010-4014.2005 Banerjee, 1994, inhA, a gene encoding a target for isoniazid and ethionamide in Mycobacterium tuberculosis, Science, 263, 227, 10.1126/science.8284673 Casali, 2006, Regulation of the Mycobacterium tuberculosis mce1 operon, J Bacteriol, 188, 441, 10.1128/JB.188.2.441-449.2006 Sala, 2009, Genome-wide regulon and crystal structure of BlaI (Rv1846c) from Mycobacterium tuberculosis, Mol Microbiol, 71, 1102, 10.1111/j.1365-2958.2008.06583.x Lew, 2011, TubercuList – 10 years after, Tuberculosis (Edinb), 91, 1, 10.1016/j.tube.2010.09.008 Betts, 2002, Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling, Mol Microbiol, 43, 717, 10.1046/j.1365-2958.2002.02779.x Archer, 1995, Transcriptional control of the nuo operon which encodes the energy-conserving NADH dehydrogenase of Salmonella typhimurium, J Bacteriol, 177, 2335, 10.1128/JB.177.9.2335-2342.1995 Quadri, 1998, Identification of a Mycobacterium tuberculosis gene cluster encoding the biosynthetic enzymes for assembly of the virulence-conferring siderophore mycobactin, Chem Biol, 5, 631, 10.1016/S1074-5521(98)90291-5 Bagchi, 2005, Transcription and autoregulation of the Rv3134c-devR-devS operon of Mycobacterium tuberculosis, Microbiology, 151, 4045, 10.1099/mic.0.28333-0 Bigi, 2000, The gene encoding P27 lipoprotein and a putative antibiotic-resistance gene form an operon in Mycobacterium tuberculosis and Mycobacterium bovis, Microbiology, 146, 1011, 10.1099/00221287-146-4-1011 Milano, 2004, The Mycobacterium tuberculosis Rv2358-furB operon is induced by zinc, Res Microbiol, 155, 192, 10.1016/j.resmic.2003.11.009 Tundup, 2006, Clusters of PE and PPE genes of Mycobacterium tuberculosis are organized in operons: evidence that PE Rv2431c is co-transcribed with PPE Rv2430c and their gene products interact with each other, FEBS Lett, 580, 1285, 10.1016/j.febslet.2006.01.042 Singh, 2003, mymA operon of Mycobacterium tuberculosis: its regulation and importance in the cell envelope, FEMS Microbiol Lett, 227, 53, 10.1016/S0378-1097(03)00648-7 Torres, 2001, Molecular analysis of Mycobacterium tuberculosis phosphate specific transport system in Mycobacterium smegmatis. Characterization of recombinant 38 kDa (PstS-1), Microb Pathog, 30, 289, 10.1006/mpat.2001.0434 Berthet, 1998, A Mycobacterium tuberculosis operon encoding ESAT-6 and a novel low-molecular-mass culture filtrate protein (CFP-10), Microbiology, 144, 3195, 10.1099/00221287-144-11-3195 Rosas-Magallanes, 2006, Horizontal transfer of a virulence operon to the ancestor of Mycobacterium tuberculosis, Mol Biol Evol, 23, 1129, 10.1093/molbev/msj120 Supply, 1997, Identification of novel intergenic repetitive units in a mycobacterial two-component system operon, Mol Microbiol, 26, 991, 10.1046/j.1365-2958.1997.6361999.x Goude, 2008, The critical role of embC in Mycobacterium tuberculosis, J Bacteriol, 190, 4335, 10.1128/JB.01825-07 Gao, 2006, A mycobacterial operon essential for virulence in vivo and invasion and intracellular persistence in macrophages, Infect Immun, 74, 1757, 10.1128/IAI.74.3.1757-1767.2006 Pasca, 2004, Rv2686c-Rv2687c-Rv2688c, an ABC fluoroquinolone efflux pump in Mycobacterium tuberculosis, Antimicrob Agents Chemother, 48, 3175, 10.1128/AAC.48.8.3175-3178.2004 Stermann, 2003, Polymorphic nucleotide within the promoter of nitrate reductase (NarGHJI) is specific for Mycobacterium tuberculosis, J Clin Microbiol, 41, 3252, 10.1128/JCM.41.7.3252-3259.2003