51
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An SQ, Lu GT, Su HZ, Li RF, He YQ, Jiang BL, Tang DJ, Tang JL. Systematic mutagenesis of all predicted gntR genes in Xanthomonas campestris pv. campestris reveals a GntR family transcriptional regulator controlling hypersensitive response and virulence. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2011; 24:1027-1039. [PMID: 21615202 DOI: 10.1094/mpmi-08-10-0180] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The GntR family is one of the most abundant and widely distributed groups of helix-turn-helix transcriptional regulators in bacteria. Six open reading frames in the genome of the plant pathogen Xanthomonas campestris pv. campestris were predicted to encode GntR regulators. All six of the predicted GntR-encoding genes were individually mutagenized and mutants from five of them were successfully obtained. Plant disease response assays revealed that one, whose product belongs to the YtrA subfamily and has been named HpaR1, is involved in the hypersensitive response (HR) and virulence. Electrophoretic mobility shift assays and in vitro transcription assays revealed that HpaR1 could repress its own transcription level through binding to its promoter sequence, indicating an autoregulatory feedback inhibition mechanism for HpaR1 expression. Promoter-gusA reporter and reverse-transcription polymerase chain reaction analyses revealed that HpaR1 positively and negatively affects the expression of HR and pathogenicity (hrp) genes in host plant and standard media, respectively. Constitutive expression of the key hrp regulator, hrpG, in the hpaR1 mutant could bypass the requirement of HpaR1 for the induction of wild-type HR, suggesting that HpaR1 regulates the expression of hrp genes that encode the type III secretion system via hrpG.
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GntR family regulators of the pathogen of fish tuberculosis Mycobacterium marinum. Biochem Biophys Res Commun 2011; 410:780-5. [PMID: 21703231 DOI: 10.1016/j.bbrc.2011.06.059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 06/08/2011] [Indexed: 11/24/2022]
Abstract
Mycobacterium marinum is a slow-growing pathogenic mycobacterium. It was first isolated by Aronson in 1926 from fish, fish mycobacteriosis or called fish tuberculosis is the common causative agent of bacterial disease in many species of freshwater and marine fish. M. marinum can infect wild fish, aquaculture and ornamental fish, and it has a close relative of the causative agent of human tuberculosis, Mycobacterium tuberculosis. The recently sequenced genome of M. marinum has been shown to contain several putative GntR regulators. This family named after gluconate regulator has a helix-turn-helix structure. Characterization of transcription regulators and their network is an important step towards the complete understanding of cellular physiology. The regulator of this family shares a similar and conserved N-terminal DNA-binding domain, but has a highly diverse C-terminal effector-binding and oligomerization domain. According to the heterogeneity, we classify the M. marinum GntR family to four subfamilies: FadR, HutC, MocR, and YtrA, and these regulators are encoded by 8, 3, 1 and 1 genes, respectively. Thus this study extends the annotation of M. marinum GntR family proteins, and can help to understand the pathogenic role of this family in M. marinum and facilitate future drug design against this pathogen.
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Genetic control of amadori product degradation in Bacillus subtilis via regulation of frlBONMD expression by FrlR. Appl Environ Microbiol 2011; 77:2839-46. [PMID: 21398478 DOI: 10.1128/aem.02515-10] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacillus subtilis is capable of degrading fructosamines. The phosphorylation and the cleavage of the resulting fructosamine 6-phosphates is catalyzed by the frlD and frlB gene products, respectively. This study addresses the physiological importance of the frlBONMD genes (formerly yurPONML), revealing the necessity of their expression for growth on fructosamines and focusing on the complex regulation of the corresponding transcription unit. In addition to the known regulation by the global transcriptional regulator CodY, the frl genes are repressed by the convergently transcribed FrlR (formerly YurK). The latter causes repression during growth on substrates other than fructosamines. Additionally, we identified in the first intergenic region of the operon an FrlR binding site which is centrally located within a 38-bp perfect palindromic sequence. There is genetic evidence that this sequence, in combination with FrlR, contributes to the remarkable decrease in the transcription downstream of the first gene of the frl operon.
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54
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Mammalian cell entry gene family of Mycobacterium tuberculosis. Mol Cell Biochem 2011; 352:1-10. [PMID: 21258845 DOI: 10.1007/s11010-011-0733-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 01/10/2011] [Indexed: 01/21/2023]
Abstract
Knowledge of virulence factors is important to understand the microbial pathogenesis and find better antibiotics. Mammalian cell entry (mce) is a crucial protein family for the virulence of Mycobacterium tuberculosis (M. tuberculosis). This review summarized the advances on mce genes. The genomic organization, characteristics of mce genes, phylogeny of this family, and their roles in M. tuberculosis virulence are emphasized in this review.
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55
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Genome-wide identification of Mycobacterium tuberculosis exported proteins with roles in intracellular growth. J Bacteriol 2010; 193:854-61. [PMID: 21148733 DOI: 10.1128/jb.01271-10] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The exported proteins of Mycobacterium tuberculosis that are localized at the bacterial cell surface or secreted into the environment are ideally situated to interact with host factors and to function in virulence. In this study, we constructed a novel β-lactamase reporter transposon and used it directly in M. tuberculosis for genome-wide identification of exported proteins. From 177 β-lactam-resistant transposon mutants, we identified 111 different exported proteins. The majority of these proteins have no known function, and for nearly half of the proteins, our demonstration that they are exported when fused to a β-lactamase reporter is the first experimental proof of their extracytoplasmic localization. The transposon mutants in our banked library were of further value as a collection of mutants lacking individual exported proteins. By individually testing each of 111 mutants for growth in macrophages, six attenuated mutants with insertions in mce1A, mce1B, mce2F, rv0199, ctaC, and lppX were identified. Given that much of the M. tuberculosis genome encodes proteins of unknown function, our library of mapped transposon mutants is a valuable resource for efforts in functional genomics. This work also demonstrates the power of a β-lactamase reporter transposon that could be applied similarly to other bacterial pathogens.
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56
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Cheigh CI, Senaratne R, Uchida Y, Casali N, Kendall LV, Riley LW. Posttreatment reactivation of tuberculosis in mice caused by Mycobacterium tuberculosis disrupted in mce1R. J Infect Dis 2010; 202:752-9. [PMID: 20629532 DOI: 10.1086/655224] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND The reactivation of tuberculosis arises in persons who are latently infected and in those who have been previously treated. The mechanism of the reactivation of tuberculosis in either situation is not well understood. A 13-gene mce1 operon of Mycobacterium tuberculosis was previously shown to be associated with latent infection in mice and may also play a role in reactivation. METHODS We tested mce1 operon M. tuberculosis mutants in a Cornell mouse model to examine disease progression and reactivation. RESULTS In BALB/c mice, the wild-type, mce1 operon mutant, and mce1R (negative transcriptional regulator of the mce1 operon) mutant M. tuberculosis strains were equally susceptible to orally administered isoniazid and pyrazinamide. However, after cessation of the treatment, the mce1R mutant rapidly and progressively proliferated in mouse lungs and spleens, whereas the other strains remained latent. The reactivation of the mce1R mutant was associated with disease progression in the mouse lungs. CONCLUSION This observation demonstrates that the constitutive expression of the mce1 genes by M. tuberculosis in the latent state can cause a reactivation of tuberculosis. The constitutive expression of the mce1 genes in the mce1R mutant may allow this mutant to maintain its lipid metabolism, enabling it to survive long-term and proliferate inside granulomas.
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Affiliation(s)
- Chan-Ick Cheigh
- Division of Infectious Diseases, School of Public Health, University of California-Berkeley, CA 94720, USA
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Ignatov D, Skvortsov T, Majorov K, Apt A, Azhikina T. Adaptive Changes in Mycobacterium avium Gene Expression Profile Following Infection of Genetically Susceptible and Resistant Mice. Acta Naturae 2010; 2:78-83. [PMID: 22649654 PMCID: PMC3347564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
We performed a comparative analysis ofMycobacterium aviumtranscriptomes (strain 724R) in infected mice of two different strains- resistant and susceptible to infection. Sets of mycobacterial genes transcribed in lung tissue were defined, and differentially transcribed genes were revealed. Our results indicate thatM. aviumgenes coding for enzymes of the Krebs cycle, oxidative phosphorylation, NO reduction, fatty acid biosynthesis, replication, translation, and genome modification are expressed at high levels in the lungs of genetically susceptible mice. The expression of genes responsible for cell wall properties, anaerobic nitrate respiration, fatty acid degradation, synthesis of polycyclic fatty acid derivatives, and biosynthesis of mycobactin and other polyketides is increased in the resistant mice. In the resistant host environment,Mycobacterium aviumapparently transitions to a latent state caused by the deficiency in divalent cations and characterised by anaerobic respiration, degradation of fatty acids, and modification of cell wall properties.
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Affiliation(s)
- D.V. Ignatov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences
| | - T.A. Skvortsov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences
| | - K.B. Majorov
- Central Research Institute for Tuberculosis, Russian Academy of Medical Sciences
| | - A.S. Apt
- Central Research Institute for Tuberculosis, Russian Academy of Medical Sciences
| | - T.L. Azhikina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences
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Vizcaíno C, Restrepo-Montoya D, Rodríguez D, Niño LF, Ocampo M, Vanegas M, Reguero MT, Martínez NL, Patarroyo ME, Patarroyo MA. Computational prediction and experimental assessment of secreted/surface proteins from Mycobacterium tuberculosis H37Rv. PLoS Comput Biol 2010; 6:e1000824. [PMID: 20585611 PMCID: PMC2891697 DOI: 10.1371/journal.pcbi.1000824] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Accepted: 05/19/2010] [Indexed: 11/19/2022] Open
Abstract
The mycobacterial cell envelope has been implicated in the pathogenicity of tuberculosis and therefore has been a prime target for the identification and characterization of surface proteins with potential application in drug and vaccine development. In this study, the genome of Mycobacterium tuberculosis H37Rv was screened using Machine Learning tools that included feature-based predictors, general localizers and transmembrane topology predictors to identify proteins that are potentially secreted to the surface of M. tuberculosis, or to the extracellular milieu through different secretory pathways. The subcellular localization of a set of 8 hypothetically secreted/surface candidate proteins was experimentally assessed by cellular fractionation and immunoelectron microscopy (IEM) to determine the reliability of the computational methodology proposed here, using 4 secreted/surface proteins with experimental confirmation as positive controls and 2 cytoplasmic proteins as negative controls. Subcellular fractionation and IEM studies provided evidence that the candidate proteins Rv0403c, Rv3630, Rv1022, Rv0835, Rv0361 and Rv0178 are secreted either to the mycobacterial surface or to the extracellular milieu. Surface localization was also confirmed for the positive controls, whereas negative controls were located on the cytoplasm. Based on statistical learning methods, we obtained computational subcellular localization predictions that were experimentally assessed and allowed us to construct a computational protocol with experimental support that allowed us to identify a new set of secreted/surface proteins as potential vaccine candidates. Since the publication of the Mycobacterium tuberculosis genome in 1998, great expectations have emerged regarding speeding up the process of developing vaccines against tuberculosis. Our group has been focused on identifying molecules localized on the mycobacterial surface that could act as ligands facilitating this pathogen's entry into host cells. Immune responses exerted against these proteins might block receptor-ligand interactions, thus hampering mycobacterial invasion. Since protein fragments involved in these interactions might serve as vaccine candidates and, taking into account that a relatively small number of mycobacterial surface proteins have been experimentally identified to date due to the inherent difficulty of proteomics studies for characterizing surface proteins, in this study, we used Machine Learning-based tools available on the World Wide Web to obtain accurate predictions of surface and secreted proteins from this pathogen and found experimental support of such predictions for a group of candidate proteins selected based on novel criteria.
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Affiliation(s)
- Carolina Vizcaíno
- Fundación Instituto de Inmunología de Colombia – FIDIC, Bogotá, Colombia
- Microbiology postgraduate program, Universidad Nacional de Colombia, Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Daniel Restrepo-Montoya
- Fundación Instituto de Inmunología de Colombia – FIDIC, Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
- Intelligent Systems Research Laboratory – LISI, Universidad Nacional de Colombia, Bogotá, Colombia
- Research Group on Combinatorial Algorithms – ALGOS-UN, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Diana Rodríguez
- Fundación Instituto de Inmunología de Colombia – FIDIC, Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Luis F. Niño
- Intelligent Systems Research Laboratory – LISI, Universidad Nacional de Colombia, Bogotá, Colombia
- Research Group on Combinatorial Algorithms – ALGOS-UN, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Marisol Ocampo
- Fundación Instituto de Inmunología de Colombia – FIDIC, Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Magnolia Vanegas
- Fundación Instituto de Inmunología de Colombia – FIDIC, Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - María T. Reguero
- Instituto de Biotecnología – IBUN, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Nora L. Martínez
- Fundación Instituto de Inmunología de Colombia – FIDIC, Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Manuel E. Patarroyo
- Fundación Instituto de Inmunología de Colombia – FIDIC, Bogotá, Colombia
- School of Medicine, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Manuel A. Patarroyo
- Fundación Instituto de Inmunología de Colombia – FIDIC, Bogotá, Colombia
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
- * E-mail:
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Joon M, Bhatia S, Pasricha R, Bose M, Brahmachari V. Functional analysis of an intergenic non-coding sequence within mce1 operon of M.tuberculosis. BMC Microbiol 2010; 10:128. [PMID: 20420720 PMCID: PMC2867952 DOI: 10.1186/1471-2180-10-128] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 04/27/2010] [Indexed: 11/29/2022] Open
Abstract
Background The mce operons play an important role in the entry of M. tuberculosis into macrophages and non-phagocytic cells. Their non-redundant function as well as complex regulation is implied by the phenotype of mce mutants. Recently, mce1 operon was found to extend over 13 genes, fadD5 (Rv0166) being the first gene of the operon. The presence of a non-coding sequence of 200 base pairs between Rv0166 and Rv0167 is peculiar to mce1 among the four mce operons of M.tuberculosis. We have examined the function of this region. Results We predicted putative promoter activity of the 200 base pairs of non-coding, intergenic region between Rv0166 and Rv0167 in silico using MEME software and designate it as intergenic promoter, IGPr. We demonstrate both promoter activity and a putative negative regulatory function of this fragment by reporter assays carried out in the surrogate host M.smegmatis. We find that the repressive elements not only control the native promoter but also repress a heterologous promoter of M.smegmatis. The higher activity of the intergenic promoter in a clinical isolate in comparison with the wild type sequence from M.tuberculosis H37Rv could be correlated with a point mutation within the negative element. We have mapped two transcription start sites for mce1 operon both of which are utilized in M.tuberculosis H37Rv as well as the clinical isolate VPCI591. Our studies show that the promoter activity in the non-coding region is relevant not only in reporter gene expression but also in the expression of mce1 operon in M. tuberculosis cells grown in synthetic medium. Conclusion The mce operon of M.tuberculosis H37Rv potentially can be transcribed from two promoters P1 and P2, former mapping upstream of Rv0166 and the latter in the non-coding intergenic region between Rv0166 and Rv0167. The transcription initiation from P1 results in a transcript with Rv0166 while that from P2 will be without it. The sequences between the translation start site of Rv0167 and the promoter P2 have a negative regulatory role, as point mutation within the sequence leads to enhanced activity of P2 as well as a heterologous promoter from M.smegmatis. The mutation detected in the clinical isolate VPCI591 therefore behaves like a gain-of-function mutation.
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Affiliation(s)
- Monika Joon
- Dr B R Ambedkar Centre for Biomedical Research, University of Delhi, Delhi-110007, India
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60
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Dunphy KY, Senaratne RH, Masuzawa M, Kendall LV, Riley LW. Attenuation of Mycobacterium tuberculosis functionally disrupted in a fatty acyl-coenzyme A synthetase gene fadD5. J Infect Dis 2010; 201:1232-9. [PMID: 20214478 DOI: 10.1086/651452] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
One key adaptation that Mycobacterium tuberculosis established to survive long term in vivo is a reliance on lipids as an energy source. M. tuberculosis H37Rv has 36 fadD genes annotated as putative fatty acyl-coenzyme A (CoA) synthetase genes, which encode enzymes that activate fatty acids for metabolism. One such gene, fadD5 (Rv0166), is located within the mce1 operon, a cluster of genes associated with M. tuberculosis persistence. We disrupted the putative fatty acid-binding site of fadD5 in H37Rv M. tuberculosis. No significant differences were found in the growth of the mutant and wild-type strains in vitro in nutrient-rich broth or in activated RAW264.7 cells. However, the fadD5 mutant was diminished in growth in minimal medium containing mycolic acid but not other long-chain fatty acids. C57BL/6 mice infected with the fadD5 mutant survived significantly longer than those infected with the wild type, and the mutant never attained the plateau phase of infection in mouse lungs. Infection in the steady-state phase was maintained for up to 168 days at a level that was 1-2 logs less than that noted in the wild type. These observations raise the rather intriguing possibility that FadD5 may serve to recycle mycolic acids for the long-term survival of the tubercle bacilli.
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Affiliation(s)
- Kathleen Y Dunphy
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720, USA
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61
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Rajagopalan M, Dziedzic R, Al Zayer M, Stankowska D, Ouimet MC, Bastedo DP, Marczynski GT, Madiraju MV. Mycobacterium tuberculosis origin of replication and the promoter for immunodominant secreted antigen 85B are the targets of MtrA, the essential response regulator. J Biol Chem 2010; 285:15816-27. [PMID: 20223818 DOI: 10.1074/jbc.m109.040097] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Efficient proliferation of Mycobacterium tuberculosis (Mtb) inside macrophage requires that the essential response regulator MtrA be optimally phosphorylated. However, the genomic targets of MtrA have not been identified. We show by chromatin immunoprecipitation and DNase I footprinting that the chromosomal origin of replication, oriC, and the promoter for the major secreted immunodominant antigen Ag85B, encoded by fbpB, are MtrA targets. DNase I footprinting analysis revealed that MtrA recognizes two direct repeats of GTCACAgcg-like sequences and that MtrA approximately P, the phosphorylated form of MtrA, binds preferentially to these targets. The oriC contains several MtrA motifs, and replacement of all motifs or of a single select motif with TATATA compromises the ability of oriC plasmids to maintain stable autonomous replication in wild type and MtrA-overproducing strains, indicating that the integrity of the MtrA motif is necessary for oriC replication. The expression of the fbpB gene is found to be down-regulated in Mtb cells upon infection when these cells overproduce wild type MtrA but not when they overproduce a nonphosphorylated MtrA, indicating that MtrA approximately P regulates fbpB expression. We propose that MtrA is a regulator of oriC replication and that the ability of MtrA to affect apparently unrelated targets, i.e. oriC and fbpB, reflects its main role as a coordinator between the proliferative and pathogenic functions of Mtb.
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Affiliation(s)
- Malini Rajagopalan
- Biomedical Research, University of Texas Health Science Center, Tyler, Texas 75708-3154, USA
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62
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Riley LW. Regulation of Mycobacterium tuberculosis cell wall lipid composition and its effects on in vitro bacterial persistence. REVISTA PORTUGUESA DE PNEUMOLOGIA 2010; 16SA:S37-42. [PMID: 25965928 DOI: 10.1016/s0873-2159(15)30091-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Lee W Riley
- MD, School of Public Health, University of California, Berkeley.
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63
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Marjanovic O, Miyata T, Goodridge A, Kendall LV, Riley LW. Mce2 operon mutant strain of Mycobacterium tuberculosis is attenuated in C57BL/6 mice. Tuberculosis (Edinb) 2009; 90:50-6. [PMID: 19963438 DOI: 10.1016/j.tube.2009.10.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2009] [Revised: 10/14/2009] [Accepted: 10/15/2009] [Indexed: 11/18/2022]
Abstract
Mycobacterium tuberculosis genome contains four related sets of an operon called mce (mce1-4). The disruption of one of these operons, mce1, causes M. tuberculosis to become hypervirulent, whereas the mce3 and mce4 operon mutants are attenuated in mice. This study examined the phenotype of the mce2 operon mutant. The deletion of mce2 operon in M. tuberculosis H37Rv had no effect on bacterial growth in 7H9 liquid broth or survival within macrophages. However, RAW macrophage-like cells infected with the mutant strain were reduced in their ability to produce TNF-alpha, IL-6 and MCP-1. In C57BL/6 mouse lungs, the mce2 operon mutant and wild type H37Rv replicated similarly up to 20 weeks of infection. However, by 56 weeks of infection, all mice infected with the wild type H37Rv had died, while 80% of those infected with the mutant remained alive (P<0.0001). The proportion of affected lung parenchyma in mice infected with the mutant was substantially less than that of mice infected with the wild type for the same time periods of infection. These observations suggest that the mce2 operon mutant is attenuated, and that this attenuation is related not to the bacterial burden but to the mutant's decreased ability to elicit a type of immune response and lung pathology detrimental to the survival of the animal.
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Affiliation(s)
- Olivera Marjanovic
- School of Public Health, University of California, Berkeley, CA 94720, USA
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64
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Li G, Che D, Xu Y. A universal operon predictor for prokaryotic genomes. J Bioinform Comput Biol 2009; 7:19-38. [PMID: 19226658 DOI: 10.1142/s0219720009003984] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 02/21/2008] [Accepted: 04/22/2008] [Indexed: 11/18/2022]
Abstract
Identification of operons at the genome scale of prokaryotic organisms represents a key step in deciphering of their transcriptional regulation machinery, biological pathways, and networks. While numerous computational methods have been shown to be effective in predicting operons for well-studied organisms such as Escherichia coli K12 and Bacillus subtilis 168, these methods generally do not generalize well to genomes other than the ones used to train the methods, or closely related genomes because they rely on organism-specific information. Several methods have been explored to address this problem through utilizing only genomic structural information conserved across multiple organisms, but they all suffer from the issue of low prediction sensitivity. In this paper, we report a novel operon prediction method that is applicable to any prokaryotic genome with high prediction accuracy. The key idea of the method is to predict operons through identification of conserved gene clusters across multiple genomes and through deriving a key parameter relevant to the distribution of intergenic distances in genomes. We have implemented this method using a graph-theoretic approach, to calculate a set of maximum gene clusters in the target genome that are conserved across multiple reference genomes. Our computational results have shown that this method has higher prediction sensitivity as well as specificity than most of the published methods. We have carried out a preliminary study on operons unique to archaea and bacteria, respectively, and derived a number of interesting new insights about operons between these two kingdoms. The software and predicted operons of 365 prokaryotic genomes are available at http://csbl.bmb.uga.edu/~dongsheng/UNIPOP.
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Affiliation(s)
- Guojun Li
- CSBL, Department of Biochemistry and Molecular Biology, Department of Computer Science, University of Georgia, Athens, GA 30602, USA.
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Hoskisson PA, Rigali S. Chapter 1 Variation in Form and Function. ADVANCES IN APPLIED MICROBIOLOGY 2009; 69:1-22. [DOI: 10.1016/s0065-2164(09)69001-8] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Santangelo MDLP, Blanco F, Campos E, Soria M, Bianco MV, Klepp L, Alito A, Zabal O, Cataldi A, Bigi F. Mce2R from Mycobacterium tuberculosis represses the expression of the mce2 operon. Tuberculosis (Edinb) 2008; 89:22-8. [PMID: 19027363 DOI: 10.1016/j.tube.2008.09.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Revised: 08/23/2008] [Accepted: 09/24/2008] [Indexed: 11/25/2022]
Abstract
The mce2 operon is one of the four mce operons present in Mycobacterium tuberculosis that encode exported proteins with a probable role in the virulence mechanisms of this bacterium. In the present study we demonstrated that Rv0586, which encodes a putative GntR-like regulator, is part of the mce2 operon. By using a promoter-lacZ fusion approach and bioinformatics tools, we found that Rv0586 represses the expression of Mce2 proteins and of a putative endonuclease IV, encoded by end (Rv0670) gene. For this reason, we have re-named the repressor protein Mce2R. By gel-shift experiments Mce2R binding was determined to be located within the mce2 promoter region. In addition, two FadR-like operator motifs were identified within the promoter regions of both the mce2 operon and the end gene. These motifs overlap putative -10 and -35 promoter boxes. M. tuberculosis carrying mce2 and end promoter-lacZ fusions were used to infect J774 macrophage-like cells. Expression of beta-galactosidase was induced after phagocytocis, suggesting that some cellular factor could be a key component of the molecular switch regulation expression of the mce2 operon. In conclusion, these results add novel evidence of the complex regulation of mce operon expression.
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ten Bokum AMC, Movahedzadeh F, Frita R, Bancroft GJ, Stoker NG. The case for hypervirulence through gene deletion in Mycobacterium tuberculosis. Trends Microbiol 2008; 16:436-41. [PMID: 18701293 DOI: 10.1016/j.tim.2008.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Revised: 06/06/2008] [Accepted: 06/18/2008] [Indexed: 10/21/2022]
Abstract
Deletion of genes in a pathogen is commonly associated with a reduction in its ability to cause disease. However, some rare cases have been described in the literature whereby deletion of a gene results in an increase in virulence. Recently, there have been several reports of hypervirulence resulting from gene deletion in Mycobacterium tuberculosis. Here, we explore this phenomenon in the context of the interaction between the pathogen and the host response.
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Affiliation(s)
- Annemieke M C ten Bokum
- Department of Pathology and Infectious Diseases, Royal Veterinary College, Royal College Street, London, NW1 0TU, UK
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The GntR-type regulators gtrA and gtrB affect cell growth and nodulation of Sinorhizobium meliloti. J Microbiol 2008; 46:137-45. [PMID: 18545962 DOI: 10.1007/s12275-007-0145-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2007] [Accepted: 01/23/2008] [Indexed: 10/22/2022]
Abstract
GntR-type transcriptional regulators are involved in the regulation of various biological processes in bacteria, but little is known about their functions in Sinorhizobium meliloti. Here, we identified two GntR-type transcriptional regulator genes, gtrA and gtrB, from S. meliloti strain 1021. Both the gtrA1 mutant and the gtrB1 mutant had lower growth rates and maximal cell yields on rich and minimal media, as well as lower cell motility on swimming plates, than did the wild-type strain. Both mutants were also symbiotically deficient. Alfalfa plants inoculated with wild-type strain 1021 formed pink elongated nodules on primary roots. In contrast, the plants inoculated with the gtrA1 and gtrB1 mutants formed relatively smaller, round, light pink nodules mainly on lateral roots. During the first 3 approximately 4 weeks post-inoculation, the plants inoculated with the gtrA1 and gtrB1 mutants were apparently stunted, with lower levels of nitrogenase activity, but there was a remarkable increase in the number of nodules compared to those inoculated with the wild-type strain. Moreover, the gtrA1 and gtrB1 mutants not only showed delayed nodulation, but also showed markedly reduced nodulation competition. These results demonstrated that both GtrA and GtrB affect cell growth and effective symbiosis of S. meliloti. Our work provides new insight into the functions of GntR-like transcriptional regulators.
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69
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Senaratne RH, Sidders B, Sequeira P, Saunders G, Dunphy K, Marjanovic O, Reader JR, Lima P, Chan S, Kendall S, McFadden J, Riley LW. Mycobacterium tuberculosis strains disrupted in mce3 and mce4 operons are attenuated in mice. J Med Microbiol 2008; 57:164-170. [PMID: 18201981 DOI: 10.1099/jmm.0.47454-0] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The Mycobacterium tuberculosis genome contains four copies of an operon called mce (mce1-4). Previously we reported that M. tuberculosis disrupted in the mce1 operon is more virulent than wild-type M. tuberculosis in mice. We generated single deletion mutants in mce3 (Deltamce3) and mce4 (Deltamce4) operons and a double deletion mutant (Deltamce3/4). Similar doubling times and growth characteristics were observed for all mutants and the wild-type (parent) M. tuberculosis H37Rv strain in culture and in macrophages. In addition, similar bacterial burdens were detected in organs from mice infected with Deltamce3 and the parent strain. However, the bacterial burdens of mice infected with Deltamce4 and Deltamce 3/4 were less than those of mice infected with the parent strain. The median survival times of mice infected with wild-type M. tuberculosis, Deltamce3, Deltamce4 and Deltamce3/4 were 40.5, 46, 58 and 62 weeks, respectively. Histopathological examination of lungs at 15 weeks post-infection showed that the extent of the lung lesions was less prominent in mice infected with Deltamce4 and Deltamce 3/4 mutants than in mice infected with the other two strains. These observations suggest that the mce3 and mce4 operons have a role distinct from that of mce1 for in vivo survival of M. tuberculosis.
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Affiliation(s)
- Ryan H Senaratne
- School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Ben Sidders
- School of Biomedical and Molecular Sciences, University of Surrey, Guildford GU2 7XH, UK.,Department of Pathology and Infectious Disease, Royal Veterinary College, Royal College Street, London NW1 0TU, UK.,School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Patricia Sequeira
- School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Grainne Saunders
- School of Biomedical and Molecular Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Kathleen Dunphy
- School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Olivera Marjanovic
- School of Public Health, University of California, Berkeley, CA 94720, USA
| | - J Rachel Reader
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Patricia Lima
- School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Stephen Chan
- School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Sharon Kendall
- Department of Pathology and Infectious Disease, Royal Veterinary College, Royal College Street, London NW1 0TU, UK
| | - Johnjoe McFadden
- School of Biomedical and Molecular Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Lee W Riley
- School of Public Health, University of California, Berkeley, CA 94720, USA
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70
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Vindal V, Ashwantha Kumar E, Ranjan A. Identification of operator sites within the upstream region of the putativemce2Rgene from mycobacteria. FEBS Lett 2008; 582:1117-22. [DOI: 10.1016/j.febslet.2008.02.074] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Revised: 02/26/2008] [Accepted: 02/29/2008] [Indexed: 10/22/2022]
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71
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Study of the role of Mce3R on the transcription of mce genes of Mycobacterium tuberculosis. BMC Microbiol 2008; 8:38. [PMID: 18304349 PMCID: PMC2277422 DOI: 10.1186/1471-2180-8-38] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Accepted: 02/27/2008] [Indexed: 11/10/2022] Open
Abstract
Background mce3 is one of the four virulence-related mce operons of Mycobacterium tuberculosis. In a previous work we showed that the overexpression of Mce3R in Mycobacterium smegmatis and M. tuberculosis abolishes the expression of lacZ fused to the mce3 promoter, indicating that Mce3R represses mce3 transcription. Results We obtained a knockout mutant strain of M. tuberculosis H37Rv by inserting a hygromycin cassette into the mce3R gene. The mutation results in a significant increase in the expression of mce3 genes either in vitro or in a murine cell macrophages line as it was determined using promoter-lacZ fusions in M. tuberculosis. The abundance of mce1, mce2 and mce4 mRNAs was not affected by this mutation as it was demonstrated by quantitative RT-PCR. The mce3R promoter activity in the presence of Mce3R was significantly reduced compared with that in the absence of the regulator, during the in vitro culture of M. tuberculosis. Conclusion Mce3R repress the transcription of mce3 operon and self regulates its own expression but does not affect the transcription of mce1, mce2 and mce4 operons of M. tuberculosis.
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Yu A, Chen A, Wang Y, Luo L, Zhu J, Yu G, Wang Y. Systematic insertion mutagenesis of GntR family transcriptional regulator genes in Sinorhizobium meliloti. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/s11434-008-0017-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Vindal V, Suma K, Ranjan A. GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization. BMC Genomics 2007; 8:289. [PMID: 17714599 PMCID: PMC2018728 DOI: 10.1186/1471-2164-8-289] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Accepted: 08/23/2007] [Indexed: 11/24/2022] Open
Abstract
Background Mycobacterium smegmatis is fast growing non-pathogenic mycobacteria. This organism has been widely used as a model organism to study the biology of other virulent and extremely slow growing species like Mycobacterium tuberculosis. Based on the homology of the N-terminal DNA binding domain, the recently sequenced genome of M. smegmatis has been shown to possess several putative GntR regulators. A striking characteristic feature of this family of regulators is that they possess a conserved N-terminal DNA binding domain and a diverse C-terminal domain involved in the effector binding and/or oligomerization. Since the physiological role of these regulators is critically dependent upon effector binding and operator sites, we have analysed and classified these regulators into their specific subfamilies and identified their potential binding sites. Results The sequence analysis of M. smegmatis putative GntRs has revealed that FadR, HutC, MocR and the YtrA-like regulators are encoded by 45, 8, 8 and 1 genes respectively. Further out of 45 FadR-like regulators, 19 were classified into the FadR group and 26 into the VanR group. All these proteins showed similar secondary structural elements specific to their respective subfamilies except MSMEG_3959, which showed additional secondary structural elements. Using the reciprocal BLAST searches, we further identified the orthologs of these regulators in Bacillus subtilis and other mycobacteria. Since the expression of many regulators is auto-regulatory, we have identified potential operator sites for a number of these GntR regulators by analyzing the upstream sequences. Conclusion This study helps in extending the annotation of M. smegmatis GntR proteins. It identifies the GntR regulators of M. smegmatis that could serve as a model for studying orthologous regulators from virulent as well as other saprophytic mycobacteria. This study also sheds some light on the nucleotide preferences in the target-motifs of GntRs thus providing important leads for initiating the experimental characterization of these proteins, construction of the gene regulatory network for these regulators and an understanding of the influence of these proteins on the physiology of the mycobacteria.
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Affiliation(s)
- Vaibhav Vindal
- Computational and Functional Genomics Group, Sun Centre of Excellence in Medical Bioinformatics, Centre for DNA Fingerprinting and Diagnostics, EMBnet India Node, Hyderabad 500076, India
| | - Katta Suma
- Computational and Functional Genomics Group, Sun Centre of Excellence in Medical Bioinformatics, Centre for DNA Fingerprinting and Diagnostics, EMBnet India Node, Hyderabad 500076, India
| | - Akash Ranjan
- Computational and Functional Genomics Group, Sun Centre of Excellence in Medical Bioinformatics, Centre for DNA Fingerprinting and Diagnostics, EMBnet India Node, Hyderabad 500076, India
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74
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Roback P, Beard J, Baumann D, Gille C, Henry K, Krohn S, Wiste H, Voskuil M, Rainville C, Rutherford R. A predicted operon map for Mycobacterium tuberculosis. Nucleic Acids Res 2007; 35:5085-95. [PMID: 17652327 PMCID: PMC1976454 DOI: 10.1093/nar/gkm518] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The prediction of operons in Mycobacterium tuberculosis (MTB) is a first step toward understanding the regulatory network of this pathogen. Here we apply a statistical model using logistic regression to predict operons in MTB. As predictors, our model incorporates intergenic distance and the correlation of gene expression calculated for adjacent gene pairs from over 474 microarray experiments with MTB RNA. We validate our findings with known examples from the literature and experimentation. From this model, we rank each potential operon pair by the strength of evidence for cotranscription, choose a classification threshold with a true positive rate of over 90% at a false positive rate of 9.1%, and use it to construct an operon map for the MTB genome.
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Affiliation(s)
- P. Roback
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - J. Beard
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - D. Baumann
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - C. Gille
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - K. Henry
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - S. Krohn
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - H. Wiste
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - M.I. Voskuil
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - C. Rainville
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
| | - R. Rutherford
- Department of Mathematics, Statistics and Computer Science, Center for Interdisciplinary Research and Department of Biology St. Olaf College, Northfield MN 55057, Department of Microbiology, University of Colorado Health Sciences Center, Aurora, CO 80045 and Department of Biology, Seattle University, 901 12th Ave, Seattle, WA 98052, USA
- *To whom correspondence should be addressed.+1 206 296 2501+1 206 296 5634
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Waddell SJ, Butcher PD. Microarray analysis of whole genome expression of intracellular Mycobacterium tuberculosis. Curr Mol Med 2007; 7:287-96. [PMID: 17504113 PMCID: PMC3123378 DOI: 10.2174/156652407780598548] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Analysis of the changing mRNA expression profile of Mycobacterium tuberculosis though the course of infection promises to advance our understanding of how mycobacteria are able to survive the host immune response. The difficulties of sample extraction from distinct mycobacterial populations, and of measuring mRNA expression profiles of multiple genes has limited the impact of gene expression studies on our interpretation of this dynamic infection process. The development of whole genome microarray technology together with advances in sample collection have allowed the expression pattern of the whole M. tuberculosis genome to be compared across a number of different in vitro conditions, murine and human tissue culture models and in vivo infection samples. This review attempts to produce a summative model of the M. tuberculosis response to infection derived from or reflected in these gene expression datasets. The mycobacterial response to the intracellular environment is characterised by the utilisation of lipids as a carbon source and the switch from aerobic/microaerophilic to anaerobic respiratory pathways. Other genes induced in the macrophage phagosome include those likely to be involved in the maintenance of the cell wall and genes related to DNA damage, heat shock, iron sequestration and nutrient limitation. The comparison of transcriptional data from in vitro models of infection with complex in vivo samples, together with the use of bacterial RNA amplification strategies to sample defined populations of bacilli, should allow us to make conclusions about M. tuberculosis physiology and host microenvironments during natural infection.
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Affiliation(s)
- Simon J Waddell
- Medical Microbiology, Division of Cellular & Molecular Medicine, St. George's University of London, Cranmer Terrace, Tooting, London, SW17 0RE, UK.
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76
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Lima P, Sidders B, Morici L, Reader R, Senaratne R, Casali N, Riley LW. Enhanced mortality despite control of lung infection in mice aerogenically infected with a Mycobacterium tuberculosis mce1 operon mutant. Microbes Infect 2007; 9:1285-90. [PMID: 17890119 PMCID: PMC2894154 DOI: 10.1016/j.micinf.2007.05.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2007] [Revised: 05/07/2007] [Accepted: 05/30/2007] [Indexed: 01/21/2023]
Abstract
Mycobacterium tuberculosis causes a variety of host clinical outcomes. We previously showed that M. tuberculosis disrupted in an operon called mce1 proliferates unchecked in BALB/c mouse lungs. The observed outcome could be attributed either to the mutant bacterial burden or to the host immunopathologic response. To differentiate these possibilities, we studied the outcomes of infection in a mouse strain (C57BL/6) less susceptible to M. tuberculosis than BALB/c. We found that the mutant infection reached a plateau in the lungs at a rate similar to that of the wild type. All mice infected with the mutant, but only half of the groups of mice infected with the wild type or complemented strain, died by 40 weeks (p<0.05). At 12-21 weeks of infection, histological examination of the lungs of mice infected with the mutant showed a diffuse pattern of lymphocyte infiltration, while that of mice infected with the other strains exhibited a nodular cellular infiltration pattern. Surprisingly, the number of bacilli recovered from the lungs was similar in all three groups. These observations suggest that rather than the bacterial burden, products of the mce1 operon may directly or indirectly modulate the host immune response that is protective to both the tubercle bacilli and the host.
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Affiliation(s)
- Patricia Lima
- Division of Infectious Diseases, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Ben Sidders
- Division of Infectious Diseases, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Lisa Morici
- Division of Infectious Diseases, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Rachel Reader
- Comparative Pathology Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Ryan Senaratne
- Division of Infectious Diseases, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Nicola Casali
- Division of Infectious Diseases, School of Public Health, University of California, Berkeley, CA 94720, USA
| | - Lee W. Riley
- Division of Infectious Diseases, School of Public Health, University of California, Berkeley, CA 94720, USA
- Corresponding author: Division of Infectious Diseases, School of Public Health, 140 Warren Hall, Berkeley, CA 94720. Phone: (510) 642-9200. Fax: (510) 642-6350.
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Uchida Y, Casali N, White A, Morici L, Kendall LV, Riley LW. Accelerated immunopathological response of mice infected with Mycobacterium tuberculosis disrupted in the mce1 operon negative transcriptional regulator. Cell Microbiol 2007; 9:1275-83. [PMID: 17223927 DOI: 10.1111/j.1462-5822.2006.00870.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis causes a variety of clinical outcomes determined by host as well as bacterial factors. M. tuberculosis disrupted in the mce1 operon causes increased mortality in immunocompetent mice. This operon is negatively regulated by mce1R (Rv0165c). We studied the role of mce1R in infection outcome in mice. At 5 x 10(4) tail vein infectious dose, the median survival time (MST) of mice infected with the mce1R mutant M. tuberculosis H37Rv was 293 days, while mice infected with the wild-type H37Rv survived more than 350 days (P < 0.0001). At a higher dose (5 x 10(6)), the MST of mutant-infected mice was 32 days, compared with 127 days for wild type-infected mice (P < 0.0001). With either tail vein or aerosol infection, mutant-infected mice developed larger granulomatous lesions in their lungs than mice infected with the wild type. Mutant-infected mice were unable to control the bacterial burden in the first 4 weeks of infection, but even after achieving control later, these mice succumbed to granulomatous pneumonia. These observations suggest that the early deregulated expression of the mce1 operon products determines later granulomatous tissue response. mce1 operon may homeostatically regulate the cell wall architecture in vivo that elicits a steady-state granuloma tissue response permitting M. tuberculosis to establish a long-term infection.
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Affiliation(s)
- Yujiro Uchida
- Division of Infectious Diseases, School of Public Health, University of California, Berkeley, CA, USA
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A phylogenomic analysis of the Actinomycetales mce operons. BMC Genomics 2007; 8:60. [PMID: 17324287 PMCID: PMC1810536 DOI: 10.1186/1471-2164-8-60] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2006] [Accepted: 02/26/2007] [Indexed: 01/29/2023] Open
Abstract
Background The genome of Mycobacterium tuberculosis harbors four copies of a cluster of genes termed mce operons. Despite extensive research that has demonstrated the importance of these operons on infection outcome, their physiological function remains obscure. Expanding databases of complete microbial genome sequences facilitate a comparative genomic approach that can provide valuable insight into the role of uncharacterized proteins. Results The M. tuberculosis mce loci each include two yrbE and six mce genes, which have homology to ABC transporter permeases and substrate-binding proteins, respectively. Operons with an identical structure were identified in all Mycobacterium species examined, as well as in five other Actinomycetales genera. Some of the Actinomycetales mce operons include an mkl gene, which encodes an ATPase resembling those of ABC uptake transporters. The phylogenetic profile of Mkl orthologs exactly matched that of the Mce and YrbE proteins. Through topology and motif analyses of YrbE homologs, we identified a region within the penultimate cytoplasmic loop that may serve as the site of interaction with the putative cognate Mkl ATPase. Homologs of the exported proteins encoded adjacent to the M. tuberculosis mce operons were detected in a conserved chromosomal location downstream of the majority of Actinomycetales operons. Operons containing linked mkl, yrbE and mce genes, resembling the classic organization of an ABC importer, were found to be common in Gram-negative bacteria and appear to be associated with changes in properties of the cell surface. Conclusion Evidence presented suggests that the mce operons of Actinomycetales species and related operons in Gram-negative bacteria encode a subfamily of ABC uptake transporters with a possible role in remodeling the cell envelope.
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Ranjan S, Gundu RK, Ranjan A. MycoperonDB: a database of computationally identified operons and transcriptional units in Mycobacteria. BMC Bioinformatics 2006; 7 Suppl 5:S9. [PMID: 17254314 PMCID: PMC1764487 DOI: 10.1186/1471-2105-7-s5-s9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background A key post genomics challenge is to identify how genes in an organism come together and perform physiological functions. An important first step in this direction is to identify transcriptional units, operons and regulons in a genome. Here we implement and report a strategy to computationally identify transcriptional units and operons of mycobacteria and construct a database-MycoperonDB. Description We have predicted transcriptional units and operons in mycobacteria and organized these predictions in the form of relational database called MycoperonDB. MycoperonDB database at present consists of 18053 genes organized as 8256 predicted operons and transcriptional units from five closely related species of mycobacteria. The database further provides literature links for experimentally characterized operons. All known promoters and related information is collected, analysed and stored. It provides a user friendly interface to allow a web based navigation of transcription units and operons. The web interface provides search tools to locate transcription factor binding DNA motif upstream to various genes. The reliability of operon prediction has been assessed by comparing the predicted operons with a set of known operons. Conclusion MycoperonDB is a publicly available structured relational database which has information about mycobacterial genes, transcriptional units and operons. We expect this database to assist molecular biologists/microbiologists in general, to hypothesize functional linkages between operonic genes of mycobacteria, their experimental characterization and validation. The database is freely available from our website .
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Affiliation(s)
- Sarita Ranjan
- Computational & Functional Genomics Group, Sun Centre of Excellence in Medical Bioinformatics, Centre for DNA Fingerprinting and Diagnostics, EMBnet India Node, Hyderabad 500076, India
| | - Ranjit Kumar Gundu
- Bioinformatics Group, Sun Centre of Excellence in Medical Bioinformatics, Centre for DNA Fingerprinting and Diagnostics, EMBnet India Node, Hyderabad 500076, India
| | - Akash Ranjan
- Computational & Functional Genomics Group, Sun Centre of Excellence in Medical Bioinformatics, Centre for DNA Fingerprinting and Diagnostics, EMBnet India Node, Hyderabad 500076, India
- Bioinformatics Group, Sun Centre of Excellence in Medical Bioinformatics, Centre for DNA Fingerprinting and Diagnostics, EMBnet India Node, Hyderabad 500076, India
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