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Urtasun-Elizari JM, Ma R, Pickford H, Farrell D, Gonzalez G, Perets V, Nakajima C, Suzuki Y, MacHugh DE, Bhatt A, Gordon SV. Functional analysis of the Mycobacterium bovis AF2122/97 PhoPR system. Tuberculosis (Edinb) 2024; 148:102544. [PMID: 39018651 DOI: 10.1016/j.tube.2024.102544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 06/25/2024] [Accepted: 07/12/2024] [Indexed: 07/19/2024]
Abstract
The PhoPR system is a master regulator in Mycobacterium tuberculosis. A key difference between M. tuberculosis and Mycobacterium bovis is a G71I substitution in the M. bovis PhoR orthologue. Functional studies of the M. bovis PhoPR system have generated conflicting findings, with some research suggesting that the M. bovis PhoPR is defective while others indicate it is functional. We sought to revisit the functionality of the M. bovis PhoPR system. To address this, we constructed a phoPR mutant in the reference strain M. bovis AF2122/97. We employed a combination of growth assays and transcriptomics analyses to assess the phenotype of the mutant vs wild type and complemented strains. We found that the M. bovis AF2122/97 ΔphoPR mutant showed a growth defect on solid and liquid media compared to the wild type and complemented strains. The transcriptome of the M. bovis AF2122/97 ΔphoPR mutant was also altered as compared to wild type, including differential expression of genes involved in lipid metabolism and secretion. Our work provides further insight into the activity of PhoPR in M. bovis and underlines the importance of the PhoPR system as a master regulator of gene expression in the Mycobacterium tuberculosis complex.
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Affiliation(s)
| | - Ruoyao Ma
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Hayleah Pickford
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Damien Farrell
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Gabriel Gonzalez
- International Institute for Vaccine Research and Development, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, 001-0021, Japan
| | - Viktor Perets
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland
| | - Chie Nakajima
- International Institute for Vaccine Research and Development, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, 001-0021, Japan; International Institute for Zoonosis Control, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan
| | - Yasuhiko Suzuki
- International Institute for Vaccine Research and Development, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, 001-0021, Japan; International Institute for Zoonosis Control, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan
| | - David E MacHugh
- UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland; UCD Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland; UCD Centre for One Health, University College Dublin, Belfield, Dublin, Ireland
| | - Apoorva Bhatt
- School of Biosciences and Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK
| | - Stephen V Gordon
- UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland; International Institute for Vaccine Research and Development, Hokkaido University, Kita 21, Nishi 11, Kita-ku, Sapporo, 001-0021, Japan; International Institute for Zoonosis Control, Hokkaido University, Kita 20, Nishi 10, Kita-ku, Sapporo, 001-0020, Japan; UCD Conway Institute of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, D04 V1W8, Ireland; UCD Centre for One Health, University College Dublin, Belfield, Dublin, Ireland; UCD Centre for Experimental Pathogen Host Research, University College Dublin, Belfield, Dublin, Ireland.
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2
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Santoshi M, Tare P, Nagaraja V. Nucleoid-associated proteins of mycobacteria come with a distinctive flavor. Mol Microbiol 2024. [PMID: 38922783 DOI: 10.1111/mmi.15287] [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: 02/16/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
In every bacterium, nucleoid-associated proteins (NAPs) play crucial roles in chromosome organization, replication, repair, gene expression, and other DNA transactions. Their central role in controlling the chromatin dynamics and transcription has been well-appreciated in several well-studied organisms. Here, we review the diversity, distribution, structure, and function of NAPs from the genus Mycobacterium. We highlight the progress made in our understanding of the effects of these proteins on various processes and in responding to environmental stimuli and stress of mycobacteria in their free-living as well as during distinctive intracellular lifestyles. We project them as potential drug targets and discuss future studies to bridge the information gap with NAPs from well-studied systems.
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Affiliation(s)
- Meghna Santoshi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Priyanka Tare
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
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3
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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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4
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Khan H, Paul P, Goar H, Bamniya B, Baid N, Sarkar D. Mycobacterium tuberculosis PhoP integrates stress response to intracellular survival by regulating cAMP level. eLife 2024; 13:RP92136. [PMID: 38739431 PMCID: PMC11090507 DOI: 10.7554/elife.92136] [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] [Indexed: 05/14/2024] Open
Abstract
Survival of Mycobacterium tuberculosis within the host macrophages requires the bacterial virulence regulator PhoP, but the underlying reason remains unknown. 3',5'-Cyclic adenosine monophosphate (cAMP) is one of the most widely used second messengers, which impacts a wide range of cellular responses in microbial pathogens including M. tuberculosis. Herein, we hypothesized that intra-bacterial cAMP level could be controlled by PhoP since this major regulator plays a key role in bacterial responses against numerous stress conditions. A transcriptomic analysis reveals that PhoP functions as a repressor of cAMP-specific phosphodiesterase (PDE) Rv0805, which hydrolyzes cAMP. In keeping with these results, we find specific recruitment of the regulator within the promoter region of rv0805 PDE, and absence of phoP or ectopic expression of rv0805 independently accounts for elevated PDE synthesis, leading to the depletion of intra-bacterial cAMP level. Thus, genetic manipulation to inactivate PhoP-rv0805-cAMP pathway decreases cAMP level, stress tolerance, and intracellular survival of the bacillus.
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Affiliation(s)
- Hina Khan
- CSIR, Institute of Microbial TechnologyChandigarhIndia
| | - Partha Paul
- CSIR, Institute of Microbial TechnologyChandigarhIndia
| | - Harsh Goar
- CSIR, Institute of Microbial TechnologyChandigarhIndia
| | - Bhanwar Bamniya
- CSIR, Institute of Microbial TechnologyChandigarhIndia
- Academy of Scientific and Innovative ResearchGhaziabadIndia
| | - Navin Baid
- CSIR, Institute of Microbial TechnologyChandigarhIndia
| | - Dibyendu Sarkar
- CSIR, Institute of Microbial TechnologyChandigarhIndia
- Academy of Scientific and Innovative ResearchGhaziabadIndia
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5
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Veerapandian R, Gadad SS, Jagannath C, Dhandayuthapani S. Live Attenuated Vaccines against Tuberculosis: Targeting the Disruption of Genes Encoding the Secretory Proteins of Mycobacteria. Vaccines (Basel) 2024; 12:530. [PMID: 38793781 PMCID: PMC11126151 DOI: 10.3390/vaccines12050530] [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: 04/08/2024] [Revised: 05/07/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Tuberculosis (TB), a chronic infectious disease affecting humans, causes over 1.3 million deaths per year throughout the world. The current preventive vaccine BCG provides protection against childhood TB, but it fails to protect against pulmonary TB. Multiple candidates have been evaluated to either replace or boost the efficacy of the BCG vaccine, including subunit protein, DNA, virus vector-based vaccines, etc., most of which provide only short-term immunity. Several live attenuated vaccines derived from Mycobacterium tuberculosis (Mtb) and BCG have also been developed to induce long-term immunity. Since Mtb mediates its virulence through multiple secreted proteins, these proteins have been targeted to produce attenuated but immunogenic vaccines. In this review, we discuss the characteristics and prospects of live attenuated vaccines generated by targeting the disruption of the genes encoding secretory mycobacterial proteins.
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Affiliation(s)
- Raja Veerapandian
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA
| | - Shrikanth S. Gadad
- Center of Emphasis in Cancer, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA
| | - Chinnaswamy Jagannath
- Department of Pathology and Genomic Medicine, Houston Methodist Research Institute & Weill Cornell Medical College, Houston, TX 77030, USA
| | - Subramanian Dhandayuthapani
- Center of Emphasis in Infectious Diseases, Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center El Paso, El Paso, TX 79905, USA
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6
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Kumar K, Dutta T. Transcriptional activation of the Mycobacterium tuberculosis virulence-associated small RNA MTS1338 by the response regulators DosR and PhoP. FEBS Lett 2024; 598:1034-1044. [PMID: 38639734 DOI: 10.1002/1873-3468.14882] [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: 07/02/2023] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/20/2024]
Abstract
MTS1338, a distinctive small RNA in pathogenic mycobacteria, plays a crucial role in host-pathogen interactions during infection. Mycobacterial cells encounter heterogeneous stresses in macrophages, which highly upregulate MTS1338. A dormancy regulatory factor DosR regulates the intracellular abundance of MTS1338. Herein, we investigated the interplay of DosR and a low pH-inducible gene regulator PhoP binding to the MTS1338 promoter. We identified that DosR strongly binds to two regions upstream of the MTS1338 gene. The proximal region possesses a threefold higher affinity than the distal site, but the presence of both regions increased the affinity for DosR by > 10-fold. PhoP did not bind to the MTS1338 gene but binds to the DosR-bound MTS1338 gene, suggesting a concerted mechanism for MTS1338 expression.
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Affiliation(s)
- Krishan Kumar
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, India
| | - Tanmay Dutta
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, India
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7
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Dechow SJ, Abramovitch RB. Targeting Mycobacterium tuberculosis pH-driven adaptation. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001458. [PMID: 38717801 PMCID: PMC11165653 DOI: 10.1099/mic.0.001458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/17/2024] [Indexed: 06/13/2024]
Abstract
Mycobacterium tuberculosis (Mtb) senses and adapts to host environmental cues as part of its pathogenesis. One important cue sensed by Mtb is the acidic pH of its host niche - the macrophage. Acidic pH induces widespread transcriptional and metabolic remodelling in Mtb. These adaptations to acidic pH can lead Mtb to slow its growth and promote pathogenesis and antibiotic tolerance. Mutants defective in pH-dependent adaptations exhibit reduced virulence in macrophages and animal infection models, suggesting that chemically targeting these pH-dependent pathways may have therapeutic potential. In this review, we discuss mechanisms by which Mtb regulates its growth and metabolism at acidic pH. Additionally, we consider the therapeutic potential of disrupting pH-driven adaptations in Mtb and review the growing class of compounds that exhibit pH-dependent activity or target pathways important for adaptation to acidic pH.
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Affiliation(s)
- Shelby J. Dechow
- Department of Microbiology, Genetics and Immunology, Michigan State University, East Lansing, MI 48824, USA
| | - Robert B. Abramovitch
- Department of Microbiology, Genetics and Immunology, Michigan State University, East Lansing, MI 48824, USA
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8
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Banerjee A, Chakraborty M, Sharma S, Chaturvedi R, Bose A, Biswas P, Singh A, Visweswariah SS. Cyclic AMP binding to a universal stress protein in Mycobacterium tuberculosis is essential for viability. J Biol Chem 2024; 300:107287. [PMID: 38636658 PMCID: PMC11107214 DOI: 10.1016/j.jbc.2024.107287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024] Open
Abstract
Mycobacterial genomes encode multiple adenylyl cyclases and cAMP effector proteins, underscoring the diverse ways these bacteria utilize cAMP. We identified universal stress proteins, Rv1636 and MSMEG_3811 in Mycobacterium tuberculosis and Mycobacterium smegmatis, respectively, as abundantly expressed, novel cAMP-binding proteins. Rv1636 is secreted via the SecA2 secretion system in M. tuberculosis but is not directly responsible for the efflux of cAMP from the cell. In slow-growing mycobacteria, intrabacterial concentrations of Rv1636 were equivalent to the concentrations of cAMP present in the cell. In contrast, levels of intrabacterial MSMEG_3811 in M. smegmatis were lower than that of cAMP and therefore, overexpression of Rv1636 increased levels of "bound" cAMP. While msmeg_3811 could be readily deleted from the genome of M. smegmatis, we found that the rv1636 gene is essential for the viability of M. tuberculosis and is dependent on the cAMP-binding ability of Rv1636. Therefore, Rv1636 may function to regulate cAMP signaling by direct sequestration of the second messenger. This is the first evidence of a "sponge" for any second messenger in bacterial signaling that would allow mycobacterial cells to regulate the available intrabacterial "free" pool of cAMP.
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Affiliation(s)
- Arka Banerjee
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Moubani Chakraborty
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Suruchi Sharma
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Ruchi Chaturvedi
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Avipsa Bose
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Priyanka Biswas
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Amit Singh
- Department of Microbiology and Cell Biology, Centre for Infectious Disease Research, Indian Institute of Science, Bengaluru, India
| | - Sandhya S Visweswariah
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India.
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9
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Gries R, Chhen J, van Gumpel E, Theobald SJ, Sonnenkalb L, Utpatel C, Metzen F, Koch M, Dallenga T, Djaout K, Baulard A, Dal Molin M, Rybniker J. Discovery of dual-active ethionamide boosters inhibiting the Mycobacterium tuberculosis ESX-1 secretion system. Cell Chem Biol 2024; 31:699-711.e6. [PMID: 38181799 DOI: 10.1016/j.chembiol.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 08/22/2023] [Accepted: 12/08/2023] [Indexed: 01/07/2024]
Abstract
Drug-resistant Mycobacterium tuberculosis (Mtb) remains a major public health concern requiring complementary approaches to standard anti-tuberculous regimens. Anti-virulence molecules or compounds that enhance the activity of antimicrobial prodrugs are promising alternatives to conventional antibiotics. Exploiting host cell-based drug discovery, we identified an oxadiazole compound (S3) that blocks the ESX-1 secretion system, a major virulence factor of Mtb. S3-treated mycobacteria showed impaired intracellular growth and a reduced ability to lyse macrophages. RNA sequencing experiments of drug-exposed bacteria revealed strong upregulation of a distinct set of genes including ethA, encoding a monooxygenase activating the anti-tuberculous prodrug ethionamide. Accordingly, we found a strong ethionamide boosting effect in S3-treated Mtb. Extensive structure-activity relationship experiments revealed that anti-virulence and ethionamide-boosting activity can be uncoupled by chemical modification of the primary hit molecule. To conclude, this series of dual-active oxadiazole compounds targets Mtb via two distinct mechanisms of action.
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Affiliation(s)
- Raphael Gries
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Jason Chhen
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Edeltraud van Gumpel
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Sebastian J Theobald
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Lindsay Sonnenkalb
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany
| | - Christian Utpatel
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany
| | - Fabian Metzen
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Tobias Dallenga
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany; Cellular Microbiology, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany
| | - Kamel Djaout
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, 59000 Lille, France
| | - Alain Baulard
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, 59000 Lille, France
| | - Michael Dal Molin
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Jan Rybniker
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany.
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10
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Coutte L, Antoine R, Slupek S, Locht C. Combined transcriptomic and ChIPseq analyses of the Bordetella pertussis RisA regulon. mSystems 2024; 9:e0095123. [PMID: 38470037 PMCID: PMC11019879 DOI: 10.1128/msystems.00951-23] [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: 09/18/2023] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
The regulation of Bordetella pertussis virulence is mediated by the two-component system BvgA/S, which activates the transcription of virulence-activated genes (vags). In the avirulent phase, the vags are not expressed, but instead, virulence-repressed genes (vrgs) are expressed, under the control of another two-component system, RisA/K. Here, we combined transcriptomic and chromatin immunoprecipitation sequencing (ChIPseq) data to examine the RisA/K regulon. We performed RNAseq analyses of RisA-deficient and RisA-phosphoablative B. pertussis mutants cultivated in virulent and avirulent conditions. We confirmed that the expression of most vrgs is regulated by phosphorylated RisA. However, the expression of some, including those involved in flagellum biosynthesis and chemotaxis, requires RisA independently of phosphorylation. Many RisA-regulated genes encode proteins with regulatory functions, suggesting multiple RisA regulation cascades. By ChIPseq analyses, we identified 430 RisA-binding sites, 208 within promoter regions, 201 within open reading frames, and 21 in non-coding regions. RisA binding was demonstrated in the promoter regions of most vrgs and, surprisingly, of some vags, as well as for other genes not identified as vags or vrgs. Unexpectedly, many genes, including some vags, like prn, brpL, bipA, and cyaA, contain a BvgA-binding site and a RisA-binding site, which increases the complexity of the RisAK/BvgAS network in B. pertussis virulence regulation.IMPORTANCEThe expression of virulence-activated genes (vags) of Bordetella pertussis, the etiological agent of whooping cough, is under the transcriptional control of the two-component system BvgA/S, which allows the bacterium to switch between virulent and avirulent phases. In addition, the more recently identified two-component system RisA/K is required for the expression of B. pertussis genes, collectively named vrgs, that are repressed during the virulent phase but activated during the avirulent phase. We have characterized the RisA/K regulon by combined transcriptomic and chromatin immunoprecipitation sequencing analyses. We identified more than 400 RisA-binding sites. Many of them are localized in promoter regions, especially vrgs, but some were found within open reading frames and in non-coding regions. Surprisingly, RisA-binding sites were also found in promoter regions of some vags, illustrating the previously underappreciated complexity of virulence regulation in B. pertussis.
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Affiliation(s)
- Loïc Coutte
- U1019–UMR9017, University of Lille, CNRS, Inserm, CHU Lille, CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France
| | - Rudy Antoine
- U1019–UMR9017, University of Lille, CNRS, Inserm, CHU Lille, CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France
| | - Stephanie Slupek
- U1019–UMR9017, University of Lille, CNRS, Inserm, CHU Lille, CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France
| | - Camille Locht
- U1019–UMR9017, University of Lille, CNRS, Inserm, CHU Lille, CIIL-Center for Infection and Immunity of Lille, Institut Pasteur de Lille, Lille, France
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11
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Orgeur M, Sous C, Madacki J, Brosch R. Evolution and emergence of Mycobacterium tuberculosis. FEMS Microbiol Rev 2024; 48:fuae006. [PMID: 38365982 PMCID: PMC10906988 DOI: 10.1093/femsre/fuae006] [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: 11/09/2023] [Revised: 01/12/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases in human history, prevailing even in the 21st century. The causative agents of TB are represented by a group of closely related bacteria belonging to the Mycobacterium tuberculosis complex (MTBC), which can be subdivided into several lineages of human- and animal-adapted strains, thought to have shared a last common ancestor emerged by clonal expansion from a pool of recombinogenic Mycobacterium canettii-like tubercle bacilli. A better understanding of how MTBC populations evolved from less virulent mycobacteria may allow for discovering improved TB control strategies and future epidemiologic trends. In this review, we highlight new insights into the evolution of mycobacteria at the genus level, describing different milestones in the evolution of mycobacteria, with a focus on the genomic events that have likely enabled the emergence and the dominance of the MTBC. We also review the recent literature describing the various MTBC lineages and highlight their particularities and differences with a focus on host preferences and geographic distribution. Finally, we discuss on putative mechanisms driving the evolution of tubercle bacilli and mycobacteria in general, by taking the mycobacteria-specific distributive conjugal transfer as an example.
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Affiliation(s)
- Mickael Orgeur
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Camille Sous
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Jan Madacki
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Unit for Human Evolutionary Genetics, 75015 Paris, France
| | - Roland Brosch
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
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12
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Belardinelli JM, Arora D, Avanzi C, Wheat WH, Bryant JM, Spencer JS, Blundell TL, Parkhill J, Floto RA, Jackson M. Clinically relevant mutations in the PhoR sensor kinase of host-adapted Mycobacterium abscessus isolates impact response to acidic pH and virulence. Microbiol Spectr 2023; 11:e0158823. [PMID: 37874174 PMCID: PMC10715180 DOI: 10.1128/spectrum.01588-23] [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: 04/17/2023] [Accepted: 09/14/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE Difficult-to-treat pulmonary infections caused by nontuberculous mycobacteria of the Mycobacterium abscessus group have been steadily increasing in the USA and globally. Owing to the relatively recent recognition of M. abscessus as a human pathogen, basic and translational research to address critical gaps in diagnosis, treatment, and prevention of diseases caused by this microorganism has been lagging behind that of the better-known mycobacterial pathogen, Mycobacterium tuberculosis. To begin unraveling the molecular mechanisms of pathogenicity of M. abscessus, we here focus on the study of a two-component regulator known as PhoPR which we found to be under strong evolutionary pressure during human lung infection. We show that PhoPR is activated at acidic pH and serves to regulate a defined set of genes involved in host adaptation. Accordingly, clinical isolates from chronically infected human lungs tend to hyperactivate this regulator enabling M. abscessus to escape macrophage killing.
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Affiliation(s)
- Juan M Belardinelli
- Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University , Fort Collins, Colorado, USA
| | - Divya Arora
- Department of Medicine, Molecular Immunity Unit, University of Cambridge, MRC-Laboratory of Molecular Biology , Cambridge, United Kingdom
| | - Charlotte Avanzi
- Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University , Fort Collins, Colorado, USA
| | - William H Wheat
- Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University , Fort Collins, Colorado, USA
| | - Josephine M Bryant
- Department of Medicine, Molecular Immunity Unit, University of Cambridge, MRC-Laboratory of Molecular Biology , Cambridge, United Kingdom
- University of Cambridge Centre for AI in Medicine , Cambridge, United Kingdom
| | - John S Spencer
- Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University , Fort Collins, Colorado, USA
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge , Cambridge, United Kingdom
| | - Julian Parkhill
- Wellcome Sanger Institute , Hinxton, United Kingdom
- Department of Veterinary Medicine, University of Cambridge , Cambridge, United Kingdom
| | - R Andres Floto
- Department of Medicine, Molecular Immunity Unit, University of Cambridge, MRC-Laboratory of Molecular Biology , Cambridge, United Kingdom
- University of Cambridge Centre for AI in Medicine , Cambridge, United Kingdom
- Cambridge Centre for Lung Infection, Papworth Hospital , Cambridge, United Kingdom
| | - Mary Jackson
- Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University , Fort Collins, Colorado, USA
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13
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Mvubu NE, Jacoby K. Mycobacterium tuberculosis complex molecular networks and their regulation: Implications of strain heterogeneity on epigenetic diversity and transcriptome regulation. Heliyon 2023; 9:e22611. [PMID: 38046135 PMCID: PMC10686871 DOI: 10.1016/j.heliyon.2023.e22611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 12/05/2023] Open
Abstract
Tuberculosis has been a public health crisis since the 1900, which has caused the highest mortalities due to a single bacterial infection worldwide, that was recently further complicated by the Coronavirus disease 2019 pandemic. The causative agent of Tuberculosis, Mycobacterium tuberculosis, belongs to a genetically well-characterized family of strains known as the Mycobacterium tuberculosis complex, which has complicated progress made towards eradicating Tuberculosis due to pathogen-specific phenotypic differences in the members of this complex. Mycobacterium tuberculosis complex strains are genetically diverse human- and animal-adapted pathogens belonging to 7 lineages (Indo-Oceanic, East-Asian, East-African Indian, Euro-American, M. africanum West Africa 1, M. africanum West Africa 2 and Ethopia), respectively and the recently identified Lineage 8 and M. africanum Lineage 9. Genomic studies have revealed that Mycobacterium tuberculosis complex members are ∼99 % similar, however, due to selective pressure and adaptation to human host, they are prone to mutations that have resulted in development of drug resistance and phenotypic heterogeneity that impact strain virulence. Furthermore, members of the Mycobacterium tuberculosis complex have preferred geographic locations and possess unique phenotypic characteristics that is linked to their pathogenicity. Due to the recent advances in development next generation sequencing platforms, several studies have revealed epigenetic changes in genomic regions combined with "unique" gene regulatory mechanisms through non-coding RNAs that are responsible for strain-specific behaviour on in vitro and in vivo infection models. The current review provides up to date epigenetic patterns, gene regulation through non-coding RNAs, together with implications of these mechanisms in down-stream proteome and metabolome, which may be responsible for "unique" responses to infection by members of the Mycobacterium tuberculosis complex. Understanding lineage-specific molecular mechanisms during infection may provide novel drug targets and disease control measures towards World Health organization END-TB strategy.
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Affiliation(s)
- Nontobeko Eunice Mvubu
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Kieran Jacoby
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
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14
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Singh PR, Goar H, Paul P, Mehta K, Bamniya B, Vijjamarri AK, Bansal R, Khan H, Karthikeyan S, Sarkar D. Dual functioning by the PhoR sensor is a key determinant to Mycobacterium tuberculosis virulence. PLoS Genet 2023; 19:e1011070. [PMID: 38100394 PMCID: PMC10723718 DOI: 10.1371/journal.pgen.1011070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023] Open
Abstract
PhoP-PhoR, one of the 12 two-component systems (TCSs) that empower M. tuberculosis to sense and adapt to diverse environmental conditions, remains essential for virulence, and therefore, represents a major target to develop novel anti-TB therapies. Although both PhoP and PhoR have been structurally characterized, the signal(s) that this TCS responds to remains unknown. Here, we show that PhoR is a sensor of acidic pH/high salt conditions, which subsequently activate PhoP via phosphorylation. In keeping with this, transcriptomic data uncover that acidic pH- inducible expression of PhoP regulon is significantly inhibited in a PhoR-deleted M. tuberculosis. Strikingly, a set of PhoP regulon genes displayed a low pH-dependent activation even in the absence of PhoR, suggesting the presence of non-canonical mechanism(s) of PhoP activation. Using genome-wide interaction-based screening coupled with phosphorylation assays, we identify a non-canonical mechanism of PhoP phosphorylation by the sensor kinase PrrB. To investigate how level of P~PhoP is regulated, we discovered that in addition to its kinase activity PhoR functions as a phosphatase of P~PhoP. Our subsequent results identify the motif/residues responsible for kinase/phosphatase dual functioning of PhoR. Collectively, these results uncover that contrasting kinase and phosphatase functions of PhoR determine the homeostatic mechanism of regulation of intra-mycobacterial P~PhoP which controls the final output of the PhoP regulon. Together, these results connect PhoR to pH-dependent activation of PhoP with downstream functioning of the regulator. Thus, PhoR plays a central role in mycobacterial adaptation to low pH conditions within the host macrophage phagosome, and a PhoR-deleted M. tuberculosis remains significantly attenuated in macrophages and animal models.
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Affiliation(s)
| | - Harsh Goar
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
| | - Partha Paul
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
| | - Khushboo Mehta
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Bhanwar Bamniya
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | - Roohi Bansal
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
| | - Hina Khan
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
| | - Subramanian Karthikeyan
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Dibyendu Sarkar
- CSIR-Institute of Microbial Technology, Sector 39 A, Chandigarh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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15
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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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16
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Bar-Oz M, Martini MC, Alonso MN, Meir M, Lore NI, Miotto P, Riva C, Angala SK, Xiao J, Masiello CS, Misiakou MA, Sun H, Moy JK, Jackson M, Johansen HK, Cirillo DM, Shell SS, Barkan D. The small non-coding RNA B11 regulates multiple facets of Mycobacterium abscessus virulence. PLoS Pathog 2023; 19:e1011575. [PMID: 37603560 PMCID: PMC10470900 DOI: 10.1371/journal.ppat.1011575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 08/31/2023] [Accepted: 07/24/2023] [Indexed: 08/23/2023] Open
Abstract
Mycobacterium abscessus causes severe disease in patients with cystic fibrosis. Little is known in M. abscessus about the roles of small regulatory RNAs (sRNA) in gene regulation. We show that the sRNA B11 controls gene expression and virulence-associated phenotypes in this pathogen. B11 deletion from the smooth strain ATCC_19977 produced a rough strain, increased pro-inflammatory signaling and virulence in multiple infection models, and increased resistance to antibiotics. Examination of clinical isolate cohorts identified isolates with B11 mutations or reduced expression. We used RNAseq and proteomics to investigate the effects of B11 on gene expression and test the impact of mutations found in clinical isolates. Over 200 genes were differentially expressed in the deletion mutant. Strains with the clinical B11 mutations showed expression trends similar to the deletion mutant, suggesting partial loss of function. Among genes upregulated in the B11 mutant, there was a strong enrichment for genes with B11-complementary sequences in their predicted ribosome binding sites (RBS), consistent with B11 functioning as a negative regulator that represses translation via base-pairing to RBSs. Comparing the proteomes similarly revealed that upregulated proteins were strongly enriched for B11-complementary sequences. Intriguingly, genes upregulated in the absence of B11 included components of the ESX-4 secretion system, critical for M. abscessus virulence. Many of these genes had B11-complementary sequences at their RBSs, which we show is sufficient to mediate repression by B11 through direct binding. Altogether, our data show that B11 acts as a direct negative regulator and mediates (likely indirect) positive regulation with pleiotropic effects on gene expression and clinically important phenotypes in M. abscessus. The presence of hypomorphic B11 mutations in clinical strains is consistent with the idea that lower B11 activity may be advantageous for M. abscessus in some clinical contexts. This is the first report on an sRNA role in M. abscessus.
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Affiliation(s)
- Michal Bar-Oz
- Koret School of Veterinary Medicine, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Maria Carla Martini
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Maria Natalia Alonso
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | | | | | - Paolo Miotto
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Camilla Riva
- IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Shiva K Angala
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Junpei Xiao
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Catherine S Masiello
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Maria-Anna Misiakou
- Center for Genomic Medicine, Copenhagen University Hospital-Rigshospitalet, Copenhagen, Denmark
| | - Huaming Sun
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Justin K Moy
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | | | | | - Scarlet S Shell
- Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Daniel Barkan
- Koret School of Veterinary Medicine, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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17
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Malaga W, Payros D, Meunier E, Frigui W, Sayes F, Pawlik A, Orgeur M, Berrone C, Moreau F, Mazères S, Gonzalo-Asensio J, Rengel D, Martin C, Astarie-Dequeker C, Mourey L, Brosch R, Guilhot C. Natural mutations in the sensor kinase of the PhoPR two-component regulatory system modulate virulence of ancestor-like tuberculosis bacilli. PLoS Pathog 2023; 19:e1011437. [PMID: 37450466 PMCID: PMC10348564 DOI: 10.1371/journal.ppat.1011437] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/22/2023] [Indexed: 07/18/2023] Open
Abstract
The molecular factors and genetic adaptations that contributed to the emergence of Mycobacterium tuberculosis (MTB) from an environmental Mycobacterium canettii-like ancestor, remain poorly investigated. In MTB, the PhoPR two-component regulatory system controls production and secretion of proteins and lipid virulence effectors. Here, we describe that several mutations, present in phoR of M. canettii relative to MTB, impact the expression of the PhoP regulon and the pathogenicity of the strains. First, we establish a molecular model of PhoR and show that some substitutions found in PhoR of M. canettii are likely to impact the structure and activity of this protein. Second, we show that STB-K, the most attenuated available M. canettii strain, displays lower expression of PhoP-induced genes than MTB. Third, we demonstrate that genetic swapping of the phoPR allele from STB-K with the ortholog from MTB H37Rv enhances expression of PhoP-controlled functions and the capacities of the recombinant strain to colonize human macrophages, the MTB target cells, as well as to cause disease in several mouse infection models. Fourth, we extended these observations to other M. canettii strains and confirm that PhoP-controlled functions are expressed at lower levels in most M. canettii strains than in M. tuberculosis. Our findings suggest that distinct PhoR variants have been selected during the evolution of tuberculosis bacilli, contributing to higher pathogenicity and persistence of MTB in the mammalian host.
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Affiliation(s)
- Wladimir Malaga
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Delphine Payros
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Eva Meunier
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Wafa Frigui
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Fadel Sayes
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Alexandre Pawlik
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Mickael Orgeur
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Céline Berrone
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Flavie Moreau
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Serge Mazères
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Jesus Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Facultad de Medicina, Departamento de Microbiologia, Pediatria, Radiologica y Salud Pùblica, Universidad de Zaragoza, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Institudo de Salud Carlos III, Madrid, Spain
| | - David Rengel
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Carlos Martin
- Grupo de Genética de Micobacterias, Facultad de Medicina, Departamento de Microbiologia, Pediatria, Radiologica y Salud Pùblica, Universidad de Zaragoza, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Institudo de Salud Carlos III, Madrid, Spain
- Servicio de Microbiologia, Hospital Universitario Miguel Servet, ISS Aragon, Zaragoza, Spain
| | - Catherine Astarie-Dequeker
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Lionel Mourey
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
| | - Roland Brosch
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
| | - Christophe Guilhot
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III – Paul Sabatier (UPS), Toulouse, France
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18
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Martini BA, Grigorov AS, Skvortsova YV, Bychenko OS, Salina EG, Azhikina TL. Small RNA MTS1338 Configures a Stress Resistance Signature in Mycobacterium tuberculosis. Int J Mol Sci 2023; 24:ijms24097928. [PMID: 37175635 PMCID: PMC10178195 DOI: 10.3390/ijms24097928] [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: 04/02/2023] [Revised: 04/21/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
In the course of evolution, Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, has developed sophisticated strategies to evade host immune response, including the synthesis of small non-coding RNAs (sRNAs), which regulate post-transcriptional pathways involved in the stress adaptation of mycobacteria. sRNA MTS1338 is upregulated in Mtb during its infection of cultured macrophages and in the model of chronic tuberculosis, suggesting involvement in host-pathogen interactions. Here, we analyzed the role of MTS1338 in the Mtb response to macrophage-like stresses in vitro. The Mtb strain overexpressing MTS1338 demonstrated enhanced survival ability under low pH, nitrosative, and oxidative stress conditions simulating the antimicrobial environment inside macrophages. Transcriptomic analysis revealed that in MTS1338-overexpressing Mtb, the stress factors led to the activation of a number of transcriptional regulators, toxin-antitoxin modules, and stress chaperones, about half of which coincided with the genes induced in Mtb phagocytosed by macrophages. We determined the MTS1338 "core regulon", consisting of 11 genes that were activated in all conditions under MTS1338 overexpression. Our findings indicate that MTS1338 is a stress-induced sRNA that promotes Mtb survival in macrophages by triggering adaptive transcriptional mechanisms in response to host antimicrobial defense reactions.
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Affiliation(s)
- Billy A Martini
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Artem S Grigorov
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Yulia V Skvortsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Oksana S Bychenko
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Elena G Salina
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Tatyana L Azhikina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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19
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Stiens J, Tan YY, Joyce R, Arnvig KB, Kendall SL, Nobeli I. Using a whole genome co-expression network to inform the functional characterisation of predicted genomic elements from Mycobacterium tuberculosis transcriptomic data. Mol Microbiol 2023; 119:381-400. [PMID: 36924313 DOI: 10.1111/mmi.15055] [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: 11/18/2022] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/18/2023]
Abstract
A whole genome co-expression network was created using Mycobacterium tuberculosis transcriptomic data from publicly available RNA-sequencing experiments covering a wide variety of experimental conditions. The network includes expressed regions with no formal annotation, including putative short RNAs and untranslated regions of expressed transcripts, along with the protein-coding genes. These unannotated expressed transcripts were among the best-connected members of the module sub-networks, making up more than half of the 'hub' elements in modules that include protein-coding genes known to be part of regulatory systems involved in stress response and host adaptation. This data set provides a valuable resource for investigating the role of non-coding RNA, and conserved hypothetical proteins, in transcriptomic remodelling. Based on their connections to genes with known functional groupings and correlations with replicated host conditions, predicted expressed transcripts can be screened as suitable candidates for further experimental validation.
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Affiliation(s)
- Jennifer Stiens
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
| | - Yen Yi Tan
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
| | - Rosanna Joyce
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
| | - Kristine B Arnvig
- Division of Biosciences, Institute of Structural and Molecular Biology, University College London, London, UK
| | - Sharon L Kendall
- Royal Veterinary College, Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Hatfield, UK
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
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20
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Rajwani R, Galata C, Lee AWT, So PK, Leung KSS, Tam KKG, Shehzad S, Ng TTL, Zhu L, Lao HY, Chan CTM, Leung JSL, Lee LK, Wong KC, Yam WC, Siu GKH. A multi-omics investigation into the mechanisms of hyper-virulence in Mycobacterium tuberculosis. Virulence 2022; 13:1088-1100. [PMID: 35791449 PMCID: PMC9262360 DOI: 10.1080/21505594.2022.2087304] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Clinical manifestations of tuberculosis range from asymptomatic infection to a life-threatening disease such as tuberculous meningitis (TBM). Recent studies showed that the spectrum of disease severity could be related to genetic diversity among clinical strains of Mycobacterium tuberculosis (Mtb). Certain strains are reported to preferentially invade the central nervous system, thus earning the label “hypervirulent strains”.However, specific genetic mutations that accounted for enhanced mycobacterial virulence are still unknown. We previously identified a set of 17 mutations in a hypervirulent Mtb strain that was from TBM patient and exhibited significantly better intracellular survivability. These mutations were also commonly shared by a cluster of globally circulating hyper-virulent strains. Here, we aimed to validate the impact of these hypervirulent-specific mutations on the dysregulation of gene networks associated with virulence in Mtb via multi-omic analysis. We surveyed transcriptomic and proteomic differences between the hyper-virulent and low-virulent strains using RNA-sequencing and label-free quantitative LC-MS/MS approach, respectively. We identified 25 genes consistently differentially expressed between the strains at both transcript and protein level, regardless the strains were growing in a nutrient-rich or a physiologically relevant multi-stress condition (acidic pH, limited nutrients, nitrosative stress, and hypoxia). Based on integrated genomic-transcriptomic and proteomic comparisons, the hypervirulent-specific mutations in FadE5 (g. 295,746 C >T), Rv0178 (p. asp150glu), higB (p. asp30glu), and pip (IS6110-insertion) were linked to deregulated expression of the respective genes and their functionally downstream regulons. The result validated the connections between mutations, gene expression, and mycobacterial pathogenicity, and identified new possible virulence-associated pathways in Mtb.
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Affiliation(s)
- Rahim Rajwani
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Chala Galata
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Annie Wing Tung Lee
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Pui-Kin So
- University Research Facility in Life Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, China
| | - Kenneth Siu Sing Leung
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Kingsley King Gee Tam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Sheeba Shehzad
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Timothy Ting Leung Ng
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Li Zhu
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Hiu Yin Lao
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Chloe Toi-Mei Chan
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Jake Siu-Lun Leung
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Lam-Kwong Lee
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
| | - Kin Chung Wong
- Department of Clinical Pathology, United Christian Hospital, Hong Kong Special Administrative Region, China
| | - Wing Cheong Yam
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Gilman Kit-Hang Siu
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region, Hong Kong, China
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Khan H, Paul P, Sevalkar RR, Kachhap S, Singh B, Sarkar D. Convergence of two global regulators to coordinate expression of essential virulence determinants of Mycobacterium tuberculosis. eLife 2022; 11:80965. [PMID: 36350294 PMCID: PMC9645806 DOI: 10.7554/elife.80965] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
Cyclic AMP (cAMP) is known to function as a global regulator of Mycobacterium tuberculosis gene expression. Sequence-based transcriptomic profiling identified the mycobacterial regulon controlled by the cAMP receptor protein, CRP. In this study, we identified a new subset of CRP-associated genes including virulence determinants which are also under the control of a major regulator, PhoP. Our results suggest that PhoP as a DNA binding transcription factor, impacts expression of these genes, and phosphorylated PhoP promotes CRP recruitment at the target promoters. Further, we uncover a distinct regulatory mechanism showing that activation of these genes requires direct recruitment of both PhoP and CRP at their target promoters. The most fundamental biological insight is derived from the inhibition of CRP binding at the regulatory regions in a PhoP-deleted strain owing to CRP-PhoP protein-protein interactions. Based on these results, a model is proposed suggesting how CRP and PhoP function as co-activators of the essential pathogenic determinants. Taken together, these results uncover a novel mode of regulation where a complex of two interacting virulence factors impact expression of virulence determinants. These results have significant implications on TB pathogenesis.
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Affiliation(s)
- Hina Khan
- CSIR-Institute of Microbial Technology
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22
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Cerezo-Cortés MI, Rodríguez-Castillo JG, Mata-Espinosa DA, Bini EI, Barrios-Payan J, Zatarain-Barrón ZL, Anzola JM, Cornejo-Granados F, Ochoa-Leyva A, Del Portillo P, Murcia MI, Hernández-Pando R. Close Related Drug-Resistance Beijing Isolates of Mycobacterium tuberculosis Reveal a Different Transcriptomic Signature in a Murine Disease Progression Model. Int J Mol Sci 2022; 23:ijms23095157. [PMID: 35563545 PMCID: PMC9100210 DOI: 10.3390/ijms23095157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 12/10/2022] Open
Abstract
Mycobacterium tuberculosis (MTB) lineage 2/Beijing is associated with high virulence and drug resistance worldwide. In Colombia, the Beijing genotype has circulated since 1997, predominantly on the pacific coast, with the Beijing-Like SIT-190 being more prevalent. This genotype conforms to a drug-resistant cluster and shows a fatal outcome in patients. To better understand virulence determinants, we performed a transcriptomic analysis with a Beijing-Like SIT-190 isolate (BL-323), and Beijing-Classic SIT-1 isolate (BC-391) in progressive tuberculosis (TB) murine model. Bacterial RNA was extracted from mice lungs on days 3, 14, 28, and 60. On average, 0.6% of the total reads mapped against MTB genomes and of those, 90% against coding genes. The strains were independently associated as determined by hierarchical cluster and multidimensional scaling analysis. Gene ontology showed that in strain BL-323 enriched functions were related to host immune response and hypoxia, while proteolysis and protein folding were enriched in the BC-391 strain. Altogether, our results suggested a differential bacterial transcriptional program when evaluating these two closely related strains. The data presented here could potentially impact the control of this emerging, highly virulent, and drug-resistant genotype.
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Affiliation(s)
- María Irene Cerezo-Cortés
- Laboratorio de Micobacterias, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (M.I.C.-C.); (J.G.R.-C.)
| | - Juan Germán Rodríguez-Castillo
- Laboratorio de Micobacterias, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (M.I.C.-C.); (J.G.R.-C.)
| | - Dulce Adriana Mata-Espinosa
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México 14080, Mexico; (D.A.M.-E.); (E.I.B.); (J.B.-P.); (Z.L.Z.-B.)
| | - Estela Isabel Bini
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México 14080, Mexico; (D.A.M.-E.); (E.I.B.); (J.B.-P.); (Z.L.Z.-B.)
| | - Jorge Barrios-Payan
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México 14080, Mexico; (D.A.M.-E.); (E.I.B.); (J.B.-P.); (Z.L.Z.-B.)
| | - Zyanya Lucia Zatarain-Barrón
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México 14080, Mexico; (D.A.M.-E.); (E.I.B.); (J.B.-P.); (Z.L.Z.-B.)
| | - Juan Manuel Anzola
- Grupo de Biotecnología Molecular, Grupo de Bioinformática y Biología Computacional, Corporación CorpoGen, Bogotá 110311, Colombia; (J.M.A.); (P.D.P.)
- Universidad Central, Facultad de Ingeniería y Ciencias Básicas Bogotá, Bogotá 100270, Colombia
| | - Fernanda Cornejo-Granados
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (F.C.-G.); (A.O.-L.)
| | - Adrian Ochoa-Leyva
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Mexico; (F.C.-G.); (A.O.-L.)
| | - Patricia Del Portillo
- Grupo de Biotecnología Molecular, Grupo de Bioinformática y Biología Computacional, Corporación CorpoGen, Bogotá 110311, Colombia; (J.M.A.); (P.D.P.)
| | - Martha Isabel Murcia
- Laboratorio de Micobacterias, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (M.I.C.-C.); (J.G.R.-C.)
- Correspondence: (M.I.M.); (R.H.-P.)
| | - Rogelio Hernández-Pando
- Sección de Patología Experimental, Departamento de Patología, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Ciudad de México 14080, Mexico; (D.A.M.-E.); (E.I.B.); (J.B.-P.); (Z.L.Z.-B.)
- Correspondence: (M.I.M.); (R.H.-P.)
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23
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Pérez I, Campos-Pardos E, Díaz C, Uranga S, Sayes F, Vicente F, Aguiló N, Brosch R, Martín C, Gonzalo-Asensio J. The Mycobacterium tuberculosis PhoPR virulence system regulates expression of the universal second messenger c-di-AMP and impacts vaccine safety and efficacy. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:1235-1248. [PMID: 35282413 PMCID: PMC8894143 DOI: 10.1016/j.omtn.2022.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/11/2022] [Indexed: 12/12/2022]
Abstract
Cyclic (di)nucleotides act as universal second messengers endogenously produced by several pathogens. Specifically, the roles of c-di-AMP in Mycobacterium tuberculosis immunity and virulence have been largely explored, although its contribution to the safety and efficacy of live tuberculosis vaccines is less understood. In this study, we demonstrate that the synthesis of c-di-AMP is negatively regulated by the M. tuberculosis PhoPR virulence system. Accordingly, the live attenuated tuberculosis vaccine candidate M. tuberculosis vaccine (MTBVAC), based on double phoP and fadD26 deletions, produces more than 25- and 45-fold c-di-AMP levels relative to wild-type M. tuberculosis or the current vaccine bacille Calmette-Guérin (BCG), respectively. Secretion of this second messenger was exclusively detected in MTBVAC but not in M. tuberculosis or in BCG. We also demonstrate that c-di-AMP synthesis during in vitro cultivation of M. tuberculosis is a growth-phase- and medium-dependent phenotype. To uncover the role of this metabolite in the vaccine properties of MTBVAC, we constructed and validated knockout and overproducing/oversecreting derivatives by inactivating the disA or cnpB gene, respectively. All MTBVAC derivatives elicited superior interleukin-1β (IL-1β) responses compared with BCG during an in vitro infection of human macrophages. However, both vaccines failed to elicit interferon β (IFNβ) activation in this cellular model. We found that increasing c-di-AMP levels remarkably correlated with a safer profile of tuberculosis vaccines in the immunodeficient mouse model. Finally, we demonstrate that overproduction of c-di-AMP due to cnpB inactivation resulted in lower protection of MTBVAC, while the absence of c-di-AMP in the MTBVAC disA derivative maintains the protective efficacy of this vaccine in mice.
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Affiliation(s)
- Irene Pérez
- Grupo de Genética de Micobacterias, Departamento de Microbiología. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, C/Domingo Miral sn, 50019 Zaragoza, Spain.,CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Av. de Monforte de Lemos 5, 28029 Madrid, Spain
| | - Elena Campos-Pardos
- Grupo de Genética de Micobacterias, Departamento de Microbiología. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, C/Domingo Miral sn, 50019 Zaragoza, Spain.,CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Av. de Monforte de Lemos 5, 28029 Madrid, Spain
| | - Caridad Díaz
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento 34, 18016 Granada, Spain
| | - Santiago Uranga
- Grupo de Genética de Micobacterias, Departamento de Microbiología. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, C/Domingo Miral sn, 50019 Zaragoza, Spain.,CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Av. de Monforte de Lemos 5, 28029 Madrid, Spain
| | - Fadel Sayes
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Francisca Vicente
- Fundación MEDINA, Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento 34, 18016 Granada, Spain
| | - Nacho Aguiló
- Grupo de Genética de Micobacterias, Departamento de Microbiología. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, C/Domingo Miral sn, 50019 Zaragoza, Spain.,CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Av. de Monforte de Lemos 5, 28029 Madrid, Spain
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Carlos Martín
- Grupo de Genética de Micobacterias, Departamento de Microbiología. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, C/Domingo Miral sn, 50019 Zaragoza, Spain.,CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Av. de Monforte de Lemos 5, 28029 Madrid, Spain.,Servicio de Microbiología Hospital Universitario Miguel Servet, Pº Isabel la Católica, 1-3, 50009 Zaragoza, Spain
| | - Jesús Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Departamento de Microbiología. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, C/Domingo Miral sn, 50019 Zaragoza, Spain.,CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Av. de Monforte de Lemos 5, 28029 Madrid, Spain.,Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), C/ Mariano Esquillor Gómez, Edificio I+D, 50018 Zaragoza, Spain
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24
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Alvarez-Eraso KLF, Muñoz-Martínez LM, Alzate JF, Barrera LF, Baena A. Modulatory Impact of the sRNA Mcr11 in Two Clinical Isolates of Mycobacterium tuberculosis. Curr Microbiol 2022; 79:39. [PMID: 34982251 DOI: 10.1007/s00284-021-02733-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/30/2021] [Indexed: 11/26/2022]
Abstract
Mycobacterium tuberculosis (Mtb) is a successful pathogen causing tuberculosis (TB) disease in humans. It has been shown, that some circulating strains of Mtb in TB endemic populations, are more virulent and more transmissible than others, which may be related to their evolved adaptations to modulate the host immune responses. Underlying these adaptations to the stressful conditions, different genetic regulatory networks involved sRNAs that are mostly unknown for Mtb. We have previously shown that Mcr11 is one of the main sRNAs that determine transcriptomic differences among the Colombian clinical isolates UT127 and UT205 compared to the laboratory strain H37Rv. We found that the knock-down of mcr11 using CRISPRi has a major impact on phenotypic traits, especially in the clinical isolate UT205. Through the analysis of RNA-seq during the knock-down of mcr11 in UT205, we found a downregulation of genes mainly involved in lipid synthesis, lipid metabolism, ribosomal proteins, transport systems, respiratory and energy systems, membrane and cell wall components, intermediary metabolism, lipoproteins and virulence genes. One of the most interesting genes showing transcriptomic changes is OprA (encoded by the gene rv0516c), which has been involved in the K+ regulation. Overall, our data may suggest that one of the prominent roles of the sRNA Mcr11 is to regulate genes that control Mtb growth and osmoregulation.
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Affiliation(s)
| | | | - Juan F Alzate
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Medellín, Colombia
- Centro Nacional de Secuenciación Genómica-CNSG, Medellín, Colombia
- Sede de Investigación Universitaria-SIU, Medellín, Colombia
| | - Luis F Barrera
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Medellín, Colombia
- Sede de Investigación Universitaria-SIU, Medellín, Colombia
- Instituto de Investigaciones Médicas, Universidad de Antioquia, Medellín, Colombia
| | - Andres Baena
- Grupo de Inmunología Celular e Inmunogenética (GICIG), Medellín, Colombia.
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad de Antioquia, Carrera 53 No. 61-30, Medellín, Colombia.
- Sede de Investigación Universitaria-SIU, Medellín, Colombia.
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25
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Transcriptomic Characterization of Tuberculous Sputum Reveals a Host Warburg Effect and Microbial Cholesterol Catabolism. mBio 2021; 12:e0176621. [PMID: 34872348 PMCID: PMC8649757 DOI: 10.1128/mbio.01766-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The crucial transmission phase of tuberculosis (TB) relies on infectious sputum and yet cannot easily be modeled. We applied one-step RNA sequencing (RNA-Seq) to sputum from infectious TB patients to investigate the host and microbial environments underlying transmission of Mycobacterium tuberculosis. In such TB sputa, compared to non-TB controls, transcriptional upregulation of inflammatory responses, including an interferon-driven proinflammatory response and a metabolic shift toward glycolysis, was observed in the host. Among all bacterial sequences in the sputum, approximately 1.5% originated from M. tuberculosis, and its transcript abundance was lower in HIV-1-coinfected patients. Commensal bacterial abundance was reduced in the presence of M. tuberculosis infection. Direct alignment to the genomes of the predominant microbiota species also reveals differential adaptation, whereby firmicutes (e.g., streptococci) displayed a nonreplicating phenotype with reduced transcription of ribosomal proteins and reduced activities of ATP synthases, while Neisseria and Prevotella spp. were less affected. The transcriptome of sputum M. tuberculosis more closely resembled aerobic replication and shared similarity in carbon metabolism to in vitro and in vivo models with significant upregulation of genes associated with cholesterol metabolism and downstream propionate detoxification pathways. In addition, and counter to previous reports on intracellular M. tuberculosis infection in vitro, M. tuberculosis in sputum was zinc, but not iron, deprived, and the phoP loci were also significantly downregulated, suggesting that the pathogen is likely extracellular in location.
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26
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Stiens J, Arnvig KB, Kendall SL, Nobeli I. Challenges in defining the functional, non-coding, expressed genome of members of the Mycobacterium tuberculosis complex. Mol Microbiol 2021; 117:20-31. [PMID: 34894010 DOI: 10.1111/mmi.14862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/14/2022]
Abstract
A definitive transcriptome atlas for the non-coding expressed elements of the members of the Mycobacterium tuberculosis complex (MTBC) does not exist. Incomplete lists of non-coding transcripts can be obtained for some of the reference genomes (e.g., M. tuberculosis H37Rv) but to what extent these transcripts have homologues in closely related species or even strains is not clear. This has implications for the analysis of transcriptomic data; non-coding parts of the transcriptome are often ignored in the absence of formal, reliable annotation. Here, we review the state of our knowledge of non-coding RNAs in pathogenic mycobacteria, emphasizing the disparities in the information included in commonly used databases. We then proceed to review ways of combining computational solutions for predicting the non-coding transcriptome with experiments that can help refine and confirm these predictions.
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Affiliation(s)
- Jennifer Stiens
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
| | - Kristine B Arnvig
- Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, UK
| | - Sharon L Kendall
- Centre for Emerging, Endemic and Exotic Diseases, Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - Irene Nobeli
- Institute of Structural and Molecular Biology, Biological Sciences, Birkbeck, University of London, London, UK
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27
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The Mycobacterium tuberculosis sRNA F6 Modifies Expression of Essential Chaperonins, GroEL2 and GroES. Microbiol Spectr 2021; 9:e0109521. [PMID: 34549992 PMCID: PMC8557902 DOI: 10.1128/spectrum.01095-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Almost 140 years after the identification of Mycobacterium tuberculosis as the etiological agent of tuberculosis, important aspects of its biology remain poorly described. Little is known about the role of posttranscriptional control of gene expression and RNA biology, including the role of most of the small RNAs (sRNAs) identified to date. We have carried out a detailed investigation of the M. tuberculosis sRNA F6 and shown it to be dependent on SigF for expression and significantly induced in starvation conditions in vitro and in a mouse model of infection. Further exploration of F6 using an in vitro starvation model of infection indicates that F6 affects the expression of the essential chaperonins GroEL2 and GroES. Our results point toward a role for F6 during periods of low metabolic activity typically associated with long-term survival of M. tuberculosis in human granulomas. IMPORTANCE Control of gene expression via small regulatory RNAs (sRNAs) is poorly understood in one of the most successful pathogens, Mycobacterium tuberculosis. Here, we present an in-depth characterization of the sRNA F6, including its expression in different infection models and the differential gene expression observed upon deletion of the sRNA. Our results demonstrate that deletion of F6 leads to dysregulation of the two essential chaperonins GroEL2 and GroES and, moreover, indicate a role for F6 in the long-term survival and persistence of M. tuberculosis in the human host.
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28
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Small RNAs Asserting Big Roles in Mycobacteria. Noncoding RNA 2021; 7:ncrna7040069. [PMID: 34842799 PMCID: PMC8628891 DOI: 10.3390/ncrna7040069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 02/07/2023] Open
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb), with 10.4 million new cases per year reported in the human population. Recent studies on the Mtb transcriptome have revealed the abundance of noncoding RNAs expressed at various phases of mycobacteria growth, in culture, in infected mammalian cells, and in patients. Among these noncoding RNAs are both small RNAs (sRNAs) between 50 and 350 nts in length and smaller RNAs (sncRNA) < 50 nts. In this review, we provide an up-to-date synopsis of the identification, designation, and function of these Mtb-encoded sRNAs and sncRNAs. The methodological advances including RNA sequencing strategies, small RNA antagonists, and locked nucleic acid sequence-specific RNA probes advancing the studies on these small RNA are described. Initial insights into the regulation of the small RNA expression and putative processing enzymes required for their synthesis and function are discussed. There are many open questions remaining about the biological and pathogenic roles of these small non-coding RNAs, and potential research directions needed to define the role of these mycobacterial noncoding RNAs are summarized.
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29
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Sharma S, Sharma M. Proline-Glutamate/Proline-Proline-Glutamate (PE/PPE) proteins of Mycobacterium tuberculosis: The multifaceted immune-modulators. Acta Trop 2021; 222:106035. [PMID: 34224720 DOI: 10.1016/j.actatropica.2021.106035] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/23/2021] [Accepted: 06/29/2021] [Indexed: 12/30/2022]
Abstract
The PE/PPE proteins encoded by seven percent (7%) of Mycobacterium tuberculosis (Mtb) genome are the chief constituents to pathogen's virulence reservoir. The fact that these genes have evolved along ESX secretory system in pathogenic Mtb strains make their investigation very intriguing. There is lot of speculation about the prominent role of these proteins at host pathogen interface and in disease pathogenesis. Nevertheless, the exact function of PE/PPE proteins still remains a mystery which calls for further research targeting these proteins. This article is an effort to document all the facts known so far with regard to these unique proteins which involves their origin, evolution, transcriptional control, and most important their role as host immune-modulators. Our understanding strongly points towards the versatile nature of these PE/PPE proteins as Mtb's host immune sensors and as decisive factors in shaping the outcome of infection. Further investigation on these proteins will surely pave way for newer and effective vaccines and therapeutics to control Tuberculosis (TB).
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Affiliation(s)
- Sadhna Sharma
- DS Kothari Central Interdisciplinary Research Centre and Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India.
| | - Monika Sharma
- DS Kothari Central Interdisciplinary Research Centre and Department of Zoology, Miranda House, University of Delhi, Delhi 110007, India.
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30
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Elimination of PknL and MSMEG_4242 in Mycobacterium smegmatis alters the character of the outer cell envelope and selects for mutations in Lsr2. ACTA ACUST UNITED AC 2021; 7:100060. [PMID: 34485766 PMCID: PMC8408660 DOI: 10.1016/j.tcsw.2021.100060] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 11/23/2022]
Abstract
Elimination of pknL and adjacent gene MSMEG_4242 in M. smegmatis produces rough & smooth colonies. All smooth colony mutants have inactivated lsr2 genes. Inactivated lsr2 leads to high expression of MSMEG_4727 and increased synthesis of LOS. Smooth mutants don’t form biofilms, have longer bacilli and increased sliding motility. Rough strains deleted for pknL and MSMEG_4242 form biofilms but have aberrant sliding motility. We propose a phosphorylation cascade of PknB phosphorylating PknL that then phosphorylates Lsr2.
Four serine/threonine kinases are present in all mycobacteria: PknA, PknB, PknG and PknL. PknA and PknB are essential for growth and replication, PknG regulates metabolism, but little is known about PknL. Inactivation of pknL and adjacent regulator MSMEG_4242 in rough colony M. smegmatis mc2155 produced both smooth and rough colonies. Upon restreaking rough colonies, smooth colonies appeared at a frequency of ~ 1/250. Smooth mutants did not form biofilms, showed increased sliding motility and anomalous lipids on thin-layer chromatography, identified by mass spectrometry as lipooligosaccharides and perhaps also glycopeptidolipids. RNA-seq and Sanger sequencing revealed that all smooth mutants had inactivated lsr2 genes due to mutations and different IS1096 insertions. When complemented with lsr2, the colonies became rough, anomalous lipids disappeared and sliding motility decreased. Smooth mutants showed increased expression of IS1096 transposase TnpA and MSMEG_4727, which encodes a protein similar to PKS5. When MSMEG_4727 was deleted, smooth pknL/MSMEG_4242/lsr2 mutants reverted to rough, formed good biofilms, their motility decreased slightly and their anomalous lipids disappeared. Rough delpknL/del4242 mutants formed poor biofilms and showed decreased, aberrant sliding motility and both phenotypes were complemented with the two deleted genes. Inactivation of lsr2 changes colony morphology from rough to smooth, augments sliding motility and increases expression of MSMEG_4727 and other enzymes synthesizing lipooligosaccharides, apparently preventing biofilm formation. Similar morphological phase changes occur in other mycobacteria, likely reflecting environmental adaptations. PknL and MSMEG_4242 regulate lipid components of the outer cell envelope and their absence selects for lsr2 inactivation. A regulatory, phosphorylation cascade model is proposed.
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31
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Engineering a new vaccine platform for heterologous antigen delivery in live-attenuated Mycobacterium tuberculosis. Comput Struct Biotechnol J 2021; 19:4273-4283. [PMID: 34429847 PMCID: PMC8355830 DOI: 10.1016/j.csbj.2021.07.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/28/2021] [Accepted: 07/28/2021] [Indexed: 12/02/2022] Open
Abstract
Live vaccines are attractive vehicles for antigen delivery as a strategy to immunize against heterologous pathogens. The live vaccine MTBVAC is based on rational attenuation of Mycobacterium tuberculosis with the objective of improving BCG protection against pulmonary tuberculosis. However, the development of recombinant mycobacteria as antigen-presenting microorganisms has been hindered due to their fastidious genetic manipulation. In this study, we used MTBVAC as a genetic platform to deliver diphtheria, tetanus, or pertussis toxoids, which are the immunogenic constituents of the DTP vaccine. When using nonoptimal genetic conditions, the expression of these immunogens was barely detectable. Accordingly, we pursued a rational, step-by-step optimization of the genetic components to achieve the expression and secretion of these toxoids. We explored variants of the L5 mycobacteriophage promoter to ensure balanced antigen expression and plasmid stability. Optimal signal sequences were identified by comparative proteomics of MTBVAC and its parental strain. It was determined that proteins secreted by the Twin Arginine Translocation pathway displayed higher secretion in MTBVAC, and the Ag85A secretion sequence was selected as the best candidate. Because the coding regions of diphtheria, tetanus, and pertussis toxoids significantly differ in G + C content relative to mycobacterial genes, their codon usage was optimized. We also placed a 3xFLAG epitope in frame with the C-terminus of these toxoids to facilitate protein detection. Altogether, these optimizations resulted in the secretion of DTP antigens by MTBVAC, as demonstrated by western blot and MRM-MS. Finally, we examined specific antibody responses in mice vaccinated with recombinant MTBVAC expressing DTP antigens.
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32
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Marques-Neto LM, Piwowarska Z, Kanno AI, Moraes L, Trentini MM, Rodriguez D, Silva JLSC, Leite LCC. Thirty years of recombinant BCG: new trends for a centenary vaccine. Expert Rev Vaccines 2021; 20:1001-1011. [PMID: 34224293 DOI: 10.1080/14760584.2021.1951243] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction: Global perception of the potential for Bacille Calmette-Guérin (BCG), and consequently recombinant BCG (rBCG), in a variety of prophylactic and therapeutic applications has been increasing. A century of information on BCG, and three decades of experience with rBCG, has generated solid knowledge in this field.Area covered: Here, we review the current state of knowledge of BCG and rBCG development. Molecular tools have facilitated the expression of a variety of molecules in BCG, with the aim of improving its efficacy as a tuberculosis vaccine, generating polyvalent vaccines against other pathogens, including viruses, bacteria, and parasites, and developing immunotherapy approaches against noninvasive bladder cancer. BCG's recently appraised heterologous effects and prospects for expanding its application to other diseases are also addressed.Expert opinion: There are high expectations for new tuberculosis vaccines currently undergoing advanced clinical trials, which could change the prospects of the field. Systems biology could reveal effective biomarkers of protection, which would greatly support vaccine development. The development of appropriate large-scale production processes would further support implementation of new vaccines and rBCG products. The next few years should consolidate the broader applications of BCG and produce insights into improvements using the recombinant BCG technology.
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Affiliation(s)
| | - Zuzanna Piwowarska
- Laboratório De Desenvolvimento De Vacinas, Instituto Butantan, São Paulo, Brazil.,UnivLyon, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Alex I Kanno
- Laboratório De Desenvolvimento De Vacinas, Instituto Butantan, São Paulo, Brazil
| | - Luana Moraes
- Laboratório De Desenvolvimento De Vacinas, Instituto Butantan, São Paulo, Brazil.,Programa De Pós-Graduação Interunidades Em Biotecnologia USP-Instituto Butantan-IPT, São Paulo, Brazil
| | - Monalisa M Trentini
- Laboratório De Desenvolvimento De Vacinas, Instituto Butantan, São Paulo, Brazil
| | - Dunia Rodriguez
- Laboratório De Desenvolvimento De Vacinas, Instituto Butantan, São Paulo, Brazil
| | - Jose L S C Silva
- Laboratório De Desenvolvimento De Vacinas, Instituto Butantan, São Paulo, Brazil.,Programa De Pós-Graduação Interunidades Em Biotecnologia USP-Instituto Butantan-IPT, São Paulo, Brazil
| | - Luciana C C Leite
- Laboratório De Desenvolvimento De Vacinas, Instituto Butantan, São Paulo, Brazil
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33
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Martín C, Marinova D, Aguiló N, Gonzalo-Asensio J. MTBVAC, a live TB vaccine poised to initiate efficacy trials 100 years after BCG. Vaccine 2021; 39:7277-7285. [PMID: 34238608 DOI: 10.1016/j.vaccine.2021.06.049] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/03/2021] [Accepted: 06/21/2021] [Indexed: 01/06/2023]
Abstract
At its 100th birthday of its first administration to a newborn, BCG has been (and continues being) an inspiration for the construction and development of hundreds of new TB vaccine candidates in the last two and a half decades. Today, 14 candidates are in clinical development inside the global TB vaccine pipeline. MTBVAC is one of these candidates. Based on a live-attenuated Mycobacterium tuberculosis clinical isolate, MTBVAC's 25 years of vaccine discovery, construction and characterisation have followed Pasteur principles, and in the process, BCG has served as a reference gold standard for establishing the safety and protective efficacy of new TB vaccine candidates. MTBVAC, which contains the antigen repertoire of M. tuberculosis, is now poised to initiate Phase 3 efficacy trials in newborns in TB-endemic countries. BCG's efficacy extends beyond that against TB, shown to confer heterologous non-specific immunity to other diseases and reduce all-cause mortality in the first months of life. Today, WHO recognises the importance that any new TB vaccine designed for administration at birth, should show similar non-specific benefits as BCG vía mechanisms of trained immunity and/or cross-reactivity of adaptive immune responses to other pathogens. Key recent studies provide strong support for MTBVAC's ability of inducing trained immunity and conferring non-specific heterologous protection similar to BCG. Research on alternative delivery routes of MTBVAC, such as a clinically feasible aerosol route, could facilitate vaccine administration for long-term TB eradication programmes in the future.
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Affiliation(s)
- Carlos Martín
- Grupo de Genética de Micobacterias, Microbiología, Facultad de Medicina Universidad de Zaragoza, Spain; CIBERES Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Hospital Universitario Miguel Servet, ISS Aragón, Zaragoza, Spain.
| | - Dessislava Marinova
- Grupo de Genética de Micobacterias, Microbiología, Facultad de Medicina Universidad de Zaragoza, Spain; CIBERES Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Nacho Aguiló
- Grupo de Genética de Micobacterias, Microbiología, Facultad de Medicina Universidad de Zaragoza, Spain; CIBERES Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Microbiología, Facultad de Medicina Universidad de Zaragoza, Spain; CIBERES Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
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34
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Ostrik AA, Azhikina TL, Salina EG. Small Noncoding RNAs and Their Role in the Pathogenesis of Mycobacterium tuberculosis Infection. BIOCHEMISTRY (MOSCOW) 2021; 86:S109-S119. [PMID: 33827403 PMCID: PMC7905965 DOI: 10.1134/s000629792114008x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Mycobacterium tuberculosis possesses a significant arsenal of strategies to combat immune defense of the host organism. Small noncoding RNAs, which constitute the largest group of regulatory RNAs, play an important role in the host–pathogen interactions and represent one of the levels of the regulation of interactions of microbial cells with their environment. The regulatory role of small RNAs in pathogenic bacteria is essential when rapid adaptation to the changing environmental conditions with further synchronization of metabolic reactions are required to ensure microbial survival and infection progression. During the past few years, eight small RNAs from M. tuberculosis have been functionally characterized, and targets for four of them have been identified. Small RNAs from M. tuberculosis and other pathogenic microorganisms were found to be one of the most important functional factors in the adaptive response to changing environmental conditions.
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Affiliation(s)
- Albina A Ostrik
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia
| | - Tatyana L Azhikina
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Elena G Salina
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, 119071, Russia.
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35
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Simeone R, Sayes F, Lawarée E, Brosch R. Breaching the phagosome, the case of the tuberculosis agent. Cell Microbiol 2021; 23:e13344. [PMID: 33860624 DOI: 10.1111/cmi.13344] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/23/2021] [Accepted: 03/25/2021] [Indexed: 12/14/2022]
Abstract
The interactions between microbes and their hosts are among the most complex biological phenomena known today. The interaction may reach from overall beneficial interaction, as observed for most microbiome/microbiota related interactions to interaction with virulent pathogens, against which host cells have evolved sophisticated defence strategies. Among the latter, the confinement of invading pathogens in a phagosome plays a key role, which often results in the destruction of the invader, whereas some pathogens may counteract phagosomal arrest and survive by gaining access to the cytosol of the host cell. In the current review, we will discuss recent insights into this dynamic process of host-pathogen interaction, using Mycobacterium tuberculosis and related pathogenic mycobacteria as main examples.
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Affiliation(s)
- Roxane Simeone
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, CNRS UMR 3525, Paris, France
| | - Fadel Sayes
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, CNRS UMR 3525, Paris, France
| | - Emeline Lawarée
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, CNRS UMR 3525, Paris, France
| | - Roland Brosch
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, CNRS UMR 3525, Paris, France
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36
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Broset E, Pardo-Seco J, Kanno AI, Aguilo N, Dacosta AI, Rivero-Calle I, Gonzalo-Asensio J, Locht C, Leite LCC, Martin C, Martinón-Torres F. BCG vaccination improves DTaP immune responses in mice and is associated with lower pertussis incidence in ecological epidemiological studies. EBioMedicine 2021; 65:103254. [PMID: 33711798 PMCID: PMC7960937 DOI: 10.1016/j.ebiom.2021.103254] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The Bacillus Calmette-Guérin (BCG), the only vaccine against tuberculosis (TB) currently in use, has shown beneficial effects against unrelated infections and to enhance immune responses to vaccines. However, there is little evidence regarding the influence of BCG vaccination on pertussis. METHODS Here, we studied the ability of BCG to improve the immune responses to diphtheria, tetanus, and acellular (DTaP) or whole-cell pertussis (DTwP) vaccination in a mouse model. We included MTBVAC, an experimental live-attenuated vaccine derived from Mycobacterium tuberculosis, in our studies to explore if it presents similar heterologous immunity as BCG. Furthermore, we explored the potential effect of routine BCG vaccination on pertussis incidence worldwide. FINDINGS We found that both BCG and MTBVAC when administered before DTaP, triggered Th1 immune responses against diphtheria, tetanus, and pertussis in mice. Immunization with DTaP alone failed to trigger a Th1 response, as measured by the production of IFN-γ. Humoral responses against DTaP antigens were also enhanced by previous immunization with BCG or MTBVAC. Furthermore, exploration of human epidemiological data showed that pertussis incidence was 10-fold lower in countries that use DTaP and BCG compared to countries that use only DTaP. INTERPRETATION BCG vaccination may have a beneficial impact on the protection against pertussis conferred by DTaP. Further randomized controlled trials are needed to properly define the impact of BCG on pertussis incidence in a controlled setting. This could be a major finding that would support changes in immunization policies. FUNDING This work was supported by the Ministry of "Economía y Competitividad"; European Commission H2020 program, "Gobierno de Aragón"; CIBERES; "Fundação Butantan"; Instituto de Salud Carlos III and "Fondo FEDER".
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Affiliation(s)
- Esther Broset
- Grupo de Genetica de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS-Aragón, Zaragoza 50009, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
| | - Jacobo Pardo-Seco
- Translational Pediatrics and Infectious Diseases, Pediatrics Department, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain; GENVIP Research Group (www.genvip.org), Instituto de Investigación Sanitaria de Santiago (SERGAS), University of Santiago de Compostela, Galicia, Spain
| | - Alex I Kanno
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Av. Vital Brasil 1500, São Paulo 05503-900, Brazil
| | - Nacho Aguilo
- Grupo de Genetica de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS-Aragón, Zaragoza 50009, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Isabel Dacosta
- Translational Pediatrics and Infectious Diseases, Pediatrics Department, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain; GENVIP Research Group (www.genvip.org), Instituto de Investigación Sanitaria de Santiago (SERGAS), University of Santiago de Compostela, Galicia, Spain
| | - Irene Rivero-Calle
- Translational Pediatrics and Infectious Diseases, Pediatrics Department, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain; GENVIP Research Group (www.genvip.org), Instituto de Investigación Sanitaria de Santiago (SERGAS), University of Santiago de Compostela, Galicia, Spain
| | - Jesus Gonzalo-Asensio
- Grupo de Genetica de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS-Aragón, Zaragoza 50009, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Zaragoza, Spain
| | - Camille Locht
- Center of Infection and Immunity of Lille, Institut Pasteur de Lille, Lille 59019, France; Inserm U1019, Lille 59019, France; CNRS UMR8204, Lille 59019, France; Univ. Lille, Lille 59019, France
| | - Luciana C C Leite
- Laboratório de Desenvolvimento de Vacinas, Instituto Butantan, Av. Vital Brasil 1500, São Paulo 05503-900, Brazil
| | - Carlos Martin
- Grupo de Genetica de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS-Aragón, Zaragoza 50009, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología, Hospital Universitario Miguel Servet, IIS Aragón, Zaragoza, Spain
| | - Federico Martinón-Torres
- Translational Pediatrics and Infectious Diseases, Pediatrics Department, Hospital Clínico Universitario de Santiago, Santiago de Compostela, Spain; GENVIP Research Group (www.genvip.org), Instituto de Investigación Sanitaria de Santiago (SERGAS), University of Santiago de Compostela, Galicia, Spain
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37
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Drever K, Lim ZL, Zriba S, Chen JM. Protein Synthesis and Degradation Inhibitors Potently Block Mycobacterium tuberculosis type-7 Secretion System ESX-1 Activity. ACS Infect Dis 2021; 7:273-280. [PMID: 33534536 DOI: 10.1021/acsinfecdis.0c00741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Mycobacterium tuberculosis (M. tb) uses its type-7 secretion system ESX-1 to translocate key virulence effector proteins. Taking a chemical genetics approach, we demonstrate for the first time the importance of mycobacterial proteostasis to ESX-1. We show that individual treatment with inhibitors of protein synthesis (chloramphenicol and kanamycin) and protein degradation (lassomycin and bortezomib), at concentrations that only reduce M. tb growth by 50% and less, specifically block ESX-1 secretion activity in the tubercle bacillus. In contrast, the mycobacterial cell-wall synthesis inhibitor isoniazid, even at a concentration that reduces M. tb growth by 90% has no effect on ESX-1 secretion activity. We also show that chloramphenicol but not isoniazid at subinhibitory concentrations specifically attenuates ESX-1-mediated M. tb virulence in macrophages. Taken together, the results of our study identify a novel vulnerability in the ESX-1 system and offer new avenues of anti-TB drug research to neutralize this critical virulence-mediating protein secretion apparatus.
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Affiliation(s)
- Kylee Drever
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B4, Canada
| | - Ze Long Lim
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan S7N 5E3, Canada
| | - Slim Zriba
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan S7N 5E3, Canada
- Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan S7N 2Z4, Canada
| | - Jeffrey M. Chen
- Vaccine and Infectious Disease Organization, Saskatoon, Saskatchewan S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5B4, Canada
- Vaccinology and Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan S7N 2Z4, Canada
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38
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Kanabalan RD, Lee LJ, Lee TY, Chong PP, Hassan L, Ismail R, Chin VK. Human tuberculosis and Mycobacterium tuberculosis complex: A review on genetic diversity, pathogenesis and omics approaches in host biomarkers discovery. Microbiol Res 2021; 246:126674. [PMID: 33549960 DOI: 10.1016/j.micres.2020.126674] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/09/2020] [Accepted: 12/16/2020] [Indexed: 12/16/2022]
Abstract
Mycobacterium tuberculosis complex (MTBC) refers to a group of mycobacteria encompassing nine members of closely related species that causes tuberculosis in animals and humans. Among the nine members, Mycobacterium tuberculosis (M. tuberculosis) remains the main causative agent for human tuberculosis that results in high mortality and morbidity globally. In general, MTBC species are low in diversity but exhibit distinctive biological differences and phenotypes among different MTBC lineages. MTBC species are likely to have evolved from a common ancestor through insertions/deletions processes resulting in species speciation with different degrees of pathogenicity. The pathogenesis of human tuberculosis is complex and remains poorly understood. It involves multi-interactions or evolutionary co-options between host factors and bacterial determinants for survival of the MTBC. Granuloma formation as a protection or survival mechanism in hosts by MTBC remains controversial. Additionally, MTBC species are capable of modulating host immune response and have adopted several mechanisms to evade from host immune attack in order to survive in humans. On the other hand, current diagnostic tools for human tuberculosis are inadequate and have several shortcomings. Numerous studies have suggested the potential of host biomarkers in early diagnosis of tuberculosis, in disease differentiation and in treatment monitoring. "Multi-omics" approaches provide holistic views to dissect the association of MTBC species with humans and offer great advantages in host biomarkers discovery. Thus, in this review, we seek to understand how the genetic variations in MTBC lead to species speciation with different pathogenicity. Furthermore, we also discuss how the host and bacterial players contribute to the pathogenesis of human tuberculosis. Lastly, we provide an overview of the journey of "omics" approaches in host biomarkers discovery in human tuberculosis and provide some interesting insights on the challenges and directions of "omics" approaches in host biomarkers innovation and clinical implementation.
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Affiliation(s)
- Renuga Devi Kanabalan
- Department of Community Health, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur, 56000, Malaysia
| | - Le Jie Lee
- Prima Nexus Sdn. Bhd., Menara CIMB, Jalan Stesen Sentral 2, Kuala Lumpur, Malaysia
| | - Tze Yan Lee
- Perdana University School of Liberal Arts, Science and Technology (PUScLST), Suite 9.2, 9th Floor, Wisma Chase Perdana, Changkat Semantan Damansara Heights, Kuala Lumpur, 50490, Malaysia
| | - Pei Pei Chong
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University Lakeside Campus, Subang Jaya, 47500, Malaysia
| | - Latiffah Hassan
- Department of Veterinary Laboratory Diagnostics, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, 43400 UPM, Malaysia
| | - Rosnah Ismail
- Department of Community Health, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur, 56000, Malaysia.
| | - Voon Kin Chin
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, 43400 UPM, Malaysia; Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Puncak Alam Campus, Bandar Puncak Alam, Selangor, 42300, Malaysia.
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Kolbe K, Bell AC, Prosser GA, Assmann M, Yang HJ, Forbes HE, Gallucci S, Mayer-Barber KD, Boshoff HI, Barry Iii CE. Development and Optimization of Chromosomally-Integrated Fluorescent Mycobacterium tuberculosis Reporter Constructs. Front Microbiol 2020; 11:591866. [PMID: 33362741 PMCID: PMC7755994 DOI: 10.3389/fmicb.2020.591866] [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: 08/05/2020] [Accepted: 11/13/2020] [Indexed: 11/25/2022] Open
Abstract
Mycobacterium tuberculosis resides in the lungs in various lesion types with unique microenvironmental conditions. This diversity is in line with heterogeneous disease progression and divergent drug efficiency. Fluorescent reporter strains can be used to decipher the micromilieu and to guide future treatment regimens. Current reporters using replicating plasmids, however, are not suitable for long-term mouse infections or studies in non-human primates. Using a combination of recombinant DNA and protein optimization techniques, we have developed reporter strains based on integrative plasmids, which exhibit stimulus-response characteristics and fluorescence intensities comparable to those based on replicating plasmids. We successfully applied the concepts by constructing a multi-color reporter strain able to detect simultaneous changes in environmental pH, Mg2+ concentrations, and protein expression levels.
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Affiliation(s)
- Katharina Kolbe
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Alice C Bell
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Gareth A Prosser
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States.,Drug Discovery Unit, College of Life Sciences, James Black Centre, University of Dundee, Dundee, United Kingdom
| | - Maike Assmann
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Hee-Jeong Yang
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - He Eun Forbes
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Sophia Gallucci
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Katrin D Mayer-Barber
- Inflammation and Innate Immunity Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Helena I Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Clifton E Barry Iii
- Tuberculosis Research Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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40
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Modeling Tubercular ESX-1 Secretion Using Mycobacterium marinum. Microbiol Mol Biol Rev 2020; 84:84/4/e00082-19. [DOI: 10.1128/mmbr.00082-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Pathogenic mycobacteria cause chronic and acute diseases ranging from human tuberculosis (TB) to nontubercular infections.
Mycobacterium tuberculosis
causes both acute and chronic human tuberculosis. Environmentally acquired nontubercular mycobacteria (NTM) cause chronic disease in humans and animals. Not surprisingly, NTM and
M. tuberculosis
often use shared molecular mechanisms to survive within the host. The ESX-1 system is a specialized secretion system that is essential for virulence and is functionally conserved between
M. tuberculosis
and
Mycobacterium marinum
.
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41
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Piattelli E, Peltier J, Soutourina O. Interplay between Regulatory RNAs and Signal Transduction Systems during Bacterial Infection. Genes (Basel) 2020; 11:E1209. [PMID: 33081172 PMCID: PMC7602753 DOI: 10.3390/genes11101209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
The ability of pathogenic bacteria to stably infect the host depends on their capacity to respond and adapt to the host environment and on the efficiency of their defensive mechanisms. Bacterial envelope provides a physical barrier protecting against environmental threats. It also constitutes an important sensory interface where numerous sensing systems are located. Signal transduction systems include Two-Component Systems (TCSs) and alternative sigma factors. These systems are able to sense and respond to the ever-changing environment inside the host, altering the bacterial transcriptome to mitigate the impact of the stress. The regulatory networks associated with signal transduction systems comprise small regulatory RNAs (sRNAs) that can be directly involved in the expression of virulence factors. The aim of this review is to describe the importance of TCS- and alternative sigma factor-associated sRNAs in human pathogens during infection. The currently available genome-wide approaches for studies of TCS-regulated sRNAs will be discussed. The differences in the signal transduction mediated by TCSs between bacteria and higher eukaryotes and the specificity of regulatory RNAs for their targets make them appealing targets for discovery of new strategies to fight against multi-resistant bacteria.
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Affiliation(s)
- Emma Piattelli
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (E.P.); (J.P.)
| | - Johann Peltier
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (E.P.); (J.P.)
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, UMR CNRS 2001, Université de Paris, 75015 Paris, France
| | - Olga Soutourina
- Institute for Integrative Biology of the Cell (I2BC), CNRS, CEA, Université Paris-Saclay, 91198 Gif-sur-Yvette, France; (E.P.); (J.P.)
- Institut Universitaire de France, CEDEX 05, 75231 Paris, France
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Ostrik AA, Salina EG, Skvortsova YV, Grigorov AS, Bychenko OS, Kaprelyants AS, Azhikina TL. Small RNAs of Mycobacterium tuberculosis in Adaptation to Host-Like Stress Conditions in vitro. APPL BIOCHEM MICRO+ 2020. [DOI: 10.1134/s0003683820040122] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Coskun FS, Srivastava S, Raj P, Dozmorov I, Belkaya S, Mehra S, Golden NA, Bucsan AN, Chapagain ML, Wakeland EK, Kaushal D, Gumbo T, van Oers NSC. sncRNA-1 Is a Small Noncoding RNA Produced by Mycobacterium tuberculosis in Infected Cells That Positively Regulates Genes Coupled to Oleic Acid Biosynthesis. Front Microbiol 2020; 11:1631. [PMID: 32849337 PMCID: PMC7399025 DOI: 10.3389/fmicb.2020.01631] [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: 05/01/2020] [Accepted: 06/23/2020] [Indexed: 12/21/2022] Open
Abstract
Nearly one third of the world’s population is infected with Mycobacterium tuberculosis (Mtb). While much work has focused on the role of different Mtb encoded proteins in pathogenesis, recent studies have revealed that Mtb also transcribes many noncoding RNAs whose functions remain poorly characterized. We performed RNA sequencing and identified a subset of Mtb H37Rv-encoded small RNAs (<30 nts in length) that were produced in infected macrophages. Designated as smaller noncoding RNAs (sncRNAs), three of these predominated the read counts. Each of the three, sncRNA-1, sncRNA-6, and sncRNA-8 had surrounding sequences with predicted stable secondary RNA stem loops. Site-directed mutagenesis of the precursor sequences suggest the existence of a hairpin loop dependent RNA processing mechanism. A functional assessment of sncRNA-1 suggested that it positively regulated two mycobacterial transcripts involved in oleic acid biosynthesis. Complementary loss- and gain- of-function approaches revealed that sncRNA-1 positively supports Mtb growth and survival in nutrient-depleted cultures as well as in infected macrophages. Overall, the findings reveal that Mtb produces sncRNAs in infected cells, with sncRNA-1 modulating mycobacterial gene expression including genes coupled to oleic acid biogenesis.
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Affiliation(s)
- Fatma S Coskun
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Shashikant Srivastava
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, United States
| | - Prithvi Raj
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Igor Dozmorov
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Serkan Belkaya
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Smriti Mehra
- Tulane National Primate Research Center, School of Medicine, Tulane University, Covington, LA, United States
| | - Nadia A Golden
- Tulane National Primate Research Center, School of Medicine, Tulane University, Covington, LA, United States
| | - Allison N Bucsan
- Tulane National Primate Research Center, School of Medicine, Tulane University, Covington, LA, United States
| | - Moti L Chapagain
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, United States
| | - Edward K Wakeland
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States
| | - Deepak Kaushal
- Tulane National Primate Research Center, School of Medicine, Tulane University, Covington, LA, United States.,Texas Biomedical Research Institute, San Antonio, TX, United States
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, United States
| | - Nicolai S C van Oers
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX, United States.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, United States
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Abstract
Bordetella pertussis, the etiological agent of whooping cough, remains a major global health problem. Despite the global usage of whole-cell vaccines since the 1950s and of acellular vaccines in the 1990s, it still is one of the most prevalent vaccine-preventable diseases in industrialized countries. Virulence of B. pertussis is controlled by BvgA/S, a two-component system responsible for upregulation of virulence-activated genes (vags) and downregulation of virulence-repressed genes (vrgs). By transcriptome sequencing (RNAseq) analyses, we identified more than 270 vags or vrgs, and chromatin immunoprecipitation sequencing (ChIPseq) analyses revealed 148 BvgA-binding sites, 91 within putative promoter regions, 52 within open reading frames, and 5 in noncoding regions. Some vags, such as dnt and fhaL, do not contain a BvgA-binding site, suggesting indirect regulation. In contrast, several vrgs and some genes not identified by RNAseq analyses under laboratory conditions contain strong BvgA-binding sites, indicating previously unappreciated complexities of BvgA/S biology. Bordetella pertussis regulates the production of its virulence factors by the two-component system BvgAS. In the virulence phase, BvgS phosphorylates BvgA, which then activates the transcription of virulence-activated genes (vags). In the avirulence phase, such as during growth in the presence of MgSO4, BvgA is not phosphorylated and the vags are not expressed. Instead, a set of virulence-repressed genes (vrgs) is expressed. Here, we performed transcriptome sequencing (RNAseq) analyses on B. pertussis cultivated with or without MgSO4 and on a BvgA-deficient Tohama I derivative. We observed that 146 genes were less expressed under modulating conditions or in the BvgA-deficient strain than under the nonmodulating condition, while 130 genes were more expressed. Some of the genes code for proteins with regulatory functions, suggesting a BvgA/S regulation cascade. To determine which genes are directly regulated by BvgA, we performed chromatin immunoprecipitation sequencing (ChIPseq) analyses. We identified 148 BvgA-binding sites, 91 within putative promoter regions, 52 within open reading frames, and 5 in noncoding regions. Among the former, 32 are in BvgA-regulated putative promoter regions. Some vags, such as dnt and fhaL, contain no BvgA-binding site, suggesting indirect BvgA regulation. Unexpectedly, BvgA also bound to some vrg putative promoter regions. Together, these observations indicate an unrecognized complexity of BvgA/S biology. IMPORTANCEBordetella pertussis, the etiological agent of whooping cough, remains a major global health problem. Despite the global usage of whole-cell vaccines since the 1950s and of acellular vaccines in the 1990s, it still is one of the most prevalent vaccine-preventable diseases in industrialized countries. Virulence of B. pertussis is controlled by BvgA/S, a two-component system responsible for upregulation of virulence-activated genes (vags) and downregulation of virulence-repressed genes (vrgs). By transcriptome sequencing (RNAseq) analyses, we identified more than 270 vags or vrgs, and chromatin immunoprecipitation sequencing (ChIPseq) analyses revealed 148 BvgA-binding sites, 91 within putative promoter regions, 52 within open reading frames, and 5 in noncoding regions. Some vags, such as dnt and fhaL, do not contain a BvgA-binding site, suggesting indirect regulation. In contrast, several vrgs and some genes not identified by RNAseq analyses under laboratory conditions contain strong BvgA-binding sites, indicating previously unappreciated complexities of BvgA/S biology.
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Pérez I, Uranga S, Sayes F, Frigui W, Samper S, Arbués A, Aguiló N, Brosch R, Martín C, Gonzalo-Asensio J. Live attenuated TB vaccines representing the three modern Mycobacterium tuberculosis lineages reveal that the Euro-American genetic background confers optimal vaccine potential. EBioMedicine 2020; 55:102761. [PMID: 32361249 PMCID: PMC7195525 DOI: 10.1016/j.ebiom.2020.102761] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 04/02/2020] [Accepted: 04/06/2020] [Indexed: 01/11/2023] Open
Abstract
Background Human tuberculosis (TB) is caused by a plethora of Mycobacterium tuberculosis complex (MTBC) strains belonging to seven phylogenetic branches. Lineages 2, 3 and 4 are considered “modern” branches of the MTBC responsible for the majority of worldwide TB. Since the current BCG vaccine confers variable protection against pulmonary TB, new candidates are investigated. MTBVAC is the unique live attenuated vaccine based on M. tuberculosis in human clinical trials. Methods MTBVAC was originally constructed by unmarked phoP and fadD26 deletions in a clinical isolate belonging to L4. Here we construct new vaccines based on isogenic gene deletions in clinical isolates of the L2 and L3 modern lineages. These three vaccine candidates were characterized at molecular level and also in animal experiments of protection and safety. Findings Safety studies in immunocompromised mice showed that MTBVAC-L2 was less attenuated than BCG Pasteur, while the original MTBVAC was found even more attenuated than BCG and MTBVAC-L3 showed an intermediate phenotype. The three MTBVAC candidates showed similar or superior protection compared to BCG in immunocompetent mice vaccinated with each MTBVAC candidate and challenged with three representative strains of the modern lineages. Interpretation MTBVAC vaccines, based on double phoP and fadD26 deletions, protect against TB independently of the phylogenetic linage used as template strain for their construction. Nevertheless, lineage L4 confers the best safety profile. Funding European Commission (TBVAC2020, H2020-PHC-643381), Spanish Ministry of Science (RTI2018-097625-B-I00), Instituto de Salud Carlos III (PI18/0336), Gobierno de Aragón/Fondo Social Europeo and the French National Research Council (ANR-10-LABX-62-IBEID, ANR-16-CE35-0009, ANR-16-CE15-0003).
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Affiliation(s)
- Irene Pérez
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Santiago Uranga
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Fadel Sayes
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris, France
| | - Wafa Frigui
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris, France
| | - Sofía Samper
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Unidad de Investigación Translacional, Instituto Aragonés de Ciencias de la Salud, Instituto de Investigación Sanitaria Aragón, Zaragoza, Spain
| | - Ainhoa Arbués
- Present adress: Medical Parasitology & Infection Biology Department, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Nacho Aguiló
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Paris, France
| | - Carlos Martín
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Servicio de Microbiología Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - Jesús Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva, Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain; CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain; Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Zaragoza, Spain.
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Zhao Y, Dong X, Hou R. lncRNA PICART1 alleviates progression of cervical cancer by upregulating TCF21. Oncol Lett 2020; 19:3719-3724. [PMID: 32382324 PMCID: PMC7202295 DOI: 10.3892/ol.2020.11486] [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: 10/23/2019] [Accepted: 12/19/2019] [Indexed: 12/23/2022] Open
Abstract
Role of long non-coding RNA (lncRNA) PICART1 in alleviating the progression of cervical cancer (CC) via targeting TCF21 was elucidated. PICART1 level in CC and paracancerous tissues was determined by quantitative real-time polymerase chain reaction (qRT-PCR). Its level in CC patients with different tumor stages (stage I+II and stage III+IV) and tumor sizes (≤4 cm and >4 cm) was examined. Survival analysis was conducted in CC patients expressing high level and low level of PICART1. Changes in proliferative, migratory and invasive abilities of HeLa and SiHa cells after transfection of si-PICART1 were assessed. Prognostic value of TCF21 in CC was determined by Kaplan-Meier curves. The interaction between PICART1, TCF21 and ARID1A was investigated through RNA immunoprecipitation (RIP) and Chromatin immunoprecipitation (ChIP) assay. PICART1 was downregulated in CC tissues and cell lines. CC patients with worse TNM staging and larger tumor size presented lower level of PICART1. Low level of PICART1 in CC patients predicted a worse prognosis. Silence of PICART1 stimulated the proliferative, migratory and invasive abilities of HeLa and SiHa cells. TCF21 expression was low in CC tissues and positively regulated by PICART1. Low level of TCF21 in CC patients predicted a worse prognosis. Potential binding relationship was verified among PICART, ARID1A and TCF21. ChIP assay confirmed the decreased enrichment of ARID1A in TCF21 promoter region after PICART1 knockdown. lncRNA PICART1 recruits ARID1A to activate TCF21 expression, thus alleviating the malignant progression of CC.
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Affiliation(s)
- Yunxia Zhao
- Department of Gynaecology and Obstetrics, Weifang People's Hospital, Weifang, Shandong 261041, P.R. China
| | - Xiuxian Dong
- Department of Gynaecology and Obstetrics, Weifang People's Hospital, Weifang, Shandong 261041, P.R. China
| | - Rong Hou
- Department of Gynaecology and Obstetrics, Weifang People's Hospital, Weifang, Shandong 261041, P.R. China
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Metabolic Switching of Mycobacterium tuberculosis during Hypoxia Is Controlled by the Virulence Regulator PhoP. J Bacteriol 2020; 202:JB.00705-19. [PMID: 31932312 DOI: 10.1128/jb.00705-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 01/06/2020] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis retains the ability to establish an asymptomatic latent infection. A fundamental question in mycobacterial physiology is to understand the mechanisms involved in hypoxic stress, a critical player in persistence. Here, we show that the virulence regulator PhoP responds to hypoxia, the dormancy signal, and effectively integrates hypoxia with nitrogen metabolism. We also provide evidence to demonstrate that both under nitrogen limiting conditions and during hypoxia, phoP locus controls key genes involved in nitrogen metabolism. Consistently, under hypoxia a ΔphoP strain shows growth attenuation even with surplus nitrogen, the alternate electron acceptor, and complementation of the mutant restores bacterial growth. Together, our observations provide new biological insights into the role of PhoP in integrating nitrogen metabolism with hypoxia by the assistance of the hypoxia regulator DosR. The results have significant implications on the mechanism of intracellular survival and growth of the tubercle bacilli under a hypoxic environment within the phagosome.IMPORTANCE M. tuberculosis retains the unique ability to establish an asymptomatic latent infection. To understand the mechanisms involved in hypoxic stress which play a critical role in persistence, we show that the virulence regulator PhoP is linked to hypoxia, the dormancy signal. In keeping with this, phoP was shown to play a major role in M. tuberculosis growth under hypoxia even in the presence of surplus nitrogen, the alternate electron acceptor. Our results showing regulation of hypoxia-responsive genes provide new biological insights into role of the virulence regulator in metabolic switching by sensing hypoxia and integrating nitrogen metabolism with hypoxia by the assistance of the hypoxia regulator DosR.
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Ami VKG, Balasubramanian R, Hegde SR. Genome-wide identification of the context-dependent sRNA expression in Mycobacterium tuberculosis. BMC Genomics 2020; 21:167. [PMID: 32070281 PMCID: PMC7029489 DOI: 10.1186/s12864-020-6573-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/10/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Tuberculosis remains one of the leading causes of morbidity and mortality worldwide. Therefore, understanding the pathophysiology of Mycobacterium tuberculosis is imperative for developing new drugs. Post-transcriptional regulation plays a significant role in microbial adaptation to different growth conditions. While the proteins associated with gene expression regulation have been extensively studied in the pathogenic strain M. tuberculosis H37Rv, post-transcriptional regulation involving small RNAs (sRNAs) remains poorly understood. RESULTS We developed a novel moving-window based approach to detect sRNA expression using RNA-Seq data. Overlaying ChIP-seq data of RNAP (RNA Polymerase) and NusA suggest that these putative sRNA coding regions are significantly bound by the transcription machinery. Besides capturing many experimentally validated sRNAs, we observe the context-dependent expression of novel sRNAs in the intergenic regions of M. tuberculosis genome. For example, ncRv11806 shows expression only in the stationary phase, suggesting its role in mycobacterial latency which is a key attribute to long term pathogenicity. Also, ncRv11875C showed expression in the iron-limited condition, which is prevalent inside the macrophages of the host cells. CONCLUSION The systems level analysis of sRNA highlights the condition-specific expression of sRNAs which might enable the pathogen survival by rewiring regulatory circuits.
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Affiliation(s)
- Vimla Kany G Ami
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560 100, India
| | - Rami Balasubramanian
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560 100, India
| | - Shubhada R Hegde
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560 100, India.
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Girardin RC, McDonough KA. Small RNA Mcr11 requires the transcription factor AbmR for stable expression and regulates genes involved in the central metabolism of Mycobacterium tuberculosis. Mol Microbiol 2020; 113:504-520. [PMID: 31782837 PMCID: PMC7064933 DOI: 10.1111/mmi.14436] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 11/25/2019] [Accepted: 11/26/2019] [Indexed: 12/31/2022]
Abstract
Mycobacterium tuberculosis (Mtb), the etiologic agent of tuberculosis, must adapt to host-associated environments during infection by modulating gene expression. Small regulatory RNAs (sRNAs) are key regulators of bacterial gene expression, but their roles in Mtb are not well understood. Here, we address the expression and function of the Mtb sRNA Mcr11, which is associated with slow bacterial growth and chronic infections in mice. We found that stable expression of Mcr11 requires multiple factors specific to TB-complex bacteria, including the AbmR transcription factor. Bioinformatic analyses used to predict regulatory targets of Mcr11 identified 7-11 nucleotide regions with potential for direct base-pairing with Mcr11 immediately upstream of Rv3282, fadA3, and lipB. mcr11-dependent regulation of these genes was demonstrated using qRT-PCR and found to be responsive to the presence of fatty acids. Mutation of the putative Mcr11 base-pairing site upstream of lipB in a promoter reporter strain resulted in significant de-repression of lipB expression, similar to that observed in mcr11-deleted Mtb. These studies establish Mcr11's roles in regulating growth and central metabolism in Mtb. Our finding that multiple TB-complex-specific factors are required for production of stable Mcr11 also emphasizes the need to better understand mechanisms of sRNA expression and stability in TB.
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Affiliation(s)
- Roxie C. Girardin
- Department of Biomedical SciencesSchool of Public HealthUniversity at AlbanyAlbanyNY
| | - Kathleen A. McDonough
- Department of Biomedical SciencesSchool of Public HealthUniversity at AlbanyAlbanyNY
- Wadsworth Center, New York State Department of HealthAlbanyNY
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50
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Kroesen VM, Madacki J, Frigui W, Sayes F, Brosch R. Mycobacterial virulence: impact on immunogenicity and vaccine research. F1000Res 2019; 8. [PMID: 32047597 PMCID: PMC6979476 DOI: 10.12688/f1000research.20572.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/21/2019] [Indexed: 12/17/2022] Open
Abstract
The borderline between virulence and efficacy in live attenuated vaccine strains is often blurred and this is also the case for the Bacillus Calmette–Guérin (BCG), the only currently licensed anti-tuberculosis vaccine used on a large, global scale, which was obtained almost 100 years ago. While BCG is more than 99% identical at the genome level to
Mycobacterium tuberculosis, the causative pathogen of human tuberculosis, some important differences in virulence factors cause naturally irreversible attenuation and safety of this vaccine in the immunocompetent host. Some of these virulence factors are involved in persistence capacities of the vaccine strains and also represent strong immunogens, responsible for inducing different host signaling pathways, which have to be taken into consideration for the development of revised and new vaccine strains. Here we discuss a number of selected mycobacterial features in relation to their biological functions and potential impact on virulence and vaccine efficacy.
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Affiliation(s)
- Vera M Kroesen
- Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Institut Pasteur, Paris, France.,Faculty VI, University of Oldenburg, Oldenburg, Germany
| | - Jan Madacki
- Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Institut Pasteur, Paris, France
| | - Wafa Frigui
- Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Institut Pasteur, Paris, France
| | - Fadel Sayes
- Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Institut Pasteur, Paris, France
| | - Roland Brosch
- Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR 3525, Institut Pasteur, Paris, France
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