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Doddam SN, Peddireddy V, Ahmed N. Mycobacterium tuberculosis DosR Regulon Gene Rv2004c Encodes a Novel Antigen with Pro-inflammatory Functions and Potential Diagnostic Application for Detection of Latent Tuberculosis. Front Immunol 2017; 8:712. [PMID: 28694808 PMCID: PMC5483032 DOI: 10.3389/fimmu.2017.00712] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 06/01/2017] [Indexed: 12/11/2022] Open
Abstract
Approximately 1.7 billion people in the world harbor latent Mycobacterium tuberculosis (Mtb) with a substantial risk of progression to clinical outcome. Containment of these seed beds of Mtb is essential to eliminate tuberculosis completely in high burden settings such as India. Hence, there is an urgent need for the identification of new serological markers for detection or vaccine candidates to prevent latent tuberculosis infection (LTBI). DosR regulon antigens of Mtb might serve as attractive targets for LTBI diagnosis or vaccine development as they are specifically expressed and are upregulated during latent phase. In this study, we investigated the role of Rv2004c, a member of DosR regulon (exclusive to Mtb complex), in host–pathogen interaction and its immunogenic potential in LTBI, active TB, and healthy control cohorts. Rv2004c elicited strong antibody response in individuals with LTBI compared to active TB patients and healthy cohorts. Recombinant Rv2004c induced pro-inflammatory cytokine response in human peripheral blood mononuclear cells and THP-1 cells via NF-κB phosphorylation. Interaction of Rv2004c with toll-like receptor (TLR)-2 was confirmed using HEK-Blue hTLR-2 and pull-down assays. Rv2004c enhanced the surface expression of TLR-2 at mRNA and protein levels in THP-1 cells. Our findings revealed that Rv2004c induces strong humoral and cell mediated immune responses. Given these observations, we propose Rv2004c to be a potential diagnostic marker or an attractive vaccine candidate that can be useful against LTBI.
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Affiliation(s)
- Sankara Narayana Doddam
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
| | - Vidyullatha Peddireddy
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India
| | - Niyaz Ahmed
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, India.,Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research Bangladesh (icddr,b), Dhaka, Bangladesh
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52
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Bigi MM, Blanco FC, Araújo FR, Thacker TC, Zumárraga MJ, Cataldi AA, Soria MA, Bigi F. Polymorphisms of 20 regulatory proteins between Mycobacterium tuberculosis and Mycobacterium bovis. Microbiol Immunol 2017; 60:552-60. [PMID: 27427512 DOI: 10.1111/1348-0421.12402] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/21/2016] [Accepted: 07/13/2016] [Indexed: 12/21/2022]
Abstract
Mycobacterium tuberculosis and Mycobacterium bovis are responsible for tuberculosis in humans and animals, respectively. Both species are closely related and belong to the Mycobacterium tuberculosis complex (MTC). M. tuberculosis is the most ancient species from which M. bovis and other members of the MTC evolved. The genome of M. bovis is over >99.95% identical to that of M. tuberculosis but with seven deletions ranging in size from 1 to 12.7 kb. In addition, 1200 single nucleotide mutations in coding regions distinguish M. bovis from M. tuberculosis. In the present study, we assessed 75 M. tuberculosis genomes and 23 M. bovis genomes to identify non-synonymous mutations in 202 coding sequences of regulatory genes between both species. We identified species-specific variants in 20 regulatory proteins and confirmed differential expression of hypoxia-related genes between M. bovis and M. tuberculosis.
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Affiliation(s)
- María M Bigi
- School of Agronomy, UBA, Buenos Aires 1417, Argentina
| | - Federico Carlos Blanco
- Biotechnology Institute, National Institute of Agricultural Technology (INTA), Hurlingham 1686, Argentina
| | | | - Tyler C Thacker
- United States Department of Agriculture, Agricultural Research Service, National Animal Disease Center, 1920 Dayton Ave, Ames, Iowa 50010, USA
| | - Martín J Zumárraga
- Biotechnology Institute, National Institute of Agricultural Technology (INTA), Hurlingham 1686, Argentina
| | - Angel A Cataldi
- Biotechnology Institute, National Institute of Agricultural Technology (INTA), Hurlingham 1686, Argentina
| | | | - Fabiana Bigi
- Biotechnology Institute, National Institute of Agricultural Technology (INTA), Hurlingham 1686, Argentina
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53
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Abstract
Haem-based sensors have emerged during the last 15 years as being a large family of proteins that occur in all kingdoms of life. These sensors are responsible mainly for detecting binding of O2, CO and NO and reporting the ligation status to an output domain with an enzymatic or macromolecule-binding property. A myriad of biological functions have been associated with these sensors, which are involved in vasodilation, bacterial symbiosis, chemotaxis and biofilm formation, among others. Here, we critically review several bacterial systems for O2 sensing that are extensively studied in many respects, focusing on the lessons that are important to advance the field.
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54
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Zheng H, Colvin CJ, Johnson BK, Kirchhoff PD, Wilson M, Jorgensen-Muga K, Larsen SD, Abramovitch RB. Inhibitors of Mycobacterium tuberculosis DosRST signaling and persistence. Nat Chem Biol 2016; 13:218-225. [PMID: 27992879 DOI: 10.1038/nchembio.2259] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 09/30/2016] [Indexed: 11/09/2022]
Abstract
The Mycobacterium tuberculosis (Mtb) DosRST two-component regulatory system promotes the survival of Mtb during non-replicating persistence (NRP). NRP bacteria help drive the long course of tuberculosis therapy; therefore, chemical inhibition of DosRST may inhibit the ability of Mtb to establish persistence and thus shorten treatment. Using a DosRST-dependent fluorescent Mtb reporter strain, a whole-cell phenotypic high-throughput screen of a ∼540,000 compound small-molecule library was conducted. The screen discovered novel inhibitors of the DosRST regulon, including three compounds that were subject to follow-up studies: artemisinin, HC102A and HC103A. Under hypoxia, all three compounds inhibit Mtb-persistence-associated physiological processes, including triacylglycerol synthesis, survival and antibiotic tolerance. Artemisinin functions by disabling the heme-based DosS and DosT sensor kinases by oxidizing ferrous heme and generating heme-artemisinin adducts. In contrast, HC103A inhibits DosS and DosT autophosphorylation activity without targeting the sensor kinase heme.
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Affiliation(s)
- Huiqing Zheng
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Christopher J Colvin
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Benjamin K Johnson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Paul D Kirchhoff
- Vahlteich Medicinal Chemistry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Michael Wilson
- Vahlteich Medicinal Chemistry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Scott D Larsen
- Vahlteich Medicinal Chemistry Core, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA
| | - Robert B Abramovitch
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
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55
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Madrona Y, Waddling CA, Ortiz de Montellano PR. Crystal structures of the CO and NOBound DosS GAF-A domain and implications for DosS signaling in Mycobacterium tuberculosis. Arch Biochem Biophys 2016; 612:1-8. [PMID: 27729224 DOI: 10.1016/j.abb.2016.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Revised: 10/06/2016] [Accepted: 10/07/2016] [Indexed: 11/29/2022]
Abstract
DosS is a sensor in Mycobacterium tuberculosis that differentially responds to O2, NO, and CO, as well as to changes in the redox state of the prosthetic heme iron atom. The ferrous protein and its Fe(II)NO and Fe(II)CO complexes undergo autophosphorylation and subsequently transfer the phosphate group to DosR, a nuclear factor, to activate it. In contrast, autophosphorylation is negligible with the ferric protein and the Fe(II)O2 complex. To clarify the basis for this differential response to gases, we have determined the crystal structures of the NO and COcomplexes of the DosS GAF-A domain, which contains the heme to which the gases bind. Comparison of these crystal structures with those reported for the phosphorylation-inactive ferric GAF-A domain suggest that the GAF-A domain is in a dynamic equilibrium between active and inactive states, and that the position of Glu87 in the heme cavity, which depends on the which gas is bound, acts as a modulator of the equilibrium, and therefore of catalytic activity.
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Affiliation(s)
- Yarrow Madrona
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, United States
| | - Christopher A Waddling
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, United States
| | - Paul R Ortiz de Montellano
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, United States.
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56
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Sharma S, Tyagi JS. Mycobacterium tuberculosis DevR/DosR Dormancy Regulator Activation Mechanism: Dispensability of Phosphorylation, Cooperativity and Essentiality of α10 Helix. PLoS One 2016; 11:e0160723. [PMID: 27490491 PMCID: PMC4973870 DOI: 10.1371/journal.pone.0160723] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 07/22/2016] [Indexed: 01/17/2023] Open
Abstract
DevR/DosR is a well-characterized regulator in Mycobacterium tuberculosis which is implicated in various processes ranging from dormancy/persistence to drug tolerance. DevR induces the expression of an ~48-gene dormancy regulon in response to gaseous stresses, including hypoxia. Strains of the Beijing lineage constitutively express this regulon, which may confer upon them a significant advantage, since they would be ‘pre-adapted’ to the environmental stresses that predominate during infection. Aerobic DevR regulon expression in laboratory-manipulated overexpression strains is also reported. In both instances, the need for an inducing signal is bypassed. While a phosphorylation-mediated conformational change in DevR was proposed as the activation mechanism under hypoxia, the mechanism underlying constitutive expression is not understood. Because DevR is implicated in bacterial dormancy/persistence and is a promising drug target, it is relevant to resolve the mechanistic puzzle of hypoxic activation on one hand and constitutive expression under ‘non-inducing’ conditions on the other. Here, an overexpression strategy was employed to elucidate the DevR activation mechanism. Using a panel of kinase and transcription factor mutants, we establish that DevR, upon overexpression, circumvents DevS/DosT sensor kinase-mediated or small molecule phosphodonor-dependent activation, and also cooperativity-mediated effects, which are key aspects of hypoxic activation mechanism. However, overexpression failed to rescue the defect of C-terminal-truncated DevR lacking the α10 helix, establishing the α10 helix as an indispensable component of DevR activation mechanism. We propose that aerobic overexpression of DevR likely increases the concentration of α10 helix-mediated active dimer species to above the threshold level, as during hypoxia, and enables regulon expression. This advance in the understanding of DevR activation mechanism clarifies a long standing question as to the mechanism of DevR overexpression-mediated induction of the regulon in the absence of the normal environmental cue and establishes the α10 helix as an universal and pivotal targeting interface for DevR inhibitor development.
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Affiliation(s)
- Saurabh Sharma
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
- * E-mail: ;
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57
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Kaur K, Kumari P, Sharma S, Sehgal S, Tyagi JS. DevS/DosS sensor is bifunctional and its phosphatase activity precludes aerobic DevR/DosR regulon expression inMycobacterium tuberculosis. FEBS J 2016; 283:2949-62. [DOI: 10.1111/febs.13787] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/04/2016] [Accepted: 06/20/2016] [Indexed: 11/26/2022]
Affiliation(s)
- Kohinoor Kaur
- Department of Biotechnology; All India Institute of Medical Sciences; New Delhi India
| | - Priyanka Kumari
- Department of Biotechnology; All India Institute of Medical Sciences; New Delhi India
| | - Saurabh Sharma
- Department of Biotechnology; All India Institute of Medical Sciences; New Delhi India
| | - Snigdha Sehgal
- Department of Biotechnology; All India Institute of Medical Sciences; New Delhi India
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology; All India Institute of Medical Sciences; New Delhi India
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58
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Saini DK, Tyagi JS. High-Throughput Microplate Phosphorylation Assays Based on DevR-DevS/Rv2027c 2-Component Signal Transduction Pathway to Screen for Novel Antitubercular Compounds. ACTA ACUST UNITED AC 2016; 10:215-24. [PMID: 15809317 DOI: 10.1177/1087057104272090] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
DevR-DevS (Rv3133c-Rv3132c) and DevR-Rv2027c have been established through their autophosphorylation and phospho-transfer properties to constitute bonafide regulatory 2-component systems of Mycobacterium tuberculosis. DevR has also been shown by others to play a key regulatory role in the expression of M. tuberculosis genes comprising the dormancy regulon. The authors describe high-throughput phosphorylation assays in a microplate format using DevS and Rv2027c histidine kinases and DevR response regulator proteins from M. tuberculosis. The assays were designed to measure [γ-32P]ATP-dependent autophosphorylation of DevS/Rv2027c and also the phosphotransfer reaction to DevR. First, the optimal reaction conditions were established using the conventional method of radiolabeling the 2-component proteins by [γ-32P]ATP and followed by gel electrophoresis-based analysis. Next, the assays were converted to a high-throughput format in which the radiolabeled protein retained on a filter using mixed cellulose ester-based 96-well filter plates was analyzed for radioactivity retention by scintillation counting. The utility of these assays to screen for inhibitors is illustrated using 2-mercaptobenzimidazole, ethidium bromide, and EDTA. The high quality and flexibility of these assays will enable their use in high-throughput screening for new antitubercular compounds directed against 2-component systems that comprise a novel target in dormant mycobacteria.
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Affiliation(s)
- Deepak Kumar Saini
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110-029, India
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59
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Basudhar D, Madrona Y, Yukl ET, Sivaramakrishnan S, Nishida CR, Moënne-Loccoz P, Ortiz de Montellano PR. Distal Hydrogen-bonding Interactions in Ligand Sensing and Signaling by Mycobacterium tuberculosis DosS. J Biol Chem 2016; 291:16100-11. [PMID: 27235395 DOI: 10.1074/jbc.m116.724815] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Indexed: 11/06/2022] Open
Abstract
Mycobacterium tuberculosis DosS is critical for the induction of M. tuberculosis dormancy genes in response to nitric oxide (NO), carbon monoxide (CO), or hypoxia. These environmental stimuli, which are sensed by the DosS heme group, result in autophosphorylation of a DosS His residue, followed by phosphotransfer to an Asp residue of the response regulator DosR. To clarify the mechanism of gaseous ligand recognition and signaling, we investigated the hydrogen-bonding interactions of the iron-bound CO and NO ligands by site-directed mutagenesis of Glu-87 and His-89. Autophosphorylation assays and molecular dynamics simulations suggest that Glu-87 has an important role in ligand recognition, whereas His-89 is essential for signal transduction to the kinase domain, a process for which Arg-204 is important. Mutation of Glu-87 to Ala or Gly rendered the protein constitutively active as a kinase, but with lower autophosphorylation activity than the wild-type in the Fe(II) and the Fe(II)-CO states, whereas the E87D mutant had little kinase activity except for the Fe(II)-NO complex. The H89R mutant exhibited attenuated autophosphorylation activity, although the H89A and R204A mutants were inactive as kinases, emphasizing the importance of these residues in communication to the kinase core. Resonance Raman spectroscopy of the wild-type and H89A mutant indicates the mutation does not alter the heme coordination number, spin state, or porphyrin deformation state, but it suggests that interdomain interactions are disrupted by the mutation. Overall, these results confirm the importance of the distal hydrogen-bonding network in ligand recognition and communication to the kinase domain and reveal the sensitivity of the system to subtle differences in the binding of gaseous ligands.
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Affiliation(s)
- Debashree Basudhar
- From the Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94158-2517 and
| | - Yarrow Madrona
- From the Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94158-2517 and
| | - Erik T Yukl
- the Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health Science University, Portland, Oregon 97239-3098
| | - Santhosh Sivaramakrishnan
- From the Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94158-2517 and
| | - Clinton R Nishida
- From the Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94158-2517 and
| | - Pierre Moënne-Loccoz
- the Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health Science University, Portland, Oregon 97239-3098
| | - Paul R Ortiz de Montellano
- From the Department of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, California 94158-2517 and
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60
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Agrawal R, Sahoo BK, Saini DK. Cross-talk and specificity in two-component signal transduction pathways. Future Microbiol 2016; 11:685-97. [PMID: 27159035 DOI: 10.2217/fmb-2016-0001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Two-component signaling systems (TCSs) are composed of two proteins, sensor kinases and response regulators, which can cross-talk and integrate information between them by virtue of high-sequence conservation and modular nature, to generate concerted and diversified responses. However, TCSs have been shown to be insulated, to facilitate linear signal transmission and response generation. Here, we discuss various mechanisms that confer specificity or cross-talk among TCSs. The presented models are supported with evidence that indicate the physiological significance of the observed TCS signaling architecture. Overall, we propose that the signaling topology of any TCSs cannot be predicted using obvious sequence or structural rules, as TCS signaling is regulated by multiple factors, including spatial and temporal distribution of the participating proteins.
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Affiliation(s)
- Ruchi Agrawal
- Department of Molecular Reproduction, Development & Genetics, Indian Institute of Science, Bangalore, India
| | - Bikash Kumar Sahoo
- Department of Molecular Reproduction, Development & Genetics, Indian Institute of Science, Bangalore, India
| | - Deepak Kumar Saini
- Department of Molecular Reproduction, Development & Genetics, Indian Institute of Science, Bangalore, India.,Centre for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, India
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61
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Nitrogen oxide cycle regulates nitric oxide levels and bacterial cell signaling. Sci Rep 2016; 6:22038. [PMID: 26912114 PMCID: PMC4766573 DOI: 10.1038/srep22038] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 02/04/2016] [Indexed: 12/28/2022] Open
Abstract
Nitric oxide (NO) signaling controls various metabolic pathways in bacteria and higher eukaryotes. Cellular enzymes synthesize and detoxify NO; however, a mechanism that controls its cellular homeostasis has not been identified. Here, we found a nitrogen oxide cycle involving nitrate reductase (Nar) and the NO dioxygenase flavohemoglobin (Fhb), that facilitate inter-conversion of nitrate, nitrite, and NO in the actinobacterium Streptomyces coelicolor. This cycle regulates cellular NO levels, bacterial antibiotic production, and morphological differentiation. NO down-regulates Nar and up-regulates Fhb gene expression via the NO-dependent transcriptional factors DevSR and NsrR, respectively, which are involved in the auto-regulation mechanism of intracellular NO levels. Nitrite generated by the NO cycles induces gene expression in neighboring cells, indicating an additional role of the cycle as a producer of a transmittable inter-cellular communication molecule.
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62
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Vashist A, Prithvi Raj D, Gupta UD, Bhat R, Tyagi JS. The α10 helix of DevR, the Mycobacterium tuberculosis dormancy response regulator, regulates its DNA binding and activity. FEBS J 2016; 283:1286-99. [PMID: 26799615 DOI: 10.1111/febs.13664] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 01/05/2016] [Accepted: 01/18/2016] [Indexed: 11/26/2022]
Abstract
The crystal structures of several bacterial response regulators provide insight into the various interdomain molecular interactions potentially involved in maintaining their 'active' or 'inactive' states. However, the requirement of high concentrations of protein, an optimal pH and ionic strength buffers during crystallization may result in a structure somewhat different from that observed in solution. Therefore, functional assessment of the physiological relevance of the crystal structure data is imperative. DevR/DosR dormancy regulator of Mycobacterium tuberculosis (Mtb) belongs to the NarL subfamily of response regulators. The crystal structure of unphosphorylated DevR revealed that it forms a dimer through the α5/α6 interface. It was proposed that phosphorylation may trigger extensive structural rearrangements in DevR that culminate in the formation of a DNA-binding competent dimeric species via α10-α10 helix interactions. The α10 helix-deleted DevR protein (DevR∆α10 ) was hyperphosphorylated but defective with respect to in vitro DNA binding. Biophysical characterization reveals that DevR∆α10 has an open but less stable conformation. The combined cross-linking and DNA-binding data demonstrate that the α10 helix is essential for the formation and stabilization of the DNA-binding proficient DevR structure in both the phosphorylated and unphosphorylated states. Genetic studies establish that Mtb strains expressing DevR∆α10 are defective with respect to dormancy regulon expression under hypoxia. The present study highlights the indispensable role of the α10 helix in DevR activation and function under hypoxia and establishes the α10-α10 helix interface as a novel target for developing inhibitors against DevR, a key regulator of hypoxia-triggered dormancy.
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Affiliation(s)
- Atul Vashist
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India.,Experimental Animal Facility, National JALMA Institute of Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, India
| | - D Prithvi Raj
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
| | - Umesh Datta Gupta
- Experimental Animal Facility, National JALMA Institute of Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, India
| | - Rajiv Bhat
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Jaya Sivaswami Tyagi
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
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63
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Abstract
Mycobacterium tuberculosis is an incredibly successful pathogen with an extraordinary penetrance of its target host population. The ability to infect many yet cause disease in few is undoubtedly central to this success. This ability relies on sensing and responding to the changing environments encountered during the course of disease in the human host. This chapter discusses these environmental cues and stresses, and explores how the genome of Mtb has evolved under the purifying selections that they exert. In analyzing the response of Mtb to a broad range of intracellular pressures it is clear that, despite genome down-sizing, Mtb has retained an extraordinary flexibility in central carbon metabolism. We believe that it is this metabolic plasticity, more than any of the virulence factors, that is the foundation for Mtb's qualities of endurance.
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64
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Tan S, Russell DG. Trans-species communication in the Mycobacterium tuberculosis-infected macrophage. Immunol Rev 2015; 264:233-48. [PMID: 25703563 DOI: 10.1111/imr.12254] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Much of the infection cycle of Mycobacterium tuberculosis (Mtb) is spent within its host cell, the macrophage. As a consequence of the chronic, enduring nature of the infection, this cell-cell interaction has become highly intimate, and the bacterium has evolved to detect, react to, and manipulate the evolving, immune-modulated phenotype of its host. In this review, we discuss the nature of the endosomal/lysosomal continuum, the characterization of the bacterium's transcriptional responses during the infection cycle, and the dominant environmental cues that shape this response. We also discuss how the metabolism of both cells is modulated by the infection and the impact that this has on the progression of the granuloma. Finally, we detail how these transcriptional responses can be exploited to construct reporter bacterial strains to probe the temporal and spatial environmental shifts experienced by Mtb during the course of experimental infections. These reporter strains provide new insights into the fitness of Mtb under immune- and drug-mediated pressure.
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Affiliation(s)
- Shumin Tan
- Department of Microbiology and Immunology, Cornell University, College of Veterinary Medicine, Ithaca, NY, USA
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65
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Wright DP, Ulijasz AT. Regulation of transcription by eukaryotic-like serine-threonine kinases and phosphatases in Gram-positive bacterial pathogens. Virulence 2015; 5:863-85. [PMID: 25603430 PMCID: PMC4601284 DOI: 10.4161/21505594.2014.983404] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bacterial eukaryotic-like serine threonine kinases (eSTKs) and serine threonine phosphatases (eSTPs) have emerged as important signaling elements that are indispensable for pathogenesis. Differing considerably from their histidine kinase counterparts, few eSTK genes are encoded within the average bacterial genome, and their targets are pleiotropic in nature instead of exclusive. The growing list of important eSTK/P substrates includes proteins involved in translation, cell division, peptidoglycan synthesis, antibiotic tolerance, resistance to innate immunity and control of virulence factors. Recently it has come to light that eSTK/Ps also directly modulate transcriptional machinery in many microbial pathogens. This novel form of regulation is now emerging as an additional means by which bacteria can alter their transcriptomes in response to host-specific environmental stimuli. Here we focus on the ability of eSTKs and eSTPs in Gram-positive bacterial pathogens to directly modulate transcription, the known mechanistic outcomes of these modifications, and their roles as an added layer of complexity in controlling targeted RNA synthesis to enhance virulence potential.
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Key Words
- OCS, one-component signaling
- PASTA, penicillin-binding protein and Ser/Thr kinase associated
- PPM, protein phosphatase metal binding
- PTM, posttranslational modification
- REC, receiver
- ROS, reactive oxygen species
- TCS, two-component signaling
- bacteria
- eSTK, eukaryotic-like serine-threonine kinase
- eSTP, eukaryotic-like serine-threonine phosphatase
- infection
- phosphorylation
- serine threonine kinase
- serine threonine phosphatase
- transcription
- wHTH, winged helix-turn-helix
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Affiliation(s)
- David P Wright
- a MRC Centre for Molecular Bacteriology and Infection (CMBI); Imperial College London ; London , UK
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66
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Kalantari A, Derouiche A, Shi L, Mijakovic I. Serine/threonine/tyrosine phosphorylation regulates DNA binding of bacterial transcriptional regulators. Microbiology (Reading) 2015. [DOI: 10.1099/mic.0.000148] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Aida Kalantari
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Chaire Agro-Biotechnologies Industrielles, AgroParisTech, Reims, France
| | - Abderahmane Derouiche
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Lei Shi
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Ivan Mijakovic
- Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark
- Systems and Synthetic Biology Division, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
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Gautam US, McGillivray A, Mehra S, Didier PJ, Midkiff CC, Kissee RS, Golden NA, Alvarez X, Niu T, Rengarajan J, Sherman DR, Kaushal D. DosS Is required for the complete virulence of mycobacterium tuberculosis in mice with classical granulomatous lesions. Am J Respir Cell Mol Biol 2015; 52:708-16. [PMID: 25322074 DOI: 10.1165/rcmb.2014-0230oc] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) must counter hypoxia within granulomas to persist. DosR, in concert with sensor kinases DosS and DosT, regulates the response to hypoxia. Yet Mtb lacking functional DosR colonize the lungs of C57Bl/6 mice, presumably owing to the lack of organized lesions with sufficient hypoxia in that model. We compared the phenotype of the Δ-dosR, Δ-dosS, and Δ-dosT mutants to Mtb using C3HeB/FeJ mice, an alternate mouse model where lesions develop hypoxia. C3HeB/FeJ mice were infected via aerosol. The progression of infection was analyzed by tissue bacterial burden and histopathology. A measure of the comparative global immune responses was also analyzed. Although Δ-dosR and Δ-dosT grew comparably to wild-type Mtb, Δ-dosS exhibited a significant defect in bacterial burden and pathology in vivo, accompanied by ablated proinflammatory response. Δ-dosS retained the ability to induce DosR. The Δ-dosS mutant was also attenuated in murine macrophages ex vivo, with evidence of reduced expression of the proinflammatory signature. Our results show that DosS, but not DosR and DosT, is required by Mtb to survive in C3HeB/FeJ mice. The attenuation of Δ-dosS is not due to its inability to induce the DosR regulon, nor is it a result of the accumulation of hypoxia. That the in vivo growth restriction of Δ-dosS could be mimicked ex vivo suggested sensitivity to macrophage oxidative burst. Anoxic caseous centers within tuberculosis lesions eventually progress to cavities. Our results provide greater insight into the molecular mechanisms of Mtb persistence within host lungs.
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Mehra S, Foreman TW, Didier PJ, Ahsan MH, Hudock TA, Kissee R, Golden NA, Gautam US, Johnson AM, Alvarez X, Russell-Lodrigue KE, Doyle LA, Roy CJ, Niu T, Blanchard JL, Khader SA, Lackner AA, Sherman DR, Kaushal D. The DosR Regulon Modulates Adaptive Immunity and Is Essential for Mycobacterium tuberculosis Persistence. Am J Respir Crit Care Med 2015; 191:1185-96. [PMID: 25730547 DOI: 10.1164/rccm.201408-1502oc] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
RATIONALE Hypoxia promotes dormancy by causing physiologic changes to actively replicating Mycobacterium tuberculosis. DosR controls the response of M. tuberculosis to hypoxia. OBJECTIVES To understand DosR's contribution in the persistence of M. tuberculosis, we compared the phenotype of various DosR regulon mutants and a complemented strain to M. tuberculosis in macaques, which faithfully model M. tuberculosis infection. METHODS We measured clinical and microbiologic correlates of infection with M. tuberculosis relative to mutant/complemented strains in the DosR regulon, studied lung pathology and hypoxia, and compared immune responses in lung using transcriptomics and flow cytometry. MEASUREMENTS AND MAIN RESULTS Despite being able to replicate initially, mutants in DosR regulon failed to persist or cause disease. On the contrary, M. tuberculosis and a complemented strain were able to establish infection and tuberculosis. The attenuation of pathogenesis in animals infected with the mutants coincided with the appearance of a Th1 response and organization of hypoxic lesions wherein M. tuberculosis expressed dosR. The lungs of animals infected with the mutants (but not the complemented strain) exhibited early transcriptional signatures of T-cell recruitment, activation, and proliferation associated with an increase of T cells expressing homing and proliferation markers. CONCLUSIONS Delayed adaptive responses, a hallmark of M. tuberculosis infection, not only lead to persistence but also interfere with the development of effective antituberculosis vaccines. The DosR regulon therefore modulates both the magnitude and the timing of adaptive immune responses in response to hypoxia in vivo, resulting in persistent infection. Hence, DosR regulates key aspects of the M. tuberculosis life cycle and limits lung pathology.
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Zhou L, Yang L, Zeng X, Danzheng J, Zheng Q, Liu J, Liu F, Xin Y, Cheng X, Su M, Ma Y, Hao X. Transcriptional and proteomic analyses of two-component response regulators in multidrug-resistant Mycobacterium tuberculosis. Int J Antimicrob Agents 2015; 46:73-81. [DOI: 10.1016/j.ijantimicag.2015.02.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 02/10/2015] [Accepted: 02/11/2015] [Indexed: 11/28/2022]
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Sikri K, Kumari P, Tyagi JS, Nandi M, Taneja NK, Batra SD. The pleiotropic transcriptional response of Mycobacterium tuberculosis to vitamin C is robust and overlaps with the bacterial response to multiple intracellular stresses. Microbiology (Reading) 2015; 161:739-53. [DOI: 10.1099/mic.0.000049] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 01/28/2015] [Indexed: 11/18/2022] Open
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Singh N, Kumar A. Virulence factor SenX3 is the oxygen-controlled replication switch of Mycobacterium tuberculosis. Antioxid Redox Signal 2015; 22:603-13. [PMID: 25333974 PMCID: PMC4333250 DOI: 10.1089/ars.2014.6020] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
AIM Morphogenetic switching between the replicating and nonreplicating states of Mycobacterium tuberculosis is regulated by oxygen, nitric oxide, and carbon monoxide levels. The mechanisms by which M. tuberculosis senses these diatomic gases remain poorly understood. In this study, we have examined whether virulence factor SenX3 plays any role in oxygen sensing. RESULTS In this study, we demonstrate that the virulence factor SenX3 is a heme protein that acts as a three-way sensor with three levels of activity. The oxidation of SenX3 heme by oxygen leads to the activation of its kinase activity, whereas the deoxy-ferrous state confers a moderate kinase activity. The binding of nitric oxide and carbon monoxide inhibits kinase activity. Consistent with these biochemical properties, the SenX3 mutant of M. tuberculosis is capable of attaining a nonreplicating persistent state in response to hypoxic stress, but its regrowth on the restoration of ambient oxygen levels is significantly attenuated compared with the wild-type and the complemented mutant strains. Furthermore, the presence of signaling concentrations of nitric oxide and carbon monoxide was able to inhibit the regrowth of M. tuberculosis in response to ambient oxygen levels. INNOVATION AND CONCLUSIONS Evidence presented in this study delineates a plausible mechanism explaining the oxygen-induced reactivation of tuberculosis diseases in humans after many years of latent infection. Furthermore, this study implicates nitric oxide and carbon monoxide in the inhibition of mycobacterial growth from the nonreplicating state.
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Affiliation(s)
- Nisha Singh
- Department of Infectious Diseases and Immunity, Council of Scientific and Industrial Research, Institute of Microbial Technology , Chandigarh, India
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Malhotra V, Agrawal R, Duncan TR, Saini DK, Clark-Curtiss JE. Mycobacterium tuberculosis response regulators, DevR and NarL, interact in vivo and co-regulate gene expression during aerobic nitrate metabolism. J Biol Chem 2015; 290:8294-309. [PMID: 25659431 DOI: 10.1074/jbc.m114.591800] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mycobacterium tuberculosis genes Rv0844c/Rv0845 encoding the NarL response regulator and NarS histidine kinase are hypothesized to constitute a two-component system involved in the regulation of nitrate metabolism. However, there is no experimental evidence to support this. In this study, we established M. tuberculosis NarL/NarS as a functional two-component system and identified His(241) and Asp(61) as conserved phosphorylation sites in NarS and NarL, respectively. Transcriptional profiling between M. tuberculosis H37Rv and a ΔnarL mutant strain during exponential growth in broth cultures with or without nitrate defined an ∼30-gene NarL regulon that exhibited significant overlap with DevR-regulated genes, thereby implicating a role for the DevR response regulator in the regulation of nitrate metabolism. Notably, expression analysis of a subset of genes common to NarL and DevR regulons in M. tuberculosis ΔdevR, ΔdevSΔdosT, and ΔnarL mutant strains revealed that in response to nitrite produced during aerobic nitrate metabolism, the DevRS/DosT regulatory system plays a primary role that is augmented by NarL. Specifically, NarL itself was unable to bind to the narK2, acg, and Rv3130c promoters in phosphorylated or unphosphorylated form; however, its interaction with DevR∼P resulted in cooperative binding, thereby enabling co-regulation of these genes. These findings support the role of physiologically derived nitrite as a metabolic signal in mycobacteria. We propose NarL-DevR binding, possibly as a heterodimer, as a novel mechanism for co-regulation of gene expression by the DevRS/DosT and NarL/NarS regulatory systems.
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Affiliation(s)
- Vandana Malhotra
- From the Center for Infectious Diseases and Vaccinology, Biodesign Institute, and
| | - Ruchi Agrawal
- the Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore 560012, India
| | - Tammi R Duncan
- From the Center for Infectious Diseases and Vaccinology, Biodesign Institute, and the School of Life Sciences, Arizona State University, Tempe, Arizona 85287 and
| | - Deepak K Saini
- the Department of Molecular Reproduction, Development, and Genetics, Indian Institute of Science, Bangalore 560012, India
| | - Josephine E Clark-Curtiss
- From the Center for Infectious Diseases and Vaccinology, Biodesign Institute, and the School of Life Sciences, Arizona State University, Tempe, Arizona 85287 and
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He X, Wang S. DNA consensus sequence motif for binding response regulator PhoP, a virulence regulator of Mycobacterium tuberculosis. Biochemistry 2014; 53:8008-20. [PMID: 25434965 PMCID: PMC4283936 DOI: 10.1021/bi501019u] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
Tuberculosis has reemerged as a serious
threat to human health
because of the increasing prevalence of drug-resistant strains and
synergetic infection with HIV, prompting an urgent need for new and
more efficient treatments. The PhoP–PhoR two-component system
of Mycobacterium tuberculosis plays an important
role in the virulence of the pathogen and thus represents a potential
drug target. To study the mechanism of gene transcription regulation
by response regulator PhoP, we identified a high-affinity DNA sequence
for PhoP binding using systematic evolution of ligands by exponential
enrichment. The sequence contains a direct repeat of two 7 bp motifs
separated by a 4 bp spacer, TCACAGC(N4)TCACAGC. The specificity
of the direct-repeat sequence for PhoP binding was confirmed by isothermal
titration calorimetry and electrophoretic mobility shift assays. PhoP
binds to the direct repeat as a dimer in a highly cooperative manner.
We found many genes previously identified to be regulated by PhoP
that contain the direct-repeat motif in their promoter sequences.
Synthetic DNA fragments at the putative promoter-binding sites bind
PhoP with variable affinity, which is related to the number of mismatches
in the 7 bp motifs, the positions of the mismatches, and the spacer
and flanking sequences. Phosphorylation of PhoP increases the affinity
but does not change the specificity of DNA binding. Overall, our results
confirm the direct-repeat sequence as the consensus motif for PhoP
binding and thus pave the way for identification of PhoP directly
regulated genes in different mycobacterial genomes.
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Affiliation(s)
- Xiaoyuan He
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences , Bethesda, Maryland 20814, United States
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Rifat D, Belchis DA, Karakousis PC. senX3-independent contribution of regX3 to Mycobacterium tuberculosis virulence. BMC Microbiol 2014; 14:265. [PMID: 25344463 PMCID: PMC4213456 DOI: 10.1186/s12866-014-0265-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 10/09/2014] [Indexed: 01/27/2023] Open
Abstract
Background Mycobacterium tuberculosis (Mtb) must adapt to various stress conditions during host infection. The two-component regulatory system (2CRS) SenX3-RegX3 is required for Mtb virulence. We showed recently that the senX3-regX3 intergenic region contains promoter activity, driving senX3-independent regX3 expression. In the current study, we tested the hypothesis that RegX3 has a SenX3-independent role in Mtb virulence. The gene expression patterns, growth, and survival of mutants containing transposon insertions in senX3 (senX3::Tn) and regX3 (regX3::Tn) were compared to those of their respective complemented strains and the isogenic wild-type parent strain during axenic growth in nutrient-rich broth, phosphate depletion, nutrient starvation, and in the lungs of BALB/c mice. Results regX3 expression was reduced in senX3::Tn during phosphate depletion and nutrient starvation, and expression of the phosphate-specific transport gene pstC2 was reduced similarly in senX3::Tn and regX3::Tn during phosphate depletion. Although senX3 and regX3 were each dispensable for Mtb growth in nutrient-rich broth, disruption of senX3 or regX3 caused a similar growth defect during phosphate depletion. Interestingly, senX3::Tn, in which monocistronic regX3 expression is preserved, showed significantly higher survival relative to regX3::Tn after 7 days of nutrient starvation (p <0.01), and in mouse lungs at Day 31 (p < 0.01), Day 62 (p < 0.01), and Day 124 (p = 0.05) after aerosol infection. Conclusion Our data demonstrate the specificity of the senX3-regX3 2CRS for sensing and responding to low ambient phosphate, but also raise the possibility that RegX3 may function independently of its cognate sensor histidine kinase.
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75
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Schreuder LJ, Parish T. Mycobacterium tuberculosis DosR is required for activity of the PmbtB and PmbtI promoters under hypoxia. PLoS One 2014; 9:e107283. [PMID: 25211224 PMCID: PMC4161423 DOI: 10.1371/journal.pone.0107283] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 08/12/2014] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis has the ability to survive for extended periods of time under conditions of low oxygen, low pH, low iron and low nutrients. The mycobactins (M. tuberculosis siderophores) play a key role in scavenging iron from the environment and are induced in response to low iron in an IdeR-regulated manner. We demonstrate that the promoters of two mycobactin gene (mbt) operons are also expressed during adaptation to low oxygen, and that this expression is dependent on the DosR regulator. Up-regulation of mbt operons induced by low iron was not DosR-dependent. DosR is a member of a two component regulatory system which responds to oxygen availability. Deletion of the DosR regulator led to increased expression of bacterioferritin and increased capacity to grow under iron depletion. These data provide a link between the mycobacterial response to two conditions likely to be encountered in vivo, low iron and low oxygen.
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Affiliation(s)
- Lise J. Schreuder
- Queen Mary University of London, Barts and The London School of Medicine and Dentistry, London, United Kingdom
| | - Tanya Parish
- Queen Mary University of London, Barts and The London School of Medicine and Dentistry, London, United Kingdom
- TB Discovery Research, Infectious Disease Research Institute, Seattle, Washington, United States of America
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DevR (DosR) mimetic peptides impair transcriptional regulation and survival of Mycobacterium tuberculosis under hypoxia by inhibiting the autokinase activity of DevS sensor kinase. BMC Microbiol 2014; 14:195. [PMID: 25048654 PMCID: PMC4110071 DOI: 10.1186/1471-2180-14-195] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 07/11/2014] [Indexed: 01/06/2023] Open
Abstract
Background Two-component systems have emerged as compelling targets for antibacterial drug design for a number of reasons including the distinct histidine phosphorylation property of their constituent sensor kinases. The DevR-DevS/DosT two component system of Mycobacterium tuberculosis (M. tb) is essential for survival under hypoxia, a stress associated with dormancy development in vivo. In the present study a combinatorial peptide phage display library was screened for DevS histidine kinase interacting peptides with the aim of isolating inhibitors of DevR-DevS signaling. Results DevS binding peptides were identified from a phage display library after three rounds of panning using DevS as bait. The peptides showed sequence similarity with conserved residues in the N-terminal domain of DevR and suggested that they may represent interacting surfaces between DevS and DevR. Two DevR mimetic peptides were found to specifically inhibit DevR-dependent transcriptional activity and restrict the hypoxic survival of M. tb. The mechanism of peptide action is majorly attributed to an inhibition of DevS autokinase activity. Conclusions These findings demonstrate that DevR mimetic peptides impede DevS activation and that intercepting DevS activation at an early step in the signaling cascade impairs M. tb survival in a hypoxia persistence model.
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Pulido PA, Novoa-Aponte L, Villamil N, Soto CY. The DosR Dormancy Regulator of Mycobacterium tuberculosis Stimulates the Na+/K+ and Ca2+ ATPase Activities in Plasma Membrane Vesicles of Mycobacteria. Curr Microbiol 2014; 69:604-10. [DOI: 10.1007/s00284-014-0632-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 04/30/2014] [Indexed: 01/14/2023]
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Gautam US, Mehra S, Ahsan MH, Alvarez X, Niu T, Kaushal D. Role of TNF in the altered interaction of dormant Mycobacterium tuberculosis with host macrophages. PLoS One 2014; 9:e95220. [PMID: 24743303 PMCID: PMC3990579 DOI: 10.1371/journal.pone.0095220] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Accepted: 03/24/2014] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) persists within lung granulomas, despite being subjected to diverse stress conditions, including hypoxia. We hypothesized that the response of host phagocytes to Mtb experiencing hypoxia is radically altered and designed in vitro experiment to study this phenomenon. Hypoxia-stressed (Mtb-H) and aerobically grown Mtb (Mtb-A) were used to infect Rhesus Macaque Bone Marrow Derived Macrophages (Rh-BMDMs) and the comparative host response to Mtb infection studied. Mechanistic insights were gained by employing RNAi. Mtb-H accumulated significantly lower bacterial burden during growth in Rh-BMDMs, concomitantly generating a drastically different host transcriptional profile (with only <2% of all genes perturbed by either infection being shared between the two groups). A key component of this signature was significantly higher TNF and apopotosis in Mtb-H- compared to Mtb-A-infected Rh-BMDMs. Silencing of TNF by RNAi reversed the significant control of Mtb replication. These results indicate a potential mechanism for the rapid clearance of hypoxia-conditioned bacilli by phagocytes. In conclusion, hypoxia-conditioned Mtb undergo significantly different interactions with host macrophages compared to Mtb grown in normoxia. These interactions result in the induction of the TNF signaling pathway, activation of apoptosis, and DNA-damage stress response. Our results show that Mtb-H bacilli are particularly susceptible to killing governed by TNF.
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Affiliation(s)
- Uma S. Gautam
- Division of Bacteriology and Parasitology, Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Smriti Mehra
- Department of Microbiology, Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Muhammad H. Ahsan
- Division of Bacteriology and Parasitology, Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Xavier Alvarez
- Department of Comparative Pathology, Tulane National Primate Research Center, Covington, Louisiana, United States of America
| | - Tianhua Niu
- Department of Biostatistics and Bioinformatics, Tulane University School of Public Health and Tropical Medicine
| | - Deepak Kaushal
- Division of Bacteriology and Parasitology, Tulane National Primate Research Center, Covington, Louisiana, United States of America
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
- * E-mail:
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Abstract
The genus Mycobacterium is comprised of Gram-positive bacteria occupying a wide range of natural habitats and includes species that range from severe intracellular pathogens to economically useful and harmless microbes. The recent upsurge in the availability of microbial genome data has shown that genes encoding haemoglobin-like proteins are ubiquitous among Mycobacteria and that multiple haemoglobins (Hbs) of different classes may be present in pathogenic and non-pathogenic species. The occurrence of truncated haemoglobins (trHbs) and flavohaemoglobins (flavoHbs) showing distinct haem active site structures and ligand-binding properties suggests that these Hbs may be playing diverse functions in the cellular metabolism of Mycobacteria. TrHbs and flavoHbs from some of the severe human pathogens such as Mycobacterium tuberculosis and Mycobacterium leprae have been studied recently and their roles in effective detoxification of reactive nitrogen and oxygen species, electron cycling, modulation of redox state of the cell and facilitation of aerobic respiration have been proposed. This multiplicity in the function of Hbs may aid these pathogens to cope with various environmental stresses and survive during their intracellular regime. This chapter provides recent updates on genomic, structural and functional aspects of Mycobacterial Hbs to address their role in Mycobacteria.
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80
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Chim N, Johnson PM, Goulding CW. Insights into redox sensing metalloproteins in Mycobacterium tuberculosis. J Inorg Biochem 2014; 133:118-26. [PMID: 24314844 PMCID: PMC3959581 DOI: 10.1016/j.jinorgbio.2013.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 11/07/2013] [Accepted: 11/08/2013] [Indexed: 12/29/2022]
Abstract
Mycobacterium tuberculosis, the pathogen that causes tuberculosis, has evolved sophisticated mechanisms for evading assault by the human host. This review focuses on M. tuberculosis regulatory metalloproteins that are sensitive to exogenous stresses attributed to changes in the levels of gaseous molecules (i.e., molecular oxygen, carbon monoxide and nitric oxide) to elicit an intracellular response. In particular, we highlight recent developments on the subfamily of Whi proteins, redox sensing WhiB-like proteins that contain iron-sulfur clusters, sigma factors and their cognate anti-sigma factors of which some are zinc-regulated, and the dormancy survival regulon DosS/DosT-DosR heme sensory system. Mounting experimental evidence suggests that these systems contribute to a highly complex and interrelated regulatory network that controls M. tuberculosis biology. This review concludes with a discussion of strategies that M. tuberculosis has developed to maintain redox homeostasis, including mechanisms to regulate endogenous nitric oxide and carbon monoxide levels.
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Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA
| | - Parker M Johnson
- Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA
| | - Celia W Goulding
- Department of Molecular Biology and Biochemistry, UCI, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, UCI, Irvine, CA 92697, USA.
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81
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Lindestam Arlehamn CS, Sette A. Definition of CD4 Immunosignatures Associated with MTB. Front Immunol 2014; 5:124. [PMID: 24715893 PMCID: PMC3970006 DOI: 10.3389/fimmu.2014.00124] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/11/2014] [Indexed: 01/05/2023] Open
Abstract
We have recently described the first true genome-wide screen for CD4(+) T-cell reactivity directed against Mycobacterium tuberculosis (MTB) in latent TB-infected individuals. The approach relied on predictions of HLA-binding capacity for a panel of DR, DP, and DQ alleles representative of those most commonly expressed in the general population, coupled with high throughput ELISPOT assays. The results identified hundreds of novel epitopes and antigens, and documented the novel observation that T cells in latent MTB infection are confined to the CXCR3(+)CCR6(+) phenotype and largely directed against three antigenic "islands" within the MTB genome. In parallel, we have made generally available to the scientific community the technical approaches and reagents developed in the process, such as motifs, algorithms, and binding assays for several common HLA class II alleles, and a panel of single allele HLA class II transfected cell lines representative of the most frequent specificities in the general population. Recent efforts have been focused on characterization of epitopes and antigens recognized by patients with active TB and individuals vaccinated with BCG, with the aim of providing the first systematic evaluation of the overlap between latent, active, and BCG cohorts. The definition of a broad range of epitopes restricted by common HLA molecules, will facilitate development of diagnostic reagents, allow a rigorous evaluation of T-cell responses associated with TB infection in humans, and enable the evaluation of the immunogenicity of different vaccine candidates. Furthermore, it might suggest new candidates for vaccine and diagnostic development.
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Affiliation(s)
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology , La Jolla, CA , USA
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82
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Singh S, Saraav I, Sharma S. Immunogenic potential of latency associated antigens against Mycobacterium tuberculosis. Vaccine 2014; 32:712-6. [DOI: 10.1016/j.vaccine.2013.11.065] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 11/17/2013] [Accepted: 11/18/2013] [Indexed: 10/26/2022]
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83
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Serine 83 in DosR, a response regulator from Mycobacterium tuberculosis, promotes its transition from an activated, phosphorylated state to an inactive, unphosphorylated state. Biochem Biophys Res Commun 2014; 444:651-5. [PMID: 24491537 DOI: 10.1016/j.bbrc.2014.01.128] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 01/25/2014] [Indexed: 11/21/2022]
Abstract
A sensor kinase, DosS, and its corresponding response regulator, DosR, constitute a two component system for regulating gene expression under hypoxic conditions in Mycobacterium tuberculosis. Among response regulators in M. tuberculosis, NarL has high sequence similarity to DosR, and autophosphorylated DosS transfers its phosphate group not only to DosR but also to NarL. Phosphorylated DosR is more rapidly dephosphorylated than phosphorylated NarL. DosR and NarL differ with respect to the amino acids at positions T+1 and T+2 around the phosphorylation sites in the N-terminal phosphoacceptor domain; NarL has S83 and Y84, whereas DosR has A90 and H91. A DosR S83A mutant shows prolonged phosphorylation. Structural comparison with a histidinol phosphate phosphatase suggests that the hydroxyl group of DosR S83 could play a role in activating the water molecule involved in the triggering of autodephosphorylation.
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84
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Essentiality of DevR/DosR interaction with SigA for the dormancy survival program in Mycobacterium tuberculosis. J Bacteriol 2013; 196:790-9. [PMID: 24317401 DOI: 10.1128/jb.01270-13] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The DevR/DosR regulator is believed to play a key role in dormancy adaptation mechanisms of Mycobacterium tuberculosis in response to a multitude of gaseous stresses, including hypoxia, which prevails within granulomas. DevR activates transcription by binding to target promoters containing a minimum of two binding sites. The proximal site overlaps with the SigA -35 element, suggesting that DevR-SigA interaction is required for activating transcription. We evaluated the roles of 14 charged residues of DevR in transcriptional activation under hypoxic stress. Seven of the 14 alanine substitution mutants were defective in regulon activation, of which K191A, R197A, and K179A+K168A (designated K179A*) mutants were significantly or completely compromised in DNA binding. Four mutants, namely, E154A, R155A, E178A, and K208A, were activation defective in spite of binding to DNA and were classified as positive-control (pc) mutants. The SigA interaction defect of the E154A and E178A proteins was established by in vitro and in vivo assays and implies that these substitutions lead to an activation defect because they disrupt an interaction(s) with SigA. The relevance of DevR interaction to the transcriptional machinery was further established by the hypoxia survival phenotype displayed by SigA interaction-defective mutants. Our findings demonstrate the role of DevR-SigA interaction in the activation mechanism and in bacterial survival under hypoxia and establish the housekeeping sigma factor SigA as a molecular target of DevR. The interaction of DevR and RNA polymerase suggests a new and novel interceptable molecular interface for future antidormancy strategies for Mycobacterium tuberculosis.
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85
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Magombedze G, Dowdy D, Mulder N. Latent Tuberculosis: Models, Computational Efforts and the Pathogen's Regulatory Mechanisms during Dormancy. Front Bioeng Biotechnol 2013; 1:4. [PMID: 25023946 PMCID: PMC4090907 DOI: 10.3389/fbioe.2013.00004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 08/12/2013] [Indexed: 01/07/2023] Open
Abstract
Latent tuberculosis is a clinical syndrome that occurs after an individual has been exposed to the Mycobacterium tuberculosis (Mtb) Bacillus, the infection has been established and an immune response has been generated to control the pathogen and force it into a quiescent state. Mtb can exit this quiescent state where it is unresponsive to treatment and elusive to the immune response, and enter a rapid replicating state, hence causing infection reactivation. It remains a gray area to understand how the pathogen causes a persistent infection and it is unclear whether the organism will be in a slow replicating state or a dormant non-replicating state. The ability of the pathogen to adapt to changing host immune response mechanisms, in which it is exposed to hypoxia, low pH, nitric oxide (NO), nutrient starvation, and several other anti-microbial effectors, is associated with a high metabolic plasticity that enables it to metabolize under these different conditions. Adaptive gene regulatory mechanisms are thought to coordinate how the pathogen changes their metabolic pathways through mechanisms that sense changes in oxygen tension and other stress factors, hence stimulating the pathogen to make necessary adjustments to ensure survival. Here, we review studies that give insights into latency/dormancy regulatory mechanisms that enable infection persistence and pathogen adaptation to different stress conditions. We highlight what mathematical and computational models can do and what they should do to enhance our current understanding of TB latency.
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Affiliation(s)
- Gesham Magombedze
- National Institute for Mathematical and Biological Synthesis, University of Tennessee, Knoxville, TN, USA
| | - David Dowdy
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Nicola Mulder
- Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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86
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Abstract
Heme is a prosthetic group best known for roles in oxygen transport, oxidative catalysis, and respiratory electron transport. Recent years have seen the roles of heme extended to sensors of gases such as O2 and NO and cell redox state, and as mediators of cellular responses to changes in intracellular levels of these gases. The importance of heme is further evident from identification of proteins that bind heme reversibly, using it as a signal, e.g. to regulate gene expression in circadian rhythm pathways and control heme synthesis itself. In this minireview, we explore the current knowledge of the diverse roles of heme sensor proteins.
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Affiliation(s)
- Hazel M. Girvan
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Andrew W. Munro
- From the Manchester Institute of Biotechnology, Faculty of Life Sciences, University of Manchester, Manchester M1 7DN, United Kingdom
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87
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Chen T, He L, Deng W, Xie J. The Mycobacterium DosR regulon structure and diversity revealed by comparative genomic analysis. J Cell Biochem 2013; 114:1-6. [PMID: 22833514 DOI: 10.1002/jcb.24302] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 07/17/2012] [Indexed: 11/12/2022]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), which claims approximately two million people annually, remains a global health concern. The non-replicating or dormancy like state of this pathogen which is impervious to anti-tuberculosis drugs is widely recognized as the culprit for this scenario. The dormancy survival regulator (DosR) regulon, composed of 48 co-regulated genes, is held as essential for Mtb persistence. The DosR regulon is regulated by a two-component regulatory system consisting of two sensor kinases-DosS (Rv3132c) and DosT (Rv2027c), and a response regulator DosR (Rv3133c). The underlying regulatory mechanism of DosR regulon expression is very complex. Many factors are involved, particularly the oxygen tension. The DosR regulon enables the pathogen to persist during lengthy hypoxia. Comparative genomic analysis demonstrated that the DosR regulon is widely distributed among the mycobacterial genomes, ranging from the pathogenic strains to the environmental strains. In-depth studies on the DosR response should provide insights into its role in TB latency in vivo and shape new measures to combat this exceeding recalcitrant pathogen.
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Affiliation(s)
- Tian Chen
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, School of Life Sciences, Southwest University, Chongqing 400715, China
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88
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Lee HN, Lee NO, Ko IJ, Kim SW, Kang BS, Oh JI. Involvement of the catalytically important Asp54 residue of Mycobacterium smegmatis DevR in protein-protein interactions between DevR and DevS. FEMS Microbiol Lett 2013; 343:26-33. [PMID: 23480849 DOI: 10.1111/1574-6968.12122] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 03/04/2013] [Accepted: 03/04/2013] [Indexed: 11/28/2022] Open
Abstract
The DevSR two-component system in Mycobacterium smegmatis consists of the DevS histidine kinase and the DevR response regulator. It is a regulatory system that is involved in the adaptation of mycobacteria to hypoxic and NO stresses. Using the yeast two-hybrid assay and pull-down assay, it was demonstrated that the phosphoaccepting Asp (Asp54) of DevR is important for protein-protein interactions between DevR and DevS. The negative charge of Asp54 of DevR was shown to play an important role in protein-protein interactions between DevR and DevS. When the Lys104 residue, which is involved in transmission of conformational changes induced by phosphorylation of the response regulator, was replaced with Ala, the mutant form of DevR was not phosphorylated by DevS and functionally inactive in vivo. However, the K104A mutation in DevR only slightly affected protein-protein interactions between DevR and DevS.
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Affiliation(s)
- Ha-Na Lee
- Department of Microbiology, Pusan National University, Busan, Korea
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89
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Cho HY, Lee YH, Bae YS, Kim E, Kang BS. Activation of ATP binding for the autophosphorylation of DosS, a Mycobacterium tuberculosis histidine kinase lacking an ATP lid motif. J Biol Chem 2013; 288:12437-47. [PMID: 23486471 DOI: 10.1074/jbc.m112.442467] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The sensor histidine kinases of Mycobacterium tuberculosis, DosS and DosT, are responsible for sensing hypoxic conditions and consist of sensor and kinase cores responsible for accepting signals and phosphorylation activity, respectively. The kinase core contains a dimerization and histidine phosphate-accepting (DHp) domain and an ATP binding domain (ABD). The 13 histidine kinase genes of M. tuberculosis can be grouped based on the presence or absence of the ATP lid motif and F box (elements known to play roles in ATP binding) in their ABDs; DosS and DosT have ABDs lacking both these elements, and the crystal structures of their ABDs indicated that they were unsuitable for ATP binding, as a short loop covers the putative ATP binding site. Although the ABD alone cannot bind ATP, the kinase core is functional in autophosphorylation. Appropriate spatial arrangement of the ABD and DHp domain within the kinase core is required for both autophosphorylation and ATP binding. An ionic interaction between Arg(440) in the DHp domain and Glu(537) in the short loop of the ABD is available and may open the ATP binding site, by repositioning the short loop away from the site. Mutations at Arg(440) and Glu(537) reduce autophosphorylation activity. Unlike other histidine kinases containing an ATP lid, which protects bound ATP, DosS is unable to accept ATP until the ABD is properly positioned relative to the histidine; this may prevent unexpected ATP reactions. ATP binding can, therefore, function as a control mechanism for histidine kinase activity.
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Affiliation(s)
- Ha Yeon Cho
- School of Life Science and Biotechnology, Kyungpook National University, Daegu 702-701, South Korea
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90
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Liebl U, Lambry JC, Vos MH. Primary processes in heme-based sensor proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1684-92. [PMID: 23485911 DOI: 10.1016/j.bbapap.2013.02.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/08/2013] [Accepted: 02/16/2013] [Indexed: 12/22/2022]
Abstract
A wide and still rapidly increasing range of heme-based sensor proteins has been discovered over the last two decades. At the molecular level, these proteins function as bistable switches in which the catalytic activity of an enzymatic domain is altered mostly by binding or dissociation of small gaseous ligands (O2, NO or CO) to the heme in a sensor domain. The initial "signal" at the heme level is subsequently transmitted within the protein to the catalytic site, ultimately leading to adapted expression levels of specific proteins. Making use of the photolability of the heme-ligand bond that mimics thermal dissociation, early processes in this intra-protein signaling pathway can be followed using ultrafast optical spectroscopic techniques; they also occur on timescales accessible to molecular dynamics simulations. Experimental studies performed over the last decade on proteins including the sensors FixL (O2), CooA (CO) and soluble guanylate cyclase (NO) are reviewed with an emphasis on emerging general mechanisms. After heme-ligand bond breaking, the ligand can escape from the heme pocket and eventually from the protein, or rebind directly to the heme. Remarkably, in all sensor proteins the rebinding, specifically of the sensed ligand, is highly efficient. This "ligand trap" property possibly provides means to smoothen the effects of fast environmental fluctuations on the switching frequency. For 6-coordinate proteins, where exchange between an internal heme-bound residue and external gaseous ligands occurs, the study of early processes starting from the unliganded form indicates that mobility of the internal ligand may facilitate signal transfer. This article is part of a Special Issue entitled: Oxygen Binding and Sensing Proteins.
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Affiliation(s)
- Ursula Liebl
- Laboratory for Optics and Biosciences, CNRS, Ecole Polytechnique, Palaiseau, France
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91
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Nambu S, Matsui T, Goulding CW, Takahashi S, Ikeda-Saito M. A new way to degrade heme: the Mycobacterium tuberculosis enzyme MhuD catalyzes heme degradation without generating CO. J Biol Chem 2013; 288:10101-10109. [PMID: 23420845 DOI: 10.1074/jbc.m112.448399] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MhuD is an oxygen-dependent heme-degrading enzyme from Mycobacterium tuberculosis with high sequence similarity (∼45%) to Staphylococcus aureus IsdG and IsdI. Spectroscopic and mutagenesis studies indicate that the catalytically active 1:1 heme-MhuD complex has an active site structure similar to those of IsdG and IsdI, including the nonplanarity (ruffling) of the heme group bound to the enzyme. Distinct from the canonical heme degradation, we have found that the MhuD catalysis does not generate CO. Product analyses by electrospray ionization-MS and NMR show that MhuD cleaves heme at the α-meso position but retains the meso-carbon atom at the cleavage site, which is removed by canonical heme oxygenases. The novel tetrapyrrole product of MhuD, termed "mycobilin," has an aldehyde group at the cleavage site and a carbonyl group at either the β-meso or the δ-meso position. Consequently, MhuD catalysis does not involve verdoheme, the key intermediate of ring cleavage by canonical heme oxygenase enzymes. Ruffled heme is apparently responsible for the heme degradation mechanism unique to MhuD. In addition, MhuD heme degradation without CO liberation is biologically significant as one of the signals of M. tuberculosis transition to dormancy is mediated by the production of host CO.
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Affiliation(s)
- Shusuke Nambu
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba, Sendai 980-8577, Japan
| | - Toshitaka Matsui
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba, Sendai 980-8577, Japan
| | - Celia W Goulding
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697; Department of Pharmaceutical Sciences, University of California, Irvine, California 92697
| | - Satoshi Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba, Sendai 980-8577, Japan
| | - Masao Ikeda-Saito
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Katahira, Aoba, Sendai 980-8577, Japan.
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92
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Sivaramakrishnan S, de Montellano PRO. The DosS-DosT/DosR Mycobacterial Sensor System. BIOSENSORS 2013; 3:259-282. [PMID: 25002970 PMCID: PMC4082495 DOI: 10.3390/bios3030259] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 06/15/2013] [Accepted: 06/26/2013] [Indexed: 11/16/2022]
Abstract
DosS/DosR is a two-component regulatory system in which DosS, a heme-containing sensor also known as DevS, under certain conditions undergoes autophosphorylation and then transfers the phosphate to DosR, a DNA-binding protein that controls the entry of Mycobacterium tuberculosis and other mycobacteria into a latent, dormant state. DosT, a second sensor closely related to DosS, is present in M. tuberculosis and participates in the control of the dormancy response mediated by DosR. The binding of phosphorylated DosR to DNA initiates the expression of approximately fifty dormancy-linked genes. DosT is accepted to be a gas sensor that is activated in the ferrous state by the absence of an oxygen ligand or by the binding of NO or CO. DosS functions in a similar fashion as a gas sensor, but contradictory evidence has led to the suggestion that it also functions as a redox state sensor. This review focuses on the structure, biophysical properties, and function of the DosS/DosT heme sensors.
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Affiliation(s)
- Santhosh Sivaramakrishnan
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94158, USA;
| | - Paul R Ortiz de Montellano
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94158, USA;
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93
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Cui T, He Z. C-di-GMP signaling and implications for pathogenesis of Mycobacterium tuberculosis. CHINESE SCIENCE BULLETIN-CHINESE 2012. [DOI: 10.1007/s11434-012-5298-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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94
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Chim N, Owens CP, Contreras H, Goulding CW. Withdrawn. Infect Disord Drug Targets 2012:CDTID-EPUB-20121116-2. [PMID: 23167715 PMCID: PMC3695056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Withdrawn by the publisher.
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Affiliation(s)
- Nicholas Chim
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Cedric P. Owens
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Heidi Contreras
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
| | - Celia W. Goulding
- Department of Molecular Biology and Biochemistry, University of California, Irvine CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine CA 92697, USA
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95
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Bhat SA, Singh N, Trivedi A, Kansal P, Gupta P, Kumar A. The mechanism of redox sensing in Mycobacterium tuberculosis. Free Radic Biol Med 2012; 53:1625-41. [PMID: 22921590 DOI: 10.1016/j.freeradbiomed.2012.08.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 08/03/2012] [Accepted: 08/03/2012] [Indexed: 12/25/2022]
Abstract
Tuberculosis epidemics have defied constraint despite the availability of effective treatment for the past half-century. Mycobacterium tuberculosis, the causative agent of TB, is continually exposed to a number of redox stressors during its pathogenic cycle. The mechanisms used by Mtb to sense redox stress and to maintain redox homeostasis are central to the success of Mtb as a pathogen. Careful analysis of the Mtb genome has revealed that Mtb lacks classical redox sensors such as FNR, FixL, and OxyR. Recent studies, however, have established that Mtb is equipped with various sophisticated redox sensors that can detect diverse types of redox stress, including hypoxia, nitric oxide, carbon monoxide, and the intracellular redox environment. Some of these sensors, such as heme-based DosS and DosT, are unique to mycobacteria, whereas others, such as the WhiB proteins and anti-σ factor RsrA, are unique to actinobacteria. This article provides a comprehensive review of the literature on these redox-sensory modules in the context of TB pathogenesis.
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Affiliation(s)
- Shabir Ahmad Bhat
- Council of Scientific and Industrial Research, Institute of Microbial Technology, Chandigarh 160036, India
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96
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Selvaraj S, Sambandam V, Sardar D, Anishetty S. In silico analysis of DosR regulon proteins of Mycobacterium tuberculosis. Gene 2012; 506:233-41. [DOI: 10.1016/j.gene.2012.06.033] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 03/01/2012] [Accepted: 06/18/2012] [Indexed: 11/28/2022]
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97
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Mak PA, Rao SPS, Ping Tan M, Lin X, Chyba J, Tay J, Ng SH, Tan BH, Cherian J, Duraiswamy J, Bifani P, Lim V, Lee BH, Ling Ma N, Beer D, Thayalan P, Kuhen K, Chatterjee A, Supek F, Glynne R, Zheng J, Boshoff HI, Barry CE, Dick T, Pethe K, Camacho LR. A high-throughput screen to identify inhibitors of ATP homeostasis in non-replicating Mycobacterium tuberculosis. ACS Chem Biol 2012; 7:1190-7. [PMID: 22500615 PMCID: PMC3401038 DOI: 10.1021/cb2004884] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Growing evidence suggests that the presence of a subpopulation
of hypoxic non-replicating, phenotypically drug-tolerant mycobacteria
is responsible for the prolonged duration of tuberculosis treatment.
The discovery of new antitubercular agents active against this subpopulation
may help in developing new strategies to shorten the time of tuberculosis
therapy. Recently, the maintenance of a low level of bacterial respiration
was shown to be a point of metabolic vulnerability in Mycobacterium
tuberculosis. Here, we describe the development of a hypoxic
model to identify compounds targeting mycobacterial respiratory functions
and ATP homeostasis in whole mycobacteria. The model was adapted to
1,536-well plate format and successfully used to screen over 600,000
compounds. Approximately 800 compounds were confirmed to reduce intracellular
ATP levels in a dose-dependent manner in Mycobacterium bovis BCG. One hundred and forty non-cytotoxic compounds with activity
against hypoxic non-replicating M. tuberculosis were
further validated. The resulting collection of compounds that disrupt
ATP homeostasis in M. tuberculosis represents a valuable
resource to decipher the biology of persistent mycobacteria.
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Affiliation(s)
- Puiying A. Mak
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
| | | | - Mai Ping Tan
- Novartis Institute for Tropical Diseases, Singapore 138670
| | - Xiuhua Lin
- Novartis Institute for Tropical Diseases, Singapore 138670
| | - Jason Chyba
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
| | - Joann Tay
- Novartis Institute for Tropical Diseases, Singapore 138670
| | - Seow Hwee Ng
- Novartis Institute for Tropical Diseases, Singapore 138670
| | - Bee Huat Tan
- Novartis Institute for Tropical Diseases, Singapore 138670
| | - Joseph Cherian
- Novartis Institute for Tropical Diseases, Singapore 138670
| | | | - Pablo Bifani
- Novartis Institute for Tropical Diseases, Singapore 138670
| | - Vivian Lim
- Novartis Institute for Tropical Diseases, Singapore 138670
| | - Boon Heng Lee
- Novartis Institute for Tropical Diseases, Singapore 138670
| | - Ngai Ling Ma
- Novartis Institute for Tropical Diseases, Singapore 138670
| | - David Beer
- Novartis Institute for Tropical Diseases, Singapore 138670
| | | | - Kelli Kuhen
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
| | - Arnab Chatterjee
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
| | - Frantisek Supek
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
| | - Richard Glynne
- Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, United States
| | - Jun Zheng
- Novartis Institute for Tropical Diseases, Singapore 138670
| | - Helena I. Boshoff
- Tuberculosis Research Section, Laboratory of Clinical
Infectious Diseases, National Institute of Allergy and Infectious
Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Clifton E. Barry
- Tuberculosis Research Section, Laboratory of Clinical
Infectious Diseases, National Institute of Allergy and Infectious
Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Thomas Dick
- Novartis Institute for Tropical Diseases, Singapore 138670
| | - Kevin Pethe
- Novartis Institute for Tropical Diseases, Singapore 138670
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98
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Larsson C, Luna B, Ammerman NC, Maiga M, Agarwal N, Bishai WR. Gene expression of Mycobacterium tuberculosis putative transcription factors whiB1-7 in redox environments. PLoS One 2012; 7:e37516. [PMID: 22829866 PMCID: PMC3400605 DOI: 10.1371/journal.pone.0037516] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 04/20/2012] [Indexed: 12/20/2022] Open
Abstract
The seven WhiB proteins of Mycobacterium tuberculosis (M.tb) are widely believed to be redox-sensing transcription factors due to their binding of iron-sulfur clusters and similarities to DNA binding proteins. Here, we explored the nature of this hypothesized relationship. We exposed M.tb to physiologic conditions such as gradual hypoxia, nitric oxide (NO), cyclic AMP and in vivo conditions, and measured transcription of the whiB genes. We found whiB3 to be induced both by hypoxia and NO, whiB7 to be induced in macrophage-like cells, and whiB4 to be induced in mouse lung. Cyclic AMP induced whiB1,−2, −4, −6 and −7. Our data indicate that the M.tb whiB genes are induced independently by various stimuli which may add versatility to their suggested redox-sensing properties.
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Affiliation(s)
- Christer Larsson
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Brian Luna
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Nicole C. Ammerman
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Mamoudou Maiga
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Nisheeth Agarwal
- Vaccine and Infectious Disease Research Center Translational Health Science and Technology Institute, Gurgaon (Haryana), India
| | - William R. Bishai
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- KwaZulu-Natal Research Institute for Tuberculosis and HIV, Durban, South Africa
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- * E-mail:
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99
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Boon C, Dick T. How Mycobacterium tuberculosis goes to sleep: the dormancy survival regulator DosR a decade later. Future Microbiol 2012; 7:513-8. [PMID: 22439727 DOI: 10.2217/fmb.12.14] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
With 2 million deaths per year, TB remains the most significant bacterial killer. The long duration of chemotherapy and the large pool of latently infected people represent challenges in disease control. To develop drugs that effectively eradicate latent infection and shorten treatment duration, the pathophysiology of the causative agent Mycobacterium tuberculosis needs to be understood. The discovery that the tubercle bacillus can develop a drug-tolerant dormant form and the identification of the underlying genetic program 10 years ago paved the way for a deeper understanding of the life of the parasite inside human lesions and for new approaches to antimycobacterial drug discovery. Here, we summarize what we have learnt since the discovery of the master regulator of dormancy, DosR, and the key gaps in our knowledge that remain. Furthermore, we discuss a possible wider clinical relevance of DosR for 'nontuberculous mycobacteria'.
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Affiliation(s)
- Calvin Boon
- Dx Assays Pte Ltd, Woodlands Central Industrial Estate, 35 Marsiling Industrial Estate Road 3, Unit 02-03/02/01, 739257, Singapore
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100
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Trauner A, Lougheed KEA, Bennett MH, Hingley-Wilson SM, Williams HD. The dormancy regulator DosR controls ribosome stability in hypoxic mycobacteria. J Biol Chem 2012; 287:24053-63. [PMID: 22544737 PMCID: PMC3390679 DOI: 10.1074/jbc.m112.364851] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 04/27/2012] [Indexed: 01/01/2023] Open
Abstract
It is thought that during latent infection, Mycobacterium tuberculosis bacilli are retained within granulomas in a low-oxygen environment. The dormancy survival (Dos) regulon, regulated by the response regulator DosR, appears to be essential for hypoxic survival in M. tuberculosis, but it is not known how the regulon promotes survival. Here we report that mycobacteria, in contrast to enteric bacteria, do not form higher-order structures (e.g. ribosomal dimers) upon entry into stasis. Instead, ribosomes are stabilized in the associated form (70S). Using a strategy incorporating microfluidic, proteomic, and ribosomal profiling techniques to elucidate the fate of mycobacterial ribosomes during hypoxic stasis, we show that the dormancy regulator DosR is required for optimal ribosome stabilization. We present evidence that the majority of this effect is mediated by the DosR-regulated protein MSMEG_3935 (a S30AE domain protein), which is associated with the ribosome under hypoxic conditions. A Δ3935 mutant phenocopies the ΔdosR mutant during hypoxia, and complementation of ΔdosR with the MSMEG_3935 gene leads to complete recovery of dosR mutant phenotypes during hypoxia. We suggest that this protein is named ribosome-associated factor under hypoxia (RafH) and that it is the major factor responsible for DosR-mediated hypoxic survival in mycobacteria.
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Affiliation(s)
- Andrej Trauner
- From the Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Kathryn E. A. Lougheed
- From the Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Mark H. Bennett
- From the Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Suzanne M. Hingley-Wilson
- From the Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Huw D. Williams
- From the Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
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