%% This BibTeX bibliography file was created using BibDesk. %% http://bibdesk.sourceforge.net/ %% Created for Ralf Stephan at 2010-03-02 11:52:26 +0100 %% Saved with string encoding Unicode (UTF-8) @article{Provvedi:2009ye, 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.}, Author = {Provvedi, Roberta and Boldrin, Francesca and Falciani, Francesco and Pal{\`u}, Giorgio and Manganelli, Riccardo}, Date-Added = {2010-03-02 11:50:45 +0100}, Date-Modified = {2010-03-02 11:50:45 +0100}, Doi = {10.1099/mic.0.024802-0}, Journal = {Microbiology}, Journal-Full = {Microbiology (Reading, England)}, Mesh = {Anti-Bacterial Agents; Bacterial Proteins; Culture Media; Dose-Response Relationship, Drug; Drug Resistance, Bacterial; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Heat-Shock Response; Humans; Molecular Sequence Data; Mycobacterium tuberculosis; Oligonucleotide Array Sequence Analysis; Vancomycin}, Month = {Apr}, Number = {Pt 4}, Pages = {1093-102}, Pmid = {19332811}, Pst = {ppublish}, Title = {Global transcriptional response to vancomycin in Mycobacterium tuberculosis}, Volume = {155}, Year = {2009}, Bdsk-Url-1 = {http://dx.doi.org/10.1099/mic.0.024802-0}} @article{Thum:2009fu, Abstract = {The Mycobacterium tuberculosis cmk gene, predicted to encode a CMP kinase (CMK), was cloned and expressed, and its product was purified to homogeneity. Steady-state kinetics confirmed that M. tuberculosis CMK is a monomer that preferentially phosphorylates CMP and dCMP by a sequential mechanism. A plausible role for CMK is discussed.}, Author = {Thum, Caroline and Schneider, Cristopher Z and Palma, Mario S and Santos, Di{\'o}genes S and Basso, Luiz A}, Date-Added = {2010-03-02 11:50:05 +0100}, Date-Modified = {2010-03-02 11:50:05 +0100}, Doi = {10.1128/JB.01337-08}, Journal = {J Bacteriol}, Journal-Full = {Journal of bacteriology}, Mesh = {Amino Acid Sequence; Cloning, Molecular; Deoxycytidine Monophosphate; Gene Expression; Kinetics; Molecular Sequence Data; Mycobacterium tuberculosis; Nucleoside-Phosphate Kinase; Phosphorylation; Recombinant Proteins; Sequence Alignment}, Month = {Apr}, Number = {8}, Pages = {2884-7}, Pmc = {PMC2668428}, Pmid = {19181797}, Pst = {ppublish}, Title = {The Rv1712 Locus from Mycobacterium tuberculosis H37Rv codes for a functional CMP kinase that preferentially phosphorylates dCMP}, Volume = {191}, Year = {2009}, Bdsk-Url-1 = {http://dx.doi.org/10.1128/JB.01337-08}} @article{Be:2008lh, Abstract = {BACKGROUND: Tuberculosis of the central nervous system (CNS) is a serious, often fatal disease primarily affecting young children. It develops after hematogenous dissemination and subsequent invasion of the CNS by Mycobacterium tuberculosis. The microbial determinants involved in CNS disease are poorly characterized. METHODS: Hematogenously disseminated M. tuberculosis infection was simulated in BALB/c mice by intravenous challenge. Bacteria were recovered using standard culture techniques. Host immune response to M. tuberculosis infection was assessed by histopathological and cytokine profile analysis. By means of a pooled infection with genotypically defined M. tuberculosis mutants, bacterial genes required for invasion or survival were determined in the CNS and lung tissue. RESULTS: M. tuberculosis were detected in whole mouse brains as early as 1 day after intravenous infection and at all time points assessed thereafter. No significant immune response was elicited in the infected brain tissue, compared with extensive inflammation in the infected lung tissue at the same time point. We identified mutants for 5 M. tuberculosis genes (Rv0311, Rv0805, Rv0931c, Rv0986, and MT3280) with CNS-specific phenotypes, absent in lung tissue. CONCLUSIONS: We have identified CNS-specific M. tuberculosis genes involved in the pathogenesis of tuberculosis. Further characterization of these genes will help in understanding the microbial pathogenesis of CNS tuberculosis.}, Author = {Be, Nicholas A and Lamichhane, Gyanu and Grosset, Jacques and Tyagi, Sandeep and Cheng, Qi-Jian and Kim, Kwang Sik and Bishai, William R and Jain, Sanjay K}, Date-Added = {2010-03-02 11:48:13 +0100}, Date-Modified = {2010-03-02 11:48:13 +0100}, Doi = {10.1086/592447}, Journal = {J Infect Dis}, Journal-Full = {The Journal of infectious diseases}, Mesh = {Animals; Central Nervous System; Cytokines; Disease Models, Animal; Female; Genes, Bacterial; Mice; Mice, Inbred BALB C; Mutation; Mycobacterium tuberculosis; Tuberculosis, Central Nervous System}, Month = {Nov}, Number = {10}, Pages = {1520-8}, Pmid = {18956986}, Pst = {ppublish}, Title = {Murine model to study the invasion and survival of Mycobacterium tuberculosis in the central nervous system}, Volume = {198}, Year = {2008}, Bdsk-Url-1 = {http://dx.doi.org/10.1086/592447}} @article{Malen:2007ff, Abstract = {Proteins secreted by Mycobacterium tuberculosis play an essential role in the pathogenesis of tuberculosis. The culture filtrates of M. tuberculosis H37Rv made by Sadamu Nagai (Japan), are considerably enriched for secreted proteins compared to other culture filtrates. Complementary approaches were used to identify the secreted proteins in these culture filtrates: (i) 2-DE combined with MALDI-TOF MS and (ii) LC coupled MS/MS. Peptides derived from a total of 257 proteins were identified of which 144 were identified by more than one peptide. Several members of the immunologically important early secretory antigenic target-6 (ESAT-6) family of proteins were found to be major components. The majority of the identified proteins, 159 (62\%), were predicted to be exported through the general secretory pathway. We experimentally verified that the signal peptides, which mediate translocation through the cell membrane, had been removed in 41 of the identified proteins, and in 35 of those, there was an AXA motif N-terminally to the cleavage site, showing that this motif is important for the recognition and cleavage of signal peptides in mycobacteria. A large fraction of the secreted proteins were unknown, suggesting that we have mapped an unexplored part of the exported proteome of M. tuberculosis. complement.}, Author = {M{\aa}len, Hiwa and Berven, Frode S and Fladmark, Kari E and Wiker, Harald G}, Date-Added = {2010-03-02 11:46:58 +0100}, Date-Modified = {2010-03-02 11:46:58 +0100}, Doi = {10.1002/pmic.200600853}, Journal = {Proteomics}, Journal-Full = {Proteomics}, Mesh = {Amino Acid Sequence; Bacterial Proteins; Electrophoresis, Gel, Two-Dimensional; Molecular Sequence Data; Molecular Weight; Mycobacterium tuberculosis; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization}, Month = {May}, Number = {10}, Pages = {1702-18}, Pmid = {17443846}, Pst = {ppublish}, Title = {Comprehensive analysis of exported proteins from Mycobacterium tuberculosis H37Rv}, Volume = {7}, Year = {2007}, Bdsk-Url-1 = {http://dx.doi.org/10.1002/pmic.200600853}} @article{Stewart:2005pi, Abstract = {The pathogenesis of mycobacterial infection is associated with an ability to interfere with maturation of the phagosomal compartment after ingestion by macrophages. Identification of the mycobacterial components that contribute to this phenomenon will allow rational design of novel approaches to the treatment and prevention of tuberculosis. Microarray-based screening of a transposon library was used to identify mutations that influence the fate of Mycobacterium bovis bacille Calmette-Gu{\'e}rin (BCG) following uptake by macrophages. A screen based on bacterial survival during a 3-d infection highlighted genes previously implicated in growth of Mycobacterium tuberculosis in macrophages and in mice, together with a number of other virulence genes including a locus encoding virulence-associated membrane proteins and a series of transporter molecules. A second screen based on separation of acidified and non-acidified phagosomes by flow cytometry identified genes involved in mycobacterial control of early acidification. This included the KefB potassium/proton antiport. Mutants unable to control early acidification were significantly attenuated for growth during 6-d infections of macrophages. Early acidification of the phagosome is associated with reduced survival of BCG in macrophages. A strong correlation exists between genes required for intracellular survival of BCG and those required for growth of M. tuberculosis in mice. In contrast, very little correlation exists between genes required for intracellular survival of BCG and those that are up-regulated during intracellular adaptation of M. tuberculosis. This study has identified targets for interventions to promote immune clearance of tuberculosis infection. The screening technologies demonstrated in this study will be useful to the study of pathogenesis in many other intracellular microorganisms.}, Author = {Stewart, Graham R and Patel, Janisha and Robertson, Brian D and Rae, Aaron and Young, Douglas B}, Date-Added = {2010-03-02 11:45:53 +0100}, Date-Modified = {2010-03-02 11:45:53 +0100}, Doi = {10.1371/journal.ppat.0010033}, Journal = {PLoS Pathog}, Journal-Full = {PLoS pathogens}, Month = {Nov}, Number = {3}, Pages = {269-78}, Pmc = {PMC1291353}, Pmid = {16322769}, Pst = {ppublish}, Title = {Mycobacterial mutants with defective control of phagosomal acidification}, Volume = {1}, Year = {2005}, Bdsk-Url-1 = {http://dx.doi.org/10.1371/journal.ppat.0010033}} @article{Siroy:2008mi, Abstract = {Mycobacteria contain an outer membrane composed of mycolic acids and a large variety of other lipids. Its protective function is an essential virulence factor of Mycobacterium tuberculosis. Only OmpA, which has numerous homologs in Gram-negative bacteria, is known to form channels in the outer membrane of M. tuberculosis so far. Rv1698 was predicted to be an outer membrane protein of unknown function. Expression of rv1698 restored the sensitivity to ampicillin and chloramphenicol of a Mycobacterium smegmatis mutant lacking the main porin MspA. Uptake experiments showed that Rv1698 partially complemented the permeability defect of the M. smegmatis porin mutant for glucose. These results indicated that Rv1698 provides an unspecific pore that can partially substitute for MspA. Lipid bilayer experiments demonstrated that purified Rv1698 is an integral membrane protein that indeed produces channels. The main single channel conductance is 4.5 +/- 0.3 nanosiemens in 1 M KCl. Zero current potential measurements revealed a weak preference for cations. Whole cell digestion of recombinant M. smegmatis with proteinase K showed that Rv1698 is surface-accessible. Taken together, these experiments demonstrated that Rv1698 is a channel protein that is likely involved in transport processes across the outer membrane of M. tuberculosis. Rv1698 has single homologs of unknown functions in Corynebacterineae and thus represents the first member of a new class of channel proteins specific for mycolic acid-containing outer membranes.}, Author = {Siroy, Axel and Mailaender, Claudia and Harder, Daniel and Koerber, Stephanie and Wolschendorf, Frank and Danilchanka, Olga and Wang, Ying and Heinz, Christian and Niederweis, Michael}, Date-Added = {2010-03-02 11:41:32 +0100}, Date-Modified = {2010-03-02 11:41:32 +0100}, Doi = {10.1074/jbc.M800866200}, Journal = {J Biol Chem}, Journal-Full = {The Journal of biological chemistry}, Mesh = {Anti-Bacterial Agents; Bacterial Outer Membrane Proteins; Cell Membrane; Endopeptidase K; Escherichia coli; Glucose; Lipid Bilayers; Models, Biological; Mutation; Mycobacterium bovis; Mycobacterium smegmatis; Mycobacterium tuberculosis; Point Mutation; Porins; Protein Structure, Secondary}, Month = {Jun}, Number = {26}, Pages = {17827-37}, Pmc = {PMC2440620}, Pmid = {18434314}, Pst = {ppublish}, Title = {Rv1698 of Mycobacterium tuberculosis represents a new class of channel-forming outer membrane proteins}, Volume = {283}, Year = {2008}, Bdsk-Url-1 = {http://dx.doi.org/10.1074/jbc.M800866200}} @article{Lavollay:2008qa, Abstract = {Our understanding of the mechanisms used by Mycobacterium tuberculosis to persist in a "dormant" state is essential to the development of therapies effective in sterilizing tissues. Gene expression profiling in model systems has revealed a complex adaptive response thought to endow M. tuberculosis with the capacity to survive several months of combinatorial antibiotic treatment. We show here that this adaptive response may involve remodeling of the peptidoglycan network by substitution of 4-->3 cross-links generated by the D,D-transpeptidase activity of penicillin-binding proteins by 3-->3 cross-links generated by a transpeptidase of L,D specificity. A candidate gene, previously shown to be upregulated upon nutrient starvation, was found to encode an L,D-transpeptidase active in the formation of 3-->3 cross-links. The enzyme, Ldt(Mt1), was inactivated by carbapenems, a class of beta-lactam antibiotics that are poorly hydrolyzed by the M. tuberculosis beta-lactamases. Ldt(Mt1) and carbapenems may therefore represent a target and a drug family relevant to the eradication of persistent M. tuberculosis.}, Author = {Lavollay, Marie and Arthur, Michel and Fourgeaud, Martine and Dubost, Lionel and Marie, Arul and Veziris, Nicolas and Blanot, Didier and Gutmann, Laurent and Mainardi, Jean-Luc}, Date-Added = {2010-03-02 11:41:14 +0100}, Date-Modified = {2010-03-02 11:41:14 +0100}, Doi = {10.1128/JB.00239-08}, Journal = {J Bacteriol}, Journal-Full = {Journal of bacteriology}, Mesh = {Anti-Bacterial Agents; Models, Biological; Mycobacterium tuberculosis; Peptidoglycan; Peptidyl Transferases; Spectrometry, Mass, Electrospray Ionization; beta-Lactams}, Month = {Jun}, Number = {12}, Pages = {4360-6}, Pmc = {PMC2446752}, Pmid = {18408028}, Pst = {ppublish}, Title = {The peptidoglycan of stationary-phase Mycobacterium tuberculosis predominantly contains cross-links generated by L,D-transpeptidation}, Volume = {190}, Year = {2008}, Bdsk-Url-1 = {http://dx.doi.org/10.1128/JB.00239-08}} @article{Slayden:2006kl, Abstract = {In Mycobacterium tuberculosis the mechanism of septum formation and regulation of cell division remains undefined. In other bacterial species FtsZ polymerization and septum formation are influenced through protein interactions in addition to transcriptional regulation, and the combination of these provides tight regulation of this process. However, homologues of proteins known to affect FtsZ assembly have not been identified and substantiated in M. tuberculosis. This suggests that M. tuberculosis may possess unique processes for regulation of septum formation. To begin to address this poorly understood aspect of M. tuberculosis physiology, FtsZ inhibitors were used to block cell division and the effects on bacterial morphology and the transcriptional response were examined. Inhibition of septum formation prevented cell division and led to bacterial filamentation. Microarray-based transcriptional profiling allowed the evaluation of multiple metabolic processes in response to inhibition of septum formation and when coupled with bioinformatics provided a means to identify regulatory elements and other gene products that probably influence septum formation.}, Author = {Slayden, Richard A and Knudson, Dennis L and Belisle, John T}, Date-Added = {2010-03-02 11:40:14 +0100}, Date-Modified = {2010-03-02 11:40:14 +0100}, Doi = {10.1099/mic.0.28762-0}, Journal = {Microbiology}, Journal-Full = {Microbiology (Reading, England)}, Mesh = {Bacterial Proteins; Cell Cycle; Cell Division; Cytoskeletal Proteins; Gene Expression Regulation, Bacterial; Humans; Microscopy, Electron; Mycobacterium tuberculosis; Oligonucleotide Array Sequence Analysis; Transcription, Genetic}, Month = {Jun}, Number = {Pt 6}, Pages = {1789-97}, Pmid = {16735741}, Pst = {ppublish}, Title = {Identification of cell cycle regulators in Mycobacterium tuberculosis by inhibition of septum formation and global transcriptional analysis}, Volume = {152}, Year = {2006}, Bdsk-Url-1 = {http://dx.doi.org/10.1099/mic.0.28762-0}} @article{Rachman:2006fu, Abstract = {As one of the world's most successful intracellular pathogens, Mycobacterium tuberculosis, the causative agent of human tuberculosis, is responsible for two to three million deaths annually. The pathogenicity of M. tuberculosis relies on its ability to survive and persist within host macrophage cells during infection. It is of central importance, therefore, to identify genes and pathways that are involved in the survival and persistence of M. tuberculosis within these cells. Utilizing genome-wide DNA arrays we have identified M. tuberculosis genes that are specifically induced during macrophage infection. To better understand the cellular context of these differentially expressed genes, we have also combined our array analyses with computational methods of protein network identification. Our combined approach reveals certain signatures of M. tuberculosis residing within macrophage cells, including the induction of genes involved in DNA damage repair, fatty acid degradation, iron metabolism, and cell wall metabolism.}, Author = {Rachman, Helmy and Strong, Michael and Schaible, Ulrich and Schuchhardt, Johannes and Hagens, Kristine and Mollenkopf, Hans and Eisenberg, David and Kaufmann, Stefan H E}, Date-Added = {2010-03-02 11:39:55 +0100}, Date-Modified = {2010-03-02 11:39:55 +0100}, Doi = {10.1016/j.micinf.2005.09.011}, Journal = {Microbes Infect}, Journal-Full = {Microbes and infection / Institut Pasteur}, Mesh = {Amino Acids; Bacterial Proteins; Biological Transport; Cell Membrane; Cell Wall; Cluster Analysis; DNA Repair; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Iron; Lipid Metabolism; Mycobacterium tuberculosis; Up-Regulation}, Month = {Mar}, Number = {3}, Pages = {747-57}, Pmid = {16513384}, Pst = {ppublish}, Title = {Mycobacterium tuberculosis gene expression profiling within the context of protein networks}, Volume = {8}, Year = {2006}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.micinf.2005.09.011}} @article{Manjunatha:2006dz, Abstract = {PA-824 is a promising new compound for the treatment of tuberculosis that is currently undergoing human trials. Like its progenitors metronidazole and CGI-17341, PA-824 is a prodrug of the nitroimidazole class, requiring bioreductive activation of an aromatic nitro group to exert an antitubercular effect. We have confirmed that resistance to PA-824 (a nitroimidazo-oxazine) and CGI-17341 (a nitroimidazo-oxazole) is most commonly mediated by loss of a specific glucose-6-phosphate dehydrogenase (FGD1) or its deazaflavin cofactor F420, which together provide electrons for the reductive activation of this class of molecules. Although FGD1 and F420 are necessary for sensitivity to these compounds, they are not sufficient and require additional accessory proteins that directly interact with the nitroimidazole. To understand more proximal events in the reductive activation of PA-824, we examined mutants that were wild-type for both FGD1 and F420 and found that, although these mutants had acquired high-level resistance to PA-824 (and another nitroimidazo-oxazine), they retained sensitivity to CGI-17341 (and a related nitroimidazo-oxazole). Microarray-based comparative genome sequencing of these mutants identified lesions in Rv3547, a conserved hypothetical protein with no known function. Complementation with intact Rv3547 fully restored sensitivity to nitroimidazo-oxazines and restored the ability of Mtb to metabolize PA-824. These results suggest that the sensitivity of Mtb to PA-824 and related compounds is mediated by a protein that is highly specific for subtle structural variations in these bicyclic nitroimidazoles.}, Author = {Manjunatha, Ujjini H and Boshoff, Helena and Dowd, Cynthia S and Zhang, Liang and Albert, Thomas J and Norton, Jason E and Daniels, Lacy and Dick, Thomas and Pang, Siew Siew and Barry, 3rd, Clifton E}, Date-Added = {2010-03-02 11:39:37 +0100}, Date-Modified = {2010-03-02 11:39:37 +0100}, Doi = {10.1073/pnas.0508392103}, Journal = {Proc Natl Acad Sci U S A}, Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America}, Mesh = {Bacterial Proteins; DNA Transposable Elements; Drug Resistance, Bacterial; Genome, Bacterial; Glucosephosphate Dehydrogenase; Molecular Sequence Data; Molecular Structure; Mutation; Mycobacterium tuberculosis; Nitroimidazoles; Oxazines; Phenotype}, Month = {Jan}, Number = {2}, Pages = {431-6}, Pmc = {PMC1326169}, Pmid = {16387854}, Pst = {ppublish}, Title = {Identification of a nitroimidazo-oxazine-specific protein involved in PA-824 resistance in Mycobacterium tuberculosis}, Volume = {103}, Year = {2006}, Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0508392103}} @article{Arcus:2005fv, Abstract = {PIN-domains (homologues of the pilT N-terminal domain) are small protein domains of approximately 140 amino acids. They are found in a diverse range of organisms and recent evidence from bioinformatics, biochemistry, structural biology and microbiology suggest that the majority of the prokaryotic PIN-domain proteins are the toxic components of toxin-antitoxin (TA) operons. Several microorganisms have a large cohort of these operons. For example, the genome of Mycobacterium tuberculosis encodes 48 PIN-domain proteins, of which 38 are thought to be involved in TA interactions. This large array of PIN-domain TA operons raises questions as to their evolutionary origin and contemporary functional significance. We suggest that the evolutionary origin of genes encoding mycobacterial PIN-domain TA operons is linked to the mobile gene pool, but that TA operons can become resident within the chromosome of host cells from where they might be recruited to fulfil a variety of roles associated with retardation of cell growth and persistence in stressful environments.}, Author = {Arcus, Vickery L and Rainey, Paul B and Turner, Susan J}, Date-Added = {2010-03-02 11:36:37 +0100}, Date-Modified = {2010-03-02 11:36:37 +0100}, Doi = {10.1016/j.tim.2005.06.008}, Journal = {Trends Microbiol}, Journal-Full = {Trends in microbiology}, Mesh = {Adenosine Triphosphatases; Amino Acid Sequence; Antitoxins; Bacterial Proteins; Models, Molecular; Molecular Motor Proteins; Molecular Sequence Data; Mycobacterium tuberculosis; Operon; Protein Structure, Tertiary; Sequence Alignment}, Month = {Aug}, Number = {8}, Pages = {360-5}, Pmid = {15993073}, Pst = {ppublish}, Title = {The PIN-domain toxin-antitoxin array in mycobacteria}, Volume = {13}, Year = {2005}, Bdsk-Url-1 = {http://dx.doi.org/10.1016/j.tim.2005.06.008}} @article{Xiong:2005bs, Abstract = {Because many membrane-associated proteins represent potential drug targets, diagnostic probes, and components of vaccines, we have chosen to study the membrane proteins of Mycobacterium tuberculosis H37Rv. To remove cytosolic proteins and facilitate access to the integral membrane proteins, membrane fractions of M. tuberculosis H37Rv were intensely washed with 5 M urea and high pH carbonate solution. One-dimensional SDS-PAGE, followed by enzymatic hydrolysis and nanoLC electrospray ionization MS/MS, proved to be the most efficient way to identify the proteins contained within the membrane fraction. Here we report 349 protein identifications in total, validated by at least two tryptic peptide matches and MOWSE scores greater than 75. Of those 349 proteins, 100 are integral membrane proteins with at least one predicted transmembrane alpha helix (excluding the possible signal sequence). 84 M. tuberculosis H37Rv proteins, including 42 integral membrane proteins, are described for the first time.}, Author = {Xiong, Ying and Chalmers, Michael J and Gao, Fei Philip and Cross, Timothy A and Marshall, Alan G}, Date = {2005 May-Jun}, Date-Added = {2010-03-02 11:36:00 +0100}, Date-Modified = {2010-03-02 11:36:00 +0100}, Doi = {10.1021/pr0500049}, Journal = {J Proteome Res}, Journal-Full = {Journal of proteome research}, Mesh = {Bacterial Proteins; Chromatography, High Pressure Liquid; Electrophoresis, Polyacrylamide Gel; Membrane Proteins; Mycobacterium tuberculosis; Proteomics; Spectrometry, Mass, Electrospray Ionization; Trypsin; Urea}, Number = {3}, Pages = {855-61}, Pmid = {15952732}, Pst = {ppublish}, Title = {Identification of Mycobacterium tuberculosis H37Rv integral membrane proteins by one-dimensional gel electrophoresis and liquid chromatography electrospray ionization tandem mass spectrometry}, Volume = {4}, Year = {2005}, Bdsk-Url-1 = {http://dx.doi.org/10.1021/pr0500049}} @article{Rengarajan:2005ij, Abstract = {Macrophages are central to host defense against microbes, but intracellular pathogens have evolved to evade their antimicrobial functions. Mycobacterium tuberculosis (MTB) has successfully exploited macrophages as its primary niche in vivo, but the bacterial genome-wide requirements that promote its intracellular survival remain undefined. Here we comprehensively identify the MTB genes required for survival by screening for transposon mutants that fail to grow within primary macrophages. We identify mutants showing decreased growth in macrophage environments that model stages of the host immune response. By systematically analyzing several biologically relevant data sets, we have been able to identify putative pathways that could not be predicted by genome organization alone. In one example, phosphate transport, requiring physically unlinked genes, was found to be critical for MTB growth in macrophages and important for establishing persistent infection in lungs. Remarkably, the majority of MTB genes found by this analysis to be required for survival are constitutively expressed rather than regulated by macrophages, revealing the host-adapted lifestyle of an evolutionarily selected intracellular pathogen.}, Author = {Rengarajan, Jyothi and Bloom, Barry R and Rubin, Eric J}, Date-Added = {2010-03-02 11:35:32 +0100}, Date-Modified = {2010-03-02 11:35:32 +0100}, Doi = {10.1073/pnas.0503272102}, Journal = {Proc Natl Acad Sci U S A}, Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America}, Mesh = {Adaptation, Physiological; Animals; Biological Transport; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Genes, Bacterial; Genome, Bacterial; Macrophages; Mice; Mice, Inbred C57BL; Mycobacterium tuberculosis; Operon; Organ Specificity; Phosphates}, Month = {Jun}, Number = {23}, Pages = {8327-32}, Pmc = {PMC1142121}, Pmid = {15928073}, Pst = {ppublish}, Title = {Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages}, Volume = {102}, Year = {2005}, Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.0503272102}} @article{Dubnau:2005hc, Abstract = {Using a promoter trap, we have identified 56 Mycobacterium tuberculosis genes preferentially expressed in the mouse lung. Quantitative real-time PCR showed that RNA levels of several genes were higher from bacteria growing in mouse lungs than from broth cultures. These results support the current hypothesis that Mycobacterium tuberculosis utilizes fatty acids as a carbon source in the mouse lung.}, Author = {Dubnau, Eugenie and Chan, John and Mohan, V P and Smith, Issar}, Date-Added = {2010-03-02 11:35:00 +0100}, Date-Modified = {2010-03-02 11:35:00 +0100}, Doi = {10.1128/IAI.73.6.3754-3757.2005}, Journal = {Infect Immun}, Journal-Full = {Infection and immunity}, Mesh = {Animals; Antigens, Bacterial; Bacterial Proteins; Drug Resistance, Bacterial; Isoniazid; Lung; Mice; Mycobacterium tuberculosis; Oxidoreductases; Reverse Transcriptase Polymerase Chain Reaction; Sequence Analysis, DNA}, Month = {Jun}, Number = {6}, Pages = {3754-7}, Pmc = {PMC1111836}, Pmid = {15908407}, Pst = {ppublish}, Title = {responses of mycobacterium tuberculosis to growth in the mouse lung}, Volume = {73}, Year = {2005}, Bdsk-Url-1 = {http://dx.doi.org/10.1128/IAI.73.6.3754-3757.2005}} @article{Hisert:2004tg, Abstract = {Tuberculosis (TB) is characterized by lifetime persistence of Mycobacterium tuberculosis. Despite the induction of a vigorous host immune response that curtails disease progression in the majority of cases, the organism is not eliminated. Subsequent immunosuppression can lead to reactivation after a prolonged period of clinical latency. Thus, while it is clear that protective immune mechanisms are engaged during M. tuberculosis infection, it also appears that the pathogen has evolved effective countermechanisms. Genetic studies with animal infection models and with patients have revealed a key role for the cytokine gamma interferon (IFN-gamma) in resistance to TB. IFN-gamma activates a large number of antimicrobial pathways. Three of these IFN-gamma-dependent mechanisms have been implicated in defense against M. tuberculosis: inducible nitric oxide synthase (iNOS), phagosome oxidase (phox), and the phagosome-associated GTPase LRG-47. In order to identify bacterial genes that provide protection against specific host immune pathways, we have developed the strategy of differential signature-tagged transposon mutagenesis. Using this approach we have identified three M. tuberculosis genes that are essential for progressive M. tuberculosis growth and rapid lethality in iNOS-deficient mice but not in IFN-gamma-deficient mice. We propose that these genes are involved in pathways that allow M. tuberculosis to counter IFN-gamma-dependent immune mechanisms other than iNOS.}, Author = {Hisert, Katherine B and Kirksey, Meghan A and Gomez, James E and Sousa, Alexandra O and Cox, Jeffery S and Jacobs, Jr, William R and Nathan, Carl F and McKinney, John D}, Date-Added = {2010-03-02 11:34:40 +0100}, Date-Modified = {2010-03-02 11:34:40 +0100}, Doi = {10.1128/IAI.72.9.5315-5321.2004}, Journal = {Infect Immun}, Journal-Full = {Infection and immunity}, Mesh = {Animals; Bacterial Proteins; DNA Transposable Elements; Female; Humans; Interferon-gamma; Lung; Male; Mice; Mice, Inbred C57BL; Mutagenesis; Mutation; Mycobacterium tuberculosis; Nitric Oxide Synthase; Nitric Oxide Synthase Type II; Tuberculosis, Pulmonary}, Month = {Sep}, Number = {9}, Pages = {5315-21}, Pmc = {PMC517420}, Pmid = {15322028}, Pst = {ppublish}, Title = {Identification of Mycobacterium tuberculosis counterimmune (cim) mutants in immunodeficient mice by differential screening}, Volume = {72}, Year = {2004}, Bdsk-Url-1 = {http://dx.doi.org/10.1128/IAI.72.9.5315-5321.2004}} @article{Daniel:2004kl, Abstract = {Mycobacterium tuberculosis enters the host by inhalation of an infectious aerosol and replicates in the alveolar macrophages until the host's immune defense causes bacteriostasis, which leads the pathogen to go into nonreplicative drug-resistant dormancy. The dormant pathogen can survive for decades till the host's immune system is weakened and active tuberculosis develops. Even though fatty acids are thought to be the major energy source required for the persistence phase, the source of fatty acids used is not known. We postulate that the pathogen uses triacylglycerol (TG) as a storage form of fatty acids. Little is known about the biosynthesis of TG in M. tuberculosis. We show that 15 mycobacterial genes that we identified as putative triacylglycerol synthase (tgs) when expressed in Escherichia coli showed TGS activity, and we report some basic catalytic characteristics of the most active enzymes. We show that several tgs genes are induced when the pathogen goes into the nonreplicative drug-resistant state caused by slow withdrawal of O(2) and also by NO treatment, which is known to induce dormancy-associated genes. The gene (Rv3130c) that shows the highest TGS activity when expressed in E. coli shows the highest induction by hypoxia and NO treatment. Biochemical evidence shows that TG synthesis and accumulation occur under both conditions. We conclude that TG may be a form of energy storage for use during long-term dormancy. Therefore, TG synthesis may be an appropriate target for novel antilatency drugs that can prevent the organism from surviving dormancy and thus assist in the control of tuberculosis.}, Author = {Daniel, Jaiyanth and Deb, Chirajyoti and Dubey, Vinod S and Sirakova, Tatiana D and Abomoelak, Bassam and Morbidoni, Hector R and Kolattukudy, Pappachan E}, Date-Added = {2010-03-02 11:34:16 +0100}, Date-Modified = {2010-03-02 11:34:16 +0100}, Doi = {10.1128/JB.186.15.5017-5030.2004}, Journal = {J Bacteriol}, Journal-Full = {Journal of bacteriology}, Mesh = {Acyltransferases; Anaerobiosis; Bacterial Proteins; Culture Media; Diacylglycerol O-Acyltransferase; Enzyme Induction; Escherichia coli; Gene Expression Regulation, Bacterial; Mycobacterium tuberculosis; Nitric Oxide; Triglycerides}, Month = {Aug}, Number = {15}, Pages = {5017-30}, Pmc = {PMC451596}, Pmid = {15262939}, Pst = {ppublish}, Title = {Induction of a novel class of diacylglycerol acyltransferases and triacylglycerol accumulation in Mycobacterium tuberculosis as it goes into a dormancy-like state in culture}, Volume = {186}, Year = {2004}, Bdsk-Url-1 = {http://dx.doi.org/10.1128/JB.186.15.5017-5030.2004}} @article{Cowley:2004oq, Abstract = {The function of the Mycobacterium tuberculosis eukaryotic-like protein serine/threonine kinase PknG was investigated by gene knock-out and by expression and biochemical analysis. The pknG gene (Rv0410c), when cloned and expressed in Escherichia coli, encodes a functional kinase. An in vitro kinase assay of the recombinant protein demonstrated that PknG can autophosphorylate its kinase domain as well as its 30 kDa C-terminal portion, which contains a tetratricopeptide (TPR) structural signalling motif. Western analysis revealed that PknG is located in the cytosol as well as in mycobacterial membrane. The pknG gene was inactivated by allelic exchange in M. tuberculosis. The resulting mutant strain causes delayed mortality in SCID mice and displays decreased viability both in vitro and upon infection of BALB/c mice. The reduced growth of the mutant was more pronounced in the stationary phase of the mycobacterial growth cycle and when grown in nutrient-depleted media. The PknG-deficient mutant accumulates glutamate and glutamine. The cellular levels of these two amino acids reached approximately threefold of their parental strain levels. Higher cellular levels of the amine sugar-containing molecules, GlcN-Ins and mycothiol, which are derived from glutamate, were detected in the DeltapknG mutant. De novo glutamine synthesis was shown to be reduced by 50\%. This is consistent with current knowledge suggesting that glutamine synthesis is regulated by glutamate and glutamine levels. These data support our hypothesis that PknG mediates the transfer of signals sensing nutritional stress in M. tuberculosis and translates them into metabolic adaptation.}, Author = {Cowley, Siobhan and Ko, Mary and Pick, Neora and Chow, Rayken and Downing, Katrina J and Gordhan, Bhavna G and Betts, Joanna C and Mizrahi, Valerie and Smith, Debbie A and Stokes, Richard W and Av-Gay, Yossef}, Date-Added = {2010-03-02 11:33:40 +0100}, Date-Modified = {2010-03-02 11:33:40 +0100}, Doi = {10.1111/j.1365-2958.2004.04085.x}, Journal = {Mol Microbiol}, Journal-Full = {Molecular microbiology}, Mesh = {Animals; Bacterial Proteins; Blotting, Western; Cell Membrane; Cloning, Molecular; Cytoplasm; Escherichia coli; Gene Deletion; Gene Expression Regulation, Bacterial; Genes, Bacterial; Glutamic Acid; Glutamine; Mice; Mice, Inbred BALB C; Mice, SCID; Mutagenesis, Insertional; Mycobacterium tuberculosis; Protein-Serine-Threonine Kinases; Recombinant Proteins; Tuberculosis; Virulence}, Month = {Jun}, Number = {6}, Pages = {1691-702}, Pmid = {15186418}, Pst = {ppublish}, Title = {The Mycobacterium tuberculosis protein serine/threonine kinase PknG is linked to cellular glutamate/glutamine levels and is important for growth in vivo}, Volume = {52}, Year = {2004}, Bdsk-Url-1 = {http://dx.doi.org/10.1111/j.1365-2958.2004.04085.x}} @article{Walburger:2004nx, Abstract = {Pathogenic mycobacteria resist lysosomal delivery after uptake into macrophages, allowing them to survive intracellularly. We found that the eukaryotic-like serine/threonine protein kinase G from pathogenic mycobacteria was secreted within macrophage phagosomes, inhibiting phagosome-lysosome fusion and mediating intracellular survival of mycobacteria. Inactivation of protein kinase G by gene disruption or chemical inhibition resulted in lysosomal localization and mycobacterial cell death in infected macrophages. Besides identifying a target for the control of mycobacterial infections, these findings suggest that pathogenic mycobacteria have evolved eukaryotic-like signal transduction mechanisms capable of modulating host cell trafficking pathways.}, Author = {Walburger, Anne and Koul, Anil and Ferrari, Giorgio and Nguyen, Liem and Prescianotto-Baschong, Cristina and Huygen, Kris and Klebl, Bert and Thompson, Charles and Bacher, Gerald and Pieters, Jean}, Date-Added = {2010-03-02 11:33:22 +0100}, Date-Modified = {2010-03-02 11:33:22 +0100}, Doi = {10.1126/science.1099384}, Journal = {Science}, Journal-Full = {Science (New York, N.Y.)}, Mesh = {Amides; Animals; Cell Line; Cyclic GMP-Dependent Protein Kinases; Enzyme Inhibitors; Gene Deletion; Lysosomes; Macrophages; Mice; Mycobacterium bovis; Mycobacterium smegmatis; Mycobacterium tuberculosis; Phagosomes; Signal Transduction; Thiophenes; Vacuoles}, Month = {Jun}, Number = {5678}, Pages = {1800-4}, Pmid = {15155913}, Pst = {ppublish}, Title = {Protein kinase G from pathogenic mycobacteria promotes survival within macrophages}, Volume = {304}, Year = {2004}, Bdsk-Url-1 = {http://dx.doi.org/10.1126/science.1099384}} @article{Shimono:2003cr, Abstract = {An estimated one-third of the world's population is latently infected with Mycobacterium tuberculosis, the etiologic agent of tuberculosis. Here, we demonstrate that, unlike wild-type M. tuberculosis, a strain of M. tuberculosis disrupted in the mce1 operon was unable to enter a stable persistent state of infection in mouse lungs. Instead, the mutant continued to replicate and killed the mice more rapidly than did the wild-type strain. Histological examination of mouse lungs infected with the mutant strain revealed diffusely organized granulomas with aberrant inflammatory cell migration. Murine macrophages infected ex vivo with the mutant strain were reduced in their ability to produce tumor necrosis factor alpha, IL-6, monocyte chemoattractant protein 1, and nitric oxide (NO), but not IL-4. The mce1 mutant strain complemented with the mce1 genes stimulated tumor necrosis factor alpha and NO production by murine macrophages at levels stimulated by the wild-type strain. These observations indicate that the mce1 operon mutant is unable to stimulate T helper 1-type immunity in mice. The hypervirulence of the mutant strain may have resulted from its inability to stimulate a proinflammatory response that would otherwise induce organized granuloma formation and control the infection without killing the organism. The mce1 operon of M. tuberculosis may be involved in modulating the host inflammatory response in such a way that the bacterium can enter a persistent state without being eliminated or causing disease in the host.}, Author = {Shimono, Nobuyuki and Morici, Lisa and Casali, Nicola and Cantrell, Sally and Sidders, Ben and Ehrt, Sabine and Riley, Lee W}, Date-Added = {2010-03-02 11:32:56 +0100}, Date-Modified = {2010-03-02 11:32:56 +0100}, Doi = {10.1073/pnas.2433882100}, Journal = {Proc Natl Acad Sci U S A}, Journal-Full = {Proceedings of the National Academy of Sciences of the United States of America}, Mesh = {Animals; Bacterial Proteins; Cytokines; Female; Lung; Macrophages; Mice; Mice, Inbred BALB C; Mycobacterium bovis; Mycobacterium tuberculosis; Operon; Tuberculosis; Virulence}, Month = {Dec}, Number = {26}, Pages = {15918-23}, Pmc = {PMC307668}, Pmid = {14663145}, Pst = {ppublish}, Title = {Hypervirulent mutant of Mycobacterium tuberculosis resulting from disruption of the mce1 operon}, Volume = {100}, Year = {2003}, Bdsk-Url-1 = {http://dx.doi.org/10.1073/pnas.2433882100}} @article{Majlessi:2003dq, Abstract = {Here we describe the identification of a new CD8(+)-T-cell epitope, the GYAGTLQSL nonamer, shared by the TB10.3 and TB10.4 proteins of the Mycobacterium tuberculosis ESAT-6 family. Cytotoxic T cells from mycobacterium-infected mice efficiently recognized this epitope. GYAGTLQSL-specific T-cell hybridomas, which were able to recognize Mycobacterium bovis BCG-infected macrophages, were generated and now allow investigation of mycobacterial-antigen processing through the major histocompatibility complex class I pathway.}, Author = {Majlessi, Laleh and Rojas, Marie-J{\'e}sus and Brodin, Priscille and Leclerc, Claude}, Date-Added = {2010-03-02 11:32:37 +0100}, Date-Modified = {2010-03-02 11:32:37 +0100}, Journal = {Infect Immun}, Journal-Full = {Infection and immunity}, Mesh = {Amino Acid Sequence; Animals; Antigens, Bacterial; Bacterial Proteins; CD8-Positive T-Lymphocytes; Epitopes, T-Lymphocyte; Histocompatibility Antigens Class I; Hybridomas; Immunization; Macrophages; Mice; Mice, Inbred BALB C; Molecular Sequence Data; Mycobacterium bovis; Mycobacterium tuberculosis; T-Lymphocytes, Cytotoxic; Tuberculosis, Pulmonary}, Month = {Dec}, Number = {12}, Pages = {7173-7}, Pmc = {PMC308897}, Pmid = {14638811}, Pst = {ppublish}, Title = {CD8+-T-cell responses of Mycobacterium-infected mice to a newly identified major histocompatibility complex class I-restricted epitope shared by proteins of the ESAT-6 family}, Volume = {71}, Year = {2003}} @article{Casali:2002bh, Abstract = {The mce1A gene of Mycobacterium tuberculosis was initially identified by its ability to promote uptake of Escherichia coli into HeLa cells. It was subsequently shown that this activity was confined to a 58-amino-acid region of the protein. A 72-amino-acid fragment (InvX) incorporating this active peptide was expressed in E. coli as a fusion to the AIDA (adhesin involved in diffuse adherence) autotransporter translocator, and its stable expression on the surface of the bacterium was demonstrated. Recombinant E. coli expressing InvX-AIDA showed extensive association with HeLa cells, and InvX was shown to be sufficient for internalization. Uptake was found to be both microtubule and microfilament dependent and required the Rho family of GTPases. Thus, the E. coli AIDA system facilitated both the qualitative and quantitative analysis of the functional domain of a heterologous protein.}, Author = {Casali, Nicola and Konieczny, Marc and Schmidt, M Alexander and Riley, Lee W}, Date-Added = {2010-03-02 11:32:09 +0100}, Date-Modified = {2010-03-02 11:32:09 +0100}, Journal = {Infect Immun}, Journal-Full = {Infection and immunity}, Mesh = {Adhesins, Escherichia coli; Bacterial Adhesion; Bacterial Proteins; Escherichia coli; Hela Cells; Humans; Microscopy, Electron; Microscopy, Fluorescence; Mycobacterium tuberculosis; Peptides; Recombinant Fusion Proteins}, Month = {Dec}, Number = {12}, Pages = {6846-52}, Pmc = {PMC133103}, Pmid = {12438361}, Pst = {ppublish}, Title = {Invasion activity of a Mycobacterium tuberculosis peptide presented by the Escherichia coli AIDA autotransporter}, Volume = {70}, Year = {2002}} @article{Rodriguez:2002qf, 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.}, Author = {Rodriguez, G Marcela and Voskuil, Martin I and Gold, Benjamin and Schoolnik, Gary K and Smith, Issar}, Date-Added = {2010-03-02 11:31:47 +0100}, Date-Modified = {2010-03-02 11:31:47 +0100}, Journal = {Infect Immun}, Journal-Full = {Infection and immunity}, Mesh = {Bacterial Proteins; Gene Expression; Hydrogen Peroxide; Iron; Mycobacterium tuberculosis; Oxidative Stress; Repressor Proteins; Siderophores}, Month = {Jul}, Number = {7}, Pages = {3371-81}, Pmc = {PMC128082}, Pmid = {12065475}, Pst = {ppublish}, Title = {ideR, An essential gene in mycobacterium tuberculosis: role of IdeR in iron-dependent gene expression, iron metabolism, and oxidative stress response}, Volume = {70}, Year = {2002}} @article{Dubnau:2002ve, Abstract = {We identified Mycobacterium tuberculosis genes preferentially expressed during infection of human macrophages using a promoter trap adapted for this pathogen. inhA encodes an enoyl-acyl carrier protein reductase that is required for mycolic acid biosynthesis (A. Quemard et al., Biochemistry 34:8235-8241, 1995) and is a major target for isoniazid (INH) in mycobacterial species (A. Banerjee et al., Science 263:227-230, 1994). Since overexpression of inhA confers INH resistance in Mycobacterium smegmatis (Banerjee et al., Science 263:227-230, 1994), we designed a promoter trap based on this gene. A library of clones, containing small fragments of M. tuberculosis DNA cloned upstream of inhA in a plasmid vector, was electroporated into M. tuberculosis, and the resulting culture was used to infect the human monocytic THP-1 cell line. Selection was made for clones surviving INH treatment during infection but retaining INH sensitivity on plates. The DNA upstream of inhA was sequenced in each clone to identify the promoter driving inhA expression. Thirteen genes identified by this method were analyzed by quantitative reverse transcription-PCR (R. Manganelli et al., Mol. Microbiol. 31:715-724, 1999), and eight of them were found to be differentially expressed from cultures grown in macrophages compared with broth-grown cultures. Several of these genes are presumed to be involved in fatty acid metabolism; one potentially codes for a unique DNA binding protein, one codes for a possible potassium channel protein, and the others code for proteins of unknown function. Genes which are induced during infection are likely to be significant for survival and growth of the pathogen; our results lend support to the view that fatty acid metabolism is essential for the virulence of M. tuberculosis.}, Author = {Dubnau, Eugenie and Font{\'a}n, Patricia and Manganelli, Riccardo and Soares-Appel, Sonia and Smith, Issar}, Date-Added = {2010-03-02 11:31:22 +0100}, Date-Modified = {2010-03-02 11:31:22 +0100}, Journal = {Infect Immun}, Journal-Full = {Infection and immunity}, Mesh = {Bacterial Proteins; Cell Line; Cloning, Molecular; Gene Expression; Genes, Bacterial; Genetic Engineering; Humans; Macrophages; Mycobacterium tuberculosis; Oxidoreductases; Promoter Regions, Genetic; Reverse Transcriptase Polymerase Chain Reaction}, Month = {Jun}, Number = {6}, Pages = {2787-95}, Pmc = {PMC127980}, Pmid = {12010964}, Pst = {ppublish}, Title = {Mycobacterium tuberculosis genes induced during infection of human macrophages}, Volume = {70}, Year = {2002}} @article{Betts:2002ly, Abstract = {The search for new TB drugs that rapidly and effectively sterilize the tissues and are thus able to shorten the duration of chemotherapy from the current 6 months has been hampered by a lack of understanding of the metabolism of the bacterium when in a 'persistent' or latent form. Little is known about the condition in which the bacilli survive, although laboratory models have shown that Mycobacterium tuberculosis can exist in a non-growing, drug-resistant state that may mimic persistence in vivo. Using nutrient starvation, we have established a model in which M. tuberculosis arrests growth, decreases its respiration rate and is resistant to isoniazid, rifampicin and metronidazole. We have used microarray and proteome analysis to investigate the response of M. tuberculosis to nutrient starvation. Proteome analysis of 6-week-starved cultures revealed the induction of several proteins. Microarray analysis enabled us to monitor gene expression during adaptation to nutrient starvation and confirmed the changes seen at the protein level. This has provided evidence for slowdown of the transcription apparatus, energy metabolism, lipid biosynthesis and cell division in addition to induction of the stringent response and several other genes that may play a role in maintaining long-term survival within the host. Thus, we have generated a model with which we can search for agents active against persistent M. tuberculosis and revealed a number of potential targets expressed under these conditions.}, Author = {Betts, Joanna C and Lukey, Pauline T and Robb, Linda C and McAdam, Ruth A and Duncan, Ken}, Date-Added = {2010-03-02 11:31:04 +0100}, Date-Modified = {2010-03-02 11:31:04 +0100}, Journal = {Mol Microbiol}, Journal-Full = {Molecular microbiology}, Mesh = {Adaptation, Physiological; Bacterial Proteins; Cell Membrane; Electrophoresis, Gel, Two-Dimensional; Energy Metabolism; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Lipids; Models, Biological; Mycobacterium tuberculosis; Oligonucleotide Array Sequence Analysis; Oxygen; Protein Biosynthesis; RNA, Bacterial; Ribosomes; Rifampin; Transcription, Genetic}, Month = {Feb}, Number = {3}, Pages = {717-31}, Pmid = {11929527}, Pst = {ppublish}, Title = {Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling}, Volume = {43}, Year = {2002}} @article{Chitale:2001vn, Abstract = {The ability to gain entry and resist the antimicrobial intracellular environment of mammalian cells is an essential virulence property of Mycobacterium tuberculosis. A purified recombinant protein expressed by a 1362 bp locus (mce1) in the M. tuberculosis genome promoted uptake into HeLa cells of polystyrene latex microspheres coated with the protein. N-terminus deletion constructs of Mce1 identified a domain located between amino acid positions 106 and 163 that was needed for this cell uptake activity. Mce1 contained hydrophobic stretches at the N-terminus predictive of a signal sequence, and colloidal gold immunoelectron microscopy indicated that the corresponding native protein is expressed on the surface of the M. tuberculosis organism. The complete M. tuberculosis genome sequence revealed that it contained four homologues of mce (mce1, mce2, mce3, mce4) and that they were all located within operons composed of genes arranged similarly at different locations in the chromosome. Recombinant Mce2, which had the highest level of identity (67\%) to Mce1, was unable to promote the association of microspheres with HeLa cells. Although the exact function of Mce1 is still unknown, it appears to serve as an effector molecule expressed on the surface of M. tuberculosis that is capable of eliciting plasma membrane perturbations in non-phagocytic mammalian cells.}, Author = {Chitale, S and Ehrt, S and Kawamura, I and Fujimura, T and Shimono, N and Anand, N and Lu, S and Cohen-Gould, L and Riley, L W}, Date-Added = {2010-03-02 11:28:58 +0100}, Date-Modified = {2010-03-02 11:28:58 +0100}, Journal = {Cell Microbiol}, Journal-Full = {Cellular microbiology}, Mesh = {Antibodies, Bacterial; Bacterial Proteins; Cell Membrane; Escherichia coli; Genes, Bacterial; Hela Cells; Humans; Immunoblotting; Microscopy, Immunoelectron; Microspheres; Mycobacterium tuberculosis; Open Reading Frames; Operon; Recombinant Proteins}, Month = {Apr}, Number = {4}, Pages = {247-54}, Pmid = {11298648}, Pst = {ppublish}, Title = {Recombinant Mycobacterium tuberculosis protein associated with mammalian cell entry}, Volume = {3}, Year = {2001}} @article{Kawai:2000kx, Abstract = {An enzyme with both inorganic polyphosphate [poly(P)]- and ATP-dependent NAD kinase activities was isolated from Micrococcus flavus. The enzyme was a dimer consisting of 34 kDa subunits, and was named poly(P)/ATP-NAD kinase. Internal amino acid sequences of the enzyme showed homologies with some function-unknown proteins released on the GenBank database. Among such proteins, hypothetical Rv1695 protein (Accession No. Z98268-16), which was encoded by a gene named "Rv1695" on genomic DNA of Mycobacterium tuberculosis H37Rv, was proposed to be poly(P)-dependent NAD kinase. By cloning and expression in Escherichia coli, Rv1695 was shown to encode poly(P)/ATP-NAD kinase and named ppnk. The ppnk product, recombinant-poly(P)/ATP-NAD kinase (Ppnk) was purified and characterized. The enzyme was a tetramaer consisting of 35 kDa subunits when expressed in E. coli. Poly(P)/ATP-NAD kinases of M. flavus and Ppnk of M. tuberculosis H37Rv specifically and completely phosphorylated NAD by utilizing commercially available poly(P)s and nucleoside triphosphates as phosphoryl donors.}, Author = {Kawai, S and Mori, S and Mukai, T and Suzuki, S and Yamada, T and Hashimoto, W and Murata, K}, Date-Added = {2010-03-02 11:28:33 +0100}, Date-Modified = {2010-03-02 11:28:33 +0100}, Doi = {10.1006/bbrc.2000.3433}, Journal = {Biochem Biophys Res Commun}, Journal-Full = {Biochemical and biophysical research communications}, Mesh = {Amino Acid Sequence; Bacterial Proteins; Micrococcus; Molecular Sequence Data; Mycobacterium tuberculosis; Phosphotransferases (Alcohol Group Acceptor); Polyphosphates}, Month = {Sep}, Number = {1}, Pages = {57-63}, Pmid = {11006082}, Pst = {ppublish}, Title = {Inorganic Polyphosphate/ATP-NAD kinase of Micrococcus flavus and Mycobacterium tuberculosis H37Rv}, Volume = {276}, Year = {2000}, Bdsk-Url-1 = {http://dx.doi.org/10.1006/bbrc.2000.3433}} @article{Rindi:1999fk, Abstract = {An mRNA differential display (DD) assay was developed to compare gene expression between Mycobacterium tuberculosis H37Rv and its avirulent mutant H37Ra. The DD protocol made use of an oligo(dT) to prime reverse-transcriptase (RT)-dependent transcription of poly-A tailed mRNAs and a PCR amplification of the RT products by using ten 12-base arbitrary primers in all their pair combinations. This analysis yielded 745 and 708 bands, including 52 and 15 differentially generated bands, in the strains H37Rv and H37Ra, respectively. Six cDNAs that appeared to be expressed in H37Rv, but not in H37Ra, were reamplified and cloned and at least 10 inserts were sequenced for each cloned cDNA. After resolving discrepant results, 6 inserts were found highly homologous to M. tuberculosis H37Rv genes. Three of these, i.e., genes Rv2770c, Rv1345, and Rv0288, coding respectively for a member of the PPE protein family, a probable polyketide synthase, and a member of the protein family containing ESAT-6, have been predictively associated to immunological or pathogenetic aspects of M. tuberculosis infection; the other genes, i.e., Rv2336, Rv1320c, and Rv2819c, code for proteins with unknown functions. These results show that mRNA DD methodology can represent a potential tool for investigation of M. tuberculosis gene expression.}, Author = {Rindi, L and Lari, N and Garzelli, C}, Date-Added = {2010-03-02 11:26:01 +0100}, Date-Modified = {2010-03-02 11:26:01 +0100}, Doi = {10.1006/bbrc.1999.0591}, Journal = {Biochem Biophys Res Commun}, Journal-Full = {Biochemical and biophysical research communications}, Mesh = {Base Sequence; Cloning, Molecular; DNA Primers; Genes, Bacterial; Mycobacterium tuberculosis; RNA, Messenger; Virulence}, Month = {Apr}, Number = {1}, Pages = {94-101}, Pmid = {10222241}, Pst = {ppublish}, Title = {Search for genes potentially involved in Mycobacterium tuberculosis virulence by mRNA differential display}, Volume = {258}, Year = {1999}, Bdsk-Url-1 = {http://dx.doi.org/10.1006/bbrc.1999.0591}}