Gene Expression Publications

Search, browse and explore data from publications with gene expression data that are stored in TBDBEcoliHub: Omics.

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	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.
	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
	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
	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
	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
	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
	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
	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)
	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
	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
	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
	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
	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.
	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)
	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
	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
	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 | Repository | Full Text Online Associated Experiment Sets Explore View Download Yang Liu and Gary Schoolnik's Unpublished Carbon Sources Data
	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.
	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
	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 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
	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
	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
	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.
	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
	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
	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
	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
	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
	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