Gene Expression Publications

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	Comparative expression studies of a complex phenotype: cord formation in Mycobacterium tuberculosis. Gao Q, Kripke K, Arinc Z, Voskuil M, Small P (2004) Tuberculosis (Edinb) 84(3-4):188-96	2004-04-21	Mycobacterium tuberculosis	Pubmed
Abstract: The aggregation of mycobacteria into structures known as cords is an intrinsic property of the human tubercle bacillus. This property is thought to be determined by the lipid composition of the bacterial cell surface and may contribute to the virulence of the organism. Using microarray technology, we compared the pattern of gene expression of H37Rv, a virulent, cording strain of Mycobacterium tuberculosis, with H37Ra, an avirulent, non-cording strain derived from the same original patient isolate, under five different nutrient combinations and growth conditions. Under all of these conditions, H37Rv formed cords and H37Ra did not. By focusing our analysis only on genes that were differentially expressed under all conditions, we hoped to enrich the resulting gene list for genes associated with cording. We identified 22 genes that were consistently expressed at higher levels in H37Rv than in H37Ra under all conditions tested. Genes involved in lipid metabolism and the cell membrane were significantly enriched in our gene list, indicating that the cell wall and the cell membrane may be the major sites of difference between these two strains. This work represents a new strategy for enriching gene lists for relevant genes, which may also be applicable for other types of problems. MESH terms: Reproducibility of Results; Genes, Bacterial; Virulence/genetics; *Gene Expression Regulation, Bacterial; Reverse Transcriptase Polymerase Chain Reaction; Mycobacterium tuberculosis/genetics/pathogenicity/*physiology; Culture Media; DNA, Bacterial/genetics; Oligonucleotide Array Sequence Analysis/methods; Phenotype; Species Specificity Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Virulent, cording strain (H37Rv) and an avirulent, non-cording strain (H37Ra) under five different nutrient combinations and growth conditions
	Reverse engineering of industrial pharmaceutical-producing actinomycete strains using DNA microarrays. Lum AM, Huang J, Hutchinson CR, Kao CM (2004) Metab Eng 6(3):186-96	2004-07-19	Streptomyces coelicolor	Pubmed
Abstract: Transcript levels in production cultures of wildtype and classically improved strains of the actinomycete bacteria Saccharopolyspora erythraea and Streptomyces fradiae were monitored using microarrays of the sequenced actinomycete S. coelicolor. Sac. erythraea and S. fradiae synthesize the polyketide antibiotics erythromycin and tylosin, respectively, and the classically improved strains contain unknown overproduction mutations. The Sac. erythraea overproducer was found to express the entire 56-kb erythromycin gene cluster several days longer than the wildtype strain. In contrast, the S. fradiae wildtype and overproducer strains expressed the 85-kb tylosin biosynthetic gene cluster similarly, while they expressed several tens of other S. fradiae genes and S. coelicolor homologs differently, including the acyl-CoA dehydrogenase gene aco and the S. coelicolor isobutyryl-CoA mutase homolog icmA. These observations indicated that overproduction mechanisms in classically improved strains can affect both the timing and rate of antibiotic synthesis, and alter the regulation of antibiotic biosynthetic enzymes and enzymes involved in precursor metabolism. MESH terms: Genetic Enhancement/*methods; Actinobacteria/genetics/*metabolism; Gene Expression Regulation, Bacterial/*physiology; Bacterial Proteins/genetics/metabolism; Genome, Bacterial; Tylosin/*biosynthesis; Gene Expression Profiling/*methods; Pharmaceutical Preparations/metabolism; Saccharopolyspora/genetics/metabolism; Streptomyces/genetics/metabolism; Anti-Bacterial Agents/biosynthesis; Drug Industry/methods; Acyl-CoA Dehydrogenase/genetics/metabolism; Erythromycin/*biosynthesis; Oligonucleotide Array Sequence Analysis/*methods; Species Specificity; Isomerases/genetics/metabolism Associated Links PubMed Link | Repository | Full Text Online Associated Experiment Sets Explore View Download S. fradiae WT and KOS155-3C R5/No Glucose S. erythraea R5 RNA Timecourse K24-1/EGFP R5 RNA Timecourse
	Gene expression diversity among Mycobacterium tuberculosis clinical isolates. Gao Q , Kripke KE , Saldanha AJ , Yan W , Holmes S , Small PM (2005) Microbiology 151(Pt 1):5-14	2005-01-01	Mycobacterium tuberculosis	Pubmed
Abstract: Intraspecies genetic diversity has been demonstrated to be important in the pathogenesis and epidemiology of several pathogens, such as HIV, influenza, Helicobacter and Salmonella. It is also important to consider strain-to-strain variation when identifying drug targets and vaccine antigens and developing tools for molecular diagnostics. Here, the authors present a description of the variability in gene expression patterns among ten clinical isolates of Mycobacterium tuberculosis, plus the laboratory strains H37Rv and H37Ra, growing in liquid culture. They identified 527 genes (15 % of those tested) that are variably expressed among the isolates studied. The remaining genes were divided into three categories based on their expression levels: unexpressed (38 %), low to undetectable expression (31 %) and consistently expressed (16 %). The expression categories were compared with functional categories and three biologically interesting gene lists: genes that are deleted among clinical isolates, T-cell antigens and essential genes. There were significant associations between expression variability and the classification of genes as T-cell antigens, involved in lipid metabolism, PE/PPE, insertion sequences and phages, and deleted among clinical isolates. This survey of mRNA expression among clinical isolates of M. tuberculosis demonstrates that genes with important functions can vary in their expression levels between strains grown under identical conditions. MESH terms: Receptors, Antigen, T-Cell/genetics/metabolism; *Genetic Variation; Genes, Essential; Gene Deletion; Mycobacterium tuberculosis/classification/genetics/*growth &; Bacterial Proteins/genetics/*metabolism; *Gene Expression; Humans; Oligonucleotide Array Sequence Analysis/methods; Tuberculosis, Pulmonary/*microbiology Associated Links PubMed Link | Full Text Online | Web Supplement | Repository Associated Experiment Sets Explore View Download Gene expression analysis of 16 Mycobacterium tuberculosis clinical isolates
	Global analysis of growth phase responsive gene expression and regulation of antibiotic biosynthetic pathways in Streptomyces coelicolor using DNA microarrays. Huang J, Lih CJ, Pan KH, Cohen SN (2001) Genes Dev 15(23):3183-92	2001-12-04	Streptomyces coelicolor	Pubmed
Abstract: The eubacterial species Streptomyces coelicolor proceeds through a complex growth cycle in which morphological differentiation/development is associated with a transition from primary to secondary metabolism and the production of antibiotics. We used DNA microarrays and mutational analysis to investigate the expression of individual genes and multigene antibiotic biosynthetic pathways during these events. We identified expression patterns in biosynthetic, regulatory, and ribosomal protein genes that were associated highly specifically with particular stages of development. A knowledge-based algorithm that correlates temporal changes in expression with chromosomal position identified groups of contiguous genes expressed at discrete stages of morphological development, inferred the boundaries of known antibiotic synthesis gene loci, and revealed novel physical clusters of coordinately regulated genes. Microarray analysis of RNA from cells mutated in genes regulating synthesis of the antibiotics actinorhodin (Act) and undecylprodigiosin (Red) identified proximate and distant sites that contain putative ABC transporter and two-component system genes expressed coordinately with genes of specific biosynthetic pathways and indicated the existence of two functionally and physically discrete regulons in the Red pathway. MESH terms: Gene Expression Regulation, Bacterial/*genetics; Genes, Bacterial/*genetics; Streptomyces/cytology/*genetics/*growth & development; Molecular Sequence Data; Multigene Family/genetics; Transcription, Genetic/genetics; Base Sequence; Anthraquinones/metabolism; Gene Deletion; Oligonucleotide Array Sequence Analysis/*methods; Open Reading Frames/genetics; Prodigiosin/analogs & derivatives/biosynthesis; Cell Division; DNA Mutational Analysis/methods; Anti-Bacterial Agents/*biosynthesis Associated Links Web Supplement | PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Expression profiles during growth of Streptomyces coelicolor
	Genome plasticity in Streptomyces: identification of 1 Mb TIRs in the S. coelicolor A3(2) chromosome. Weaver D, Karoonuthaisiri N, Tsai HH, Huang CH, Ho ML, Gai S, Patel KG, Huang J, Cohen SN, Hopwood DA, Chen CW, Kao CM (2004) Mol Microbiol 51(6):1535-50	2004-03-01	Streptomyces coelicolor	Pubmed
Abstract: The chromosomes of several widely used laboratory derivatives of Streptomyces coelicolor A3(2) were found to have 1.06 Mb inverted repeat sequences at their termini (i.e. long-terminal inverted repeats; L-TIRs), which are 50 times the length of the 22 kb TIRs of the sequenced S. coelicolor strain M145. The L-TIRs include 1005 annotated genes and increase the overall chromosome size to 9.7 Mb. The 1.06 Mb L-TIRs are the longest reported thus far for an actinomycete, and are proposed to represent the chromosomal state of the original soil isolate of S. coelicolor A3(2). S. coelicolor A3(2), M600 and J1501 possess L-TIRs, whereas approximately half the examined early mutants of A3(2) generated by ultraviolet (UV) or X-ray mutagenesis have truncated their TIRs to the 22 kb length. UV radiation was found to stimulate L-TIR truncation. Two copies of a transposase gene (SCO0020) flank 1.04 Mb of DNA in the right L-TIR, and recombination between them appears to generate strains containing short TIRs. This TIR reduction mechanism may represent a general strategy by which transposable elements can modulate the structure of chromosome ends. The presence of L-TIRs in certain S. coelicolor strains represents a major chromosomal alteration in strains previously thought to be genetically similar. MESH terms: RNA, Bacterial/*chemistry/isolation & purification; Cloning, Molecular; DNA, Bacterial/*chemistry/isolation & purification; Sequence Analysis, DNA; *Terminal Repeat Sequences/genetics; Transposases/genetics/metabolism; Molecular Sequence Data; Recombination, Genetic/genetics; Base Sequence; Chromosome Mapping/methods; Electrophoresis, Gel, Pulsed-Field; *Genome, Bacterial; Nucleic Acid Hybridization; *Streptomyces/genetics; Animals; Chromosomes, Bacterial/*genetics; Humans; Amino Acid Sequence; Genes, Bacterial/genetics Associated Links PubMed Link | Full Text Online | Web Supplement | Repository Associated Experiment Sets Explore View Download Identification of 1 Mb TIRs in the S. coelicolor A3(2) chromosome
	Regional organization of gene expression in Streptomyces coelicolor. Karoonuthaisiri N, Weaver D, Huang J, Cohen SN, Kao CM (2005) Gene 353(1):53-66	2005-06-20	Streptomyces coelicolor	Pubmed
Abstract: Based on the chromosomal locations of genes inferred from sequence analysis to be essential for the viability of Streptomyces coelicolor, Bentley et al. [Bentley, S.D., et al. 2002. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2), Nature 417, 141-147.] have suggested that a 4.9 Mb central region of the linear S. coelicolor chromosome encodes 'core' functions expressed during vegetative growth of this species, while 1.5 Mb and 2.3 Mb chromosomal DNA segments lateral to this core encode auxiliary functions proposed to be required under other growth conditions. To examine this hypothesis and experimentally identify genes expressed during vegetative growth of S. coelicolor cultures, we used DNA microarrays to measure globally the abundance of S. coelicolor transcripts in cells growing in liquid medium. We found that, overall, genes corresponding to the 4.9 Mb core region of the S. coelicolor M145 chromosome were more highly expressed under non-limiting growth conditions than genes in the 1.5 Mb left and 2.3 Mb right chromosome arms, supporting the notion of the core versus auxiliary organization of genes on the chromosome. To examine how this chromosomal distribution of transcripts changes under other growth conditions, we also measured gene expression changes during stationary phase and several stress conditions. During stationary phase, the composition of S. coelicolor transcripts appears to shift from large quantities of growth-related transcripts encoded in the core region to those of less characterized genes, which may be essential for differentiation and other physiological responses, encoded throughout the chromosome. After temperature and osmotic upshifts, we found that S. coelicolor transiently induces a set of several hundred genes located throughout the chromosome, which may function in response mechanisms common to the two stress conditions. MESH terms: Gene Expression Regulation, Bacterial/drug effects/*genetics; Cluster Analysis; Streptomyces coelicolor/*genetics/growth & development; Phosphates/pharmacology; Ethanol/pharmacology; Sucrose/pharmacology; Chromosomes, Bacterial/*genetics; Oligonucleotide Array Sequence Analysis/methods; Temperature; Gene Expression Profiling Associated Links PubMed Link | Repository | Full Text Online Associated Experiment Sets Explore View Download Regional organization of gene expression in Streptomyces coelicolor
	Role of stress response sigma factor SigG in Mycobacterium tuberculosis. Lee JH, Geiman DE, Bishai WR (2008) J Bacteriol 190(3):1128-33	2008-02-01	Mycobacterium tuberculosis	Pubmed
Abstract: The sigG gene of Mycobacterium tuberculosis was disrupted by homologous recombination, and the genes regulated by SigG were examined by real-time reverse-transcription PCR and microarray studies. The SigG consensus promoter recognition sequence was identified as GCGNGT-N15-18-CGANCA. A DeltasigG mutant was found to be more resistant to mitomycin C treatment than the wild-type strain, indicating that it may be involved in the SOS response in M. tuberculosis. MESH terms: Oligonucleotide Array Sequence Analysis; Recombination, Genetic; *SOS Response (Genetics); Cell Line; *Heat-Shock Response; Sigma Factor/genetics/*metabolism; *Gene Expression Regulation, Bacterial; Macrophages, Alveolar/microbiology; Molecular Sequence Data; Base Sequence; Mice; Reverse Transcriptase Polymerase Chain Reaction; DNA-Directed RNA Polymerases/genetics/*metabolism; Mycobacterium tuberculosis/metabolism/pathogenicity/*physiology; Promoter Regions, Genetic; Animals; Bacterial Proteins/genetics/*metabolism; Humans Associated Links PubMed Link | Full Text Online | Web Supplement Associated Experiment Sets Explore View Download Control vs SigG knockout
	Fibrotic response as a distinguishing feature of resistance and susceptibility to pulmonary infection with Mycobacterium tuberculosis in mice. Marquis JF, Nantel A, LaCourse R, Ryan L, North RJ, Gros P (2008) Infect Immun 76(1):78-88	2008-01-01	Mus musculus	Pubmed
Abstract: The differential susceptibility of inbred mouse strains DBA/2J (susceptible) and C57BL/6J (resistant) to pulmonary tuberculosis following aerosol infection is under complex genetic control. In this report, transcriptional profiling with RNAs from Mycobacterium tuberculosis-infected lungs was used to investigate the physiological response, cell type, and biochemical pathways underlying differential susceptibility to infection. Statistical analysis of cDNA-based microarrays revealed that 1,097 transcripts showed statistically significant changes in abundance (changes of > or = 1.5-fold) in at least one of four experimental group comparisons (C57BL/6J [day 0] versus DBA/2J [day 0] mice, C57BL/6J [day 90] versus DBA/2J [day 90] mice, C57BL/6J [day 90] versus C57BL/6J [day 0] mice, or DBA/2J [day 90] versus DBA/2J [day 0] mice). A group of genes showing very high degrees of significance (changes of > or = 2.0-fold) displayed enrichment for transcripts associated with tissue remodeling and the fibrotic response. The differential expression of fibrotic response genes (Sparc, Col1a1, Col1a2, Col4a1, and Col4a2) in the infected lungs of the two mouse strains was validated by another microarray platform (Affymetrix oligonucleotide chips) and by reverse transcription-PCR. Furthermore, the differential expression of additional genes known to be associated with fibrosis (Mmp2, Timp1, and Arg1) was also validated by these approaches. Overall, these results identify the differential fibrotic response as a pathological basis for the high susceptibility of DBA/2J mice to pulmonary tuberculosis. MESH terms: Oligonucleotide Array Sequence Analysis; Male; Fibrosis/*genetics/*microbiology/pathology; *Mycobacterium tuberculosis; Mice; Tuberculosis, Pulmonary/*genetics/*microbiology/pathology; Mice, Inbred DBA; *Genetic Predisposition to Disease; Lung/pathology; Animals; Mice, Inbred C57BL; Gene Expression Profiling Associated Links PubMed Link | Full Text Online | Web Supplement
	Transcriptional regulation of multi-drug tolerance and antibiotic-induced responses by the histone-like protein Lsr2 in M. tuberculosis. Colangeli R, Helb D, Vilcheze C, Hazbon MH, Lee CG, Safi H, Sayers B, Sardone I, Jones MB, Fleischmann RD, Peterson SN, Jacobs WR Jr, Alland D (2007) PLoS Pathog 3(6):e87	2007-06-22	Mycobacterium tuberculosis	Pubmed
Abstract: Multi-drug tolerance is a key phenotypic property that complicates the sterilization of mammals infected with Mycobacterium tuberculosis. Previous studies have established that iniBAC, an operon that confers multi-drug tolerance to M. bovis BCG through an associated pump-like activity, is induced by the antibiotics isoniazid (INH) and ethambutol (EMB). An improved understanding of the functional role of antibiotic-induced genes and the regulation of drug tolerance may be gained by studying the factors that regulate antibiotic-mediated gene expression. An M. smegmatis strain containing a lacZ gene fused to the promoter of M. tuberculosis iniBAC (PiniBAC) was subjected to transposon mutagenesis. Mutants with constitutive expression and increased EMB-mediated induction of PiniBAC::lacZ mapped to the lsr2 gene (MSMEG6065), a small basic protein of unknown function that is highly conserved among mycobacteria. These mutants had a marked change in colony morphology and generated a new polar lipid. Complementation with multi-copy M. tuberculosis lsr2 (Rv3597c) returned PiniBAC expression to baseline, reversed the observed morphological and lipid changes, and repressed PiniBAC induction by EMB to below that of the control M. smegmatis strain. Microarray analysis of an lsr2 knockout confirmed upregulation of M. smegmatis iniA and demonstrated upregulation of genes involved in cell wall and metabolic functions. Fully 121 of 584 genes induced by EMB treatment in wild-type M. smegmatis were upregulated ("hyperinduced") to even higher levels by EMB in the M. smegmatis lsr2 knockout. The most highly upregulated genes and gene clusters had adenine-thymine (AT)-rich 5-prime untranslated regions. In M. tuberculosis, overexpression of lsr2 repressed INH-mediated induction of all three iniBAC genes, as well as another annotated pump, efpA. The low molecular weight and basic properties of Lsr2 (pI 10.69) suggested that it was a histone-like protein, although it did not exhibit sequence homology with other proteins in this class. Consistent with other histone-like proteins, Lsr2 bound DNA with a preference for circular DNA, forming large oligomers, inhibited DNase I activity, and introduced a modest degree of supercoiling into relaxed plasmids. Lsr2 also inhibited in vitro transcription and topoisomerase I activity. Lsr2 represents a novel class of histone-like proteins that inhibit a wide variety of DNA-interacting enzymes. Lsr2 appears to regulate several important pathways in mycobacteria by preferentially binding to AT-rich sequences, including genes induced by antibiotics and those associated with inducible multi-drug tolerance. An improved understanding of the role of lsr2 may provide important insights into the mechanisms of action of antibiotics and the way that mycobacteria adapt to stresses such as antibiotic treatment. MESH terms: Oligonucleotide Array Sequence Analysis; *Transcription, Genetic; DNA Topoisomerases, Type I/physiology; Gene Expression Regulation, Bacterial/*drug effects; DNA/metabolism; DNA, Superhelical/chemistry; *Drug Resistance, Multiple, Bacterial; Genes, Bacterial/physiology; Anti-Bacterial Agents/*pharmacology; Antigens, Bacterial/*physiology; Bacterial Proteins/genetics/*physiology; Promoter Regions, Genetic; Membrane Transport Proteins/genetics; Mycobacterium tuberculosis/*drug effects/genetics; Lipids/analysis; Operon; Permeability Associated Links PubMed Link | Full Text Online | Web Supplement
	The enduring hypoxic response of Mycobacterium tuberculosis. Rustad TR, Harrell MI, Liao R, Sherman DR (2008) PLoS ONE 3(1):e1502	2008-01-30	Mycobacterium tuberculosis	Pubmed
Abstract: BACKGROUND: A significant body of evidence accumulated over the last century suggests a link between hypoxic microenvironments within the infected host and the latent phase of tuberculosis. Studies to test this correlation have identified the M. tuberculosis initial hypoxic response, controlled by the two-component response regulator DosR. The initial hypoxic response is completely blocked in a dosR deletion mutant. METHODOLOGY/PRINCIPAL FINDINGS: We show here that a dosR deletion mutant enters bacteriostasis in response to in vitro hypoxia with only a relatively mild decrease in viability. In the murine infection model, the phenotype of the mutant was indistinguishable from that of the parent strain. These results suggested that additional genes may be essential for entry into and maintenance of bacteriostasis. Detailed microarray analysis of oxygen starved cultures revealed that DosR regulon induction is transient, with induction of nearly half the genes returning to baseline within 24 hours. In addition, a larger, sustained wave of gene expression follows the DosR-mediated initial hypoxic response. This Enduring Hypoxic Response (EHR) consists of 230 genes significantly induced at four and seven days of hypoxia but not at initial time points. These genes include a surprising number of transcriptional regulators that could control the program of bacteriostasis. We found that the EHR is independent of the DosR-mediated initial hypoxic response, as EHR expression is virtually unaltered in the dosR mutant. CONCLUSIONS/SIGNIFICANCE: Our results suggest a reassessment of the role of DosR and the initial hypoxic response in MTB physiology. Instead of a primary role in survival of hypoxia induced bacteriostasis, DosR may regulate a response that is largely optional in vitro and in mouse infections. Analysis of the EHR should help elucidate the key regulatory factors and enzymatic machinery exploited by M. tuberculosis for long-term bacteriostasis in the face of oxygen deprivation. MESH terms: Oligonucleotide Array Sequence Analysis; Genes, Bacterial; Mycobacterium tuberculosis/genetics/*physiology; Mice; Mice, Inbred CBA; Mice, Inbred DBA; Transcription, Genetic; Anoxia/*microbiology; Gene Deletion; Animals; Mice, Inbred C57BL Associated Links Full Text Online | PubMed Link | Repository | Web Supplement Associated Experiment Sets Explore View Download H37Rv wild type strain grown under normal vs hypoxic (0.2% Oxygen) conditions H37dosR mutant strain grown under normal vs hypoxic (0.2% Oxygen) conditions
	Identification of tuberculosis susceptibility genes with human macrophage gene expression profiles. Thuong NT, Dunstan SJ, Chau TT, Thorsson V, Simmons CP, Quyen NT, Thwaites GE, Thi Ngoc Lan N, Hibberd M, Teo YY, Seielstad M, Aderem A, Farrar JJ, Hawn TR (2008) PLoS Pathog 4(12):e1000229	2008-12-01	Homo sapiens	Pubmed
Abstract: Although host genetics influences susceptibility to tuberculosis (TB), few genes determining disease outcome have been identified. We hypothesized that macrophages from individuals with different clinical manifestations of Mycobacterium tuberculosis (Mtb) infection would have distinct gene expression profiles and that polymorphisms in these genes may also be associated with susceptibility to TB. We measured gene expression levels of >38,500 genes from ex vivo Mtb-stimulated macrophages in 12 subjects with 3 clinical phenotypes: latent, pulmonary, and meningeal TB (n = 4 per group). After identifying differentially expressed genes, we confirmed these results in 34 additional subjects by real-time PCR. We also used a case-control study design to examine whether polymorphisms in differentially regulated genes were associated with susceptibility to these different clinical forms of TB. We compared gene expression profiles in Mtb-stimulated and unstimulated macrophages and identified 1,608 and 199 genes that were differentially expressed by >2- and >5-fold, respectively. In an independent sample set of 34 individuals and a subset of highly regulated genes, 90% of the microarray results were confirmed by RT-PCR, including expression levels of CCL1, which distinguished the 3 clinical groups. Furthermore, 6 single nucleotide polymorphisms (SNPs) in CCL1 were found to be associated with TB in a case-control genetic association study with 273 TB cases and 188 controls. To our knowledge, this is the first identification of CCL1 as a gene involved in host susceptibility to TB and the first study to combine microarray and DNA polymorphism studies to identify genes associated with TB susceptibility. These results suggest that genome-wide studies can provide an unbiased method to identify critical macrophage response genes that are associated with different clinical outcomes and that variation in innate immune response genes regulate susceptibility to TB. MESH terms: Mycobacterium tuberculosis/*immunology; Oligonucleotide Array Sequence Analysis; Reproducibility of Results; Tuberculosis/*genetics/*immunology; Tuberculosis, Meningeal/genetics/immunology; Cluster Analysis; Polymerase Chain Reaction; *Polymorphism, Single Nucleotide; Tuberculosis, Pulmonary/genetics/immunology; Case-Control Studies; *Genetic Predisposition to Disease; Macrophage Activation; Macrophages/*immunology; Chemokine CCL1/*genetics/metabolism; Humans; Databases, Genetic; Gene Expression Regulation; RNA, Messenger/genetics/metabolism Associated Links PubMed Link | Full Text Online | Repository | Web Supplement Associated Experiment Sets Explore View Download Identification of tuberculosis susceptibility genes with human macrophage gene expression profiles (CEL data) Identification of tuberculosis susceptibility genes with human macrophage gene expression profiles (Probe Set data)
	Candidate biomarkers for discrimination between infection and disease caused by Mycobacterium tuberculosis. Jacobsen M, Repsilber D, Gutschmidt A, Neher A, Feldmann K, Mollenkopf HJ, Ziegler A, Kaufmann SH (2007) J Mol Med 85(6):613-21	2007-06-01	Homo sapiens	Pubmed
Abstract: Infection with Mycobacterium tuberculosis is controlled by an efficacious immune response in about 90% of infected individuals who do not develop disease. Although essential mediators of protection, e.g., interferon-gamma, have been identified, these factors are insufficient to predict the outcome of M. tuberculosis infection. As a first step to determine additional biomarkers, we compared gene expression profiles of peripheral blood mononuclear cells from tuberculosis patients and M. tuberculosis-infected healthy donors by microarray analysis. Differentially expressed candidate genes were predominantly derived from monocytes and comprised molecules involved in the antimicrobial defense, inflammation, chemotaxis, and intracellular trafficking. We verified differential expression for alpha-defensin 1, alpha-defensin 4, lactoferrin, Fcgamma receptor 1A (cluster of differentiation 64 [CD64]), bactericidal permeability-increasing protein, and formyl peptide receptor 1 by quantitative polymerase chain reaction analysis. Moreover, we identified increased protein expression of CD64 on monocytes from tuberculosis patients. Candidate biomarkers were then assessed for optimal study group discrimination. Using a linear discriminant analysis, a minimal group of genes comprising lactoferrin, CD64, and the Ras-associated GTPase 33A was sufficient for classification of (1) tuberculosis patients, (2) M. tuberculosis-infected healthy donors, and (3) noninfected healthy donors. MESH terms: Biological Markers/metabolism; Male; Receptors, IgG/metabolism; Tissue Donors; Tuberculosis/*genetics; Adult; Discriminant Analysis; Mycobacterium tuberculosis/*physiology; Transcription, Genetic; Case-Control Studies; Monocytes/metabolism/microbiology; Humans; Immunity, Innate/genetics; Female; Gene Expression Profiling; Health; Up-Regulation/genetics Associated Links PubMed Link | Web Supplement | Repository | Full Text Online Associated Experiment Sets Explore View Download Biomarkers for discrimination between infection and disease caused by Mycobacterium tuberculosis
	Roles of SigB and SigF in the Mycobacterium tuberculosis sigma factor network. Lee JH, Karakousis PC, Bishai WR (2008) J Bacteriol 190(2):699-707	2008-01-01	Mycobacterium tuberculosis	Pubmed
Abstract: To characterize the roles of SigB and SigF in sigma factor regulation in Mycobacterium tuberculosis, we used chemically inducible recombinant strains to conditionally overexpress sigB and sigF. Using whole genomic microarray analysis and quantitative reverse transcription-PCR, we investigated the resulting global transcriptional changes after sigB induction, and we specifically tested the relative expression of other sigma factor genes after knock-in expression of sigB and sigF. Overexpression of sigB resulted in significant upregulation of genes encoding several early culture filtrate antigens (ESAT-6-like proteins), ribosomal proteins, PE-PGRS proteins, the keto-acyl synthase, KasA, and the regulatory proteins WhiB2 and IdeR. Of note, the induction of sigB did not alter the expression of other sigma factor genes, indicating that SigB is likely to serve as an end regulator for at least one branch of the M. tuberculosis sigma factor regulatory cascade. Analysis of the 5'-untranslated region (UTR) of SigB-dependent transcripts revealed a putative consensus sequence of NGTGG-N(14-18)-NNGNNG. This sequence appeared upstream of both sigB (Rv2710) and the gene following it, ideR (Rv2711), and in vitro transcription analysis with recombinant SigB-reconstituted RNA polymerase confirmed SigB-dependent transcription from each of these promoters. Knock-in expression of sigF revealed that only the sigC gene was significantly upregulated 6 and 12 h after sigF induction. The previously identified SigF promoter consensus sequence AGTTTG-N(15)-GGGTTT was identified in the 5' UTR of the sigC gene, and SigF-dependent in vitro transcription of the promoter upstream of sigC was confirmed by using recombinant SigF-reconstituted RNA polymerase. These two knock-in recombinant strains were tested in a macrophage model of infection which showed that overexpression of sigB and sigF resulted in reduced rates of M. tuberculosis intracellular growth. These results define the SigB promoter consensus recognition sequence and members of the SigB regulon. Moreover, the data suggest that, in addition to serving as an end regulator in a sigma factor cascade, SigB may auto-amplify its own expression under certain conditions. MESH terms: Oligonucleotide Array Sequence Analysis; Sigma Factor/genetics/*physiology; Binding Sites; Genes, Bacterial; Macrophages, Alveolar/microbiology; Reverse Transcriptase Polymerase Chain Reaction; Mice; Bacterial Proteins/genetics/*physiology; Consensus Sequence; Mycobacterium tuberculosis/genetics/pathogenicity/*physiology; 5 Untranslated Regions/genetics; Regulon; Animals; Gene Expression Profiling; Gene Expression Regulation, Bacterial/genetics/*physiology Associated Links Full Text Online | PubMed Link | Web Supplement Associated Experiment Sets Explore View Download Ctrl vs sigB overexpression
	Differential gene expression between Mycobacterium bovis and Mycobacterium tuberculosis. Rehren G, Walters S, Fontan P, Smith I, Zarraga AM (2007) Tuberculosis (Edinb) 87(4):347-59	2007-07-01	Mycobacterium tuberculosis	Pubmed
Abstract: The high sequence identity among the Mycobacterium bovis and Mycobacterium tuberculosis genomes contrasts with the physiological differences reported between these pathogens, suggesting that variations in gene expression may be involved. In this study, microarray hybridization was used to compare the total transcriptome of M. bovis and M. tuberculosis, during the exponential phase of growth. Differential expression was detected in 258 genes, representing a 6% of the total genome. Variable genes were grouped according to functional categories. The main variations were found in genes encoding proteins involved in intermediary metabolism and respiration, cell wall processes, and hypothetical proteins. It is noteworthy that, compared to M. tuberculosis, the expression of a higher number of transcriptional regulators were detected in M. bovis. Likewise, in M. tuberculosis we found a higher expression of the PE/PPE genes, some of which code for cell wall related proteins. Also, in both pathogens we detected the expression of a number of genes not annotated in the M. tuberculosis H37Rv or M. bovis 2122 genomes, but annotated in the M. tuberculosis CDC1551 genome. Our results provide new evidence concerning differences in gene expression between both pathogens, and confirm previous hypotheses inferred from genome comparisons and proteome analysis. This study may shed some new light on our understanding of the mechanisms relating to differences in gene expression and pathogenicity in mycobacteria. MESH terms: RNA, Bacterial/isolation & purification; Genes, Bacterial/*genetics; Mycobacterium tuberculosis/*genetics; *Gene Expression Profiling; Reverse Transcriptase Polymerase Chain Reaction; Transcription, Genetic; Mycobacterium bovis/*genetics; *Oligonucleotide Array Sequence Analysis Associated Links Full Text Online | Repository | PubMed Link Associated Experiment Sets Explore View Download M. tuberculosis vs M. bovis transcriptional comparison
	Functional genomics reveals extended roles of the Mycobacterium tuberculosis stress response factor sigmaH. Mehra S, Kaushal D Mehra S and Kaushal D (2009) J Bacteriol 191(12):3965-80	2009-06-01	Mycobacterium tuberculosis	Pubmed
Abstract: Mycobacterium tuberculosis is one of the most successful pathogens of humankind. During infection, M. tuberculosis must cope with and survive against a variety of different environmental conditions. Sigma factors likely facilitate the modulation of the pathogen's gene expression in response to changes in its extracellular milieu during infection. sigma(H), an alternate sigma factor encoded by the M. tuberculosis genome, is induced by thiol-oxidative stress, heat shock, and phagocytosis. In response to these conditions, sigma(H) induces the expression of sigma(B), sigma(E), and the thioredoxin regulon. In order to more effectively characterize the transcriptome controlled by sigma(H), we studied the long-term effects of the induction of sigma(H) on global transcription in M. tuberculosis. The M. tuberculosis isogenic mutant of sigma(H) (Delta-sigma(H)) is more susceptible to diamide stress than wild-type M. tuberculosis. To study the long-term effects of sigma(H) induction, we exposed both strains to diamide, rapidly washed it away, and resumed culturing in diamide-free medium (post-diamide stress culturing). Analysis of the effects of sigma(H) induction in this experiment revealed a massive temporal programming of the M. tuberculosis transcriptome. Immediately after the induction of sigma(H), genes belonging to the functional categories "virulence/detoxification" and "regulatory proteins" were induced in large numbers. Fewer genes belonging to the "lipid metabolism" category were induced, while a larger number of genes belonging to this category were downregulated. sigma(H) caused the induction of the ATP-dependent clp proteolysis regulon, likely mediated by a transcription factor encoded by Rv2745c, several members of the mce1 virulence regulon, and the sulfate acquisition/transport network. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository
	The transcriptional regulator Rv0485 modulates the expression of a pe and ppe gene pair and is required for Mycobacterium tuberculosis virulence. Goldstone RM, Goonesekera SD, Bloom BR, Sampson SL (2009) Infect Immun 77(10):4654-67	2009-10-01	Mycobacterium tuberculosis	Pubmed
Abstract: The pe and ppe genes are unique to mycobacteria and are widely speculated to play a role in tuberculosis pathogenesis. However, little is known about how expression of these genes is controlled. Elucidating the regulatory control of genes found exclusively in mycobacteria, such as the pe and ppe gene families, may be key to understanding the success of this pathogen. In this study, we used a transposon mutagenesis approach to elucidate pe and ppe regulation. This resulted in the identification of Rv0485, a previously uncharacterized transcriptional regulator. Microarray and quantitative real-time PCR analysis confirmed that disruption of Rv0485 reduced the expression of the pe13 and ppe18 gene pair (Rv1195 and Rv1196), defined the Rv0485 regulon, and emphasized the lack of global regulation of pe and ppe genes. The in vivo phenotype of the Rv0485 transposon mutant strain (Rv0485::Tn) was investigated in the mouse model, where it was demonstrated that the mutation has minimal effect on bacterial organ burden. Despite this, disruption of Rv0485 allowed mice to survive for significantly longer, with substantially reduced lung pathology in comparison with mice infected with wild-type Mycobacterium tuberculosis. Infection of immune-deficient SCID mice with the Rv0485::Tn strain also resulted in extended survival times, suggesting that Rv0485 plays a role in modulation of innate immune responses. This is further supported by the finding that disruption of Rv0485 resulted in reduced secretion of proinflammatory cytokines by infected murine macrophages. In summary, we have demonstrated that disruption of a previously uncharacterized transcriptional regulator, Rv0485, results in reduced expression of pe13 and ppe18 and attenuation of M. tuberculosis virulence. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download The Transcriptional Regulator Rv0485 Modulates the Expression of a PE and PPE Genes.
	A member of the cAMP receptor protein family of transcription regulators in Mycobacterium tuberculosis is required for virulence in mice and controls transcription of the rpfA gene coding for a resuscitation promoting factor. Rickman L, Scott C, Hunt DM, Hutchinson T, Menendez MC, Whalan R, Hinds J, Colston MJ, Green J, Buxton RS (2005) Mol Microbiol 56(5):1274-86	2005-03-30	Mycobacterium tuberculosis	Pubmed
Abstract: Deletion of gene Rv3676 in Mycobacterium tuberculosis coding for a transcription factor belonging to the cAMP receptor protein (CRP) family caused growth defects in laboratory medium, in bone marrow-derived macrophages and in a mouse model of tuberculosis. Transcript profiling of M. tuberculosis grown in vitro identified 16 genes with significantly altered expression in the mutant compared with the wild type. Analysis of the DNA sequences upstream of the corresponding open reading frames revealed that 12 possessed sequences related to a consensus CRP binding site that could represent the sites of action of Rv3676. These included rpfA, lprQ, whiB1 and ahpC among genes with enhanced expression in the wild type, and Rv3616c-Rv3613c, Rv0188 and lipQ among genes exhibiting enhanced expression in the mutant. The activity of an rpfA::lacZ promoter fusion was lowered in the Rv3676 mutant and by mutation of the predicted Rv3676 binding site. Moreover, the product of Rv3676 (isolated as a TrxA fusion protein) interacted specifically with the rpfA promoter, and binding was inhibited by mutation of the Rv3676 site. Although Rv3676 retains four of the six amino acid residues that bind cAMP in Escherichia coli CRP addition of cAMP did not enhance Rv3676 binding at the rpfA promoter in vitro. In summary, it has been shown that Rv3676 is a direct regulator of rpfA expression, and because rpfA codes for a resuscitation promoting factor this may implicate Rv3676 in reactivation of dormant M. tuberculosis infections. MESH terms: Artificial Gene Fusion; Colony Count, Microbial; Mycobacterium tuberculosis/genetics/growth & development/*pathogenicity; Oligonucleotide Array Sequence Analysis; Spleen/microbiology; *Transcription, Genetic; Virulence/genetics; Disease Models, Animal; *Gene Expression Regulation, Bacterial; Molecular Sequence Data; Tuberculosis/microbiology; Aconitate Hydratase/*biosynthesis/genetics; Cyclic AMP Receptor Protein/genetics/*physiology; Genes, Bacterial/physiology; Mice; Regulatory Sequences, Nucleic Acid; beta-Galactosidase/genetics/metabolism; Macrophages/microbiology; Mice, Inbred BALB C; Gene Deletion; Lung/microbiology; Animals; Lac Operon/physiology; Amino Acid Sequence; Bacterial Proteins/*biosynthesis/genetics; Female; Genes, Reporter/physiology Associated Links Full Text Online | PubMed Link | Web Supplement | Repository Associated Experiment Sets Explore View Download Wild type vs CRP mutant of Mycobacterium tuberculosis
	Genetic and functional characterization of the mouse Trl3 locus in defense against tuberculosis. Marquis JF, Lacourse R, Ryan L, North RJ, Gros P (2009) J Immunol 182(6):3757-67	2009-03-15	Mus musculus	Pubmed
Abstract: The genetic control of susceptibility to tuberculosis in DBA/2J and C57BL/6J mice is complex and influenced by at least four tuberculosis resistance loci (Trl1-Trl4). To further study the Trl3 and Trl4 loci, we have created congenic mouse lines D2.B6-Chr7 and D2.B6-Chr19, in which resistant B6-derived portions of chromosome 7 (Chr.7) and chromosome 19 (Chr.19) overlapping Trl3 and Trl4, respectively, were independently introgressed onto susceptible D2 background. Transfer of B6-derived Trl3 chromosome 7 segment significantly increased resistance of D2 mice, as measured by reduced pulmonary microbial replication at day 70, and increased host survival following aerosol infection. However, transfer of B6-derived chromosome 19 (Trl4) onto D2 mice did not increase resistance by itself and does not improve on the protective effect of chromosome 7. Further study of the protective effect of Trl3 in D2.B6-Chr7 mice indicates that it does not involve modulation of timing or magnitude of Th1 response in the lung, as investigated by measuring the number of Ag-specific, IFN-gamma-producing CD4(+) and CD8(+) T cells. Rather, Trl3 appears to affect the intrinsic ability of activated macrophages to restrict intracellular mycobacterial replication in an NO synthase 2-independent fashion. Microarray experiments involving parental and congenic mouse lines identified a number of genes in the Trl3 interval on chromosome 7 the level of expression of which before infection or in response to Mycobacterium tuberculosis infection is differentially regulated in a parental haplotype-dependent fashion. This gene list represents a valuable entry point for the identification and prioritization of positional candidate genes for the Trl3 effect on chromosome 7. MESH terms: Chromosomal Proteins, Non-Histone/chemistry/*genetics/physiology; Male; Gene Expression Regulation/immunology; Signal Transduction/genetics/immunology; Mice; Mice, Inbred DBA; Genetic Markers/immunology; *Genetic Predisposition to Disease; Mice, Congenic; Animals; Immunity, Innate/*genetics; Mice, Inbred C57BL; Phenotype; Species Specificity; Tuberculosis, Pulmonary/*genetics/*immunology/mortality/pathology; Mycobacterium tuberculosis/growth & development/*immunology Associated Links PubMed Link | Full Text Online | Web Supplement | Repository Associated Experiment Sets Explore View Download Genetic and Functional Characterization of the Mouse Trl3/Trl4 Locus in Defense against Tuberculosis (CEL data) Genetic and Functional Characterization of the Mouse Trl3/Trl4 Locus in Defense against Tuberculosis (Probe Set Data)
	Transcriptional responses of Mycobacterium tuberculosis to lung surfactant. Schwab U, Rohde KH, Wang Z, Chess PR, Notter RH, Russell DG (2009) Microb Pathog 46(4):185-93	2009-04-01	Mycobacterium tuberculosis	Pubmed
Abstract: This study uses microarray analyses to examine gene expression profiles for Mycobacterium tuberculosis (Mtb) induced by exposure in vitro to bovine lung surfactant preparations that vary in apoprotein content: (i) whole lung surfactant (WLS) containing the complete mixture of endogenous lipids and surfactant proteins (SP)-A, -B, -C, and -D; (ii) extracted lung surfactant (CLSE) containing lipids plus SP-B and -C; (iii) column-purified surfactant lipids (PPL) containing no apoproteins, and (iv) purified human SP-A. Exposure to WLS evoked a multitude of transcriptional responses in Mtb, with 52 genes up-regulated and 23 genes down-regulated at 30min exposure, plus 146 genes up-regulated and 27 genes down-regulated at 2h. Notably, WLS rapidly induced several membrane-associated lipases that presumptively act on surfactant lipids as substrates, and a large number of genes involved in the synthesis of phthiocerol dimycocerosate (PDIM), a cell wall component known to be important in macrophage interactions and Mtb virulence. Exposure of Mtb to CLSE, PPL, or purified SP-A caused a substantially weaker transcriptional response (<=20 genes were induced) suggesting that interactions among multiple lipid-protein components of WLS may contribute to its effects on Mtb transcription. MESH terms: Oligonucleotide Array Sequence Analysis; Pulmonary Surfactants/*metabolism; *Stress, Physiological; Animals; Humans; Cattle; Gene Expression Profiling; Mycobacterium tuberculosis/*drug effects Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Transcriptional responses of Mycobacterium tuberculosis to lung surfactant
	Inhibition of respiration by nitric oxide induces a Mycobacterium tuberculosis dormancy program. Voskuil MI, Schnappinger D, Visconti KC, Harrell MI, Dolganov GM, Sherman DR, Schoolnik GK (2003) J Exp Med 198(5):705-13	2003-09-01	Mycobacterium tuberculosis	Pubmed
Abstract: An estimated two billion persons are latently infected with Mycobacterium tuberculosis. The host factors that initiate and maintain this latent state and the mechanisms by which M. tuberculosis survives within latent lesions are compelling but unanswered questions. One such host factor may be nitric oxide (NO), a product of activated macrophages that exhibits antimycobacterial properties. Evidence for the possible significance of NO comes from murine models of tuberculosis showing progressive infection in animals unable to produce the inducible isoform of NO synthase and in animals treated with a NO synthase inhibitor. Here, we show that O2 and low, nontoxic concentrations of NO competitively modulate the expression of a 48-gene regulon, which is expressed in vivo and prepares bacilli for survival during long periods of in vitro dormancy. NO was found to reversibly inhibit aerobic respiration and growth. A heme-containing enzyme, possibly the terminal oxidase in the respiratory pathway, likely senses and integrates NO and O2 levels and signals the regulon. These data lead to a model postulating that, within granulomas, inhibition of respiration by NO production and O2 limitation constrains M. tuberculosis replication rates in persons with latent tuberculosis. MESH terms: Nitric Oxide Synthase/*drug effects; Nitric Oxide Donors/*pharmacology; Triazenes/*pharmacology; Nitric Oxide/*physiology; Mycobacterium tuberculosis/drug effects/growth & development/*metabolism; Oxygen Consumption/*drug effects Associated Links Full Text Online | Web Supplement | PubMed Link | Repository Associated Experiment Sets Explore View Download Inhibition of Respiration by Nitric Oxide Induces a Mycobacterium tuberculosis Dormancy Program
	Mycobacterium tuberculosis modulates its cell surface via an oligopeptide permease (Opp) transport system. Flores-Valdez MA, Morris RP, Laval F, Daffe M, Schoolnik GK (2009) FASEB J 23(12):4091-104	2009-08-11	Mycobacterium tuberculosis	Pubmed
Abstract: Bacterial species utilize a vast repertoire of surface structures to interact with their surroundings, and employ a number of strategies to reconfigure the cellular envelope according to specific stimuli. Gram-positive bacteria exemplified by Streptomyces and Bacillus species, control production of some exposed molecules by importing oligopeptide signals via permeases (Opp). Such oligopeptides modulate intracellular signaling pathways. In this work, we functionally characterized an Opp of the human pathogen Mycobacterium tuberculosis (Mtb), and propose its reannotation. Using genome-wide transcriptional profiling, we found that Opp was required to modulate (fold-change ranging from -3.5 to 2.0) the expression of several genes, most of them encoding surface-exposed molecules. These included the virulence-associated lipids mycolic acids and phthiocerol dimycocerosates (PDIM), as well as PE-family proteins. By thin layer chromatography, and MALDI-TOF-MS we confirmed changes in the lipid profile, including an altered accumulation of triacylglycerides and an affected ratio of mycolic acids to PDIM. An Opp loss of function mutant showed no in vitro growth defect, but had diminished burden during chronic infection and produced a slightly delayed time-to-death of animals when compared to WT Mtb infection. MESH terms: null Associated Links Full Text Online | PubMed Link | Repository Associated Experiment Sets Explore View Download Characterization of mycobacterial oligopeptide permease system
	The mechanism of action of PA-824: Novel insights from transcriptional profiling. Manjunatha U, Boshoff HI, Barry CE (2009) Commun Integr Biol 2(3):215-8	2009-05-01	Mycobacterium tuberculosis	Pubmed
Abstract: The bicyclic nitroimidazole PA-824 is a pro-drug with a very complex mechanism of action active against both replicating and hypoxic, non-replicating Mycobacterium tuberculosis. Microarray analysis of the mode of action of PA-824 showed a puzzling mixed effect both on genes responsive to both cell wall inhibition (like isoniazid) and respiratory poisoning (like cyanide). The aerobic killing mechanism of this drug appears to involve inhibition of cell wall mycolic acid biosynthesis through an as yet unknown molecular mechanism. However, the structure-activity relationships governing aerobic activity do not parallel the relationships determining anaerobic activity. Based on the metabolite profiling of PA-824 and various derivatives by Ddn-mediated activation, we have shown that PA-824 acts directly as an NO donor.1 This respiratory poisoning through nitric oxide release seemed to be a crucial element of anaerobic activity by PA-824. The effect of PA-824 on the respiratory complex under hypoxic non-replicating conditions was also manifested in a rapid drop in intracellular ATP levels, again similar to that observed by cyanide treatment. Thus, transcriptional profiling provided valuable clues to elucidating the molecular mechanism of mycobacterial killing. MESH terms: null Associated Links PubMed Link | Full Text Online Associated Experiment Sets Explore View Download The mechanism of action of PA-824: Novel insights from transcriptional profiling.
	Global transcriptional profile of Mycobacterium tuberculosis during THP-1 human macrophage infection. Fontan P, Aris V, Ghanny S, Soteropoulos P, Smith I (2008) Infect Immun 76(2):717-25	2008-02-01	Mycobacterium tuberculosis	Pubmed
Abstract: During lung infection, Mycobacterium tuberculosis resides in macrophages and subverts the bactericidal mechanisms of these professional phagocytes. Comprehension of this host-pathogen relationship is fundamental for the development of new therapies to cure and prevent tuberculosis. In this work, we analyzed the transcriptional profile of M. tuberculosis infecting human macrophage-like THP-1 cells in order to identify putative bacterial pathogenic factors that can be relevant for the intracellular survival of M. tuberculosis. We compared the gene expression profile of M. tuberculosis H37Rv after 4 h and 24 h of infection of human macrophage-like THP-1 cells with the gene expression profile of the strain growing exponentially in broth cultures. We found 585 genes expressed differentially by intracellular M. tuberculosis. An analysis of the gene expression profile of M. tuberculosis inside THP-1 cells suggests the perturbation of the cell envelope as a major intracellular stress inside THP-1 macrophages. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Global Transcriptional Profile of Mycobacterium tuberculosis during THP-1 Human Macrophage Infection
	Mycobacterium tuberculosis sigma factor E regulon modulates the host inflammatory response. Fontan PA, Aris V, Alvarez ME, Ghanny S, Cheng J, Soteropoulos P, Trevani A, Pine R, Smith I (2008) J Infect Dis 198(6):877-85	2008-09-15	Mycobacterium tuberculosis	Pubmed
Abstract: Mycobacterium tuberculosis survives in macrophages and usually subverts the bactericidal mechanisms of these phagocytes. The understanding of this host-pathogen interaction is relevant for the development of new treatments for tuberculosis. The adaptation of M. tuberculosis to intracellular life depends on its ability to regulate the expression of its genes. Sigma factors are important bacterial transcription activators that bind to the RNA polymerase and give it promoter specificity. Sigma factor E (SigE) controls the expression of genes that are essential for virulence. We have identified the SigE regulon during infection of macrophages, and we analyzed the impact of this regulon on the transcriptional response of phagocytes. Our results indicate that SigE regulates the expression of genes involved in the maintenance of M. tuberculosis cell envelope integrity and function during macrophage infection. Analysis of the phagocytes' transcriptional response indicates that the SigE regulon is involved in the modulation of the inflammatory response. MESH terms: null Associated Links PubMed Link | Repository | Full Text Online Associated Experiment Sets Explore View Download Sigma factor E of Mycobacterium tuberculosis controls the expression of bacterial components that modulate macrophages.
	The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Balazsi G, Heath AP, Shi L, Gennaro ML (2008) Mol Syst Biol 4():225	2008-11-01	Mycobacterium tuberculosis	Pubmed
Abstract: The virulence of Mycobacterium tuberculosis depends on the ability of the bacilli to switch between replicative (growth) and non-replicative (dormancy) states in response to host immunity. However, the gene regulatory events associated with transition to dormancy are largely unknown. To address this question, we have assembled the largest M. tuberculosis transcriptional-regulatory network to date, and characterized the temporal response of this network during adaptation to stationary phase and hypoxia, using published microarray data. Distinct sets of transcriptional subnetworks (origons) were responsive at various stages of adaptation, showing a gradual progression of network response under both conditions. Most of the responsive origons were in common between the two conditions and may help define a general transcriptional signature of M. tuberculosis growth arrest. These results open the door for a systems-level understanding of transition to non-replicative persistence, a phenotypic state that prevents sterilization of infection by the host immune response and promotes the establishment of latent M. tuberculosis infection, a condition found in two billion people worldwide. MESH terms: Mycobacterium tuberculosis/*genetics/growth & development/metabolism; Transcription Factors/metabolism; *Genes, Bacterial Associated Links PubMed Link | Web Supplement | Full Text Online
	Global transcriptional response to vancomycin in Mycobacterium tuberculosis. Provvedi R, Boldrin F, Falciani F, Palu G, Manganelli R (2009) Microbiology 155(Pt 4):1093-102	2009-04-01	Mycobacterium tuberculosis	Pubmed
Abstract: In order to gain additional understanding of the physiological mechanisms used by bacteria to maintain surface homeostasis and to identify potential targets for new antibacterial drugs, we analysed the variation of the Mycobacterium tuberculosis transcriptional profile in response to inhibitory and subinhibitory concentrations of vancomycin. Our analysis identified 153 genes differentially regulated after exposing bacteria to a concentration of the drug ten times higher than the MIC, and 141 genes differentially expressed when bacteria were growing in a concentration of the drug eightfold lower than the MIC. Hierarchical clustering analysis indicated that the response to these different conditions is different, although with some overlap. This approach allowed us to identify several genes whose products could be involved in the protection from antibiotic stress targeting the envelope and help to confer the basal level of M. tuberculosis resistance to antibacterial drugs, such as Rv2623 (UspA-like), Rv0116c, PE20-PPE31, PspA and proteins related to toxin-antitoxin systems. Moreover, we also demonstrated that the alternative sigma factor sigma(E) confers basal resistance to vancomycin, once again underlining its importance in the physiology of the mycobacterial surface stress response. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository
	A thiolase of Mycobacterium tuberculosis is required for virulence and production of androstenedione and androstadienedione from cholesterol. Nesbitt NM, Yang X, Fontan P, Kolesnikova I, Smith I, Sampson NS, Dubnau E (2010) Infect Immun 78(1):275-82	2009-10-12	Mycobacterium tuberculosis	Pubmed
Abstract: Mycobacterium tuberculosis (M. tb), the causative agent of tuberculosis, is an intracellular pathogen that shifts to a lipid-based metabolism in the host. Moreover, metabolism of the host lipid cholesterol plays an important role in M. tuberculosis (M. tb) infection. We used transcriptional profiling to identify genes transcriptionally regulated by cholesterol and KstR (Rv3574), a Tet-R like repressor. The fadA5 (Rv3546) gene, annotated as a lipid metabolizing thiolase, the expression of which is upregulated by cholesterol and repressed by KstR, was deleted in M. tb H37Rv. We demonstrated that fadA5 is required for utilization of cholesterol as a sole carbon source in vitro and for full virulence of M. tb in the chronic stage of mouse lung infection. Cholesterol is not toxic to the fadA5 mutant strain, and therefore, toxicity does not account for its attenuation. We show that the wild-type strain, H37Rv, metabolizes cholesterol to androst-4-ene-3,17-dione and androsta-1,4-diene-3,17-dione and exports these metabolites into the medium, whereas the fadA5 mutant strain is defective for this activity. We demonstrate that FadA5 catalyzes the thiolysis of acetoacetyl CoA. This catalytic activity is consistent with a beta-ketoacyl CoA thiolase function in cholesterol beta-oxidation that is required for the production of androsterones. We conclude that the attenuated phenotype of the fadA5 mutant is a consequence of disrupted cholesterol metabolism that is only essential in the persistent stage of M. tb infection and may be caused by the inability to produce AD/ADD from cholesterol. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download M. tuberculosis Grown in Cholesterol Supplemented Medium M. tuberculosis CDC1551 Wild Type vs kstR Mutant With or Without Cholesterol
	Combination of host susceptibility and Mycobacterium tuberculosis virulence define gene expression profile in the host. Beisiegel M, Mollenkopf HJ, Hahnke K, Koch M, Dietrich I, T Reece S, Kaufmann SH (2009) Eur J Immunol 39(12):3369-3384	2009-09-30	Mus musculus	Pubmed
Abstract: Progression and outcome of tuberculosis is governed by extensive crosstalk between pathogen and host. Analyses of global changes in gene expression during immune response to infection with Mycobacterium tuberculosis (M.tb) can help identify molecular markers of disease state and progression. Global distribution of M.tb strains with different degrees of virulence and drug resistance, especially for the immunocompromised host, make closer analyses of host responses more pressing than ever. Here, we describe global transcriptional responses of inducible nitric oxide synthase-deficient (iNOS(-/-)) and WT mice infected with two related M.tb strains of markedly different virulence, namely the M.tb laboratory strains H37Rv and H37Ra. Both hosts exhibited highly similar resistance to infection with H37Ra. In contrast, iNOS(-/-) mice rapidly succumbed to H37Rv, whereas WT mice developed chronic course of disease. By differential analyses, virulence-specific changes in global host gene expression were analyzed to identify molecular markers characteristic for chronic versus acute infection. We identified several markers unique for different stages of disease progression and not previously associated with virulence-specific host responses in tuberculosis. MESH terms: null Associated Links PubMed Link | Full Text Online | Web Supplement Associated Experiment Sets Explore View Download Combination of host susceptibility and Mycobacterium tuberculosis virulence define gene expression profile in the host
	Transcriptional profiling of mycobacterial antigen-induced responses in infants vaccinated with BCG at birth. Fletcher HA, Keyser A, Bowmaker M, Sayles PC, Kaplan G, Hussey G, Hill AV, Hanekom WA (2009) BMC Med Genomics 2():10	2009-02-24	Homo sapiens	Pubmed
Abstract: ABSTRACT: BACKGROUND: Novel tuberculosis (TB) vaccines recently tested in humans have been designed to boost immunity induced by the current vaccine, Mycobacterium bovis Bacille Calmette-Guerin (BCG). Because BCG vaccination is used extensively in infants, this population group is likely to be the first in which efficacy trials of new vaccines will be conducted. However, our understanding of the complexity of immunity to BCG in infants is inadequate, making interpretation of vaccine-induced immune responses difficult. METHODS: To better understand BCG-induced immunity, we performed gene expression profiling in five 10-week old infants routinely vaccinated with BCG at birth. RNA was extracted from 12 hour BCG-stimulated or purified protein derivative of tuberculin (PPD)-stimulated PBMC, isolated from neonatal blood collected 10 weeks after vaccination. RNA was hybridised to the Sentrix(R) HumanRef-8 Expression BeadChip (Illumina) to measure expression of >16,000 genes. RESULTS: We found that ex vivo stimulation of PBMC with PPD and BCG induced largely similar gene expression profiles, except that BCG induced greater macrophage activation. The peroxisome proliferator-activated receptor (PPAR) signaling pathway, including PPAR-gamma, involved in activation of the alternative, anti-inflammatory macrophage response was down-regulated following stimulation with both antigens. In contrast, up-regulation of genes associated with the classic, pro-inflammatory macrophage response was noted. Further analysis revealed a decrease in the expression of cell adhesion molecules (CAMs), including integrin alpha M (ITGAM), which is known to be important for entry of mycobacteria into the macrophage. Interestingly, more leukocyte genes were down-regulated than up-regulated. CONCLUSION: Our results suggest that a combination of suppressed and up-regulated genes may be key in determining development of protective immunity to TB induced by vaccination with BCG. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository | Web Supplement Associated Experiment Sets Explore View Download Transcriptional profiling of mycobacterial antigen-induced responses in infants vaccinated with BCG at birth
	Transcriptional Adaptation of Mycobacterium tuberculosis within Macrophages: Insights into the Phagosomal Environment. Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, Monahan IM, Dolganov G, Efron B, Butcher PD, Nathan C, Schoolnik GK (2003) J Exp Med 198(5):693-704	2003-09-01	Mycobacterium tuberculosis	Pubmed
Abstract: Little is known about the biochemical environment in phagosomes harboring an infectious agent. To assess the state of this organelle we captured the transcriptional responses of Mycobacterium tuberculosis (MTB) in macrophages from wild-type and nitric oxide (NO) synthase 2-deficient mice before and after immunologic activation. The intraphagosomal transcriptome was compared with the transcriptome of MTB in standard broth culture and during growth in diverse conditions designed to simulate features of the phagosomal environment. Genes expressed differentially as a consequence of intraphagosomal residence included an interferon gamma- and NO-induced response that intensifies an iron-scavenging program, converts the microbe from aerobic to anaerobic respiration, and induces a dormancy regulon. Induction of genes involved in the activation and beta-oxidation of fatty acids indicated that fatty acids furnish carbon and energy. Induction of sigmaE-dependent, sodium dodecyl sulfate-regulated genes and genes involved in mycolic acid modification pointed to damage and repair of the cell envelope. Sentinel genes within the intraphagosomal transcriptome were induced similarly by MTB in the lungs of mice. The microbial transcriptome thus served as a bioprobe of the MTB phagosomal environment, showing it to be nitrosative, oxidative, functionally hypoxic, carbohydrate poor, and capable of perturbing the pathogen's cell envelope. MESH terms: null Associated Links PubMed Link | Full Text Online | Web Supplement
	Phthiocerol dimycocerosate transport is required for resisting interferon-gamma-independent immunity. Murry JP, Pandey AK, Sassetti CM, Rubin EJ (2009) J Infect Dis 200(5):774-82	2009-09-01	Mycobacterium tuberculosis	Pubmed
Abstract: Nitric oxide (NO), which is an important component of immunity to Mycobacterium tuberculosis, has both cytotoxic and immune regulatory functions. We examined the way that this molecule interacts with M. tuberculosis in vivo by screening for bacterial mutations that alter growth in mice that are unable to produce inducible NO synthase (iNOS), the dominant source of NO during infection. We found that very few bacterial genes appeared to be specifically required for resistance to NO in vivo. Instead, mutations in several virulence factors caused greater attenuation in the absence of iNOS. Among these were mutants incapable of transporting the lipid phthiocerol dimycocerosate (PDIM). Although PDIM has been implicated in NO defense, this result indicates that PDIM has other roles during infection. We additionally found that PDIM transport is required for virulence in mice lacking interferon-gamma . Thus, PDIM is important for resisting an interferon-gamma-independent mechanism of immunity. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Mycobacterium tuberculosis TraSH experiment: Growth in wild type C57BL/6J versus iNOS-/- mice
	Global analysis of the Mycobacterium tuberculosis Zur (FurB) regulon. Maciag A, Dainese E, Rodriguez GM, Milano A, Provvedi R, Pasca MR, Smith I, Palu G, Riccardi G, Manganelli R (2007) J Bacteriol 189(3):730-40	2007-02-01	Mycobacterium tuberculosis	Pubmed
Abstract: The proteins belonging to the Fur family are global regulators of gene expression involved in the response to several environmental stresses and to the maintenance of divalent cation homeostasis. The Mycobacterium tuberculosis genome encodes two Fur-like proteins, FurA and a protein formerly annotated FurB. Since in this paper we show that it represents a zinc uptake regulator, we refer to it as Zur. The gene encoding Zur is found in an operon together with the gene encoding a second transcriptional regulator (Rv2358). In a previous work we demonstrated that Rv2358 is responsible for the zinc-dependent repression of the Rv2358-zur operon, favoring the hypothesis that these genes represent key regulators of zinc homeostasis. In this study we generated a zur mutant in M. tuberculosis, examined its phenotype, and characterized the Zur regulon by DNA microarray analysis. Thirty-two genes, presumably organized in 16 operons, were found to be upregulated in the zur mutant. Twenty-four of them belonged to eight putative transcriptional units preceded by a conserved 26-bp palindrome. Electrophoretic mobility shift experiments demonstrated that Zur binds to this palindrome in a zinc-dependent manner, suggesting its direct regulation of these genes. The proteins encoded by Zur-regulated genes include a group of ribosomal proteins, three putative metal transporters, the proteins belonging to early secretory antigen target 6 (ESAT-6) cluster 3, and three additional proteins belonging to the ESAT-6/culture filtrate protein 10 (CFP-10) family known to contain immunodominant epitopes in the T-cell response to M. tuberculosis infection. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository
	The influence of reduced oxygen availability on pathogenicity and gene expression in Mycobacterium tuberculosis. Bacon J, James BW, Wernisch L, Williams A, Morley KA, Hatch GJ, Mangan JA, Hinds J, Stoker NG, Butcher PD, Marsh PD (2004) Tuberculosis (Edinb) 84(3-4):205-17	2004-04-01	Mycobacterium tuberculosis	Pubmed
Abstract: We investigated how Mycobacterium tuberculosis responded to a reduced oxygen tension in terms of its pathogenicity and gene expression by growing cells under either aerobic or low-oxygen conditions in chemostat culture. The chemostat enabled us to control and vary the oxygen tension independently of other environmental parameters, so that true cause-and-effect relationships of reduced oxygen availability could be established. Cells grown under low oxygen were more pathogenic for guinea pigs than those grown aerobically. The effect of reduced oxygen on global gene expression was determined using DNA microarray. Spearman rank correlation confirmed that microarray expression profiles were highly reproducible between repeat cultures. Using microarray analysis we have identified genes that respond to a low-oxygen environment without the influence of other parameters such as nutrient depletion. Some of these genes appear to be involved in the biosynthesis of cell wall precursors and their induction may have contributed to increased infectivity in the guinea pig. This study has shown that a combination of chemostat culture and microarray presents a biologically robust and statistically reliable experimental approach for studying the effect of relevant and specific environmental stimuli on mycobacterial virulence and gene expression. MESH terms: null Associated Links PubMed Link | Repository | Full Text Online
	Bioactive Pyridine-N-oxide Disulfides from Allium stipitatum O'Donnell G, Poeschl R, Zimhony O, Gunaratnam M, Moreira JB, Neidle S, Evangelopoulos D, Bhakta S, Malkinson JP, Boshoff HI, Lenaerts A, Gibbons S (2009) J Nat Prod 72(3):360-365	2009-03-01	Mycobacterium tuberculosis	Pubmed
Abstract: From Allium stipitatum, three pyridine-N-oxide alkaloids (1-3) possessing disulfide functional groups were isolated. The structures of these natural products were elucidated by spectroscopic means as 2-(methyldithio)pyridine-N-oxide (1), 2-[(methylthiomethyl)dithio]pyridine-N-oxide (2), and 2,2'-dithio-bis-pyridine-N-oxide (3). The proposed structure of 1 was confirmed by synthetic S-methylthiolation of commercial 2-thiopyridine-N-oxide. Compounds 1 and 2 are new natural products, and 3 is reported for the first time from an Allium species. All compounds were evaluated for activity against fast-growing species of Mycobacterium, methicillin-resistant Staphylococcus aureus, and a multidrug-resistant (MDR) variants of S. aureus. Compounds 1 and 2 exhibited minimum inhibitory concentrations (MICs) of 0.5-8 mug/mL against these strains. A small series of analogues of 1 were synthesized in an attempt to optimize antibacterial activity, although the natural product had the most potent in vitro activity. In a whole-cell assay at 30 mug/mL, 1 was shown to give complete inhibition of the incorporation of (14)C-labeled acetate into soluble fatty acids, indicating that it is potentially an inhibitor of fatty acid biosynthesis. In a human cancer cell line antiproliferative assay, 1 and 2 displayed IC(50) values ranging from 0.3 to 1.8 muM with a selectivity index of 2.3 when compared to a human somatic cell line. Compound 1 was evaluated in a microarray analysis that indicated a similar mode of action to menadione and 8-quinolinol by interfering with the thioredoxin system and up-regulating the production of various heat shock proteins. This compound was also assessed in a mouse model for in vivo toxicity. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Bioactive Pyridine-N-oxide Disulfides from Allium stipitatum
	Regulation of morphological differentiation in S. coelicolor by RNase III (AbsB) cleavage of mRNA encoding the AdpA transcription factor. Xu W, Huang J, Lin R, Shi J, Cohen SN (2010) Mol Microbiol 75(3):781-91	2010-01-03	Streptomyces coelicolor	Pubmed
Abstract: Summary RNase III family enzymes, which are perhaps the most widely conserved of all ribonucleases, are known primarily for their role in the processing and maturation of small RNAs. The RNase III gene of Streptomyces coelicolor, which was discovered initially as a global regulator of antibiotic production in this developmentally complex bacterial species and named absB (antibiotic biosynthesis gene B), has subsequently also been found to modulate the cellular abundance of multiple messenger RNAs implicated in morphological differentiation. We report here that regulation of differentiation-related mRNAs by the S. coelicolor AbsB/RNase III enzyme occurs largely by ribonucleolytic cleavage of transcripts encoding the pleiotropic transcription factor, AdpA, and that AdpA and AbsB participate in a novel feedback-control loop that reciprocally regulates the cellular levels of both proteins. Our results reveal a previously unsuspected mechanism for global ribonuclease-mediated control of gene expression in streptomycetes. MESH terms: null Associated Links PubMed Link | Full Text Online Associated Experiment Sets Explore View Download Gene expression pattern of adpA knock-out strains in Streptomyces coelicolor
	Unique roles of DosT and DosS in DosR regulon induction and Mycobacterium tuberculosis dormancy. Honaker RW, Leistikow RL, Bartek IL, Voskuil MI (2009) Infect Immun 77(8):3258-63	2009-08-01	Mycobacterium tuberculosis	Pubmed
Abstract: In Mycobacterium tuberculosis, the sensor kinases DosT and DosS activate the transcriptional regulator DosR, resulting in the induction of the DosR regulon, which is important for anaerobic survival and perhaps latent infection. The individual and collective roles of these sensors have been postulated biochemically, but their roles in vivo have remained unclear. This work demonstrates distinct and additive roles for each sensor during anaerobic dormancy. Both sensors are necessary for wild-type levels of DosR regulon induction, and concomitantly, full induction of the regulon is required for wild-type anaerobic survival. In the anaerobic model, DosT plays an early role, responding to hypoxia. DosT then induces the regulon and with it DosS, which sustains and further induces the regulon. DosT then loses its functionality as oxygen becomes limited, and DosS alone maintains induction of the genes from that point forward. Thus, M. tuberculosis has evolved a system whereby it responds to hypoxic conditions in a stepwise fashion as it enters an anaerobic state. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Unique roles of DosT and DosS in DosR regulon induction and Mycobacterium tuberculosis dormancy
	Activation of the eis gene in a W-Beijing strain of Mycobacterium tuberculosis correlates with increased SigA levels and enhanced intracellular growth. Wu S, Barnes PF, Samten B, Pang X, Rodrigue S, Ghanny S, Soteropoulos P, Gaudreau L, Howard ST (2009) Microbiology 155(Pt 4):1272-81	2009-04-01	Mycobacterium tuberculosis	Pubmed
Abstract: There is growing evidence that strains of Mycobacterium tuberculosis differ in pathogenicity and transmissibility, but little is understood about the contributory factors. We have previously shown that increased expression of the principal sigma factor, SigA, mediates the capacity of M. tuberculosis strain 210 to grow more rapidly in human monocytes, compared with other strains. Strain 210 is part of the widespread W-Beijing family of M. tuberculosis strains and includes clinical isolate TB294. To identify genes that respond to changes in SigA levels and that might enhance intracellular growth, we examined RNA and protein expression patterns in TB294-pSigA, a recombinant strain of TB294 that overexpresses sigA from a multicopy plasmid. Lysates from broth-grown cultures of TB294-pSigA contained high levels of Eis, a protein known to modulate host-pathogen interactions. DNA microarray analysis indicated that the eis gene, Rv2416c, was expressed at levels in TB294-pSigA 40-fold higher than in the vector control strain TB294-pCV, during growth in the human monocyte cell line MonoMac6. Other genes with elevated expression in TB294-pSigA showed much smaller changes from TB294-pCV, and the majority of genes with expression differences between the two strains had reduced expression in TB294-pSigA, including an unexpected number of genes associated with the DNA-damage response. Real-time PCR analyses confirmed that eis was expressed at very high levels in TB294-pSigA in monocytes as well as in broth culture, and further revealed that, like sigA, eis was also more highly expressed in wild-type TB294 than in the laboratory strain H37Rv, during growth in monocytes. These findings suggested an association between increased SigA levels and eis activation, and results of chromatin immunoprecipitation confirmed that SigA binds the eis promoter in live TB294 cells. Deletion of eis reduced growth of TB294 in monocytes, and complementation of eis reversed this effect. We conclude that SigA regulates eis, that there is a direct correlation between upregulation of SigA and high expression levels of eis, and that eis contributes to the enhanced capacity of a clinical isolate of M. tuberculosis strain 210 to grow in monocytes. MESH terms: Oligonucleotide Array Sequence Analysis; Cell Line; Immunoglobulin A, Secretory/genetics/*metabolism; *Gene Expression Regulation, Bacterial; Monocytes/microbiology; Antigens, Bacterial/genetics/*metabolism; Chromatin Immunoprecipitation; *Host-Pathogen Interactions; Gene Deletion; Bacterial Proteins/genetics/*metabolism; Humans; Mycobacterium tuberculosis/genetics/*growth &; Up-Regulation Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Activation of the eis gene in a W-Beijing strain of Mycobacterium tuberculosis (TB294) with SigA overexpression
	Mycobacterial cells have dual nickel-cobalt sensors: sequence relationships and metal sites of metal-responsive repressors are not congruent. Campbell DR, Chapman KE, Waldron KJ, Tottey S, Kendall S, Cavallaro G, Andreini C, Hinds J, Stoker NG, Robinson NJ, Cavet JS (2007) J Biol Chem 282(44):32298-310	2007-11-02	Mycobacterium tuberculosis	Pubmed
Abstract: A novel ArsR-SmtB family transcriptional repressor, KmtR, has been characterized from mycobacteria. Mutants of Mycobacterium tuberculosis lacking kmtR show elevated expression of Rv2025c encoding a deduced CDF-family metal exporter. KmtR-dependent repression of the cdf and kmtR operator-promoters was alleviated by nickel and cobalt in minimal medium. Electrophoretic mobility shift assays and fluorescence anisotropy show binding of purified KmtR to nucleotide sequences containing a region of dyad symmetry from the cdf and kmtR operator-promoters. Incubation of KmtR with cobalt inhibits DNA complex assembly and metal-protein binding was confirmed. KmtR is the second, to NmtR, characterized ArsR-SmtB sensor of nickel and cobalt from M. tuberculosis suggesting special significance for these ions in this pathogen. KmtR-dependent expression is elevated in complete medium with no increase in response to metals, whereas NmtR retains a response to nickel and cobalt under these conditions. KmtR has tighter affinities for nickel and cobalt than NmtR consistent with basal levels of these metals being sensed by KmtR but not NmtR in complete medium. More than a thousand genes encoding ArsR-SmtB-related proteins are listed in databases. KmtR has none of the previously defined metal-sensing sites. Substitution of His88, Glu101, His102, His110, or His111 with Gln generated KmtR variants that repress the cdf and kmtR operator-promoters even in elevated nickel and cobalt, revealing a new sensory site. Importantly, ArsR-SmtB sequence groupings do not correspond with the different sensory motifs revealing that only the latter should be used to predict metal sensing. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository
	The Mycobacterium tuberculosis sigma factor sigmaB is required for full response to cell envelope stress and hypoxia in vitro, but it is dispensable for in vivo growth. Fontan PA, Voskuil MI, Gomez M, Tan D, Pardini M, Manganelli R, Fattorini L, Schoolnik GK, Smith I (2009) J Bacteriol 191(18):5628-33	2009-09-01	Mycobacterium tuberculosis	Pubmed
Abstract: The numerous sigma (sigma) factors present in Mycobacterium tuberculosis are indicative of the adaptability of this pathogen to different environmental conditions. In this report, we describe the M. tuberculosis sigma(B) regulon and the phenotypes of an M. tuberculosis sigB mutant strain exposed to cell envelope stress, oxidative stress, and hypoxia. The sigB mutant was especially defective in survival under hypoxic conditions in vitro, but it was not attenuated for growth in THP-1 cells or during mouse and guinea pig infection. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Sigma factor B (sigB) response to stress conditions (0.05% SDS and 5mM Diamide)
	Azole resistance in Mycobacterium tuberculosis is mediated by the MmpS5-MmpL5 efflux system. Milano A, Pasca MR, Provvedi R, Lucarelli AP, Manina G, Ribeiro AL, Manganelli R, Riccardi G (2009) Tuberculosis (Edinb) 89(1):84-90	2009-01-01	Mycobacterium tuberculosis	Pubmed
Abstract: Tuberculosis (TB) remains the leading cause of mortality due to a bacterial pathogen, Mycobacterium tuberculosis. Moreover, the recent isolation of M. tuberculosis strains resistant to both first- and second-line antitubercular drugs (XDR-TB) threatens to make the treatment of this disease extremely difficult and becoming a threat to public health worldwide. Recently, it has been shown that azoles are potent inhibitors of mycobacterial cell growth and have antitubercular activity in mice, thus favoring the hypothesis that these drugs may constitute a novel strategy against tuberculosis disease. To investigate the mechanisms of resistance to azoles in mycobacteria, we isolated and characterized several spontaneous azoles resistant mutants from M. tuberculosis and Mycobacterium bovis BCG. All the analyzed resistant mutants exhibited both increased econazole efflux and increased transcription of mmpS5-mmpL5 genes, encoding a hypothetical efflux system belonging to the resistance-nodulation-division (RND) family of transporters. We found that the up-regulation of mmpS5-mmpL5 genes was linked to mutations either in the Rv0678 gene, hypothesized to be involved in the transcriptional regulation of this efflux system, or in its putative promoter/operator region. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository
	Mycobacterium tuberculosis invasion of macrophages: linking bacterial gene expression to environmental cues. Rohde KH, Abramovitch RB, Russell DG (2007) Cell Host Microbe 2(5):352-64	2007-11-15	Mycobacterium tuberculosis	Pubmed
Abstract: A central feature of Mycobacterium tuberculosis (Mtb) pathogenesis is the ability of Mtb to survive within macrophages (MO). Despite its critical importance, our appreciation of the interplay between these two cells remains superficial. We employed microarrays to conduct a stepwise dissection of Mtb-MO interaction during the invasion of resting bone marrow MO. Contrary to many bacterial pathogens, engagement by MO receptors without internalization did not alter Mtb gene expression. Subsequently, a high-resolution profile of Mtb invasion-linked gene expression was generated by assaying the Mtb transcriptome at 20 min intervals up to 2 hr postinfection. Transcriptional responses were detected within minutes of phagocytosis, including gene subsets with distinct temporal profiles. Pharmacological manipulation of phagosomal pH and in vitro acid stress studies revealed that vacuole acidification is an important trigger for differential gene expression. Finally, there are marked species-specific differences in the response of Mtb and M. bovis BCG to intraphagosomal cues. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository
	PepD participates in the mycobacterial stress response mediated through MprAB and SigE. White MJ, He H, Penoske RM, Twining SS, Zahrt TC (2010) J Bacteriol 192(6):1498-510	2010-03-01	Mycobacterium tuberculosis	Pubmed
Abstract: Currently, one-third of the world's population is believed to be latently infected with Mycobacterium tuberculosis. The mechanisms by which M. tuberculosis establishes latent infection remain largely undefined. mprAB encodes a two-component signal transduction system required by M. tuberculosis for aspects of persistent infection. MprAB regulates a large and diverse group of genetic determinants in response to membrane stress, including the extracytoplasmic function (ECF) sigma factor sigE and the HtrA-like serine protease pepD. Recent studies have demonstrated that PepD functions as both a protease and chaperone in vitro. In addition, inactivation of pepD alters the virulence of M. tuberculosis in a mouse model system of infection. Here, we demonstrate that PepD plays an important role in the stress response network of Mycobacterium mediated through MprAB and SigE. In particular, we demonstrate that the protease activity of PepD requires the PDZ domain, in addition to the catalytic serine at position 317. pepD expression initiates from at least three promoters in M. tuberculosis, including one that is regulated by SigE and is located upstream of the mprA coding sequence. Deletion of pepD or mprAB in Mycobacterium smegmatis and M. tuberculosis alters the stress response phenotypes of these strains, including increasing sensitivity to SDS and cell wall antibiotics and upregulating the expression of stress-responsive determinants, including sigE. Taking these data together, we hypothesize that PepD utilizes its PDZ domain to recognize and process misfolded proteins at the cell membrane, leading to activation of the MprAB and SigE signaling pathways and subsequent establishment of a positive feedback loop that facilitates bacterial adaptation. MESH terms: null Associated Links PubMed Link | Repository | Full Text Online Associated Experiment Sets Explore View Download M. tuberculosis transcriptional profile of delta pepD null mutant vs wild-type
	DosR-regulon genes induction in Mycobacterium bovis BCG under aerobic conditions. Flores Valdez MA, Schoolnik GK Flores Valdez MA and Schoolnik GK (2010) Tuberculosis (Edinb) 90(3):197-200	2010-04-24	Mycobacterium tuberculosis	Pubmed
Abstract: In this report we demonstrated that under aerobic conditions, Mycobacterium bovis BCG expressing an hsp60-driven second copy of the hypoxia-related transcriptional regulator DosR increased 2-fold or greater the expression of 38 out of the 48 genes belonging to the DosR regulon, including the latency antigens Rv1733c, Rv2029, Rv2627, and Rv2628. Expression of DosR under these conditions slightly delayed in vitro growth, but did not promote a non-replicating state as opposed to microaerobic and hypoxic adaptation. Our results suggest BCG producing DosR can be cultured under standard in vitro conditions, allowing evaluation of this strain as a latency-specific vaccine candidate.CI - Copyright (c) 2010 Elsevier Ltd. All rights reserved. MESH terms: null Associated Links PubMed Link Associated Experiment Sets Explore View Download DosR-regulon genes induction in Mycobacterium bovis BCG under aerobic conditions
	Secreted transcription factor controls Mycobacterium tuberculosis virulence. Raghavan S, Manzanillo P, Chan K, Dovey C, Cox JS (2008) Nature 454(7205):717-21	2008-08-07	Mycobacterium tuberculosis	Pubmed
Abstract: Bacterial pathogens trigger specialized virulence factor secretion systems on encountering host cells. The ESX-1 protein secretion system of Mycobacterium tuberculosis-the causative agent of the human disease tuberculosis-delivers bacterial proteins into host cells during infection and is critical for virulence, but how it is regulated is unknown. Here we show that EspR (also known as Rv3849) is a key regulator of ESX-1 that is required for secretion and virulence in mice. EspR activates transcription of an operon that includes three ESX-1 components, Rv3616c-Rv3614c, whose expression in turn promotes secretion of ESX-1 substrates. EspR directly binds to and activates the Rv3616c-Rv3614c promoter and, unexpectedly, is itself secreted from the bacterial cell by the ESX-1 system that it regulates. Efflux of the DNA-binding regulator results in reduced Rv3616c-Rv3614c transcription, and thus reduced ESX-1 secretion. Our results reveal a direct negative feedback loop that regulates the activity of a secretion system essential for virulence. As the virulence factors secreted by the ESX-1 system are highly antigenic, fine control of secretion may be critical to successful infection. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository
	A highly conserved transcriptional repressor controls a large regulon involved in lipid degradation in Mycobacterium smegmatis and Mycobacterium tuberculosis. Kendall SL, Withers M, Soffair CN, Moreland NJ, Gurcha S, Sidders B, Frita R, Ten Bokum A, Besra GS, Lott JS, Stoker NG (2007) Mol Microbiol 65(3):684-99	2007-08-01	Mycobacterium Smegmatis MC2 155	Pubmed
Abstract: The Mycobacterium tuberculosis TetR-type regulator Rv3574 has been implicated in pathogenesis as it is induced in vivo, and genome-wide essentiality studies show it is required for infection. As the gene is highly conserved in the mycobacteria, we deleted the Rv3574 orthologue in Mycobacterium smegmatis (MSMEG_6042) and used real-time quantitative polymerase chain reaction and microarray analyses to show that it represses the transcription both of itself and of a large number of genes involved in lipid metabolism. We identified a conserved motif within its own promoter (TnnAACnnGTTnnA) and showed that it binds as a dimer to 29 bp probes containing the motif. We found 16 and 31 other instances of the motif in intergenic regions of M. tuberculosis and M. smegmatis respectively. Combining the results of the microarray studies with the motif analyses, we predict that Rv3574 directly controls the expression of 83 genes in M. smegmatis, and 74 in M. tuberculosis. Many of these genes are known to be induced by growth on cholesterol in rhodococci, and palmitate in M. tuberculosis. We conclude that this regulator, designated elsewhere as kstR, controls the expression of genes used for utilizing diverse lipids as energy sources, possibly imported through the mce4 system. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository
	The Differential Gene Expression Pattern of Mycobacterium tuberculosis in Response to Capreomycin and PA-824 versus First-Line TB Drugs Reveals Stress- and PE/PPE-Related Drug Targets. Fu LM, Tai SC Fu LM and Tai SC (2009) Int J Microbiol 2009():879621	2009-07-22	Mycobacterium tuberculosis	Pubmed
Abstract: Tuberculosis is a leading infectious disease causing millions of deaths each year. How to eradicate mycobacterial persistence has become a central research focus for developing next-generation TB drugs. Yet, the knowledge in this area is fundamentally limited and only a few drugs, notably capreomycin and PA-824, have been shown to be active against non-replicating persistent TB bacilli. In this study, we performed a new bioinformatics analysis on microarray-based gene expression data obtained from the public domain to explore genes that were differentially induced by drugs between the group of capreomycin and PA-824 and the group of mainly the first-line TB drugs. Our study has identified 42 genes specifically induced by capreomycin and PA-824. Many of these genes are related to stress responses. In terms of the distribution of identified genes in a specific category relative to the whole genome, only the categories of PE/PPE and conserved hypotheticals have statistical significance. Six among the 42 genes identified in this study are on the list of the top 100 persistence targets selected by the TB Structural Genomics Consortium. Further biological elucidation of their roles in mycobacterial persistence is warranted. MESH terms: null Associated Links Repository | PubMed Link | Full Text Online Associated Experiment Sets Explore View Download Differential Gene Expression Pattern of MTB in Response to Capreomycin and PA-824 versus First-Line TB Drugs
	Cross-regulation among disparate antibiotic biosynthetic pathways of Streptomyces coelicolor. Huang J , Shi J , Molle V , Sohlberg B , Weaver D , Bibb MJ , Karoonuthaisiri N , Lih CJ , Kao CM , Buttner MJ , Cohen SN (2005) Mol Microbiol 58(5):1276-87	2005-12-01	Streptomyces coelicolor	Pubmed
Abstract: A complex programme of regulation governs gene expression during development of the morphologically and biochemically complex eubacterial genus Streptomyces. Earlier work has suggested a model in which 'higher level' pleiotropic regulators activate 'pathway-specific' regulators located within chromosomal gene clusters encoding biosynthesis of individual antibiotics. We used mutational analysis and adventitious overexpression of key Streptomyces coelicolor regulators to investigate functional interactions among them. We report here that cluster-situated regulators (CSRs) thought to be pathway-specific can also control other antibiotic biosynthetic gene clusters, and thus have pleiotropic actions. Surprisingly, we also find that CSRs exhibit growth-phase-dependent control over afsR2/afsS, a 'higher level' pleiotropic regulatory locus not located within any of the chromosomal gene clusters it targets, and further demonstrate that cross-regulation by CSRs is modulated globally and differentially during the S. coelicolor growth cycle by the RNaseIII homologue AbsB. Our results, which reveal a network of functional interactions among regulators that govern production of antibiotics and other secondary metabolites in S. coelicolor, suggest that revision of the currently prevalent view of higher-level versus pathway-specific regulation of secondary metabolism in Streptomyces species is warranted. MESH terms: *Multigene Family; Mutation; Oligonucleotide Array Sequence Analysis; Streptomyces coelicolor/genetics/growth & development/*metabolism; *Gene Expression Regulation, Bacterial; Transcription Factors/genetics/metabolism; Reverse Transcriptase Polymerase Chain Reaction; DNA-Binding Proteins/genetics/metabolism; Bacterial Proteins/genetics/*metabolism; Anti-Bacterial Agents/*biosynthesis; *Genes, Regulator Associated Links PubMed Link | Full Text Online | Web Supplement | User Specified Associated Experiment Sets Explore View Download Transcriptional profiling of antibiotic biosynthetic pathways of S. coelicolor: Transcriptional effects of absB on secondary metabolite pathways Transcriptional profiling of antibiotic biosynthetic pathways of S. coelicolor: Expression of secondary metabolite genes M145, mutant M512 (delta redD delta actII-ORF4) and M550 (delta redZ) Transcriptional profiling of antibiotic biosynthetic pathways of S. coelicolor: Effects on secondary metabolite pathways during induction of regulatory genes in the absence or presence of absB
	rag genes: novel components of the RamR regulon that trigger morphological differentiation in Streptomyces coelicolor. Paolo SS, Huang J, Cohen SN, Thompson CJ (2006) Mol Microbiol 61(5):1167-86	2006-09-01	Streptomyces coelicolor	Pubmed
Abstract: The filamentous bacterium, Streptomyces coelicolor, undergoes a complex cycle of growth and development in which morphological differentiation coincides with the activation of the orphan response regulator RamR and the biosynthesis of a morphogenic peptide called SapB. SapB is a lantibiotic-like molecule derived from the product of the ramS gene that promotes formation of aerial hyphae by breaking the aqueous tension on the surface of the substrate mycelium. A ramR-disrupted mutant is delayed in aerial hyphae formation while constitutive overexpression of ramR accelerates aerial hyphae formation in the wild-type strain and restores SapB biosynthesis and aerial hyphae formation in all developmental mutants (bld) tested. Using DNA microarrays to globally identify S. coelicolor genes whose transcription was affected by ramR mutation or overexpression, we discovered a ramR-activated locus of contiguous cotranscribed developmental genes that modulate both aerial hyphae formation and sporulation. The genes of this cluster of ramR-activated genes (rag), which are chromosomally distant from previously known RamR-regulated genes, include: ragA (sco4075) and ragB (sco4074), which encode two subunits of an ABC transporter, ragK (sco4073), a putative histidine kinase, and ragR (sco4072), a ramR paralogue. Promoter mapping and protein-DNA binding experiments indicate that RamR activates ragABKR transcription directly, by binding to three sequence motifs in the ragABKR promoter region. A constructed ragABKR null mutant was able to synthesize SapB and erect aerial hyphae; however, these hyphae were unusually branched, reminiscent of substrate hyphae. Subsequent stages of differentiation, septation and sporogenesis were delayed. The role of ragABKR in aerial hyphae formation was shown both by epistasis (ragR-activated aerial hyphae formation in bld mutants) and extracellular complementation (ragR-induced synthesis of an activity allowing aerial hyphae formation in bld mutants) experiments. In conclusion, the ragABKR locus activates a SapB-independent developmental pathway that is involved in both aerial hyphae formation and sporulation, serving to integrate sequential morphogenic changes. MESH terms: Recombinant Proteins/genetics/metabolism; Oligonucleotide Array Sequence Analysis; Hyphae/genetics/growth & development; Molecular Sequence Data; Mutagenesis, Site-Directed; Bacterial Proteins/*genetics/physiology; Base Sequence; Reverse Transcriptase Polymerase Chain Reaction; Transcription Factors/*genetics/physiology; Transcription, Genetic/genetics; Genes, Bacterial/genetics/physiology; DNA-Binding Proteins/*genetics/physiology; Gene Expression Regulation, Bacterial; Microscopy, Electron, Scanning; Models, Biological; Operon/genetics; Promoter Regions, Genetic/genetics; Regulon/*genetics; Streptomyces coelicolor/*genetics/physiology/ultrastructure; Mutation/genetics Associated Links Full Text Online | PubMed Link Associated Experiment Sets Explore View Download Transcriptional profile of Streptomyces coelicolor RamR null or RamR over expression mutants
	Regulation of the Mycobacterium tuberculosis hypoxic response gene encoding alpha -crystallin. Sherman DR, Voskuil M, Schnappinger D, Liao R, Harrell MI, Schoolnik GK (2001) Proc Natl Acad Sci U S A 98(13):7534-9	2001-06-19	Mycobacterium tuberculosis	Pubmed
Abstract: Unlike many pathogens that are overtly toxic to their hosts, the primary virulence determinant of Mycobacterium tuberculosis appears to be its ability to persist for years or decades within humans in a clinically latent state. Since early in the 20th century latency has been linked to hypoxic conditions within the host, but the response of M. tuberculosis to a hypoxic signal remains poorly characterized. The M. tuberculosis alpha-crystallin (acr) gene is powerfully and rapidly induced at reduced oxygen tensions, providing us with a means to identify regulators of the hypoxic response. Using a whole genome microarray, we identified >100 genes whose expression is rapidly altered by defined hypoxic conditions. Numerous genes involved in biosynthesis and aerobic metabolism are repressed, whereas a high proportion of the induced genes have no known function. Among the induced genes is an apparent operon that includes the putative two-component response regulator pair Rv3133c/Rv3132c. When we interrupted expression of this operon by targeted disruption of the upstream gene Rv3134c, the hypoxic regulation of acr was eliminated. These results suggest a possible role for Rv3132c/3133c/3134c in mycobacterial latency. MESH terms: Mycobacterium tuberculosis/*genetics/growth & development/physiology; Aerobiosis; *Gene Expression Regulation, Bacterial; Crystallins/*genetics; Time Factors; Bacterial Proteins/*genetics; Anaerobiosis; Kinetics Associated Links Web Supplement | Full Text Online | PubMed Link | Repository Associated Experiment Sets Explore View Download Adaptation to Hypoxia in Mycobacterium tuberculosis
	Mycobacterium tuberculosis gene expression during adaptation to stationary phase and low-oxygen dormancy. Voskuil MI, Visconti KC, Schoolnik GK (2004) Tuberculosis (Edinb) 84(3-4):218-27	2004-03-21	Mycobacterium tuberculosis	Pubmed
Abstract: The innate mechanisms used by Mycobacterium tuberculosis to persist during periods of non-proliferation are central to understanding the physiology of the bacilli during latent disease. We have used whole genome expression profiling to expose adaptive mechanisms initiated by M. tuberculosis in two common models of M. tuberculosis non-proliferation. The first of these models was a standard growth curve in which gene expression changes were followed from exponential growth through the transition to stationary phase. In the second model, we followed the adaptive process of M. tuberculosis during transition from aerobic growth to a state of anaerobic non-replicating persistence. The most striking finding from these experiments was the strong induction of the entire DosR "dormancy" regulon over approximately 20 days during the long transition to an anaerobic state. This is contrasted by the muted overall response to aerated stationary phase with only a partial dormancy regulon response. From the results presented here we conclude that the respiration-limited environment of the oxygen-depleted NRP model recreates at least one fundamental factor for which the genome of M. tuberculosis encodes a decisive adaptive program. MESH terms: Mycobacterium tuberculosis/*genetics/growth & development/physiology; Oligonucleotide Array Sequence Analysis; Adaptation, Physiological/genetics; RNA, Messenger/genetics; Cluster Analysis; Gene Expression Regulation, Bacterial/*physiology; RNA, Bacterial/genetics; Anaerobiosis/physiology; DNA, Bacterial/genetics; Genes, Bacterial/genetics Associated Links Full Text Online | PubMed Link | Repository Associated Experiment Sets Explore View Download Stationary phase and dormancy gene expression
	Ancestral antibiotic resistance in Mycobacterium tuberculosis. Morris RP, Nguyen L, Gatfield J, Visconti K, Nguyen K, Schnappinger D, Ehrt S, Liu Y, Heifets L, Pieters J, Schoolnik G, Thompson CJ (2005) Proc Natl Acad Sci U S A 102(34):12200-5	2005-08-23	Mycobacterium tuberculosis	Pubmed
Abstract: Chemotherapeutic options to treat tuberculosis are severely restricted by the intrinsic resistance of Mycobacterium tuberculosis to the majority of clinically applied antibiotics. Such resistance is partially provided by the low permeability of their unique cell envelope. Here we describe a complementary system that coordinates resistance to drugs that have penetrated the envelope, allowing mycobacteria to tolerate diverse classes of antibiotics that inhibit cytoplasmic targets. This system depends on whiB7, a gene that pathogenic Mycobacterium shares with Streptomyces, a phylogenetically related genus known as the source of diverse antibiotics. In M. tuberculosis, whiB7 is induced by subinhibitory concentrations of antibiotics (erythromycin, tetracycline, and streptomycin) and whiB7 null mutants (Streptomyces and Mycobacterium) are hypersusceptible to antibiotics in vitro. M. tuberculosis is also antibiotic sensitive within a monocyte model system. In addition to antibiotics, whiB7 is induced by exposure to fatty acids that pathogenic Mycobacterium species may accumulate internally or encounter within eukaryotic hosts during infection. Gene expression profiling analyses demonstrate that whiB7 transcription determines drug resistance by activating expression of a regulon including genes involved in ribosomal protection and antibiotic efflux. Components of the whiB7 system may serve as attractive targets for the identification of inhibitors that render M. tuberculosis or multidrug-resistant derivatives more antibiotic-sensitive. MESH terms: *Evolution, Molecular; Plasmids/genetics; Sequence Analysis, DNA; Streptomyces coelicolor/genetics; *Gene Expression Regulation, Bacterial; Molecular Sequence Data; Mycobacterium tuberculosis/drug effects/*genetics/pathogenicity; Base Sequence; Fatty Acids/metabolism; Reverse Transcriptase Polymerase Chain Reaction; Bacterial Proteins/genetics; DNA Mutational Analysis; Drug Resistance, Multiple, Bacterial/*genetics; Transcription Factors/genetics; Anti-Bacterial Agents/*toxicity; Gene Expression Profiling; Regulon/*genetics Associated Links PubMed Link | Full Text Online Associated Experiment Sets Explore View Download Ancestral antibiotic resistance in Mycobacterium tuberculosis
	Role of the extracytoplasmic-function sigma factor sigma(H) in Mycobacterium tuberculosis global gene expression. Manganelli R, Voskuil MI, Schoolnik GK, Dubnau E, Gomez M, Smith I (2002) Mol Microbiol 45(2):365-74	2002-07-18	Mycobacterium tuberculosis	Pubmed
Abstract: Like other bacterial species, Mycobacterium tuberculosis has multiple sigma (sigma) factors encoded in its genome. In previously published work, we and others have shown that mutations in some of these transcriptional activators render M. tuberculosis sensitive to various environmental stresses and, in some cases, cause attenuated virulence phenotypes. In this paper, we characterize a M. tuberculosis mutant lacking the ECF sigma factor sigma(H). This mutant was more sensitive than the wild type to heat shock and to various oxidative stresses, but did not show decreased ability to grow inside macrophages. Using quantitative reverse transcription-PCR and microarray technology, we have started to define the sigma(H) regulon and its involvement in the global regulation of the response to heat shock and the thiol-specific oxidizing agent diamide. We identified 48 genes whose expression increased after exposure of M. tuberculosis to diamide; out of these, 39 were not induced in the sigH mutant, showing their direct or indirect dependence on sigma(H). Some of these genes encode proteins whose predicted function is related to thiol metabolism, such as thioredoxin, thioredoxin reductase and enzymes involved in cysteine and molybdopterine biosynthesis. Other genes under sigma(H) control encode transcriptional regulators such as sigB, sigE, and sigH itself. MESH terms: Sigma Factor/genetics/*physiology; Virulence; Genes, Bacterial; Hot Temperature; Sulfhydryl Reagents/pharmacology; *Gene Expression Regulation, Bacterial; Molecular Sequence Data; Mycobacterium tuberculosis/drug effects/*genetics/pathogenicity; Sequence Alignment; Sequence Homology, Nucleic Acid; Base Sequence; Mice; Bacterial Proteins/genetics/*physiology; Macrophages/microbiology; Transcription, Genetic; Consensus Sequence; Animals; Cell Line/microbiology; Diamide/pharmacology; Humans; Oxidative Stress; Gene Expression Profiling Associated Links Full Text Online | Web Supplement | PubMed Link | Repository Associated Experiment Sets Explore View Download H37Rv wild type vs H37Rv sigma H null mutant exposed to 5 mM diamide for 1hr H37Rv wild type vs H37 sigma H null mutant
	The Mycobacterium tuberculosis ECF sigma factor sigmaE: role in global gene expression and survival in macrophages. Manganelli R , Voskuil MI , Schoolnik GK , Smith I (2001) Mol Microbiol 41(2):423-37	2001-12-21	Mycobacterium tuberculosis	Pubmed
Abstract: In previously published work, we identified three Mycobacterium tuberculosis sigma (sigma) factor genes responding to heat shock (sigB, sigE and sigH). Two of them (sigB and sigE) also responded to SDS exposure. As these responses to stress suggested that the sigma factors encoded by these genes could be involved in pathogenicity, we are studying their role in physiology and virulence. In this work, we characterize a sigE mutant of M. tuberculosis H37Rv. The sigE mutant strain was more sensitive than the wild-type strain to heat shock, SDS and various oxidative stresses. It was also defective in the ability to grow inside both human and murine unactivated macrophages and was more sensitive than the wild-type strain to the killing activity of activated murine macrophages. Using microarray technology and quantitative reverse transcription-polymerase chain reaction (RT-PCR), we started to define the sigmaE regulon of M. tuberculosis and its involvement in the global regulation of the stress induced by SDS. We showed the requirement for a functional sigE gene for full expression of sigB and for its induction after SDS exposure but not after heat shock. We also identified several genes that are no longer induced when sigmaE is absent. These genes encode proteins belonging to different classes including transcriptional regulators, enzymes involved in fatty acid degradation and classical heat shock proteins. MESH terms: Mutation; Oligonucleotide Array Sequence Analysis; Cell Line; Hot Temperature; Sigma Factor/genetics/*metabolism; Base Sequence; Macrophages/immunology/*microbiology; Mice; Heat-Shock Response/genetics; Consensus Sequence/genetics; Sodium Dodecyl Sulfate/pharmacology; Animals; Bacterial Proteins/genetics/*metabolism; Humans; Mycobacterium tuberculosis/*genetics/growth & development/*physiology; Oxidative Stress; Promoter Regions, Genetic/genetics; Regulon/genetics; Gene Expression Profiling; *Gene Expression Regulation, Bacterial/drug effects; Genetic Complementation Test; Heat-Shock Proteins/genetics; RNA, Messenger/genetics/metabolism Associated Links Web Supplement | Full Text Online | PubMed Link | Repository Associated Experiment Sets Explore View Download SDS exposure(0.05%) of wild type and sigE mutant of M. tuberculosis
	Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis. Park HD, Guinn KM, Harrell MI, Liao R, Voskuil MI, Tompa M, Schoolnik GK, Sherman DR (2003) Mol Microbiol 48(3):833-43	2003-04-09	Mycobacterium tuberculosis	Pubmed
Abstract: Unlike many pathogens that are overtly harmful to their hosts, Mycobacterium tuberculosis can persist for years within humans in a clinically latent state. Latency is often linked to hypoxic conditions within the host. Among M. tuberculosis genes induced by hypoxia is a putative transcription factor, Rv3133c/DosR. We performed targeted disruption of this locus followed by transcriptome analysis of wild-type and mutant bacilli. Nearly all the genes powerfully regulated by hypoxia require Rv3133c/DosR for their induction. Computer analysis identified a consensus motif, a variant of which is located upstream of nearly all M. tuberculosis genes rapidly induced by hypoxia. Further, Rv3133c/DosR binds to the two copies of this motif upstream of the hypoxic response gene alpha-crystallin. Mutations within the binding sites abolish both Rv3133c/DosR binding as well as hypoxic induction of a downstream reporter gene. Also, mutation experiments with Rv3133c/DosR confirmed sequence-based predictions that the C-terminus is responsible for DNA binding and that the aspartate at position 54 is essential for function. Together, these results demonstrate that Rv3133c/DosR is a transcription factor of the two-component response regulator class, and that it is the primary mediator of a hypoxic signal within M. tuberculosis. MESH terms: Gene Targeting; Oligonucleotide Array Sequence Analysis; *Gene Expression Regulation, Bacterial; Regulatory Sequences, Nucleic Acid; Transcription Factors/genetics/*metabolism; Mycobacterium tuberculosis/genetics/*metabolism; Oxygen/metabolism; Tuberculosis/metabolism; Anoxia/*metabolism; Aspartic Acid/metabolism; Bacterial Proteins/genetics/*metabolism; Humans; Genes, Reporter; Protein Binding Associated Links PubMed Link | Web Supplement | Repository | Full Text Online Associated Experiment Sets Explore View Download Hypoxic treatment of wildtype and dosR (devR) mutant strains
	ideR, An essential gene in mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response. Rodriguez GM, Voskuil MI, Gold B, Schoolnik GK, Smith I (2002) Infect Immun 70(7):3371-81	2002-07-01	Mycobacterium tuberculosis	Pubmed
Abstract: The mycobacterial IdeR protein is a metal-dependent regulator of the DtxR (diphtheria toxin repressor) family. In the presence of iron, it binds to a specific DNA sequence in the promoter regions of the genes that it regulates, thus controlling their transcription. In this study, we provide evidence that ideR is an essential gene in Mycobacterium tuberculosis. ideR cannot normally be disrupted in this mycobacterium in the absence of a second functional copy of the gene. However, a rare ideR mutant was obtained in which the lethal effects of ideR inactivation were alleviated by a second-site suppressor mutation and which exhibited restricted iron assimilation capacity. Studies of this strain and a derivative in which IdeR expression was restored allowed us to identify phenotypic effects resulting from ideR inactivation. Using DNA microarrays, the iron-dependent transcriptional profiles of the wild-type, ideR mutant, and ideR-complemented mutant strains were analyzed, and the genes regulated by iron and IdeR were identified. These genes encode a variety of proteins, including putative transporters, proteins involved in siderophore synthesis and iron storage, members of the PE/PPE family, a membrane protein involved in virulence, transcriptional regulators, and enzymes involved in lipid metabolism. MESH terms: Bacterial Proteins/genetics/metabolism/*physiology; *Oxidative Stress; *Repressor Proteins; Hydrogen Peroxide/pharmacology; Mycobacterium tuberculosis/drug effects/*genetics/metabolism; Iron/*metabolism; *Gene Expression; Siderophores/biosynthesis Associated Links Web Supplement | Full Text Online | PubMed Link | Repository Associated Experiment Sets Explore View Download Role of IdeR in M. tuberculosis
	Evidence for complex interactions of stress-associated regulons in an mprAB deletion mutant of Mycobacterium tuberculosis. Pang X, Vu P, Byrd TF, Ghanny S, Soteropoulos P, Mukamolova GV, Wu S, Samten B, Howard ST (2007) Microbiology 153(Pt 4):1229-42	2007-04-01	Mycobacterium tuberculosis	Pubmed
Abstract: Two-component systems are important constituents of bacterial regulatory networks. Results of this investigation into the role of the MprAB two-component system of Mycobacterium tuberculosis indicate that it is associated with the regulation of several stress-responsive regulons. Using a deletion mutant lacking portions of the response regulator, MprA, and the histidine kinase, MprB, it was demonstrated by real-time PCR, primer extension analyses and DNA microarrays that MprAB activates sigma factor genes sigE and sigB, under SDS stress and during exponential growth. SDS-inducible, MprA-dependent transcriptional start points were identified for mprA, sigE and sigB, and variations in distance between these points and MprA-binding sites suggest that MprA is involved in different mechanisms of promoter activation. Although most of the SigE regulon was downregulated in the deletion mutant, the cluster of genes Rv1129c, Rv1130 and Rv1131, which is associated with growth in monoctyes, was upregulated in the deletion mutant under SDS stress, and this upregulation was dependent upon atmospheric growth conditions. Multiple stress-associated genes of the DosR, SigD and IdeR regulons were also upregulated in the deletion mutant, during exponential growth and/or in the presence of SDS. Surprisingly, the deletion mutant had increased resistance to SDS compared to the parental strain, and enhanced growth in human peripheral blood monocytes, characteristics which may result from a loss of repression of stress-associated genes. MESH terms: Leukocytes, Mononuclear/*microbiology; Protein Kinases/genetics/*metabolism; *Regulon; Sigma Factor/genetics; *Gene Expression Regulation, Bacterial; Mycobacterium tuberculosis/*genetics; Gene Deletion; Promoter Regions, Genetic; Bacterial Proteins/genetics/*metabolism; Humans Associated Links Repository | PubMed Link | Full Text Online Associated Experiment Sets Explore View Download MprAB modulates multiple regulons in M. tuberculosis
	Cell population heterogeneity in Mycobacterium tuberculosis H37Rv. Andreu N, Gibert I Andreu N and Gibert I (2008) Tuberculosis (Edinb) 88(6):553-9	2008-11-01	Mycobacterium tuberculosis	Pubmed
Abstract: The laboratory strain H37Rv represents one of the most commonly used strains in the study of Mycobacterium tuberculosis. Despite the apparent stability of the strain, the absence of a selective pressure for virulence factors could lead to the in vitro accumulation of attenuated mutants. To assess this hypothesis, we performed a systematic analysis of individual clones isolated from subcultured M. tuberculosis H37Rv and from a non-subcultured frozen stock. First, we studied two virulence indicators: neutral red staining and content of phthiocerol dimycocerosates (PDIMs). We found that H37Rv formed a mixed population containing wild-type cells, as well as neutral red and PDIM mutants. Then, we compared the global gene expression of 3 isolated clones (which displayed various phenotypes) and the non-subcultured stock, by microarray analysis. This transcriptional profiling confirmed that a significant heterogeneity existed despite, and in addition to, the neutral red and PDIM phenotypes. These results strongly suggest that great caution must be taken in extrapolating data obtained with M. tuberculosis H37Rv grown in vitro, and it would be prudent to study several independent clones to obtain valid conclusions. For this purpose, the neutral red and PDIM phenotypes might be useful indicators of undesired heterogeneity. MESH terms: Coloring Agents; Mutation; Oligonucleotide Array Sequence Analysis; Tuberculosis, Pulmonary/*genetics/metabolism; Virulence; Genetic Variation; Lipids; Neutral Red; Gene Expression Regulation, Bacterial/genetics; Mycobacterium tuberculosis/*genetics/metabolism/pathogenicity; RNA, Messenger; Humans; Phenotype; Genes, Bacterial/genetics; Genetic Heterogeneity; Staining and Labeling Associated Links PubMed Link | Full Text Online | Web Supplement Associated Experiment Sets Explore View Download Cell population heterogeneity in Mycobacterium tuberculosis H37Rv
	The chaplins: a family of hydrophobic cell-surface proteins involved in aerial mycelium formation in Streptomyces coelicolor. Elliot MA, Karoonuthaisiri N, Huang J, Bibb MJ, Cohen SN, Kao CM, Buttner MJ (2003) Genes Dev 17(14):1727-40	2003-07-15	Streptomyces coelicolor	Pubmed
Abstract: The filamentous bacterium Streptomyces coelicolor differentiates by forming specialized, spore-bearing aerial hyphae that grow into the air. Using microarrays, we identified genes that are down-regulated in a mutant unable to erect aerial hyphae. Through this route, we identified a previously unknown layer of aerial mycelium surface proteins (the "chaplins"). The chaplins share a hydrophobic domain of approximately 40 residues (the "chaplin domain"), and all have a secretion signal. The five short chaplins (ChpD,E,F,G,H) have one chaplin domain, whereas the three long chaplins (ChpA,B,C) have two chaplin domains and a C-terminal "sorting signal" that targets them for covalent attachment to the cell wall by sortase enzyme. Expression of the two chaplin genes examined (chpE, chpH) depended on aerial hyphae formation but not sporulation, and egfp fusions showed their expression localized to aerial structures. Mass spectrometry of cell wall extracts confirmed that the short chaplins localized to the cell surface. Deletion of chaplin genes caused severe delays in aerial hyphae formation, a phenotype rescued by exogenous application of chaplin proteins. These observations implicate the chaplins in aerial mycelium formation, and suggest that coating of the envelope by the chaplins is required for aerial hyphae to grow out of the aqueous environment of the substrate mycelium into the air. MESH terms: *Hydrophobicity; Molecular Sequence Data; Sequence Alignment; Streptomyces/*growth & development; Hyphae/*growth & development; Proteins/*metabolism; Amino Acid Sequence; Cell Wall/metabolism; Gene Expression Profiling Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Transcriptional profile of wild type (J1915) vs bldN mutant
	A master regulator sigmaB governs osmotic and oxidative response as well as differentiation via a network of sigma factors in Streptomyces coelicolor. Lee EJ, Karoonuthaisiri N, Kim HS, Park JH, Cha CJ, Kao CM, Roe JH (2005) Mol Microbiol 57(5):1252-64	2005-09-01	Streptomyces coelicolor	Pubmed
Abstract: The differentiating bacterium Streptomyces coelicolor harbours some 66 sigma factors, which support its complex life cycle. sigma(B), a functional homologue of sigma(S) from Escherichia coli, controls both osmoprotection and differentiation in S. coelicolor A3(2). Microarray analysis revealed sigma(B)-dependent induction of more than 280 genes by 0.2 M KCl. These genes encode several sigma factors, oxidative defence proteins, chaperones, systems to provide osmolytes, cysteine, mycothiol, and gas vesicle. sigma(B) controlled induction of itself and its two paralogues (sigma(L) and sigma(M)) in a hierarchical order of sigma(B)-->sigma(L)-->sigma(M), as revealed by S1 mapping and Western blot analyses. The phenotype of each sigma mutant suggested a sequential action in morphological differentiation; sigma(B) in forming aerial mycelium, sigma(L) in forming spores and sigma(M) for efficient sporulation. sigma(B) was also responsible for the increase in cysteine and mycothiol, the major thiol buffer in actinomycetes, upon osmotic shock, revealing an overlap between protections against osmotic and oxidative stresses. Proteins in sigB mutant were more oxidized (carbonylated) than the wild type. These results support a hypothesis that sigma(B) serves as a master regulator that triggers other related sigma factors in a cascade, and thus regulates differentiation and osmotic and oxidative response in S. coelicolor. MESH terms: Gene Expression/drug effects; Oligonucleotide Array Sequence Analysis; Osmotic Pressure; Sigma Factor/genetics/*physiology; Oxidative Stress/*genetics; *Gene Expression Regulation, Bacterial; Streptomyces coelicolor/*genetics/*growth & development; Bacterial Proteins/genetics/*physiology; Potassium Chloride/pharmacology; Phenotype; Genes, Bacterial/genetics; Oxidation-Reduction Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Osmotic stress response in wild type and sigB null mutant of S. coelicolor
	The transcriptional responses of Mycobacterium tuberculosis to inhibitors of metabolism: novel insights into drug mechanisms of action. Boshoff HI, Myers TG, Copp BR, McNeil MR, Wilson MA, Barry CE 3rd (2004) J Biol Chem 279(38):40174-84	2004-09-17	Mycobacterium tuberculosis	Pubmed
Abstract: The differential transcriptional response of Mycobacterium tuberculosis to drugs and growth-inhibitory conditions was monitored to generate a data set of 430 microarray profiles. Unbiased grouping of these profiles independently clustered agents of known mechanism of action accurately and was successful at predicting the mechanism of action of several unknown agents. These predictions were validated biochemically for two agents of previously uncategorized mechanism, pyridoacridones and phenothiazines. Analysis of this data set further revealed 150 underlying clusters of coordinately regulated genes offering the first glimpse at the full metabolic potential of this organism. A signature subset of these gene clusters was sufficient to classify all known agents as to mechanism of action. Transcriptional profiling of both crude and purified natural products can provide critical information on both mechanism and detoxification prior to purification that can be used to guide the drug discovery process. Thus, the transcriptional profile generated by a crude marine natural product recapitulated the mechanistic prediction from the pure active component. The underlying gene clusters further provide fundamental insights into the metabolic response of bacteria to drug-induced stress and provide a rational basis for the selection of critical metabolic targets for screening for new agents with improved activity against this important human pathogen. MESH terms: Transcriptional Activation/drug effects; Ethambutol/pharmacology; Fluoroquinolones/pharmacology; Genome, Bacterial; Mycobacterium tuberculosis/drug effects/*genetics/*metabolism; Phenothiazines/pharmacology; Gene Expression Regulation, Bacterial/*drug effects/physiology; Antipsychotic Agents/pharmacology; Cell Wall/drug effects/metabolism; Azoles/pharmacology; Energy Metabolism/*drug effects; *Oligonucleotide Array Sequence Analysis; Antitubercular Agents/pharmacology; DNA Gyrase/antagonists & inhibitors/metabolism; Drug Design; Electron Transport/drug effects; Enzyme Inhibitors/pharmacology Associated Links Full Text Online | Web Supplement | Repository | PubMed Link Associated Experiment Sets Explore View Download M. tuberculosis transcriptional response to inhibitors of metabolism
	Characterization of a large, stable, high-copy-number Streptomyces plasmid that requires stability and transfer functions for heterologous polyketide overproduction. Fong R , Hu Z , Hutchinson CR , Huang J , Cohen S , Kao C (2007) Appl Environ Microbiol 73(4):1296-307	2007-02-01	Streptomyces coelicolor	Pubmed
Abstract: A major limitation to improving small-molecule pharmaceutical production in streptomycetes is the inability of high-copy-number plasmids to tolerate large biosynthetic gene cluster inserts. A recent finding has overcome this barrier. In 2003, Hu et al. discovered a stable, high-copy-number, 81-kb plasmid that significantly elevated production of the polyketide precursor to the antibiotic erythromycin in a heterologous Streptomyces host (J. Ind. Microbiol. Biotechnol. 30:516-522, 2003). Here, we have identified mechanisms by which this SCP2*-derived plasmid achieves increased levels of metabolite production and examined how the 45-bp deletion mutation in the plasmid replication origin increased plasmid copy number. A plasmid intramycelial transfer gene, spd, and a partition gene, parAB, enhance metabolite production by increasing the stable inheritance of large plasmids containing biosynthetic genes. Additionally, high product titers required both activator (actII-ORF4) and biosynthetic genes (eryA) at high copy numbers. DNA gel shift experiments revealed that the 45-bp deletion abolished replication protein (RepI) binding to a plasmid site which, in part, supports an iteron model for plasmid replication and copy number control. Using the new information, we constructed a large high-copy-number plasmid capable of overproducing the polyketide 6-deoxyerythronolide B. However, this plasmid was unstable over multiple culture generations, suggesting that other SCP2* genes may be required for long-term, stable plasmid inheritance. MESH terms: DNA Replication; Streptomyces/chemistry/*metabolism; Anti-Bacterial Agents/biosynthesis; Gene Dosage; Plasmids/genetics/*physiology; Macrolides/*metabolism Associated Links PubMed Link | Full Text Online | Repository | Repository Associated Experiment Sets Explore View Download Transcriptional profile of Streptomyces coelicolor containg pKOS011-26 plasmid
	Functional Genetic Diversity among Mycobacterium tuberculosis Complex Clinical Isolates: Delineation of Conserved Core and Lineage-Specific Transcriptomes during Intracellular Survival. Homolka S, Niemann S, Russell DG, Rohde KH (2010) PLoS Pathog 6(7):e1000988	2010-07-08	Mycobacterium tuberculosis	Pubmed
Abstract: Tuberculosis exerts a tremendous burden on global health, with approximately 9 million new infections and approximately 2 million deaths annually. The Mycobacterium tuberculosis complex (MTC) was initially regarded as a highly homogeneous population; however, recent data suggest the causative agents of tuberculosis are more genetically and functionally diverse than appreciated previously. The impact of this natural variation on the virulence and clinical manifestations of the pathogen remains largely unknown. This report examines the effect of genetic diversity among MTC clinical isolates on global gene expression and survival within macrophages. We discovered lineage-specific transcription patterns in vitro and distinct intracellular growth profiles associated with specific responses to host-derived environmental cues. Strain comparisons also facilitated delineation of a core intracellular transcriptome, including genes with highly conserved regulation across the global panel of clinical isolates. This study affords new insights into the genetic information that M. tuberculosis has conserved under selective pressure during its long-term interactions with its human host. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Basal in vitro transcriptomes of Mycobacterium tuberculosis complex (MTC) clinical isolates Intracellular transcriptional adaptation of Mycobacterium tuberculosis complex (MTC) clinical isolates inside resting murine macrophages Intracellular transcriptional adaptation of Mycobacterium tuberculosis complex (MTC) clinical isolates inside activated murine macrophages
	Altered expression of isoniazid-regulated genes in drug-treated dormant Mycobacterium tuberculosis. Karakousis PC, Williams EP, Bishai WR (2008) J Antimicrob Chemother 61(2):323-31	2008-02-01	Mycobacterium tuberculosis	Pubmed
Abstract: OBJECTIVES: Despite having potent activity against actively replicating Mycobacterium tuberculosis, isoniazid has very limited activity against dormant bacilli. In order to investigate the lack of bactericidal activity of this drug under conditions leading to mycobacterial dormancy, we studied the transcriptional pattern of M. tuberculosis in different physiological states following exposure to isoniazid. METHODS: Global gene expression analysis was used to study M. tuberculosis treated with isoniazid in dormancy models of nutrient depletion and progressive hypoxia in vitro, as well as in an in vivo hollow fibre model of dormancy. Mycobacterial expression of the drug's putative transcriptional signature was investigated by RT-PCR in each dormancy model, and during the early and chronic phases of infection in the mouse aerosol model. Transcriptional responses were correlated with the bactericidal activity of isoniazid in the respective models. RESULTS: A small group of genes directly relevant to the mechanism of action of isoniazid was confirmed to constitute a transcriptional signature of the drug, as differential regulation of these genes was abrogated in an isoniazid-resistant, katG-deficient M. tuberculosis strain following isoniazid exposure. Isoniazid-induced expression of this transcriptional signature was abolished in dormant bacilli which had acquired phenotypic tolerance to isoniazid, regardless of the specific conditions responsible for the induction of the dormancy phenotype. Quantitative RT-PCR revealed that expression of isoniazid-regulated genes (IRGs) is dramatically altered under conditions of nutrient depletion and progressive hypoxia in vitro. Although these IRGs are highly induced following drug exposure early in infection in the mouse hollow fibre and aerosol models, correlating with potent bactericidal activity of the drug, their expression levels are markedly diminished during late-stage infection in these two models, coinciding with the greatly reduced bactericidal activity of isoniazid against these organisms. CONCLUSIONS: The reduced susceptibility of bacilli to the bactericidal drug isoniazid, as well as lack of expression of IRGs upon exposure to the drug, may be defining features of M. tuberculosis dormancy. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Effect of Isoniazid treatment on Mycobacterium tuberculosis gene expression in various dormancy models
	The three RelE homologs of Mycobacterium tuberculosis have individual, drug-specific effects on bacterial antibiotic tolerance. Singh R, Barry CE 3rd, Boshoff HI (2010) J Bacteriol 192(5):1279-91	2010-03-01	Mycobacterium tuberculosis	Pubmed
Abstract: In Escherichia coli, expression of the RelE and HipA toxins in the absence of their cognate antitoxins has been associated with generating multidrug-tolerant "persisters." Here we show that unlike persisters of E. coli, persisters of Mycobacterium tuberculosis selected with one drug do not acquire cross-resistance to other classes of drugs. M. tuberculosis has three homologs of RelE arranged in operons with their apparent antitoxins. Each toxin individually arrests growth of both M. tuberculosis and E. coli, an effect that is neutralized by coexpression of the cognate antitoxin. Overexpression or deletion of each of the RelE toxins had a toxin- and drug-specific effect on the proportion of bacilli surviving antibiotic killing. All three toxins were upregulated in vivo, but none of the deletions affected survival during murine infection. RelE2 overexpression increased bacterial survival rates in the presence of rifampin in vitro, while deletion significantly decreased survival rates. Strikingly, deletion of this toxin had no discernible effect on the level of persisters seen in rifampin-treated mice. Our results suggest that, in vivo, RelE-generated persisters are unlikely to play a significant role in the generation of bacilli that survive in the face of multidrug therapy or in the generation of multidrug-resistant M. tuberculosis. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Transcriptional analysis of RelE family toxin overexpression in Mycobacterium tuberculosis
	Characterization of a Clp protease gene regulator and the reaeration response in Mycobacterium tuberculosis. Sherrid AM, Rustad TR, Cangelosi GA, Sherman DR (2010) PLoS One 5(7):e11622	2010-07-16	Mycobacterium tuberculosis	Pubmed
Abstract: Mycobacterium tuberculosis (MTB) enters a non-replicating state when exposed to low oxygen tension, a condition the bacillus encounters in granulomas during infection. Determining how mycobacteria enter and maintain this state is a major focus of research. However, from a public health standpoint the importance of latent TB is its ability to reactivate. The mechanism by which mycobacteria return to a replicating state upon re-exposure to favorable conditions is not understood. In this study, we utilized reaeration from a defined hypoxia model to characterize the adaptive response of MTB following a return to favorable growth conditions. Global transcriptional analysis identified the approximately 100 gene Reaeration Response, induced relative to both log-phase and hypoxic MTB. This response includes chaperones and proteases, as well as the transcription factor Rv2745c, which we characterize as a Clp protease gene regulator (ClgR) orthologue. During reaeration, genes repressed during hypoxia are also upregulated in a wave of transcription that includes genes crucial to transcription, translation and oxidative phosphorylation and culminates in bacterial replication. In sum, this study defines a new transcriptional response of MTB with potential relevance to disease, and implicates ClgR as a regulator involved in resumption of replication following hypoxia. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Reaeration timecourse from a defined hypoxia model in Mycobacterium tuberculosis.
	Yang Liu and Gary Schoolnik's Unpublished Carbon Sources Data. Yang Liu and Gary Schoolnik (Unpublished Results)	2010-06-01	Mycobacterium tuberculosis
Abstract: Yang Liu and Gary Schoolnik studied transcriptional profiles of H37Rv and several other strains and mutants when grown on different carbon sources and/or treated with different drugs or subjected to different growth conditions. All the samples/slides from these studies were organized into this unpublished experiment set and made available to public users. whiB4, Rv3524 null mutants and strains like H37Rv, MT106, MT71, MT90, MT95, MT96, MTB1248, MTB1254, MTB1255, MTB1370, MTB6548, MTB889, TM106, TM85 were used in this study. Various carbon sources used in this study include arachidonic acid, glucose, glycerol, linoleic acid, oleic acid, palmitic acid etc. Cells were exposed to treatment conditions like starvation, different temperatures etc. Drugs used in this study include dipyridyl, eicosatetraynoic acid isoniazid, ndomechacin, nordihydroguaiaretic acid, SDS, tetracycline etc. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Yang Liu and Gary Schoolnik's Unpublished Carbon Sources Data
	A Mycobacterium tuberculosis sigma factor network responds to cell-envelope damage by the promising anti-mycobacterial thioridazine. Dutta NK, Mehra S, Kaushal D (2010) PLoS One 5(4):e10069	2010-04-08	Mycobacterium tuberculosis	Pubmed
Abstract: BACKGROUND: Novel therapeutics are urgently needed to control tuberculosis (TB). Thioridazine (THZ) is a candidate for the therapy of multidrug and extensively drug-resistant TB. METHODOLOGY/PRINCIPAL FINDINGS: We studied the impact of THZ on Mycobacterium tuberculosis (Mtb) by analyzing gene expression profiles after treatment at the minimal inhibitory (1x MIC) or highly inhibitory (4x MIC) concentrations between 1-6 hours. THZ modulated the expression of genes encoding membrane proteins, efflux pumps, oxido-reductases and enzymes involved in fatty acid metabolism and aerobic respiration. The Rv3160c-Rv3161c operon, a multi-drug transporter and the Rv3614c/3615c/3616c regulon, were highly induced in response to THZ. A significantly high number of Mtb genes co-expressed with sigma(B) (the sigma(B) regulon) was turned on by THZ treatment. sigma(B) has recently been shown to protect Mtb from envelope-damage. We hypothesized that THZ damages the Mtb cell-envelope, turning on the expression of the sigma(B) regulon. Consistent with this hypothesis, we present electron-microscopy data which shows that THZ modulates cell-envelope integrity. Moreover, the Mtb mutants in sigma(H) and sigma(E), two alternate stress response sigma factors that induce the expression of sigma(B), exhibited higher sensitivity to THZ, indicating that the presence and expression of sigma(B) allows Mtb to resist the impact of THZ. Conditional induction of sigma(B) levels increased the survival of Mtb in the presence of THZ. CONCLUSIONS/SIGNIFICANCE: THZ targets different pathways and can thus be used as a multi-target inhibitor itself as well as provide strategies for multi-target drug development for combination chemotherapy. Our results show that the Mtb sigma factor network comprising of sigma(H), sigma(E) and sigma(B) plays a crucial role in protecting the pathogen against cell-envelope damage. MESH terms: null Associated Links PubMed Link | Full Text Online | Repository Associated Experiment Sets Explore View Download Mycobacterium tuberculosis gene expression in response to thioridazine (THZ)