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Gosain TP, Chugh S, Rizvi ZA, Chauhan NK, Kidwai S, Thakur KG, Awasthi A, Singh R. Mycobacterium tuberculosis strain with deletions in menT3 and menT4 is attenuated and confers protection in mice and guinea pigs. Nat Commun 2024; 15:5467. [PMID: 38937463 PMCID: PMC11211403 DOI: 10.1038/s41467-024-49246-5] [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: 08/06/2023] [Accepted: 05/29/2024] [Indexed: 06/29/2024] Open
Abstract
The genome of Mycobacterium tuberculosis encodes for a large repertoire of toxin-antitoxin systems. In the present study, MenT3 and MenT4 toxins belonging to MenAT subfamily of TA systems have been functionally characterized. We demonstrate that ectopic expression of these toxins inhibits bacterial growth and this is rescued upon co-expression of their cognate antitoxins. Here, we show that simultaneous deletion of menT3 and menT4 results in enhanced susceptibility of M. tuberculosis upon exposure to oxidative stress and attenuated growth in guinea pigs and mice. We observed reduced expression of transcripts encoding for proteins that are essential or required for intracellular growth in mid-log phase cultures of ΔmenT4ΔT3 compared to parental strain. Further, the transcript levels of proteins involved in efficient bacterial clearance were increased in lung tissues of ΔmenT4ΔT3 infected mice relative to parental strain infected mice. We show that immunization of mice and guinea pigs with ΔmenT4ΔT3 confers significant protection against M. tuberculosis infection. Remarkably, immunization of mice with ΔmenT4ΔT3 results in increased antigen-specific TH1 bias and activated memory T cell response. We conclude that MenT3 and MenT4 are important for M. tuberculosis pathogenicity and strains lacking menT3 and menT4 have the potential to be explored further as vaccine candidates.
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Affiliation(s)
- Tannu Priya Gosain
- Centre for Tuberculosis Research, Translational Health Sciences and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, India
| | - Saurabh Chugh
- Centre for Tuberculosis Research, Translational Health Sciences and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, India
| | - Zaigham Abbas Rizvi
- Centre for Immunobiology and Immunotherapy, Translational Health Sciences and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, India
| | - Neeraj Kumar Chauhan
- Centre for Tuberculosis Research, Translational Health Sciences and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, India
| | - Saqib Kidwai
- Centre for Tuberculosis Research, Translational Health Sciences and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, 160036, India
| | - Amit Awasthi
- Centre for Immunobiology and Immunotherapy, Translational Health Sciences and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, India
| | - Ramandeep Singh
- Centre for Tuberculosis Research, Translational Health Sciences and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, 121001, India.
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Xu M, Liu M, Liu T, Pan X, Ren Q, Han T, Gou L. HigA2 (Rv2021c) Is a Transcriptional Regulator with Multiple Regulatory Targets in Mycobacterium tuberculosis. Microorganisms 2024; 12:1244. [PMID: 38930627 PMCID: PMC11205783 DOI: 10.3390/microorganisms12061244] [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: 05/25/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Toxin-antitoxin (TA) systems are the major mechanism for persister formation in Mycobacterium tuberculosis (Mtb). Previous studies found that HigBA2 (Rv2022c-Rv2021c), a predicted type II TA system of Mtb, could be activated for transcription in response to multiple stresses such as anti-tuberculosis drugs, nutrient starvation, endure hypoxia, acidic pH, etc. In this study, we determined the binding site of HigA2 (Rv2021c), which is located in the coding region of the upstream gene higB2 (Rv2022c), and the conserved recognition motif of HigA2 was characterized via oligonucleotide mutation. Eight binding sites of HigA2 were further found in the Mtb genome according to the conserved motif. RT-PCR showed that HigA2 can regulate the transcription level of all eight of these genes and three adjacent downstream genes. DNA pull-down experiments showed that twelve functional regulators sense external regulatory signals and may regulate the transcription of the HigBA2 system. Of these, Rv0903c, Rv0744c, Rv0474, Rv3124, Rv2603c, and Rv3583c may be involved in the regulation of external stress signals. In general, we identified the downstream target genes and possible upstream regulatory genes of HigA2, which paved the way for the illustration of the persistence establishment mechanism in Mtb.
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Affiliation(s)
- Mingyan Xu
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063210, China; (M.X.); (M.L.); (T.L.); (X.P.); (Q.R.)
| | - Meikun Liu
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063210, China; (M.X.); (M.L.); (T.L.); (X.P.); (Q.R.)
| | - Tong Liu
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063210, China; (M.X.); (M.L.); (T.L.); (X.P.); (Q.R.)
| | - Xuemei Pan
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063210, China; (M.X.); (M.L.); (T.L.); (X.P.); (Q.R.)
| | - Qi Ren
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063210, China; (M.X.); (M.L.); (T.L.); (X.P.); (Q.R.)
| | - Tiesheng Han
- Hebei Province Key Laboratory of Occupational Health and Safety for Coal Industry, School of Public Health, North China University of Science and Technology, Tangshan 063210, China; (M.X.); (M.L.); (T.L.); (X.P.); (Q.R.)
| | - Lixia Gou
- School of Life Science, North China University of Science and Technology, Tangshan 063210, China
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3
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Tulin G, Figueroa NR, Checa SK, Soncini FC. The multifarious MerR family of transcriptional regulators. Mol Microbiol 2024; 121:230-242. [PMID: 38105009 DOI: 10.1111/mmi.15212] [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: 08/10/2023] [Revised: 11/28/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023]
Abstract
The MerR family of transcriptional regulators includes a variety of bacterial cytoplasmic proteins that respond to a wide range of signals, including toxins, metal ions, and endogenous metabolites. Its best-characterized members share similar structural and functional features with the family founder, the mercury sensor MerR, although most of them do not respond to metal ions. The group of "canonical" MerR homologs displays common molecular mechanisms for controlling the transcriptional activation of their target genes in response to inducer signals. This includes the recognition of distinctive operator sequences located at suboptimal σ70 -dependent promoters. Interestingly, an increasing number of proteins assigned to the MerR family based on their DNA-binding domain do not match in structure, sequence, or mode of action with any of the canonical MerR-like regulators. Here, we analyzed several members of the family, including this last group. Based on a phylogenetic analysis, and similarities in structural/functional features and position of their target operators relative to the promoter elements, we propose to assign these "atypical/divergent" MerR regulators to a phylogenetically separated group. These atypical/divergent homologs represent a new class of transcriptional regulators with novel regulatory mechanisms.
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Affiliation(s)
- Gonzalo Tulin
- Instituto de Biología Molecular y Celular de Rosario, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Nicolás R Figueroa
- Centro de Estudios Fotosintéticos y Bioquímicos, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Susana K Checa
- Instituto de Biología Molecular y Celular de Rosario, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
| | - Fernando C Soncini
- Instituto de Biología Molecular y Celular de Rosario, Departamento de Microbiología, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Consejo Nacional de Investigaciones Científicas y Técnicas, Rosario, Argentina
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4
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Gopi Reji J, K Edison L, Raghunandanan S, Pushparajan AR, Kurthkoti K, Ajay Kumar R. Rv1255c, a dormancy-related transcriptional regulator of TetR family in Mycobacterium tuberculosis, enhances isoniazid tolerance in Mycobacterium smegmatis. J Antibiot (Tokyo) 2023; 76:720-727. [PMID: 37821540 DOI: 10.1038/s41429-023-00661-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 08/29/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023]
Abstract
Mycobacterium tuberculosis is exposed to diverse stresses inside the host during dormancy. Meanwhile, many metabolic and transcriptional regulatory changes occur, resulting in physiological modifications that help M. tuberculosis to adapt to these stresses. The same physiological changes also cause antibiotic tolerance in dormant M. tuberculosis. However, the transcriptional regulatory mechanism of antibiotic tolerance during dormancy remains unclear. Here, we showed that the expression of Rv1255c, an uncharacterised member of the tetracycline repressor family of transcriptional regulators, is upregulated during different stresses and hypoxia-induced dormancy. Antibiotic tolerance and efflux activities of Mycobacterium smegmatis constitutively expressing Rv1255c were analysed, and interestingly, it showed increased isoniazid tolerance and efflux activity. The intrabacterial isoniazid concentrations were found to be low in M. smegmatis expressing Rv1255c. Moreover, orthologs of the M. tuberculosis katG, gene of the enzyme which activates the first-line prodrug isoniazid, are overexpressed in this strain. Structural analysis of isoforms of KatG enzymes in M. smegmatis identified major amino acid substitutions associated with isoniazid resistance. Thus, we showed that Rv1255c helps M. smegmatis tolerate isoniazid by orchestrating drug efflux machinery. In addition, we showed that Rv1255c also causes overexpression of katG isoform in M. smegmatis which has amino acid substitutions as found in isoniazid-resistant katG in M. tuberculosis.
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Affiliation(s)
- Jijimole Gopi Reji
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Lakshmi K Edison
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Sajith Raghunandanan
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Akhil Raj Pushparajan
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Krishna Kurthkoti
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India
| | - Ramakrsihnan Ajay Kumar
- Mycobacterium Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, India.
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5
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Mahatha AC, Banerjee SK, Ghosh A, Lata S, Saha S, Basu J, Kundu M. A systems approach to decipher a role of transcription factor RegX3 in the adaptation of Mycobacterium tuberculosis to hypoxic stress. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35980355 DOI: 10.1099/mic.0.001229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Two-component systems (TCSs) are required for the ability of Mycobacterium tuberculosis to respond to stress. The paired TCS, SenX3-RegX3 is known to respond to phosphate starvation and acid stress. The other stress conditions under which RegX3 is required for M. tuberculosis to mount an appropriate response, remain incompletely understood. Here we have employed genome-wide microarray profiling to compare gene expression in a ΔregX3 mutant with the wild-type under phosphate stress, in order to gain information on the probable RegX3 regulon. We pulled out a set of 128 hypoxia-associated genes, which could potentially be regulated by RegX3, by overlapping the gene set downregulated at least twofold in ΔregX3 with the gene set reported in the literature to be associated with the response to hypoxia. We identified potential RegX3 binding inverted repeats at the loci of 41 of these genes, in silico. We also observed that ΔregX3 was attenuated in terms of its ability to withstand hypoxia, and this was reversed upon complementation with regX3, corroborating a role of RegX3 in the response of M. tuberculosis to hypoxia. We validated the binding of RegX3 at the upstream regions of a selected set of these genes. Electrophoretic mobility shift assays (EMSAs) confirmed that RegX3 binds to the upstream regions of the hypoxia-associated genes Rv3334, whiB7, Rv0195, Rv0196 and Rv1960c. Gene expression analyses showed that the expression of these genes is regulated by RegX3 under hypoxia. We also show that the expression of whiB7, Rv3334 and Rv0195 in macrophage-grown M. tuberculosis, is dependent on RegX3. Finally, we show that attenuation of survival of ΔregX3 under hypoxia is partly reversed upon overexpression of either Rv0195 or Rv3334, suggesting that the RegX3-Rv0195 and the RegX3-Rv3334 axis are involved in the adaptation of M. tuberculosis to a hypoxic environment.
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Affiliation(s)
- Amar Chandra Mahatha
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India
| | - Srijon Kaushik Banerjee
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India.,Present address: Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, PA 15217, USA
| | - Abhirupa Ghosh
- Division of Bioinformatics, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Suruchi Lata
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India
| | - Sudipto Saha
- Division of Bioinformatics, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, India
| | - Joyoti Basu
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India
| | - Manikuntala Kundu
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata 700009, India
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6
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Lata S, Mahatha AC, Mal S, Gupta UD, Kundu M, Basu J. Unravelling novel roles of the Mycobacterium tuberculosis transcription factor Rv0081 in regulation of the nucleoid-associated proteins Lsr2 and EspR, cholesterol utilization and subversion of lysosomal trafficking in macrophages. Mol Microbiol 2022; 117:1104-1120. [PMID: 35304930 DOI: 10.1111/mmi.14895] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 11/30/2022]
Abstract
The transcriptional network of Mycobacterium tuberculosis is designed to enable the organism to withstand host-associated stresses and to exploit the host milieu for its own survival and multiplication. Rv0081 (MT0088) is a transcriptional regulator whose interplay with other gene regulatory proteins and role in enabling M. tuberculosis to thrive within its host is incompletely understood. M. tuberculosis utilizes cholesterol within the granuloma. We show that deletion of Rv0081 compromises the ability of M. tuberculosis to utilize cholesterol as sole carbon source, to subvert lysosomal trafficking, and to form granulomas in vitro. Rv0081 downregulates expression of the nucleoid associated repressor Lsr2, leading to increased expression of the cholesterol catabolism-linked gene kshA and genes of the cholesterol importing operon, accounting for the requirement of Rv0081 in cholesterol utilization. Further, Rv0081 activates EspR which is required for secretion of ESX-1 substrates, which in turn are involved in subversion of lysosomal traffickingof M. tuberculosisand granuloma expansion. These results provide new insight into the role of Rv0081 under conditions which resemble the environment encountered by M. tuberculosis within its host. Rv0081 emergesas a central regulator of genes linked to various pathways which are crucial for the survival of the bacterium in vivo.
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Affiliation(s)
- Suruchi Lata
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata, 700009, India
| | - Amar Chandra Mahatha
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata, 700009, India
| | - Soumya Mal
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata, 700009, India
| | - Umesh D Gupta
- National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India
| | - Manikuntala Kundu
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata, 700009, India
| | - Joyoti Basu
- Department of Chemistry, Bose Institute, 93/1 Acharya Prafulla Chandra Road, Kolkata, 700009, India
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Willemse D, Moodley C, Mehra S, Kaushal D. Transcriptional Response of Mycobacterium tuberculosis to Cigarette Smoke Condensate. Front Microbiol 2021; 12:744800. [PMID: 34721344 PMCID: PMC8554204 DOI: 10.3389/fmicb.2021.744800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
Smoking is known to be an added risk factor for tuberculosis (TB), with nearly a quarter of the TB cases attributed to cigarette smokers in the 22 countries with the highest TB burden. Many studies have indicated a link between risk of active TB and cigarette smoke. Smoking is also known to significantly decrease TB cure and treatment completion rate and increase mortality rates. Cigarette smoke contains thousands of volatile compounds including carcinogens, toxins, reactive solids, and oxidants in both particulate and gaseous phase. Yet, to date, limited studies have analyzed the impact of cigarette smoke components on Mycobacterium tuberculosis (Mtb), the causative agent of TB. Here we report the impact of cigarette smoke condensate (CSC) on survival, mutation frequency, and gene expression of Mtb in vitro. We show that exposure of virulent Mtb to cigarette smoke increases the mutation frequency of the pathogen and strongly induces the expression of the regulon controlled by SigH—a global transcriptional regulator of oxidative stress. SigH has previously been shown to be required for Mtb to respond to oxidative stress, survival, and granuloma formation in vivo. A high-SigH expression phenotype is known to be associated with greater virulence of Mtb. In patients with pulmonary TB who smoke, these changes may therefore play an important, yet unexplored, role in the treatment efficacy by potentially enhancing the virulence of tubercle bacilli.
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Affiliation(s)
- Danicke Willemse
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Chivonne Moodley
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States.,Tulane National Primate Research Center, Tulane University Health Sciences Center, Covington, LA, United States
| | - Smriti Mehra
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States.,Tulane National Primate Research Center, Tulane University Health Sciences Center, Covington, LA, United States
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, TX, United States
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Peterson EJR, Abidi AA, Arrieta-Ortiz ML, Aguilar B, Yurkovich JT, Kaur A, Pan M, Srinivas V, Shmulevich I, Baliga NS. Intricate Genetic Programs Controlling Dormancy in Mycobacterium tuberculosis. Cell Rep 2021; 31:107577. [PMID: 32348771 PMCID: PMC7605849 DOI: 10.1016/j.celrep.2020.107577] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 12/18/2019] [Accepted: 04/06/2020] [Indexed: 11/24/2022] Open
Abstract
Mycobacterium tuberculosis (MTB) displays the remarkable ability to transition in and out of dormancy, a hallmark of the pathogen’s capacity to evade the immune system and exploit susceptible individuals. Uncovering the gene regulatory programs that underlie the phenotypic shifts in MTB during disease latency and reactivation has posed a challenge. We develop an experimental system to precisely control dissolved oxygen levels in MTB cultures in order to capture the transcriptional events that unfold as MTB transitions into and out of hypoxia-induced dormancy. Using a comprehensive genome-wide transcription factor binding map and insights from network topology analysis, we identify regulatory circuits that deterministically drive sequential transitions across six transcriptionally and functionally distinct states encompassing more than three-fifths of the MTB genome. The architecture of the genetic programs explains the transcriptional dynamics underlying synchronous entry of cells into a dormant state that is primed to infect the host upon encountering favorable conditions. Mycobacterium tuberculosis (MTB) persists within the host by counteracting disparate stressors including hypoxia. Peterson et al. report a transcriptional program that coordinates sequential state transitions to drive MTB in and out of hypoxia-induced dormancy. Among varied properties, this program encodes advanced preparedness to infect the host in favorable conditions.
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Affiliation(s)
| | - Abrar A Abidi
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Boris Aguilar
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | - Amardeep Kaur
- Institute for Systems Biology, Seattle, WA 98109, USA
| | - Min Pan
- Institute for Systems Biology, Seattle, WA 98109, USA
| | | | | | - Nitin S Baliga
- Institute for Systems Biology, Seattle, WA 98109, USA; Molecular and Cellular Biology Program, Departments of Microbiology and Biology, University of Washington, Seattle, WA; Lawrence Berkeley National Laboratories, Berkeley, CA.
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9
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Dissecting the RecA-(In)dependent Response to Mitomycin C in Mycobacterium tuberculosis Using Transcriptional Profiling and Proteomics Analyses. Cells 2021; 10:cells10051168. [PMID: 34064944 PMCID: PMC8151990 DOI: 10.3390/cells10051168] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 02/06/2023] Open
Abstract
Mycobacteria exploit at least two independent global systems in response to DNA damage: the LexA/RecA-dependent SOS response and the PafBC-regulated pathway. Intracellular pathogens, such as Mycobacterium tuberculosis, are exposed to oxidative and nitrosative stress during the course of infection while residing inside host macrophages. The current understanding of RecA-independent responses to DNA damage is based on the saprophytic model of Mycobacterium smegmatis, a free-living and nonpathogenic mycobacterium. The aim of the present study was to identify elements of RecA-independent responses to DNA damage in pathogenic intracellular mycobacteria. With the help of global transcriptional profiling, we were able to dissect RecA-dependent and RecA-independent pathways. We profiled the DNA damage responses of an M. tuberculosis strain lacking the recA gene, a strain with an undetectable level of the PafBC regulatory system, and a strain with both systems tuned down simultaneously. RNA-Seq profiling was correlated with the evaluation of cell survival in response to DNA damage to estimate the relevance of each system to the overall sensitivity to genotoxic agents. We also carried out whole-cell proteomics analysis of the M. tuberculosis strains in response to mitomycin C. This approach highlighted that LexA, a well-defined key element of the SOS system, is proteolytically inactivated during RecA-dependent DNA repair, which we found to be transcriptionally repressed in response to DNA-damaging agents in the absence of RecA. Proteomics profiling revealed that AlkB was significantly overproduced in the ΔrecA pafBCCRISPRi/dCas9 strain and that Holliday junction resolvase RuvX was a DNA damage response factor that was significantly upregulated regardless of the presence of functional RecA and PafBC systems, thus falling into a third category of DNA damage factors: RecA- and PafBC-independent. While invisible to the mass spectrometer, the genes encoding alkA, dnaB, and dnaE2 were significantly overexpressed in the ΔrecA pafBCCRISPRi/dCas9 strain at the transcript level.
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10
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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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11
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Sousa EH, Carepo MS, Moura JJ. Nitrate-nitrite fate and oxygen sensing in dormant Mycobacterium tuberculosis: A bioinorganic approach highlighting the importance of transition metals. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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12
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Jiang J, Lin C, Zhang J, Wang Y, Shen L, Yang K, Xiao W, Li Y, Zhang L, Liu J. Transcriptome Changes of Mycobacterium marinum in the Process of Resuscitation From Hypoxia-Induced Dormancy. Front Genet 2020; 10:1359. [PMID: 32117415 PMCID: PMC7025489 DOI: 10.3389/fgene.2019.01359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 12/11/2019] [Indexed: 12/22/2022] Open
Abstract
Nearly one-third of the world's population is latently infected with Mycobacterium tuberculosis (M. tb), which represents a huge disease reservoir for reactivation and a major obstacle for effective control of tuberculosis. During latent infection, M. tb is thought to enter nonreplicative dormant states by virtue of its response to hypoxia and nutrient-deprived conditions. Knowledge of the genetic programs used to facilitate entry into and exit from the nonreplicative dormant states remains incomplete. In this study, we examined the transcriptional changes of Mycobacterium marinum (M. marinum), a pathogenic mycobacterial species closely related to M. tb, at different stages of resuscitation from hypoxia-induced dormancy. RNA-seq analyses were performed on M. marinum cultures recovered at multiple time points after resuscitation. Differentially expressed genes (DEGs) at each time period were identified and analyzed. Co-expression networks of transcription factors and DEGs in each period were constructed. In addition, we performed a weighted gene co-expression network analysis (WGCNA) on all genes and obtained 12 distinct gene modules. Collectively, these data provided valuable insight into the transcriptome changes of M. marinum upon resuscitation as well as gene module function of the bacteria during active metabolism and growth.
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Affiliation(s)
- Jun Jiang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Chen Lin
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Junli Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Yuchen Wang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Lifang Shen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Kunpeng Yang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Wenxuan Xiao
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Yao Li
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China
| | - Lu Zhang
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China.,State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Science, Fudan University, Shanghai, China
| | - Jun Liu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Science, Fudan University, Shanghai, China.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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13
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Banerjee SK, Lata S, Sharma AK, Bagchi S, Kumar M, Sahu SK, Sarkar D, Gupta P, Jana K, Gupta UD, Singh R, Saha S, Basu J, Kundu M. The sensor kinase MtrB of Mycobacterium tuberculosis regulates hypoxic survival and establishment of infection. J Biol Chem 2019; 294:19862-19876. [PMID: 31653701 PMCID: PMC6937564 DOI: 10.1074/jbc.ra119.009449] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 10/24/2019] [Indexed: 12/16/2022] Open
Abstract
Paired two-component systems (TCSs), having a sensor kinase (SK) and a cognate response regulator (RR), enable the human pathogen Mycobacterium tuberculosis to respond to the external environment and to persist within its host. Here, we inactivated the SK gene of the TCS MtrAB, mtrB, generating the strain ΔmtrB We show that mtrB loss reduces the bacterium's ability to survive in macrophages and increases its association with autophagosomes and autolysosomes. Notably, the ΔmtrB strain was markedly defective in establishing lung infection in mice, with no detectable lung pathology following aerosol challenge. ΔmtrB was less able to withstand hypoxic and acid stresses and to form biofilms and had decreased viability under hypoxia. Transcriptional profiling of ΔmtrB by gene microarray analysis, validated by quantitative RT-PCR, indicated down-regulation of the hypoxia-associated dosR regulon, as well as genes associated with other pathways linked to adaptation of M. tuberculosis to the host environment. Using in vitro biochemical assays, we demonstrate that MtrB interacts with DosR (a noncognate RR) in a phosphorylation-independent manner. Electrophoretic mobility shift assays revealed that MtrB enhances the binding of DosR to the hspX promoter, suggesting an unexpected role of MtrB in DosR-regulated gene expression in M. tuberculosis Taken together, these findings indicate that MtrB functions as a regulator of DosR-dependent gene expression and in the adaptation of M. tuberculosis to hypoxia and the host environment. We propose that MtrB may be exploited as a chemotherapeutic target against tuberculosis.
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Affiliation(s)
| | - Suruchi Lata
- Department of Chemistry, Bose Institute, Kolkata 700009, India
| | | | - Shreya Bagchi
- Department of Chemistry, Bose Institute, Kolkata 700009, India
| | - Manish Kumar
- Department of Chemistry, Bose Institute, Kolkata 700009, India
| | | | - Debasree Sarkar
- Division of Bioinformatics, Bose Institute, Kolkata 700054, India
| | - Pushpa Gupta
- National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India
| | - Kuladip Jana
- Division of Molecular Medicine, Bose Institute, Kolkata 700054, India
| | - Umesh Datta Gupta
- National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra 282004, India
| | - Ramandeep Singh
- Vaccine and Infectious Disease Research Centre, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad, Haryana 121001, India
| | - Sudipto Saha
- Division of Bioinformatics, Bose Institute, Kolkata 700054, India
| | - Joyoti Basu
- Department of Chemistry, Bose Institute, Kolkata 700009, India
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14
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Yousefi Avarvand A, Khademi F, Tafaghodi M, Ahmadipour Z, Moradi B, Meshkat Z. The roles of latency-associated antigens in tuberculosis vaccines. ACTA ACUST UNITED AC 2019; 66:487-491. [DOI: 10.1016/j.ijtb.2019.04.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/26/2019] [Indexed: 11/27/2022]
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15
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Gordhan BG, Peters J, Kana BD. Application of model systems to study adaptive responses of Mycobacterium tuberculosis during infection and disease. ADVANCES IN APPLIED MICROBIOLOGY 2019; 108:115-161. [PMID: 31495404 DOI: 10.1016/bs.aambs.2019.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) claims more human lives than any other infectious organism. The lethal synergy between TB-HIV infection and the rapid emergence of drug resistant strains has created a global public health threat that requires urgent attention. Mycobacterium tuberculosis, the causative agent of TB is an exquisitely well-adapted human pathogen, displaying the ability to promptly remodel metabolism when encountering stressful environments during pathogenesis. A careful study of the mechanisms that enable this adaptation will enhance the understanding of key aspects related to the microbiology of TB disease. However, these efforts require microbiological model systems that mimic host conditions in the laboratory. Herein, we describe several in vitro model systems that generate non-replicating and differentially culturable mycobacteria. The changes that occur in the metabolism of M. tuberculosis in some of these models and how these relate to those reported for human TB disease are discussed. We describe mechanisms that tubercle bacteria use to resuscitate from these non-replicating conditions, together with phenotypic heterogeneity in terms of culturabiliy of M. tuberculosis in sputum. Transcriptional changes in M. tuberculosis that allow for adaptation of the organism to the lung environment are also summarized. Finally, given the emerging importance of the microbiome in various infectious diseases, we provide a description of how the lung and gut microbiome affect susceptibility to TB infection and response to treatment. Consideration of these collective aspects will enhance the understanding of basic metabolism, physiology, drug tolerance and persistence in M. tuberculosis to enable development of new therapeutic interventions.
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Affiliation(s)
- Bhavna Gowan Gordhan
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Julian Peters
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Bavesh Davandra Kana
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa.
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16
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Kumar A, Phulera S, Rizvi A, Sonawane PJ, Panwar HS, Banerjee S, Sahu A, Mande SC. Structural basis of hypoxic gene regulation by the Rv0081 transcription factor ofMycobacterium tuberculosis. FEBS Lett 2019; 593:982-995. [DOI: 10.1002/1873-3468.13375] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 03/26/2019] [Accepted: 03/28/2019] [Indexed: 01/01/2023]
Affiliation(s)
- Ashwani Kumar
- National Centre for Cell Science SP Pune University Campus Pune India
| | - Swastik Phulera
- National Centre for Cell Science SP Pune University Campus Pune India
| | - Arshad Rizvi
- Department of Biochemistry University of Hyderabad Hyderabad India
| | | | | | | | - Arvind Sahu
- National Centre for Cell Science SP Pune University Campus Pune India
| | - Shekhar C. Mande
- National Centre for Cell Science SP Pune University Campus Pune India
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