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Novak JK, Gardner JG. Current models in bacterial hemicellulase-encoding gene regulation. Appl Microbiol Biotechnol 2024; 108:39. [PMID: 38175245 PMCID: PMC10766802 DOI: 10.1007/s00253-023-12977-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 01/05/2024]
Abstract
The discovery and characterization of bacterial carbohydrate-active enzymes is a fundamental component of biotechnology innovation, particularly for renewable fuels and chemicals; however, these studies have increasingly transitioned to exploring the complex regulation required for recalcitrant polysaccharide utilization. This pivot is largely due to the current need to engineer and optimize enzymes for maximal degradation in industrial or biomedical applications. Given the structural simplicity of a single cellulose polymer, and the relatively few enzyme classes required for complete bioconversion, the regulation of cellulases in bacteria has been thoroughly discussed in the literature. However, the diversity of hemicelluloses found in plant biomass and the multitude of carbohydrate-active enzymes required for their deconstruction has resulted in a less comprehensive understanding of bacterial hemicellulase-encoding gene regulation. Here we review the mechanisms of this process and common themes found in the transcriptomic response during plant biomass utilization. By comparing regulatory systems from both Gram-negative and Gram-positive bacteria, as well as drawing parallels to cellulase regulation, our goals are to highlight the shared and distinct features of bacterial hemicellulase-encoding gene regulation and provide a set of guiding questions to improve our understanding of bacterial lignocellulose utilization. KEY POINTS: • Canonical regulatory mechanisms for bacterial hemicellulase-encoding gene expression include hybrid two-component systems (HTCS), extracytoplasmic function (ECF)-σ/anti-σ systems, and carbon catabolite repression (CCR). • Current transcriptomic approaches are increasingly being used to identify hemicellulase-encoding gene regulatory patterns coupled with computational predictions for transcriptional regulators. • Future work should emphasize genetic approaches to improve systems biology tools available for model bacterial systems and emerging microbes with biotechnology potential. Specifically, optimization of Gram-positive systems will require integration of degradative and fermentative capabilities, while optimization of Gram-negative systems will require bolstering the potency of lignocellulolytic capabilities.
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Affiliation(s)
- Jessica K Novak
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA
| | - Jeffrey G Gardner
- Department of Biological Sciences, University of Maryland - Baltimore County, Baltimore, MD, USA.
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2
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Garg R, Manhas I, Chaturvedi D. Unveiling the orchestration: mycobacterial small RNAs as key mediators in host-pathogen interactions. Front Microbiol 2024; 15:1399280. [PMID: 38903780 PMCID: PMC11188477 DOI: 10.3389/fmicb.2024.1399280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
Small RNA (sRNA) molecules, a class of non-coding RNAs, have emerged as pivotal players in the regulation of gene expression and cellular processes. Mycobacterium tuberculosis and other pathogenic mycobacteria produce diverse small RNA species that modulate bacterial physiology and pathogenesis. Recent advances in RNA sequencing have enabled identification of novel small RNAs and characterization of their regulatory functions. This review discusses the multifaceted roles of bacterial small RNAs, covering their biogenesis, classification, and functional diversity. Small RNAs (sRNAs) play pivotal roles in orchestrating diverse cellular processes, ranging from gene silencing to epigenetic modifications, across a broad spectrum of organisms. While traditionally associated with eukaryotic systems, recent research has unveiled their presence and significance within bacterial domains as well. Unlike their eukaryotic counterparts, which primarily function within the context of RNA interference (RNAi) pathways, bacterial sRNAs predominantly act through base-pairing interactions with target mRNAs, leading to post-transcriptional regulation. This fundamental distinction underscores the necessity of elucidating the unique roles and regulatory mechanisms of bacterial sRNAs in bacterial adaptation and survival. By doing these myriad functions, they regulate bacterial growth, metabolism, virulence, and drug resistance. In Mycobacterium tuberculosis, apart from having various roles in the bacillus itself, small RNA molecules have emerged as key regulators of gene expression and mediators of host-pathogen interactions. Understanding sRNA regulatory networks in mycobacteria can drive our understanding of significant role they play in regulating virulence and adaptation to the host environment. Detailed functional characterization of Mtb sRNAs at the host-pathogen interface is required to fully elucidate the complex sRNA-mediated gene regulatory networks deployed by Mtb, to manipulate the host. A deeper understanding of this aspect could pave the development of novel diagnostic and therapeutic strategies for tuberculosis.
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Affiliation(s)
- Rajni Garg
- Department of Human Genetics and Molecular Medicine, Amity School of Health Sciences, Amity University, Mohali, Punjab, India
| | - Ishali Manhas
- Department of Biotechnology, Amity School of Biological Sciences, Amity University, Mohali, Punjab, India
| | - Diksha Chaturvedi
- Department of Biotechnology and Medical Engineering, National Institute of Technology, Rourkela, Odisha, India
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3
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Gupta VK, Vaishnavi VV, Arrieta-Ortiz ML, P S A, K M J, Jeyasankar S, Raghunathan V, Baliga NS, Agarwal R. 3D Hydrogel Culture System Recapitulates Key Tuberculosis Phenotypes and Demonstrates Pyrazinamide Efficacy. Adv Healthc Mater 2024:e2304299. [PMID: 38655817 DOI: 10.1002/adhm.202304299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/29/2024] [Indexed: 04/26/2024]
Abstract
The mortality caused by tuberculosis (TB) infections is a global concern, and there is a need to improve understanding of the disease. Current in vitro infection models to study the disease have limitations such as short investigation durations and divergent transcriptional signatures. This study aims to overcome these limitations by developing a 3D collagen culture system that mimics the biomechanical and extracellular matrix (ECM) of lung microenvironment (collagen fibers, stiffness comparable to in vivo conditions) as the infection primarily manifests in the lungs. The system incorporates Mycobacterium tuberculosis (Mtb) infected human THP-1 or primary monocytes/macrophages. Dual RNA sequencing reveals higher mammalian gene expression similarity with patient samples than 2D macrophage infections. Similarly, bacterial gene expression more accurately recapitulates in vivo gene expression patterns compared to bacteria in 2D infection models. Key phenotypes observed in humans, such as foamy macrophages and mycobacterial cords, are reproduced in the model. This biomaterial system overcomes challenges associated with traditional platforms by modulating immune cells and closely mimicking in vivo infection conditions, including showing efficacy with clinically relevant concentrations of anti-TB drug pyrazinamide, not seen in any other in vitro infection model, making it reliable and readily adoptable for tuberculosis studies and drug screening.
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Affiliation(s)
- Vishal K Gupta
- Department of Bioengineering, Indian Institute of Science, CV Raman Road, Bengaluru, Karnataka, 560012, India
| | - Vijaya V Vaishnavi
- Department of Bioengineering, Indian Institute of Science, CV Raman Road, Bengaluru, Karnataka, 560012, India
| | | | - Abhirami P S
- Department of Bioengineering, Indian Institute of Science, CV Raman Road, Bengaluru, Karnataka, 560012, India
| | - Jyothsna K M
- Department of Electrical Communication Engineering, Indian Institute of Science, CV Raman Road, Bengaluru, Karnataka, 560012, India
| | - Sharumathi Jeyasankar
- Department of Bioengineering, Indian Institute of Science, CV Raman Road, Bengaluru, Karnataka, 560012, India
| | - Varun Raghunathan
- Department of Electrical Communication Engineering, Indian Institute of Science, CV Raman Road, Bengaluru, Karnataka, 560012, India
| | - Nitin S Baliga
- Institute of Systems Biology, 401 Terry Ave N, Seattle, WA, 98109, USA
| | - Rachit Agarwal
- Department of Bioengineering, Indian Institute of Science, CV Raman Road, Bengaluru, Karnataka, 560012, India
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4
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Mitermite M, Elizari JMU, Ma R, Farrell D, Gordon SV. Exploring virulence in Mycobacterium bovis: clues from comparative genomics and perspectives for the future. Ir Vet J 2023; 76:26. [PMID: 37770951 PMCID: PMC10540498 DOI: 10.1186/s13620-023-00257-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 09/19/2023] [Indexed: 09/30/2023] Open
Abstract
Here we provide a summary of a plenary lecture delivered on Mycobacterium bovis, the bovine TB bacillus, at the M. bovis 2022 meeting held in Galway, Ireland, in June 2022. We focus on the analysis of genetic differences between M. bovis and the human pathogen Mycobacterium tuberculosis as a route to gain knowledge on what makes M. bovis function as an animal pathogen. We provide a brief historical background around M. bovis and comparative virulence experiments with M. tuberculosis, before moving to what we have learned from the studies of the M. bovis genome sequence. We discuss the need to translate knowledge on the molecular basis of virulence in M. bovis into improved control of bovine tuberculosis.
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Affiliation(s)
- Morgane Mitermite
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Jose Maria Urtasun Elizari
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Ruoyao Ma
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland.
- UCD School of Medicine, University College Dublin, Dublin, Ireland.
- UCD School of Biomolecular and Biomedical Science, University College Dublin, Dublin, Ireland.
- UCD Conway Institute, University College Dublin, Dublin, Ireland.
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5
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Singha B, Behera D, Khan MZ, Singh NK, Sowpati DT, Gopal B, Nandicoori VK. The unique N-terminal region of Mycobacterium tuberculosis sigma factor A plays a dominant role in the essential function of this protein. J Biol Chem 2023; 299:102933. [PMID: 36690275 PMCID: PMC10011835 DOI: 10.1016/j.jbc.2023.102933] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/22/2023] Open
Abstract
SigA (σA) is an essential protein and the primary sigma factor in Mycobacterium tuberculosis (Mtb). However, due to the absence of genetic tools, our understanding of the role and regulation of σA activity and its molecular attributes that help modulate Mtb survival is scant. Here, we generated a conditional gene replacement of σA in Mtb and showed that its depletion results in a severe survival defect in vitro, ex vivo, and in vivo in a murine infection model. Our RNA-seq analysis suggests that σA either directly or indirectly regulates ∼57% of the Mtb transcriptome, including ∼28% of essential genes. Surprisingly, we note that despite having ∼64% similarity with σA, overexpression of the primary-like σ factor SigB (σB) fails to compensate for the absence of σA, suggesting minimal functional redundancy. RNA-seq analysis of the Mtb σB deletion mutant revealed that 433 genes are regulated by σB, of which 283 overlap with the σA transcriptome. Additionally, surface plasmon resonance, in vitro transcription, and functional complementation experiments reveal that σA residues between 132-179 that are disordered and missing from all experimentally determined σA-RNAP structural models are imperative for σA function. Moreover, phosphorylation of σA in the intrinsically disordered N-terminal region plays a regulatory role in modulating its activity. Collectively, these observations and analysis provide a rationale for the centrality of σA for the survival and pathogenicity of this bacillus.
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Affiliation(s)
- Biplab Singha
- National Institute of Immunology, New Delhi, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Debashree Behera
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | | | | | | | | | - Vinay Kumar Nandicoori
- National Institute of Immunology, New Delhi, India; CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
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Rehna EA, Munavar H, Dharmalingam K, Shakila M, Natesan S. Mycobacterium leprae hsp18 promoter-EGFP transcriptional fusion construct: Environmental stress and strain-specific expression. Gene 2022; 851:147034. [DOI: 10.1016/j.gene.2022.147034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 10/25/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
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Chhaya A, Sharma A, Dattu Hade M, Kaur J, Dikshit KL. Transcript analysis and expression of the glbO gene, encoding truncated hemoglobin,O, of M. smegmatis implicate its role under hypoxia and oxidative stress. Gene X 2022; 841:146759. [PMID: 35933051 DOI: 10.1016/j.gene.2022.146759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 07/24/2022] [Indexed: 12/12/2022] Open
Abstract
Although truncated hemoglobin O, (trHbO), is ubiquitous among mycobacteria, its physiological function is not very obvious and may be diverse. In an attempt to understand role of trHbO in cellular metabolism of a non-pathogenic mycobacterium, we analysed expression profile of the glbO gene, encoding trHbO, in M. smegmatis and studied implications of its overexpression on physiology of its host under different environmental conditions. Quantitative RT-PCR indicated that transcript level of the glbO gene remains low at a basal level under aerobic growth cycle of M. smegmatis but its level gets induced significantly during low oxygen, oxidative stress and macrophage infection. Overexpression of the glbO gene enhanced growth of M. smegmatis under hypoxia, promoted pellicle biofilm formation and provided resistance towards oxidative stress. Additionally, glbO gene overexpressing M. smegmatis exhibited enhanced cell survival over isogenic control cells and altered the level of pro- and anti- inflammatory cytokines during intracellular infection. These results suggested important role of trHbO, in supporting the cellular metabolism and survival of M, smegmatis both under low oxygen and oxidative stress.
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Affiliation(s)
- Ajay Chhaya
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Aashish Sharma
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Mangesh Dattu Hade
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Jagdeep Kaur
- Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Kanak L Dikshit
- Department of Biotechnology, Panjab University, Chandigarh 160014, India.
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Sengupta S, Bhawsinghka N, Shaw R, Patra MM, Das Gupta SK. Mycobacteriophage D29 induced association of Mycobacterial RNA polymerase with ancillary factors leads to increased transcriptional activity. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35353035 DOI: 10.1099/mic.0.001158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Mycobacteriophage D29 infects species belonging to the genus Mycobacterium including the deadly pathogen Mycobacterium tuberculosis. D29 is a lytic phage, although, related to the lysogenic mycobacteriophage L5. This phage is unable to lysogenize in mycobacteria as it lacks the gene encoding the phage repressor. Infection by many mycobacteriophages cause various changes in the host that ultimately leads to inactivation of the latter. One of the host targets often modified in the process is RNA polymerase. During our investigations with phage D29 infected Mycobacterium smegmatis (Msm) we observed that the promoters from both phage, and to a lesser extent those of the host were found to be more active in cells that were exposed to D29, as compared to the unexposed. Further experiments indicate that the RNA polymerase purified from phage infected cells possessed higher affinity for promoters particularly those that were phage derived. Comparison of the purified RNA polymerase preparations from infected and uninfected cells showed that several ancillary transcription factors, Sigma factor F, Sigma factor H, CarD and RbpA are prominently associated with the RNA polymerase from infected cells. Based on our observations we conclude that the higher activity of RNA polymerase observed in D29 infected cells is due to its increased association with ancillary transcription factors.
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Affiliation(s)
- Shreya Sengupta
- Department of Microbiology, Bose Institute, P-1/12 C.I.T Road. Scheme VIIM, Kolkata-700054, West Bengal, India
| | - Niketa Bhawsinghka
- Department of Microbiology, Bose Institute, P-1/12 C.I.T Road. Scheme VIIM, Kolkata-700054, West Bengal, India.,Present address: Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Rahul Shaw
- Department of Microbiology, Bose Institute, P-1/12 C.I.T Road. Scheme VIIM, Kolkata-700054, West Bengal, India
| | - Madhu Manti Patra
- Department of Microbiology, Bose Institute, P-1/12 C.I.T Road. Scheme VIIM, Kolkata-700054, West Bengal, India
| | - Sujoy K Das Gupta
- Department of Microbiology, Bose Institute, P-1/12 C.I.T Road. Scheme VIIM, Kolkata-700054, West Bengal, India
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Jiang Z, Zhuang Z, Mi K. Experimental Evolution Reveals Redox State Modulates Mycobacterial Pathogenicity. Front Genet 2022; 13:758304. [PMID: 35368697 PMCID: PMC8965865 DOI: 10.3389/fgene.2022.758304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 02/10/2022] [Indexed: 11/19/2022] Open
Abstract
Understanding how Mycobacterium tuberculosis has evolved into a professional pathogen is helpful in studying its pathogenesis and for designing vaccines. We investigated how the evolutionary adaptation of M. smegmatis mc251 to an important clinical stressor H2O2 allows bacteria to undergo coordinated genetic mutations, resulting in increased pathogenicity. Whole-genome sequencing identified a mutation site in the fur gene, which caused increased expression of katG. Using a Wayne dormancy model, mc251 showed a growth advantage over its parental strain mc2155 in recovering from dormancy under anaerobic conditions. Meanwhile, the high level of KatG in mc251 was accompanied by a low level of ATP, which meant that mc251 is at a low respiratory level. Additionally, the redox-related protein Rv1996 showed different phenotypes in different specific redox states in M. smegmatis mc2155 and mc251, M. bovis BCG, and M. tuberculosis mc27000. In conclusion, our study shows that the same gene presents different phenotypes under different physiological conditions. This may partly explain why M. smegmatis and M. tuberculosis have similar virulence factors and signaling transduction systems such as two-component systems and sigma factors, but due to the different redox states in the corresponding bacteria, M. smegmatis is a nonpathogen, while M. tuberculosis is a pathogen. As mc251 overcomes its shortcomings of rapid removal, it can potentially be developed as a vaccine vector.
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Affiliation(s)
- Zheng Jiang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Zengfang Zhuang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
| | - Kaixia Mi
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing, China
- *Correspondence: Kaixia Mi,
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An extracytoplasmic function (ECF) sigma/anti-sigma factor system regulates hypochlorous acid resistance and impacts expression of the type IV secretion system in Brucella melitensis. J Bacteriol 2021; 203:e0012721. [PMID: 33820796 PMCID: PMC8315932 DOI: 10.1128/jb.00127-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The intracellular bacterial pathogen Brucella causes persistent infections in various mammalian species. To survive and replicate within macrophages, these bacteria must be able to withstand oxidative stresses and express the type IV secretion system (T4SS) to evade host immune responses. The extracytoplasmic function (ECF) sigma factor system is a major signal transduction mechanism in bacteria that senses environmental cues and responds by regulating gene expression. In this study, we defined an ECF σ bcrS and its cognate anti-σ factor abcS in Brucella melitensis M28 by conserved domain analysis and a protein interaction assay. BcrS directly activates an adjacent operon, bcrXQP, that encodes a methionine-rich peptide and a putative methionine sulfoxide reductase system, whereas AbcS is a negative regulator of bcrS and bcrXQP. The bcrS-abcS and bcrXQP operons can be induced by hypochlorous acid and contribute to hypochlorous acid resistance in vitro. Next, RNA sequencing analysis and genome-wide recognition sequence search identified the regulons of BcrS and AbcS. Interestingly, we found that BcrS positively influences T4SS expression in an AbcS-dependent manner and that AbcS also affects T4SS expression independently of BcrS. Last, we demonstrate that abcS is required for the maintenance of persistent infection, while bcrS is dispensable in a mouse infection model. Collectively, we conclude that BcrS and AbcS influence expression of multiple genes responsible for Brucella virulence traits. IMPORTANCEBrucella is a notorious intracellular pathogen that induces chronic infections in animals and humans. To survive and replicate within macrophages, these bacteria require a capacity to withstand oxidative stresses and to express the type IV secretion system (T4SS) to combat host immune responses. In this study, we characterized an extracytoplasmic function sigma/anti-sigma factor system that regulates resistance to reactive chlorine species and T4SS expression, thereby establishing a potential link between two crucial virulence traits of Brucella. Furthermore, the anti-sigma factor AbcS contributes to Brucella persistent infection of mice. Thus, this work provides novel insights into Brucella virulence regulation as well as a potential drug target for fighting Brucella infections.
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Grosse-Siestrup BT, Gupta T, Helms S, Tucker SL, Voskuil MI, Quinn FD, Karls RK. A Role for Mycobacterium tuberculosis Sigma Factor C in Copper Nutritional Immunity. Int J Mol Sci 2021; 22:2118. [PMID: 33672733 PMCID: PMC7924339 DOI: 10.3390/ijms22042118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 02/09/2021] [Accepted: 02/17/2021] [Indexed: 11/22/2022] Open
Abstract
Sigma factor C (SigC) contributes to Mycobacterium tuberculosis virulence in various animal models, but the stress response coordinated by this transcription factor was undefined. The results presented here indicate that SigC prevents copper starvation. Whole genome expression studies demonstrate short-term (4-h) induction of sigC, controlled from a tetracycline-inducible promoter, upregulates ctpB and genes in the nonribosomal peptide synthase (nrp) operon. These genes are expressed at higher levels after 48-h sigC induction, but also elevated are genes encoding copper-responsive regulator RicR and RicR-regulated copper toxicity response operon genes rv0846-rv0850, suggesting prolonged sigC induction results in excessive copper uptake. No growth and global transcriptional differences are observed between a sigC null mutant relative to its parent strain in 7H9 medium. In a copper-deficient medium, however, growth of the sigC deletion strain lags the parent, and 40 genes (including those in the nrp operon) are differentially expressed. Copper supplementation reverses the growth defect and silences most transcriptional differences. Together, these data support SigC as a transcriptional regulator of copper acquisition when the metal is scarce. Attenuation of sigC mutants in severe combined immunodeficient mice is consistent with an inability to overcome innate host defenses that sequester copper ions to deprive invading microbes of this essential micronutrient.
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Affiliation(s)
- Benjamin T. Grosse-Siestrup
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (B.T.G.-S.); (T.G.); (S.H.); (S.L.T.); (F.D.Q.)
| | - Tuhina Gupta
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (B.T.G.-S.); (T.G.); (S.H.); (S.L.T.); (F.D.Q.)
| | - Shelly Helms
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (B.T.G.-S.); (T.G.); (S.H.); (S.L.T.); (F.D.Q.)
| | - Samantha L. Tucker
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (B.T.G.-S.); (T.G.); (S.H.); (S.L.T.); (F.D.Q.)
| | - Martin I. Voskuil
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA;
| | - Frederick D. Quinn
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (B.T.G.-S.); (T.G.); (S.H.); (S.L.T.); (F.D.Q.)
| | - Russell K. Karls
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (B.T.G.-S.); (T.G.); (S.H.); (S.L.T.); (F.D.Q.)
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Dey U, Sarkar S, Teronpi V, Yella VR, Kumar A. G-quadruplex motifs are functionally conserved in cis-regulatory regions of pathogenic bacteria: An in-silico evaluation. Biochimie 2021; 184:40-51. [PMID: 33548392 DOI: 10.1016/j.biochi.2021.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 02/06/2023]
Abstract
The role of G-quadruplexes in the cellular physiology of human pathogenesis is an intriguing area of research. Nonetheless, their functional roles and evolutionary conservation have not been compared comprehensively in pathogenic forms of various bacterial genera and species. In the current in silico study, we addressed the role of G-quadruplex-forming sequences (G4 motifs) in the context of cis-regulation, expression variation, regulatory networks, gene orthology and ontology. Genome-wide screening across seven pathogenic genomes using the G4Hunter tool revealed the significant prevalence of G4 motifs in cis-regulatory regions compared to the intragenic regions. Significant conservation of G4 motifs was observed in the regulatory region of 300 orthologous genes. Further analysis of published ChIP-Seq data (Minch et al., 2015) of 91 DNA-binding proteins of the M. tuberculosis genome revealed significant links between G4 motifs and target sites of transcriptional regulators. Interestingly, the transcription factors entangled with virulence, in specific, CsoR, Rv0081, DevR/DosR, and TetR family are found to have G4 motifs in their target regulatory regions. Overall the current study applies positional-functional relationship computation to delve into the cis-regulation of G-quadruplex structures in the context of gene orthology in pathogenic bacteria.
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Affiliation(s)
- Upalabdha Dey
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India
| | - Sharmilee Sarkar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India
| | - Valentina Teronpi
- Department of Zoology, Pandit Deendayal Upadhyaya Adarsha Mahavidyalaya, Behali, Biswanath, 784184, Assam, India
| | - Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, 522502, Andhra Pradesh, India.
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, 784028, Assam, India.
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BCG and BCGΔBCG1419c protect type 2 diabetic mice against tuberculosis via different participation of T and B lymphocytes, dendritic cells and pro-inflammatory cytokines. NPJ Vaccines 2020; 5:21. [PMID: 32194998 PMCID: PMC7067831 DOI: 10.1038/s41541-020-0169-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/20/2020] [Indexed: 02/08/2023] Open
Abstract
Comorbidity between Tuberculosis (TB) and type 2 diabetes (T2D) is one of the greatest contributors to the spread of Mycobacterium tuberculosis (M. tuberculosis) in low- and middle-income countries. T2D compromises key steps of immune responses against M. tuberculosis and it might affect the protection afforded by vaccine candidates against TB. We compared the protection and immune response afforded by the BCGΔBCG1419c vaccine candidate versus that of wild-type BCG in mice with T2D. Vaccination with both BCGΔBCG1419c, BCG or infection with M. tuberculosis reduced weight loss, hyperglycemia, and insulin resistance during T2D progression, suggesting that metabolic changes affecting these parameters were affected by mycobacteria. For control of acute TB, and compared with non-vaccinated controls, BCG showed a dominant T CD4+ response whereas BCGΔBCG1419c showed a dominant T CD8+/B lymphocyte response. Moreover, BCG maintained an increased response in lung cells via IFN-γ, TNF-α, and IL-4, while BCGΔBCG1419c increased IFN-γ but reduced IL-4 production. As for chronic TB, and compared with non-vaccinated controls, both BCG strains had a predominant presence of T CD4+ lymphocytes. In counterpart, BCGΔBCG1419c led to increased presence of dendritic cells and an increased production of IL-1 β. Overall, while BCG effectively reduced pneumonia in acute infection, it failed to reduce it in chronic infection, whereas we hypothesize that increased production of IL-1 β induced by BCGΔBCG1419c contributed to reduced pneumonia and alveolitis in chronic TB. Our results show that BCG and BCGΔBCG1419c protect T2D mice against TB via different participation of T and B lymphocytes, dendritic cells, and pro-inflammatory cytokines.
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14
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Behra PRK, Pettersson BMF, Ramesh M, Dasgupta S, Kirsebom LA. Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members. Sci Rep 2019; 9:19259. [PMID: 31848383 PMCID: PMC6917791 DOI: 10.1038/s41598-019-55464-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/12/2019] [Indexed: 11/09/2022] Open
Abstract
Nontuberculous mycobacteria, NTM, are of growing concern and among these members of the Mycobacterium mucogenicum (Mmuc) and Mycobacterium neoaurum (Mneo) clades can cause infections in humans and they are resistant to first-line anti-tuberculosis drugs. They can be isolated from different ecological niches such as soil, tap water and ground water. Mycobacteria, such as Mmuc and Mneo, are classified as rapid growing mycobacteria, RGM, while the most familiar, Mycobacterium tuberculosis, belongs to the slow growing mycobacteria, SGM. Modern “omics” approaches have provided new insights into our understanding of the biology and evolution of this group of bacteria. Here we present comparative genomics data for seventeen NTM of which sixteen belong to the Mmuc- and Mneo-clades. Focusing on virulence genes, including genes encoding sigma/anti-sigma factors, serine threonine protein kinases (STPK), type VII (ESX genes) secretion systems and mammalian cell entry (Mce) factors we provide insight into their presence as well as phylogenetic relationship in the case of the sigma/anti-sigma factors and STPKs. Our data further suggest that these NTM lack ESX-5 and Mce2 genes, which are known to affect virulence. In this context, Mmuc- and Mneo-clade members lack several of the genes in the glycopeptidolipid (GLP) locus, which have roles in colony morphotype appearance and virulence. For the M. mucogenicum type strain, MmucT, we provide RNASeq data focusing on mRNA levels for sigma factors, STPK, ESX proteins and Mce proteins. These data are discussed and compared to in particular the SGM and fish pathogen Mycobacterium marinum. Finally, we provide insight into as to why members of the Mmuc- and Mneo-clades show resistance to rifampin and isoniazid, and why MmucT forms a rough colony morphotype.
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Affiliation(s)
- Phani Rama Krishna Behra
- Department of Cell and Molecular Biology, Box 596, BMC, Uppsala University, SE 751 24, Uppsala, Sweden
| | - B M Fredrik Pettersson
- Department of Cell and Molecular Biology, Box 596, BMC, Uppsala University, SE 751 24, Uppsala, Sweden
| | - Malavika Ramesh
- Department of Cell and Molecular Biology, Box 596, BMC, Uppsala University, SE 751 24, Uppsala, Sweden
| | - Santanu Dasgupta
- Department of Cell and Molecular Biology, Box 596, BMC, Uppsala University, SE 751 24, Uppsala, Sweden
| | - Leif A Kirsebom
- Department of Cell and Molecular Biology, Box 596, BMC, Uppsala University, SE 751 24, Uppsala, Sweden.
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15
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Dutta D, Srivastava V, Tripathi A, Singh V, Ansari MM, Pant G, Mishra M, Sharma S, Thota JR, Singh PK, Singh BN. Mycobacterium bovis sigF mutant exhibits altered surface phenotype and compromised pathogenesis. Tuberculosis (Edinb) 2019; 118:101855. [PMID: 31430695 DOI: 10.1016/j.tube.2019.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Debashis Dutta
- Department of Immunology and Microbiology, The Scripps Research Institute, 130 Scripps Way, 3C1, FL33458, USA; Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| | - Vishal Srivastava
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| | - Ashutosh Tripathi
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| | - Vandana Singh
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| | - Mohd Mustkim Ansari
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| | - Garima Pant
- Electron Microscopy Unit, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| | - Manisha Mishra
- CSIR-National Botanical Research Institute, Lucknow, 226001, India.
| | - Sharad Sharma
- Division of Toxicology and Experimental Medicine, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| | - Jagadehswar Reddy Thota
- Sophisticated Analytical Instrument Facility, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
| | | | - Bhupendra N Singh
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, India.
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16
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Li X, Lv X, Lin Y, Zhen J, Ruan C, Duan W, Li Y, Xie J. Role of two-component regulatory systems in intracellular survival of Mycobacterium tuberculosis. J Cell Biochem 2019; 120:12197-12207. [PMID: 31026098 DOI: 10.1002/jcb.28792] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 01/11/2019] [Accepted: 01/14/2019] [Indexed: 11/06/2022]
Abstract
The typical two-component regulatory systems (TCSs), consisting of response regulator and histidine kinase, play a central role in survival of pathogenic bacteria under stress conditions such as nutrient starvation, hypoxia, and nitrosative stress. A total of 11 complete paired two-component regulatory systems have been found in Mycobacterium tuberculosis, including a few isolated kinase and regulatory genes. Increasing evidence has shown that TCSs are closely associated with multiple physiological process like intracellular persistence, pathogenicity, and metabolism. This review gives the two-component signal transduction systems in M. tuberculosis and their signal transduction roles in adaption to the environment.
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Affiliation(s)
- Xue Li
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Xi Lv
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Yanping Lin
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Junfeng Zhen
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Cao Ruan
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Wei Duan
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Yue Li
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
| | - Jianping Xie
- State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Institute of Modern Biopharmaceuticals, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
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17
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Martini MC, Zhou Y, Sun H, Shell SS. Defining the Transcriptional and Post-transcriptional Landscapes of Mycobacterium smegmatis in Aerobic Growth and Hypoxia. Front Microbiol 2019; 10:591. [PMID: 30984135 PMCID: PMC6448022 DOI: 10.3389/fmicb.2019.00591] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 03/08/2019] [Indexed: 12/13/2022] Open
Abstract
The ability of Mycobacterium tuberculosis to infect, proliferate, and survive during long periods in the human lungs largely depends on the rigorous control of gene expression. Transcriptome-wide analyses are key to understanding gene regulation on a global scale. Here, we combine 5′-end-directed libraries with RNAseq expression libraries to gain insight into the transcriptome organization and post-transcriptional mRNA cleavage landscape in mycobacteria during log phase growth and under hypoxia, a physiologically relevant stress condition. Using the model organism Mycobacterium smegmatis, we identified 6,090 transcription start sites (TSSs) with high confidence during log phase growth, of which 67% were categorized as primary TSSs for annotated genes, and the remaining were classified as internal, antisense, or orphan, according to their genomic context. Interestingly, over 25% of the RNA transcripts lack a leader sequence, and of the coding sequences that do have leaders, 53% lack a strong consensus Shine-Dalgarno site. This indicates that like M. tuberculosis, M. smegmatis can initiate translation through multiple mechanisms. Our approach also allowed us to identify over 3,000 RNA cleavage sites, which occur at a novel sequence motif. To our knowledge, this represents the first report of a transcriptome-wide RNA cleavage site map in mycobacteria. The cleavage sites show a positional bias toward mRNA regulatory regions, highlighting the importance of post-transcriptional regulation in gene expression. We show that in low oxygen, a condition associated with the host environment during infection, mycobacteria change their transcriptomic profiles and endonucleolytic RNA cleavage is markedly reduced, suggesting a mechanistic explanation for previous reports of increased mRNA half-lives in response to stress. In addition, a number of TSSs were triggered in hypoxia, 56 of which contain the binding motif for the sigma factor SigF in their promoter regions. This suggests that SigF makes direct contributions to transcriptomic remodeling in hypoxia-challenged mycobacteria. Taken together, our data provide a foundation for further study of both transcriptional and posttranscriptional regulation in mycobacteria.
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Affiliation(s)
- M Carla Martini
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Ying Zhou
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Huaming Sun
- Program in Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA, United States
| | - Scarlet S Shell
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA, United States.,Program in Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, MA, United States
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18
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Vashist A, Malhotra V, Sharma G, Tyagi JS, Clark-Curtiss JE. Interplay of PhoP and DevR response regulators defines expression of the dormancy regulon in virulent Mycobacterium tuberculosis. J Biol Chem 2018; 293:16413-16425. [PMID: 30181216 PMCID: PMC6200940 DOI: 10.1074/jbc.ra118.004331] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/15/2018] [Indexed: 11/06/2022] Open
Abstract
The DevR response regulator of Mycobacterium tuberculosis is an established regulator of the dormancy response in mycobacteria and can also be activated during aerobic growth conditions in avirulent strains, suggesting a complex regulatory system. Previously, we reported culture medium-specific aerobic induction of the DevR regulon genes in avirulent M. tuberculosis H37Ra that was absent in the virulent H37Rv strain. To understand the underlying basis of this differential response, we have investigated aerobic expression of the Rv3134c-devR-devS operon using M. tuberculosis H37Ra and H37Rv devR overexpression strains, designated as LIX48 and LIX50, respectively. Overexpression of DevR led to the up-regulation of a large number of DevR regulon genes in aerobic cultures of LIX48, but not in LIX50. To ascertain the involvement of PhoP response regulator, also known to co-regulate a subset of DevR regulon genes, we complemented the naturally occurring mutant phoPRa gene of LIX48 with the WT phoPRv gene. PhoPRv dampened the induced expression of the DevR regulon by >70-80%, implicating PhoP in the negative regulation of devR expression. Electrophoretic mobility shift assays confirmed phosphorylation-independent binding of PhoPRv to the Rv3134c promoter and further revealed that DevR and PhoPRv proteins exhibit differential DNA binding properties to the target DNA. Through co-incubations with DNA, ELISA, and protein complementation assays, we demonstrate that DevR forms a heterodimer with PhoPRv but not with the mutant PhoPRa protein. The study puts forward a new possible mechanism for coordinated expression of the dormancy regulon, having implications in growth adaptations critical for development of latency.
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Affiliation(s)
- Atul Vashist
- the Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Vandana Malhotra
- the Center for Infectious Diseases and Vaccinology, Biodesign Institute, and
- From the Department of Biochemistry, Sri Venkateswara College, University of Delhi, New Delhi 110021, India
| | - Gunjan Sharma
- the Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Jaya Sivaswami Tyagi
- the Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Josephine E Clark-Curtiss
- 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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19
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Gomide ACP, Ibraim IC, Alves JTC, de Sá PG, de Oliveira Silva YR, Santana MP, Silva WM, Folador EL, Mariano DCB, de Paula Castro TL, Barbosa S, Dorella FA, Carvalho AF, Pereira FL, Leal CAG, Figueiredo HCP, Azevedo V, Silva A, Folador ARC. Transcriptome analysis of Corynebacterium pseudotuberculosis biovar Equi in two conditions of the environmental stress. Gene 2018; 677:349-360. [PMID: 30098432 DOI: 10.1016/j.gene.2018.08.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 07/10/2018] [Accepted: 08/06/2018] [Indexed: 11/30/2022]
Abstract
Corynebacterium pseudotuberculosis has been widely studied in an effort to understand its biological evolution. Transcriptomics has revealed possible candidates for virulence and pathogenicity factors of strain 1002 (biovar Ovis). Because C. pseudotuberculosis is classified into two biovars, Ovis and Equi, it was interesting to assess the transcriptional profile of biovar Equi strain 258, the causative agent of ulcerative lymphangitis. The genome of this strain was re-sequenced; the reassembly was completed using optical mapping technology, and the sequence was subsequently re-annotated. Two growth conditions that occur during the host infection process were simulated for the transcriptome: the osmotic and acid medium. Genes that may be associated with the microorganism's resilience under unfavorable conditions were identified through RNAseq, including genes present in pathogenicity islands. The RT-qPCR was performed to confirm the results in biological triplicate for each condition for some genes. The results extend our knowledge of the factors associated with the spread and persistence of C. pseudotuberculosis during the infection process and suggest possible avenues for studies related to the development of vaccines, diagnosis, and therapies that might help minimize damage to agribusinesses.
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Affiliation(s)
- Anne Cybelle Pinto Gomide
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil.
| | - Izabela Coimbra Ibraim
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil
| | - Jorianne T C Alves
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil
| | - Pablo Gomes de Sá
- Federal Rural University of Amazonia, Rodovia PA 140, 2428 Tomé-Açu, PA, Brazil
| | - Yuri Rafael de Oliveira Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil
| | - Mariana Passos Santana
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil
| | - Wanderson Marques Silva
- National Institute of Agricultural Technology, Los Reseros y Nicolás Repetto, Hurlingham 1686, Argentina
| | - Edson Luiz Folador
- Biotechnology Center, Federal University of Paraíba, João Pessoa, Brazil.
| | - Diego C B Mariano
- Department of Computer Sciences, Institute of Exact Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil.
| | - Thiago Luiz de Paula Castro
- Department of Biointeraction, Institute of Health Sciences, Federal University of Bahia, Av. Reitor Miguel Calmon, s/n, Vale do Canela, Bahia, Brazil
| | - Silvanira Barbosa
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil
| | - Fernanda Alves Dorella
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Alex F Carvalho
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Felipe L Pereira
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| | - Carlos A G Leal
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil.
| | - Henrique C P Figueiredo
- AQUACEN - National Reference Laboratory of Aquatic Animal Diseases, Ministry of Fisheries and Aquaculture, Veterinary School, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Vasco Azevedo
- Department of General Biology, Institute of Biological Sciences, Federal University of Minas Gerais, Av. Antônio Carlos, Belo Horizonte 31.270-901, Brazil.
| | - Artur Silva
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil.
| | - Adriana Ribeiro Carneiro Folador
- Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Institute of Biological Science, Federal University of Para, Belém, Pará, Brazil, Rua Augusto Corrêa, Belém 66.075-110, Brazil.
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20
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Identification of new antibacterial targets in RNA polymerase of Mycobacterium tuberculosis by detecting positive selection sites. Comput Biol Chem 2018; 73:25-30. [PMID: 29413813 DOI: 10.1016/j.compbiolchem.2017.11.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 10/07/2017] [Accepted: 11/03/2017] [Indexed: 01/22/2023]
Abstract
Bacterial RNA polymerase (RNAP) is an effective target for antibacterial treatment. In order to search new potential targets in RNAP of Mycobacterium, we detected adaptive selections of RNAP related genes in 13 strains of Mycobacterium by phylogenetic analysis. We first collected sequences of 17 genes including rpoA, rpoB, rpoC, rpoZ, and sigma factor A-M. Then maximum likelihood trees were constructed, followed by positive selection detection. We found that sigG shows positive selection along the clade (M. tuberculosis, M. bovis), suggesting its important evolutionary role and its potential to be a new antibacterial target. Moreover, the regions near 933Cys and 935His on the rpoB subunit of M. tuberculosis showed significant positive selection, which could also be a new attractive target for anti-tuberculosis drugs.
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21
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Bansal R, Anil Kumar V, Sevalkar RR, Singh PR, Sarkar D. Mycobacterium tuberculosis virulence-regulator PhoP interacts with alternative sigma factor SigE during acid-stress response. Mol Microbiol 2017; 104:400-411. [PMID: 28142206 DOI: 10.1111/mmi.13635] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/24/2017] [Indexed: 12/17/2022]
Abstract
The ability to sense acid stress and mount an appropriate adaptive response by Mycobacterium tuberculosis, which adapts a long-term residence in the macrophage phagosome, remains one of the critical features that defines mycobacterial physiology and its intracellular location. To understand the mechanistic basis of adaptation of the intracellular pathogen, we studied global regulation of M. tuberculosis gene expression in response to acid stress. Although recent studies indicate a role for the virulence-associated phoP locus in pH-driven adaptation, in this study, we discovered a strikingly novel regulatory mechanism, which controls acid-stress homeostasis. Using mycobacterial protein fragment complementation and in vitro interaction analyses, we demonstrate that PhoP interacts with acid-inducible extracytoplasmic SigE (one of the 13 M. tuberculosis sigma factors) to regulate a complex transcriptional program. Based on these results, we propose a model to suggest that PhoP-SigE interaction represents a major requirement for the global acid stress response, absence of which leads to strongly reduced survival of the bacilli under acidic pH conditions. These results account for the significant growth attenuation of the phoP mutant in both cellular and animal models, and unravel the underlying global mechanism of how PhoP induces an adaptive program in response to acid stress.
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Affiliation(s)
- Roohi Bansal
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, 160036, India
| | | | | | | | - Dibyendu Sarkar
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, 160036, India
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22
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Mycobacterium tuberculosis Transcription Machinery: Ready To Respond to Host Attacks. J Bacteriol 2016; 198:1360-73. [PMID: 26883824 DOI: 10.1128/jb.00935-15] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Regulating responses to stress is critical for all bacteria, whether they are environmental, commensal, or pathogenic species. For pathogenic bacteria, successful colonization and survival in the host are dependent on adaptation to diverse conditions imposed by the host tissue architecture and the immune response. Once the bacterium senses a hostile environment, it must enact a change in physiology that contributes to the organism's survival strategy. Inappropriate responses have consequences; hence, the execution of the appropriate response is essential for survival of the bacterium in its niche. Stress responses are most often regulated at the level of gene expression and, more specifically, transcription. This minireview focuses on mechanisms of regulating transcription initiation that are required by Mycobacterium tuberculosis to respond to the arsenal of defenses imposed by the host during infection. In particular, we highlight how certain features of M. tuberculosis physiology allow this pathogen to respond swiftly and effectively to host defenses. By enacting highly integrated and coordinated gene expression changes in response to stress,M. tuberculosis is prepared for battle against the host defense and able to persist within the human population.
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23
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Toyoda K, Inui M. The extracytoplasmic function σ factor σ(C) regulates expression of a branched quinol oxidation pathway in Corynebacterium glutamicum. Mol Microbiol 2016; 100:486-509. [PMID: 26789738 DOI: 10.1111/mmi.13330] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2016] [Indexed: 11/30/2022]
Abstract
Bacteria modify their expression of different terminal oxidases in response to oxygen availability. Corynebacterium glutamicum, a facultative anaerobic bacterium of the phylum Actinobacteria, possesses aa3 -type cytochrome c oxidase and cytochrome bd-type quinol oxidase, the latter of which is induced by oxygen limitation. We report that an extracytoplasmic function σ factor, σ(C) , is responsible for the regulation of this process. Chromatin immunoprecipitation with microarray analysis detected eight σ(C) -binding regions in the genome, facilitating the identification of a consensus promoter sequence for σ(C) recognition. The promoter sequences were found upstream of genes for cytochrome bd, heme a synthesis enzymes and uncharacterized membrane proteins, all of which were upregulated by sigC overexpression. However, one consensus promoter sequence found on the antisense strand upstream of an operon encoding the cytochrome bc1 complex conferred a σ(C) -dependent negative effect on expression of the operon. The σ(C) regulon was induced by cytochrome aa3 deficiency without modifying sigC expression, but not by bc1 complex deficiency. These findings suggest that σ(C) is activated in response to impaired electron transfer via cytochrome aa3 and not directly to a shift in oxygen levels. Our results reveal a new paradigm for transcriptional regulation of the aerobic respiratory system in bacteria.
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Affiliation(s)
- Koichi Toyoda
- Research institute of Innovative Technology for the Earth (RITE), 9-2 Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan
| | - Masayuki Inui
- Research institute of Innovative Technology for the Earth (RITE), 9-2 Kizugawadai, Kizugawa, Kyoto, 619-0292, Japan.,Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0101, Japan
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24
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In Streptomyces coelicolor SigR, methionine at the -35 element interacting region 4 confers the -31'-adenine base selectivity. Biochem Biophys Res Commun 2016; 470:257-262. [PMID: 26775842 DOI: 10.1016/j.bbrc.2016.01.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/12/2016] [Indexed: 11/20/2022]
Abstract
In Gram-positive Streptomyces coelicolor A3(2), SigR (Sc σ(R)) of the group IV ECF sigma factor singly activates expression of more than 30 oxidation responsive genes. Of the two promoter-binding domains--individually called region 2 and region 4 - within Sc σ(R), we hereby report a 2.6 Å resolution structure of the -35 element interacting carboxyl-terminal region 4 (Sc σ(R)4). Structural comparison of Sc σ(R)4 with the Escherichia coli SigE (Ec σ(E)) in complex with Ec σ(E) -35 element suggested that a single residue (Sc σ(R) Met188 and Ec σ(E) Arg171) may be responsible for distinguishing the one-base pair difference of the -35 elements--Sc σ(R)(-31')ATTCC(-35') ((-31')A) vs. Ec σ(E)(-31')GTTCC(-35') ((-31')G)--by interacting with the -31'-base. Further studies using expressed Sc σ(R) indicate that the wild-type Sc σ(R) with Met188 selectively interacted with the (-31')A sequence over the (-31')G sequence, whereas a mutation of Met188 to arginine resulted in interaction with both (-31')A and (-31')G sequences. Hence, we conclude that Met188 of Sc σ(R) confers the (-31')A-selectivity in -35 element interaction by disfavoured interaction with the (-31')G base.
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Abstract
Two-component regulatory systems (2CRSs) are widely used by bacteria to sense and respond to environmental stimuli with coordinated changes in gene expression. Systems are normally comprised of a sensory kinase protein that activates a transcriptional regulator by phosphorylation. Mycobacteria have few 2CRSs, but they are of key importance for bacterial survival and play important roles in pathogenicity. Mycobacterium tuberculosis has 12 paired two-component regulatory systems (which include a system with two regulators and one sensor, and a split sensor system), as well as four orphan regulators. Several systems are involved in virulence, and disruption of different systems leads to attenuation or hypervirulence. PhoPR plays a major role in regulating cell wall composition, and its inactivation results in sufficient attenuation of M. tuberculosis that deletion strains are live vaccine candidates. MprAB controls the stress response and is required for persistent infections. SenX3-RegX3 is required for control of aerobic respiration and phosphate uptake, and PrrAB is required for adaptation to intracellular infection. MtrAB is an essential system that controls DNA replication and cell division. The remaining systems (KdpDE, NarL, TrcRS, TcrXY, TcrA, PdtaRS, and four orphan regulators) are less well understood. The structure and binding motifs for several regulators have been characterized, revealing variations in function and operation. The sensors are less well characterized, and stimuli for many remain to be confirmed. This chapter reviews our current understanding of the role of two-component systems in mycobacteria, in particular M. tuberculosis.
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Sigma Factors: Key Molecules in Mycobacterium tuberculosis Physiology and Virulence. Microbiol Spectr 2015; 2:MGM2-0007-2013. [PMID: 26082107 DOI: 10.1128/microbiolspec.mgm2-0007-2013] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid adaptation to changing environments is one of the keys to the success of microorganisms. Since infection is a dynamic process, it is possible to predict that Mycobacterium tuberculosis adaptation involves continuous modulation of its global transcriptional profile in response to the changing environment found in the human body. In the last 18 years several studies have stressed the role of sigma (σ) factors in this process. These are small interchangeable subunits of the RNA polymerase holoenzyme that are required for transcriptional initiation and that determine promoter specificity. The M. tuberculosis genome encodes 13 of these proteins, one of which--the principal σ factor σA--is essential. Of the other 12 σ factors, at least 6 are required for virulence. In this article we review our current knowledge of mycobacterial σ factors, their regulons, the complex mechanisms determining their regulation, and their roles in M. tuberculosis physiology and virulence.
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Sharma A, Rustad T, Mahajan G, Kumar A, Rao KVS, Banerjee S, Sherman DR, Mande SC. Towards understanding the biological function of the unusual chaperonin Cpn60.1 (GroEL1) of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2015; 97:137-46. [PMID: 26822628 DOI: 10.1016/j.tube.2015.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 11/05/2015] [Accepted: 11/08/2015] [Indexed: 12/19/2022]
Abstract
The 60 kDa heat shock proteins, also known as Cpn60s (GroELs) are components of the essential protein folding machinery of the cell, but are also dominant antigens in many infectious diseases. Although generally essential for cellular survival, in some organisms such as Mycobacterium tuberculosis, one or more paralogous Cpn60s are known to be dispensable. In M. tuberculosis, Cpn60.2 (GroEL2) is essential for cell survival, but the biological role of the non-essential Cpn60.1 (GroEL1) is still elusive. To understand the relevance of Cpn60.1 (GroEL1) in M. tuberculosis physiology, detailed transcriptomic analyses for the wild type H37Rv and cpn60.1 knockout (groEL1-KO) were performed under in vitro stress conditions: stationary phase, cold shock, low aeration, mild cold shock and low pH. Additionally, the survival of the groEL1-KO was assessed in macrophages at multiplicity of infection (MOI) of 1:1 and 1:5. We observed that survival under low aeration was significantly compromised in the groEL1-KO. Further, the gene expression analyses under low aeration showed change in expression of several key virulence factors like two component system PhoP/R and MprA/B, sigma factors SigM and C and adversely affected known hypoxia response regulators Rv0081, Rv0023 and DosR. Our work is therefore suggestive of an important role of Cpn60.1 (GroEL1) for survival under low aeration by affecting the expression of genes known for hypoxia response.
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Affiliation(s)
- Aditi Sharma
- Centre for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad 500 001, India; Graduate Studies, Manipal University, Manipal 576104, India; National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Tige Rustad
- Center for Infectious Diseases Research (formerly known as Seattle Biomedical Research Institute), Seattle, WA, USA
| | - Gaurang Mahajan
- National Centre for Cell Science, Ganeshkhind, Pune 411 007, India
| | - Arun Kumar
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Kanury V S Rao
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | | | - David R Sherman
- Center for Infectious Diseases Research (formerly known as Seattle Biomedical Research Institute), Seattle, WA, USA; University of Washington Department of Global Health, Seattle, WA, USA
| | - Shekhar C Mande
- Centre for DNA Fingerprinting and Diagnostics, Nampally, Hyderabad 500 001, India; National Centre for Cell Science, Ganeshkhind, Pune 411 007, India.
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Gutka HJ, Wang Y, Franzblau SG, Movahedzadeh F. glpx Gene in Mycobacterium tuberculosis Is Required for In Vitro Gluconeogenic Growth and In Vivo Survival. PLoS One 2015; 10:e0138436. [PMID: 26397812 PMCID: PMC4580611 DOI: 10.1371/journal.pone.0138436] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/31/2015] [Indexed: 11/18/2022] Open
Abstract
Several enzymes involved in central carbon metabolism and gluconeogenesis play a critical role in survival and pathogenesis of Mycobacterium tuberculosis (Mtb). The only known functional fructose 1,6-bisphosphatase (FBPase) in Mtb is encoded by the glpX gene and belongs to the Class II sub-family of FBPase. We describe herein the generation of a ΔglpX strain using homologous recombination. Although the growth profile of ΔglpX is comparable to that of wild type Mtb when grown on the standard enrichment media, its growth is dysgonic with individual gluconeogenic substrates such as oleic acid, glycerol and acetate. In mice lung CFU titers of ΔglpX were 2-3 log10 lower than the wild-type Mtb strain. The results indicate that glpX gene encodes a functional FBPase and is essential for both in vitro and in vivo growth and survival of Mtb. Loss of glpX results in significant reduction of FBPase activity but not complete abolition. These findings verify that the glpX encoded FBPase II in Mtb can be a potential target for drug discovery.
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Affiliation(s)
- Hiten J. Gutka
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Yuehong Wang
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Scott G. Franzblau
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Farahnaz Movahedzadeh
- Institute for Tuberculosis Research, College of Pharmacy, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
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Dou Y, Aruni W, Muthiah A, Roy F, Wang C, Fletcher HM. Studies of the extracytoplasmic function sigma factor PG0162 in Porphyromonas gingivalis. Mol Oral Microbiol 2015. [PMID: 26216199 DOI: 10.1111/omi.12122] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
PG0162, annotated as an extracytoplasmic function (ECF) sigma factor in Porphyromonas gingivalis, is composed of 193 amino acids. As previously reported, the PG0162-deficient mutant, P. gingivalis FLL350 showed significant reduction in gingipain activity compared with the parental strain. Because this ECF sigma factor could be involved in the virulence regulation in P. gingivalis, its genetic properties were further characterized. A 5'-RACE analysis showed that the start of transcription of the PG0162 gene occurred from a guanine (G) residue 69 nucleotides upstream of the ATG translation initiation codon. The function of PG0162 as a sigma factor was confirmed in a run-off in vitro transcription assay using the purified rPG0162 and RNAP core enzyme from Escherichia coli with the PG0162 promoter as template. As an appropriate PG0162 inducing environmental signal is unknown, a strain overexpressing the PG0162 gene designated P. gingivalis FLL391 was created. Compared with the wild-type strain, transcriptome analysis of P. gingivalis FLL391 showed that approximately 24% of the genome displayed altered gene expression (260 upregulated genes; 286 downregulated genes). Two other ECF sigma factors (PG0985 and PG1660) were upregulated more than two-fold. The autoregulation of PG0162 was confirmed with the binding of the rPG0162 protein to the PG0162 promoter in electrophoretic mobility shift assay. In addition, the rPG0162 protein also showed the ability to bind to the promoter region of two genes (PG0521 and PG1167) that were most upregulated in P. gingivalis FLL391. Taken together, our data suggest that PG0162 is a sigma factor that may play an important role in the virulence regulatory network in P. gingivalis.
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Affiliation(s)
- Y Dou
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - W Aruni
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - A Muthiah
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - F Roy
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - C Wang
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - H M Fletcher
- Division of Microbiology and Molecular Genetics, Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA.,Institute of Oral Biology, Kyung Hee University, Seoul, Republic of Korea
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Li W, Fan X, Long Q, Xie L, Xie J. Mycobacterium tuberculosis effectors involved in host-pathogen interaction revealed by a multiple scales integrative pipeline. INFECTION GENETICS AND EVOLUTION 2015; 32:1-11. [PMID: 25709069 DOI: 10.1016/j.meegid.2015.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/02/2015] [Accepted: 02/14/2015] [Indexed: 01/04/2023]
Abstract
BACKGROUND Mycobacterium tuberculosis (Mtb) has evolved multiple strategies to counter host immunity. Proteins are one important player in the host-pathogen interaction. A comprehensive list of such proteins will benefit our understanding of pathogenesis of Mtb. METHODS A genome-scale dataset was created from different sources of published data: global gene expression studies in disease models; genome-wide insertional mutagenesis defining gene essentiality under different conditions; genes lost in clinical isolates; subcellular localization analysis and non-homology analysis. Using data mining and meta-analysis, expressed proteins critical for intracellular survival of Mtb are first identified, followed by subcellular localization analysis, finally filtering a series of subtractive channel of analysis to find out promising drug target candidates. RESULTS The analysis found 54 potential candidates essential for the intracellular survival of the pathogen and non-homologous to host or gut flora, and might be promising drug targets. CONCLUSION Based on our meta-analysis and bioinformatics analysis, 54 hits were found from Mtb around 4000 open reading frames. These hits can be good candidates for further experimental investigation.
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Affiliation(s)
- Wu Li
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiangyu Fan
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China; School of Biological Science and Technology, University of Jinan, Shandong 250022, China
| | - Quanxin Long
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China; The Second Affiliated Hospital and the Key Laboratory of Molecular Biology of Infectious Diseases of the Ministry of Education, Chongqing Medical University, 1 Medical Road, Yuzhong District, Chongqing 400016, China
| | - Longxiang Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China.
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Different behaviours of promoters in Mycobacterium tuberculosis H37Rv and H37Ra. World J Microbiol Biotechnol 2015; 31:407-13. [DOI: 10.1007/s11274-014-1794-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 12/28/2014] [Indexed: 10/24/2022]
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Souza BM, Castro TLDP, Carvalho RDDO, Seyffert N, Silva A, Miyoshi A, Azevedo V. σ(ECF) factors of gram-positive bacteria: a focus on Bacillus subtilis and the CMNR group. Virulence 2014; 5:587-600. [PMID: 24921931 PMCID: PMC4105308 DOI: 10.4161/viru.29514] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The survival of bacteria to different environmental conditions depends on the activation of adaptive mechanisms, which are intricately driven through gene regulation. Because transcriptional initiation is considered to be the major step in the control of bacterial genes, we discuss the characteristics and roles of the sigma factors, addressing (1) their structural, functional and phylogenetic classification; (2) how their activity is regulated; and (3) the promoters recognized by these factors. Finally, we focus on a specific group of alternative sigma factors, the so-called σ(ECF) factors, in Bacillus subtilis and some of the main species that comprise the CMNR group, providing information on the roles they play in the microorganisms' physiology and indicating some of the genes whose transcription they regulate.
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Affiliation(s)
- Bianca Mendes Souza
- Laboratório de Genética Celular e Molecular; Instituto de Ciências Biológicas; Departamento de Biologia Geral; Universidade Federal de Minas Gerais; Belo Horizonte, MG Brazil
| | - Thiago Luiz de Paula Castro
- Laboratório de Genética Celular e Molecular; Instituto de Ciências Biológicas; Departamento de Biologia Geral; Universidade Federal de Minas Gerais; Belo Horizonte, MG Brazil
| | - Rodrigo Dias de Oliveira Carvalho
- Laboratório de Genética Celular e Molecular; Instituto de Ciências Biológicas; Departamento de Biologia Geral; Universidade Federal de Minas Gerais; Belo Horizonte, MG Brazil
| | - Nubia Seyffert
- Laboratório de Genética Celular e Molecular; Instituto de Ciências Biológicas; Departamento de Biologia Geral; Universidade Federal de Minas Gerais; Belo Horizonte, MG Brazil
| | - Artur Silva
- Laboratório de Polimorfismo de DNA; Instituto de Ciências Biológicas; Departamento de Genética; Universidade Federal do Pará; Belém, PA Brazil
| | - Anderson Miyoshi
- Laboratório de Genética Celular e Molecular; Instituto de Ciências Biológicas; Departamento de Biologia Geral; Universidade Federal de Minas Gerais; Belo Horizonte, MG Brazil
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular; Instituto de Ciências Biológicas; Departamento de Biologia Geral; Universidade Federal de Minas Gerais; Belo Horizonte, MG Brazil
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Rifat D, Karakousis PC. Differential regulation of the two-component regulatory system senX3-regX3 in Mycobacterium tuberculosis. MICROBIOLOGY-SGM 2014; 160:1125-1133. [PMID: 24722908 DOI: 10.1099/mic.0.077180-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The highly successful pathogen Mycobacterium tuberculosis (Mtb) has evolved strategies to adapt to various stress conditions, thus promoting survival within the infected host. The two-component regulatory system (2CRS) senX3-regX3, which has been implicated in the Mtb response to inorganic phosphate depletion, is believed to behave as an auto-regulatory bicistronic operon. Unlike other 2CRS, Mtb senX3-regX3 features an intergenic region (IR) containing several mycobacterium interspersed repetitive units (MIRU) of unknown function. In this study, we used a lacZ reporter system to study the promoter activity of the 5' untranslated region of senX3, and that of various numbers of MIRUs in the senX3-regX3 IR, during axenic Mtb growth in nutrient-rich broth, and upon exposure to growth-restricting conditions. Activity of the senX3 promoter was induced during phosphate depletion and nutrient starvation, and IR promoter activity under these conditions was directly proportional to the number of MIRUs present. Quantitative reverse transcriptase (qRT)-PCR analysis of exponentially growing Mtb revealed monocistronic transcription of senX3 and regX3, and, to a lesser degree, bicistronic transcription of the operon. In addition, we observed primarily monocistronic upregulation of regX3 during phosphate depletion of Mtb, which was confirmed by Northern analysis in wild-type Mtb and by RT-PCR in a senX3-disrupted mutant, while upregulation of regX3 in nutrient-starved Mtb was chiefly bicistronic. Our findings of differential regulation of senX3-regX3 highlight the potential regulatory role of MIRUs in the Mtb genome and provide insight into the regulatory mechanisms underlying Mtb adaptation to physiologically relevant conditions.
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Affiliation(s)
- Dalin Rifat
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Petros C Karakousis
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Zhao Q, Li W, Chen T, He Y, Deng W, Luo H, Xie J. Mycobacterium tuberculosis serine protease Rv3668c can manipulate the host-pathogen interaction via Erk-NF-κB axis-mediated cytokine differential expression. J Interferon Cytokine Res 2014; 34:686-98. [PMID: 24684623 DOI: 10.1089/jir.2013.0071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Tuberculosis caused by Mycobacterium tuberculosis (MTB) remains a serious global public health concern. About one-third of the global population has been latently infected with this pathogen. MTB proteases are important virulence factors and involve in subverting the host immunity. MTB protease Rv3668c was implicated in drug action and dormancy by Gene Expression Omnibus data. To define the role of Rv3668c in pathogen-host interaction, we constructed recombinant strain Mycobacterium smegmatis-Rv3668c (Ms-Rv3668c). The resultant strains were used to challenge the human macrophage cell line U937. The cytokine levels and the survival of recombinants and macrophages were monitored. The results showed that recombinant Ms-Rv3668c specifically upregulated the secretion of proinflammatory cytokines TNF-α, IL-1β, and IL-6 and downregulated the secretion of anti-inflammatory cytokine IL-10 by U937 cells, consistent with the upregulated transcription of TNF-α and IL-1β. Rv3668c recombinants demonstrated prolonged survival within the U937 cells and accelerated the death of the host cells. Inhibitor experiments showed that the ERK-NF-κB axis was involved in the Rv3668c-triggered TNF-α and IL-1β changes. These results provided evidence for the engagement of Rv3668c in the interaction between Mycobacterium and host.
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Affiliation(s)
- Quanju Zhao
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, and Key Laboratory of Ministry of Education and Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University , Chongqing, China
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Cossu A, Sechi LA, Bandino E, Zanetti S, Rosu V. Expression profiling of Mycobacterium tuberculosis H37Rv and Mycobacterium smegmatis in acid-nitrosative multi-stress displays defined regulatory networks. Microb Pathog 2013; 65:89-96. [PMID: 24184341 DOI: 10.1016/j.micpath.2013.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 10/17/2013] [Accepted: 10/23/2013] [Indexed: 11/26/2022]
Abstract
Several studies regarding the transcriptome of Mycobacterium tuberculosis following the exposure to various in vitro simulated phagosomal stressors, have already tried to elucidate the bacterium behavior during the intracellular infection. An in vitro acid-nitrosative multi-stress was carried out for M. tuberculosis H37Rv and Mycobacterium smegmatis MC(2)155 in order to analyze by DNA-microarray the gene expression changes associated respectively to pathogenic and non-pathogenic mycobacterial species. During acid-nitrosative multi-stress both mycobacteria shift their transcriptome to allow the anaerobic respiratory state and energy pathways characteristic of starvation. M. tuberculosis counteracts the combined acid-nitrosative stress more efficiently than M. smegmatis as also shown by the up-regulation of glbN and hmp genes, that are specifically directed to NO detoxification. Moreover, the down-regulation of some virulence factors involved in phthiocerol dimycocerosates synthesis strengthens the hypothesis that these major virulence determinants may be attenuated by M. tuberculosis in the presence of reactive nitrogen species. In fact, it down-regulates other genes implicated in the synthesis of membrane structural lipids but in contrast to M. smegmatis, M. tuberculosis up-regulates many genes annotated for the synthesis of peptidoglycan. Results suggest a gene regulation of M. tuberculosis which reveals a distinctive expression pattern under stressful environment.
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Affiliation(s)
- Andrea Cossu
- Department of Food Science, Division of Food Microbiology, University of Massachusetts, Amherst, MA 01003, USA.
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Nambu T, Yamane K, Yamanaka T, Mashimo C, Maruyama H, Yoshida M, Hayashi H, Leung KP, Fukushima H. Identification of disulphide stress-responsive extracytoplasmic function sigma factors in Rothia mucilaginosa. Arch Oral Biol 2013; 58:681-9. [PMID: 23399044 DOI: 10.1016/j.archoralbio.2012.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 08/21/2012] [Accepted: 10/23/2012] [Indexed: 11/17/2022]
Abstract
Rothia mucilaginosa is known as a member of commensal bacterial flora in the oral cavity and has received attention as a potential opportunistic pathogen. We previously determined the genomic sequence of R. mucilaginosa DY-18, a clinical strain with biofilm-like structures isolated from an infected root canal of a tooth with persistent apical periodontitis. We found that the DY-18 genome had only two sigma factor genes that encoded the primary and extracytoplasmic function (ECF) sigma factors. Genomic analysis on the available database of R. mucilaginosa ATCC 25296 (a type strain for R. mucilaginosa) revealed that ATCC 25296 has three sigma factors: one primary sigma factor and two ECF sigma factors, one of which was highly homologous to that of DY-18. ECF sigma factors play an important role in the response to environmental stress and to the production of virulence factors. Therefore, we first examined gene-encoding sigma factors on R. mucilaginosa genome in silico. The homologous ECF sigma factors found in strains DY-18 and ATCC 25296 formed a distinct SigH (SigR) clade in a phylogenetic tree and their cognate anti-sigma factor has a HXXXCXXC motif known to respond against disulphide stress. Quantitative reverse transcription polymerase chain reaction (PCR) and microarray analysis showed that the transcriptional levels of sigH were markedly up-regulated under disulphide stress in both strains. Microarray data also demonstrated that several oxidative-stress-related genes (thioredoxin, mycothione reductase, reductase and oxidoreductase) were significantly up-regulated under the diamide stress. On the basis of these results, we conclude that the alternative sigma factor SigH of R. mucilaginosa is a candidate regulator in the redox state.
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Affiliation(s)
- Takayuki Nambu
- Department of Bacteriology, Osaka Dental University, 8-1 Kuzuha-Hanazono, Hirakata, 573-1121 Japan.
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Forrellad MA, Klepp LI, Gioffré A, Sabio y García J, Morbidoni HR, de la Paz Santangelo M, Cataldi AA, Bigi F. Virulence factors of the Mycobacterium tuberculosis complex. Virulence 2012; 4:3-66. [PMID: 23076359 PMCID: PMC3544749 DOI: 10.4161/viru.22329] [Citation(s) in RCA: 379] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The Mycobacterium tuberculosis complex (MTBC) consists of closely related species that cause tuberculosis in both humans and animals. This illness, still today, remains to be one of the leading causes of morbidity and mortality throughout the world. The mycobacteria enter the host by air, and, once in the lungs, are phagocytated by macrophages. This may lead to the rapid elimination of the bacillus or to the triggering of an active tuberculosis infection. A large number of different virulence factors have evolved in MTBC members as a response to the host immune reaction. The aim of this review is to describe the bacterial genes/proteins that are essential for the virulence of MTBC species, and that have been demonstrated in an in vivo model of infection. Knowledge of MTBC virulence factors is essential for the development of new vaccines and drugs to help manage the disease toward an increasingly more tuberculosis-free world.
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Newton-Foot M, Gey van Pittius NC. The complex architecture of mycobacterial promoters. Tuberculosis (Edinb) 2012; 93:60-74. [PMID: 23017770 DOI: 10.1016/j.tube.2012.08.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 07/31/2012] [Accepted: 08/06/2012] [Indexed: 01/02/2023]
Abstract
The genus Mycobacterium includes a variety of species with differing phenotypic properties, including growth rate, pathogenicity and environment- and host-specificity. Although many mycobacterial species have been extensively studied and their genomes sequenced, the reasons for phenotypic variation between closely related species remain unclear. Variation in gene expression may contribute to these characteristics and enable the bacteria to respond to changing environmental conditions. Gene expression is controlled primarily at the level of transcription, where the main element of regulation is the promoter. Transcriptional regulation and associated promoter sequences have been studied extensively in E. coli. This review describes the complex structure and characteristics of mycobacterial promoters, in comparison to the classical E. coli prokaryotic promoter structure. Some components of mycobacterial promoters are similar to those of E. coli. These include the predominant guanine residue at the transcriptional start point, conserved -10 hexamer, similar interhexameric distances, the use of ATG as a start codon, the guanine- and adenine-rich ribosome binding site and the presence of extended -10 (TGn) motifs in strong promoters. However, these components are much more variable in sequence in mycobacterial promoters and no conserved -35 hexamer sequence (clearly defined in E. coli) can be identified. This may be a result of the high G+C content of mycobacterial genomes, as well as the large number of sigma factors present in mycobacteria, which may recognise different promoter sequences. Mycobacteria possess a complex transcriptional regulatory network. Numerous regulatory motifs have been identified in mycobacterial promoters, predominantly in the interhexameric region. These are bound by specific transcriptional regulators in response to environmental changes. The combination of specific promoter sequences, transcriptional regulators and a variety of sigma factors enables rapid and specific responses to diverse conditions and different stages of infection. This review aims to provide an overview of the complex architecture of mycobacterial transcriptional regulation.
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Affiliation(s)
- Mae Newton-Foot
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 19063, Francie van Zijl Drive, Tygerberg 7505, South Africa.
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James JN, Hasan ZU, Ioerger TR, Brown AC, Personne Y, Carroll P, Ikeh M, Tilston-Lunel NL, Palavecino C, Sacchettini JC, Parish T. Deletion of SenX3-RegX3, a key two-component regulatory system of Mycobacterium smegmatis, results in growth defects under phosphate-limiting conditions. MICROBIOLOGY-SGM 2012; 158:2724-2731. [PMID: 22956756 DOI: 10.1099/mic.0.060319-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two component regulatory systems are key elements in the control of bacterial gene expression in response to environmental perturbations. The SenX3-RegX3 system is implicated in the control of phosphate uptake in Mycobacterium smegmatis and Mycobacterium tuberculosis. regX3 is reported to be essential in M. smegmatis, but not in M. tuberculosis. We attempted to construct complete senX3-regX3 operon deletion strains of M. smegmatis; initially we found that the operon could only be deleted when another functional copy was provided. Using a strain in which the only functional copy of the operon was present on an integrating plasmid, we attempted to replace the functional copy with an empty vector. Surprisingly, we obtained strains in which the functional copy had been deleted from the chromosome at a low frequency. We deleted the senX3 gene in a similar fashion, but it was not possible to delete regX3 alone. To identify possible compensatory mutations we sequenced the whole genome of two deletion strains and the wild-type. A synonymous single nucleotide polymorphism (SNP) in a lipoprotein was found in all deletion strains, but not the parental strains, and a frameshift mutation in nhaA was identified in three of the four deletion strains. Operon deletion strains were more sensitive to phosphate limitation, showing a reduced ability to grow at lower phosphate concentrations. The M. tuberculosis operon was able to functionally complement the growth phenotype in M. smegmatis under phosphate-replete conditions, but not under low phosphate conditions, reinforcing the difference between the two species. Our data show that, in contrast with previous reports, it is possible to delete the operon in M. smegmatis, possibly due to the accumulation of compensatory mutations, and that the deletion does affect growth in phosphate.
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Affiliation(s)
- Jade N James
- Queen Mary University of London, Barts and the London, London, UK
| | | | - Thomas R Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, USA
| | - Amanda C Brown
- Queen Mary University of London, Barts and the London, London, UK
| | - Yoann Personne
- Queen Mary University of London, Barts and the London, London, UK
| | - Paul Carroll
- Queen Mary University of London, Barts and the London, London, UK
| | - Melanie Ikeh
- Queen Mary University of London, Barts and the London, London, UK
| | | | | | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Tanya Parish
- TB Discovery Research, Infectious Disease Research Institute, Seattle, WA, USA.,Queen Mary University of London, Barts and the London, London, UK
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WAN BS, ZHANG QF, ZHOU AP, ZHAO GP, YAO YF. Genomics and Genome Evolution of Mycobacterium tuberculosis*. PROG BIOCHEM BIOPHYS 2012. [DOI: 10.3724/sp.j.1206.2011.00469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Evolutionary link between the mycobacterial plasmid pAL5000 replication protein RepB and the extracytoplasmic function family of σ factors. J Bacteriol 2012; 194:1331-41. [PMID: 22247504 DOI: 10.1128/jb.06218-11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Mycobacterial plasmid pAL5000 represents a family of plasmids found mostly in the Actinobacteria. It replicates using two plasmid-encoded proteins, RepA and RepB. While BLAST searches indicate that RepA is a replicase family protein, the evolutionary connection of RepB cannot be established, as no significant homologous partner (E < 10(-3)) outside the RepB family can be identified. To obtain insight into the structure-function and evolutionary connections of RepB, an investigation was undertaken using homology modeling, phylogenetic, and mutational analysis methods. The results indicate that although they are synthesized from the same operon, the phylogenetic affinities of RepA and RepB differ. Thus, the operon may have evolved through random breaking and joining events. Homology modeling predicted the presence of a three-helical helix-turn-helix domain characteristic of region 4 of extracytoplasmic function (ECF) σ factors in the C-terminal region of RepB. At the N-terminal region, there is a helical stretch, which may be distantly related to region 3 of σ factors. Mutational analysis identified two arginines indispensable for RepB activity, one each located within the C- and N-terminal conserved regions. Apart from analyzing the domain organization of the protein, the significance of the presence of a highly conserved A/T-rich element within the RepB binding site was investigated. Mutational analysis revealed that although this motif does not bind RepB, its integrity is important for efficient DNA-protein interactions and replication to occur. The present investigation unravels the possibility that RepB-like proteins and their binding sites represent ancient DNA-protein interaction modules.
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Arnvig KB, Comas I, Thomson NR, Houghton J, Boshoff HI, Croucher NJ, Rose G, Perkins TT, Parkhill J, Dougan G, Young DB. Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis. PLoS Pathog 2011; 7:e1002342. [PMID: 22072964 PMCID: PMC3207917 DOI: 10.1371/journal.ppat.1002342] [Citation(s) in RCA: 163] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 09/15/2011] [Indexed: 01/21/2023] Open
Abstract
RNA sequencing provides a new perspective on the genome of Mycobacterium tuberculosis by revealing an extensive presence of non-coding RNA, including long 5' and 3' untranslated regions, antisense transcripts, and intergenic small RNA (sRNA) molecules. More than a quarter of all sequence reads mapping outside of ribosomal RNA genes represent non-coding RNA, and the density of reads mapping to intergenic regions was more than two-fold higher than that mapping to annotated coding sequences. Selected sRNAs were found at increased abundance in stationary phase cultures and accumulated to remarkably high levels in the lungs of chronically infected mice, indicating a potential contribution to pathogenesis. The ability of tubercle bacilli to adapt to changing environments within the host is critical to their ability to cause disease and to persist during drug treatment; it is likely that novel post-transcriptional regulatory networks will play an important role in these adaptive responses.
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Affiliation(s)
- Kristine B Arnvig
- Division of Mycobacterial Research, MRC National Institute for Medical Research, London, United Kingdom.
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Chang A, Smollett KL, Gopaul KK, Chan BHY, Davis EO. Mycobacterium tuberculosis H37Rv sigC is expressed from two promoters but is not auto-regulatory. Tuberculosis (Edinb) 2011; 92:48-55. [PMID: 22015173 DOI: 10.1016/j.tube.2011.09.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 09/15/2011] [Accepted: 09/20/2011] [Indexed: 11/29/2022]
Abstract
The extracytoplasmic function (ECF) sigma factor SigC has been implicated in the pathogenesis of Mycobacterium tuberculosis but control of its expression and activity is poorly understood. No proteins that interact with SigC have been detected leading to the suggestion that this sigma factor may be primarily controlled at the level of transcription. It has been suggested that SigC may be autoregulatory and a role has also been proposed for SigF in the expression of sigC. In this study we identified two promoters that were active under standard growth conditions by a combination of transcript start site mapping and promoter-lacZ fusion assays. The dominant promoter, P1, closely resembled mycobacterial SigA-dependent promoters, and introduction of a single base change at the conserved A of the -10 region eliminated promoter activity. Although the sequence of the other, P2, closely resembled the reported SigC consensus motifs, expression directed by this promoter was unaltered in a ΔsigC mutant strain, or in strains defective in other ECF sigma factors for which some similarity in consensus sequences was apparent. Comparison of the effects of different changes in the -10 region suggested that the P2 promoter was most likely recognised by SigA.
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Affiliation(s)
- Anchi Chang
- MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, United Kingdom
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PrsW is required for colonization, resistance to antimicrobial peptides, and expression of extracytoplasmic function σ factors in Clostridium difficile. Infect Immun 2011; 79:3229-38. [PMID: 21628514 DOI: 10.1128/iai.00019-11] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Clostridium difficile is an anaerobic, Gram-positive, spore-forming, opportunistic pathogen that is the most common cause of hospital-acquired infectious diarrhea. In numerous pathogens, stress response mechanisms are required for survival within the host. Extracytoplasmic function (ECF) σ factors are a major family of signal transduction systems, which sense and respond to extracellular stresses. We have identified three C. difficile ECF σ factors. These ECF σ factors, CsfT, CsfU, and CsfV, induce their own expressions and are negatively regulated by their cognate anti-σ factors, RsiT, RsiU, and RsiV, respectively. The levels of expression of these ECF σ factors increase following exposure to the antimicrobial peptides bacitracin and/or lysozyme. The expressions of many ECF σ factors are controlled by site 1 and site 2 proteases, which cleave anti-σ factors. Using a retargeted group II intron, we generated a C. difficile mutation in prsW, a putative site 1 protease. The C. difficile prsW mutant exhibited decreased levels of expression of CsfT and CsfU but not of CsfV. When expressed in a heterologous host, C. difficile PrsW was able to induce the degradation of RsiT but not of RsiU. When the prsW mutant was tested in competition assays against its isogenic parent in the hamster model of C. difficile infection, we found that the prsW mutant was 30-fold less virulent than the wild type. The prsW mutant was also significantly more sensitive to bacitracin and lysozyme than the wild type in in vitro competition assays. Taken together, these data suggest that PrsW likely regulates the activation of the ECF σ factor CsfT in C. difficile and controls the resistance of C. difficile to antimicrobial peptides that are important for survival in the host.
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Gupta RK, Chauhan S, Tyagi JS. K182G substitution in DevR or C₈G mutation in the Dev box impairs protein-DNA interaction and abrogates DevR-mediated gene induction in Mycobacterium tuberculosis. FEBS J 2011; 278:2131-9. [PMID: 21518251 DOI: 10.1111/j.1742-4658.2011.08130.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The DevR response regulator mediates adaptation of Mycobacterium tuberculosis to various signals that are likely to be encountered within the host such as hypoxia, nitric oxide, carbon monoxide and ascorbic acid. DevR is proposed as a promising target for developing drugs against dormant bacteria. It induces the expression of target genes by interacting with DNA motifs located in their promoter regions. An understanding of DNA-protein interactions is expected to facilitate the development of inhibitors targeting DevR. Only three amino acids in DevR, namely Lys179, Lys182 and Asn183, directly contact nucleotide bases in the DNA motif. The present study was designed to decipher the contribution of Lys182 in DevR function. M. tuberculosis fdxA (Rv2007c), a member of the DevR regulon, was selected for this analysis. Its transcriptional start point was mapped at -1 or -2 with respect to the putative translational start site suggesting that fdxA is expressed as a leaderless mRNA. DNase I footprinting led to the discovery of a secondary binding site and induction of the fdxA promoter is explained by the cooperative binding of DevR to two binding sites. Mutation of Lys182 lowers the DNA binding affinity of DevR and abrogates induction of fdxA and other regulon genes. Mutational analyses also highlight the singular importance of Lys182-G(13) nucleotide interaction for DevR binding and regulon induction. Our findings demonstrate that impairment of Lys182-mediated interactions alone abolishes DevR function and provide valuable insights for designing molecules that interfere with DevR-mediated dormancy adaptation.
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Affiliation(s)
- Rajesh Kumar Gupta
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, India
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Awasthy D, Ambady A, Bhat J, Sheikh G, Ravishankar S, Subbulakshmi V, Mukherjee K, Sambandamurthy V, Sharma U. Essentiality and functional analysis of type I and type III pantothenate kinases of Mycobacterium tuberculosis. MICROBIOLOGY-SGM 2010; 156:2691-2701. [PMID: 20576686 DOI: 10.1099/mic.0.040717-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Pantothenate kinase, an essential enzyme in bacteria and eukaryotes, is involved in catalysing the first step of conversion of pantothenate to coenzyme A (CoA). Three isoforms (type I, II and III) of this enzyme have been reported from various organisms, which can be differentiated from each other on the basis of their biochemical and structural characteristics. Though most bacteria carry only one of the isoforms of pantothenate kinases, some of them possess two isoforms. The physiological relevance of the presence of two types of isozymes in a single organism is not clear. Mycobacterium tuberculosis, an intracellular pathogen, possesses two isoforms of pantothenate kinases (CoaA and CoaX) belonging to type I and III. In order to determine which pantothenate kinase is essential in mycobacteria, we performed gene inactivation of coaA and coaX of M. tuberculosis individually. It was found that coaA could only be inactivated in the presence of an extra copy of the gene, while coaX could be inactivated in the wild-type cells, proving that CoaA is the essential pantothenate kinase in M. tuberculosis. Additionally, the coaA gene of M. tuberculosis was able to complement a temperature-sensitive coaA mutant of Escherichia coli at a non-permissive temperature while coaX could not. The coaX deletion mutant showed no growth defects in vitro, in macrophages or in mice. Taken together, our data suggest that CoaX, which is essential in Bacillus anthracis and thus had been suggested to be a drug target in this organism, might not be a valid target in M. tuberculosis. We have established that the type I isoform, CoaA, is the essential pantothenate kinase in M. tuberculosis and thus can be explored as a drug target.
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Affiliation(s)
- Disha Awasthy
- AstraZeneca R & D, 'Avishkar' Bellary Road, Hebbal, Bangalore, India
| | - Anisha Ambady
- AstraZeneca R & D, 'Avishkar' Bellary Road, Hebbal, Bangalore, India
| | - Jyothi Bhat
- AstraZeneca R & D, 'Avishkar' Bellary Road, Hebbal, Bangalore, India
| | - Gulebahar Sheikh
- AstraZeneca R & D, 'Avishkar' Bellary Road, Hebbal, Bangalore, India
| | - Sudha Ravishankar
- AstraZeneca R & D, 'Avishkar' Bellary Road, Hebbal, Bangalore, India
| | | | - Kakoli Mukherjee
- AstraZeneca R & D, 'Avishkar' Bellary Road, Hebbal, Bangalore, India
| | | | - Umender Sharma
- AstraZeneca R & D, 'Avishkar' Bellary Road, Hebbal, Bangalore, India
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Hingley-Wilson SM, Lougheed KEA, Ferguson K, Leiva S, Williams HD. Individual Mycobacterium tuberculosis universal stress protein homologues are dispensable in vitro. Tuberculosis (Edinb) 2010; 90:236-44. [PMID: 20541977 PMCID: PMC2914252 DOI: 10.1016/j.tube.2010.03.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 03/16/2010] [Accepted: 03/31/2010] [Indexed: 01/25/2023]
Abstract
Mycobacterium tuberculosis has 10 universal stress proteins, whose function is unknown. However, proteomic and transcriptomic analyses have shown that a number of usp genes are significantly upregulated under hypoxic conditions and in response to nitric oxide and carbon monoxide, as well as during M. tuberculosis infection of macrophage cell lines. Six of these USPs are part of the DosR regulon and this, along with their expression pattern and the phenotypes of usp mutants in other bacterial species, suggests a potential role in the persistence and/or intracellular survival of Mtb. Knock-out mutants of individual usp genes encoding the USPs Rv1996, Rv2005c, Rv2026c and Rv2028c were generated and their growth and survival under hypoxic and other stress conditions examined. Although the majority of usp genes are highly induced in hypoxic conditions, mutation did not affect the long term survival of Mtb under these conditions, or in response to a range of stress conditions chosen to represent the environmental onslaughts experienced by the bacillus during an infection, nor during infection of mouse and human - derived macrophage cell lines. The possibility remains that these USPs are functionally redundant in Mtb.
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Affiliation(s)
- S M Hingley-Wilson
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
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Ohol YM, Goetz DH, Chan K, Shiloh MU, Craik CS, Cox JS. Mycobacterium tuberculosis MycP1 protease plays a dual role in regulation of ESX-1 secretion and virulence. Cell Host Microbe 2010; 7:210-20. [PMID: 20227664 DOI: 10.1016/j.chom.2010.02.006] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 12/05/2009] [Accepted: 02/09/2010] [Indexed: 11/19/2022]
Abstract
Mycobacterium tuberculosis uses the ESX-1 secretion system to deliver virulence proteins during infection of host cells. Here we report a mechanism of posttranscriptional control of ESX-1 mediated by MycP1, a M. tuberculosis serine protease. We show that MycP1 is required for ESX-1 secretion but that, unexpectedly, genetic inactivation of MycP1 protease activity increases secretion of ESX-1 substrates. We demonstrate that EspB, an ESX-1 substrate required for secretion, is a target of MycP1 in vitro and in vivo. During macrophage infection, an inactive MycP1 protease mutant causes hyperactivation of ESX-1-stimulated innate signaling pathways. MycP1 is required for growth in mice during acute infection, while loss of its protease activity leads to attenuated virulence during chronic infection. As the key ESX-1 substrates ESAT-6 and CFP-10 are highly immunogenic, fine-tuning of their secretion by MycP1 may balance virulence and immune detection and be essential for successful maintenance of long-term M. tuberculosis infection.
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Affiliation(s)
- Yamini M Ohol
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94158, USA
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Abstract
In this review, we summarize the present understanding of the Mycobacterium tuberculosis transcriptome and catalog both experimentally verified findings and computationally derived predictions. We also provide a new analysis for a range of discoveries by comparing the results of previously independent research papers. Bringing these data together and improving their accessibility should help catalyze further discoveries. This minireview also provides some general insights that may be valuable to those working to characterize the transcriptome of less-studied prokaryotes.
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Converse PJ, Eisenach KD, Theus SA, Nuermberger EL, Tyagi S, Ly LH, Geiman DE, Guo H, Nolan ST, Akar NC, Klinkenberg LG, Gupta R, Lun S, Karakousis PC, Lamichhane G, McMurray DN, Grosset JH, Bishai WR. The impact of mouse passaging of Mycobacterium tuberculosis strains prior to virulence testing in the mouse and guinea pig aerosol models. PLoS One 2010; 5:e10289. [PMID: 20422019 PMCID: PMC2858211 DOI: 10.1371/journal.pone.0010289] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2010] [Accepted: 03/20/2010] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND It has been hypothesized that the virulence of lab-passaged Mycobacterium tuberculosis and recombinant M. tuberculosis mutants might be reduced due to multiple in vitro passages, and that virulence might be augmented by passage of these strains through mice before quantitative virulence testing in the mouse or guinea pig aerosol models. METHODOLOGY/PRINCIPAL FINDINGS By testing three M. tuberculosis H37Rv samples, one deletion mutant, and one recent clinical isolate for survival by the quantitative organ CFU counting method in mouse or guinea pig aerosol or intravenous infection models, we could discern no increase in bacterial fitness as a result of passaging of M. tuberculosis strains in mice prior to quantitative virulence testing in two animal models. Surface lipid expression as assessed by neutral red staining and thin-layer chromatography for PDIM analysis also failed to identify virulence correlates. CONCLUSIONS/SIGNIFICANCE These results indicate that animal passaging of M. tuberculosis strains prior to quantitative virulence testing in mouse or guinea pig models does not enhance or restore potency to strains that may have lost virulence due to in vitro passaging. It is critical to verify virulence of parental strains before genetic manipulations are undertaken and comparisons are made.
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Affiliation(s)
- Paul J Converse
- Department of Medicine, Center for Tuberculosis Research, Johns Hopkins University, Baltimore, Maryland, United States of America.
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