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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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2
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Xia X. Horizontal Gene Transfer and Drug Resistance Involving Mycobacterium tuberculosis. Antibiotics (Basel) 2023; 12:1367. [PMID: 37760664 PMCID: PMC10526031 DOI: 10.3390/antibiotics12091367] [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: 07/14/2023] [Revised: 08/13/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) acquires drug resistance at a rate comparable to that of bacterial pathogens that replicate much faster and have a higher mutation rate. One explanation for this rapid acquisition of drug resistance in Mtb is that drug resistance may evolve in other fast-replicating mycobacteria and then be transferred to Mtb through horizontal gene transfer (HGT). This paper aims to address three questions. First, does HGT occur between Mtb and other mycobacterial species? Second, what genes after HGT tend to survive in the recipient genome? Third, does HGT contribute to antibiotic resistance in Mtb? I present a conceptual framework for detecting HGT and analyze 39 ribosomal protein genes, 23S and 16S ribosomal RNA genes, as well as several genes targeted by antibiotics against Mtb, from 43 genomes representing all major groups within Mycobacterium. I also included mgtC and the insertion sequence IS6110 that were previously reported to be involved in HGT. The insertion sequence IS6110 shows clearly that the Mtb complex participates in HGT. However, the horizontal transferability of genes depends on gene function, as was previously hypothesized. HGT is not observed in functionally important genes such as ribosomal protein genes, rRNA genes, and other genes chosen as drug targets. This pattern can be explained by differential selection against functionally important and unimportant genes after HGT. Functionally unimportant genes such as IS6110 are not strongly selected against, so HGT events involving such genes are visible. For functionally important genes, a horizontally transferred diverged homologue from a different species may not work as well as the native counterpart, so the HGT event involving such genes is strongly selected against and eliminated, rendering them invisible to us. In short, while HGT involving the Mtb complex occurs, antibiotic resistance in the Mtb complex arose from mutations in those drug-targeted genes within the Mtb complex and was not gained through HGT.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, ON K1N 9A7, Canada; ; Tel.: +1-613-562-5718
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON K1H 8M5, Canada
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3
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Pepperell CS. Evolution of Tuberculosis Pathogenesis. Annu Rev Microbiol 2022; 76:661-680. [PMID: 35709500 DOI: 10.1146/annurev-micro-121321-093031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mycobacterium tuberculosis is a globally distributed, lethal pathogen of humans. The virulence armamentarium of M. tuberculosis appears to have been developed on a scaffold of antiphagocytic defenses found among diverse, mostly free-living species of Mycobacterium. Pathoadaptation was further aided by the modularity, flexibility, and interactivity characterizing mycobacterial effectors and their regulators. During emergence of M. tuberculosis, novel genetic material was acquired, created, and integrated with existing tools. The major mutational mechanisms underlying these adaptations are discussed in this review, with examples. During its evolution, M. tuberculosis lost the ability and/or opportunity to engage in lateral gene transfer, but despite this it has retained the adaptability that characterizes mycobacteria. M. tuberculosis exemplifies the evolutionary genomic mechanisms underlying adoption of the pathogenic niche, and studies of its evolution have uncovered a rich array of discoveries about how new pathogens are made. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Caitlin S Pepperell
- Division of Infectious Diseases, Department of Medicine, and Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA;
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Comparative Genomics of Mycobacterium avium Complex Reveals Signatures of Environment-Specific Adaptation and Community Acquisition. mSystems 2021; 6:e0119421. [PMID: 34665012 PMCID: PMC8525567 DOI: 10.1128/msystems.01194-21] [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] [Indexed: 11/20/2022] Open
Abstract
Nontuberculous mycobacteria, including those in the Mycobacterium avium complex (MAC), constitute an increasingly urgent threat to global public health. Ubiquitous in soil and water worldwide, MAC members cause a diverse array of infections in humans and animals that are often multidrug resistant, intractable, and deadly. MAC lung disease is of particular concern and is now more prevalent than tuberculosis in many countries, including the United States. Although the clinical importance of these microorganisms continues to expand, our understanding of their genomic diversity is limited, hampering basic and translational studies alike. Here, we leveraged a unique collection of genomes to characterize MAC population structure, gene content, and within-host strain dynamics in unprecedented detail. We found that different MAC species encode distinct suites of biomedically relevant genes, including antibiotic resistance genes and virulence factors, which may influence their distinct clinical manifestations. We observed that M. avium isolates from different sources—human pulmonary infections, human disseminated infections, animals, and natural environments—are readily distinguished by their core and accessory genomes, by their patterns of horizontal gene transfer, and by numerous specific genes, including virulence factors. We identified highly similar MAC strains from distinct patients within and across two geographically distinct clinical cohorts, providing important insights into the reservoirs which seed community acquisition. We also discovered a novel MAC genomospecies in one of these cohorts. Collectively, our results provide key genomic context for these emerging pathogens and will facilitate future exploration of MAC ecology, evolution, and pathogenesis. IMPORTANCE Members of the Mycobacterium avium complex (MAC), a group of mycobacteria encompassing M. avium and its closest relatives, are omnipresent in natural environments and emerging pathogens of humans and animals. MAC infections are difficult to treat, sometimes fatal, and increasingly common. Here, we used comparative genomics to illuminate key aspects of MAC biology. We found that different MAC species and M. avium isolates from different sources encode distinct suites of clinically relevant genes, including those for virulence and antibiotic resistance. We identified highly similar MAC strains in patients from different states and decades, suggesting community acquisition from dispersed and stable reservoirs, and we discovered a novel MAC species. Our work provides valuable insight into the genomic features underlying these versatile pathogens.
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The ATP-Binding Cassette (ABC) Transport Systems in Mycobacterium tuberculosis: Structure, Function, and Possible Targets for Therapeutics. BIOLOGY 2020; 9:biology9120443. [PMID: 33291531 PMCID: PMC7761784 DOI: 10.3390/biology9120443] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Revised: 11/06/2020] [Accepted: 11/12/2020] [Indexed: 12/22/2022]
Abstract
Simple Summary Mycobacterium tuberculosis is a bacterium of great medical importance because it causes tuberculosis, a disease that affects millions of people worldwide. Two important features are related to this bacterium: its ability to infect and survive inside the host, minimizing the immune response, and the burden of clinical isolates that are highly resistant to antibiotics treatment. These two phenomena are directly affected by cell envelope proteins, such as proteins from the ATP-Binding Cassette (ABC transporters) superfamily. In this review, we have compiled information on all the M. tuberculosis ABC transporters described so far, both from a functional and structural point of view, and show their relevance for the bacillus and the potential targets for studies aiming to control the microorganism and structural features. Abstract Mycobacterium tuberculosis is the etiological agent of tuberculosis (TB), a disease that affects millions of people in the world and that is associated with several human diseases. The bacillus is highly adapted to infect and survive inside the host, mainly because of its cellular envelope plasticity, which can be modulated to adapt to an unfriendly host environment; to manipulate the host immune response; and to resist therapeutic treatment, increasing in this way the drug resistance of TB. The superfamily of ATP-Binding Cassette (ABC) transporters are integral membrane proteins that include both importers and exporters. Both types share a similar structural organization, yet only importers have a periplasmic substrate-binding domain, which is essential for substrate uptake and transport. ABC transporter-type importers play an important role in the bacillus physiology through the transport of several substrates that will interfere with nutrition, pathogenesis, and virulence. Equally relevant, exporters have been involved in cell detoxification, nutrient recycling, and antibiotics and drug efflux, largely affecting the survival and development of multiple drug-resistant strains. Here, we review known ABC transporters from M. tuberculosis, with particular focus on the diversity of their structural features and relevance in infection and drug resistance.
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Sapriel G, Brosch R. Shared Pathogenomic Patterns Characterize a New Phylotype, Revealing Transition toward Host-Adaptation Long before Speciation of Mycobacterium tuberculosis. Genome Biol Evol 2020; 11:2420-2438. [PMID: 31368488 PMCID: PMC6736058 DOI: 10.1093/gbe/evz162] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis remains one of the deadliest infectious diseases of humanity. To better understand the evolutionary history of host-adaptation of tubercle bacilli (MTB), we sought for mycobacterial species that were more closely related to MTB than the previously used comparator species Mycobacterium marinum and Mycobacterium kansasii. Our phylogenomic approach revealed some recently sequenced opportunistic mycobacterial pathogens, Mycobacterium decipiens, Mycobacterium lacus, Mycobacterium riyadhense, and Mycobacterium shinjukuense, to constitute a common clade with MTB, hereafter called MTB-associated phylotype (MTBAP), from which MTB have emerged. Multivariate and clustering analyses of genomic functional content revealed that the MTBAP lineage forms a clearly distinct cluster of species that share common genomic characteristics, such as loss of core genes, shift in dN/dS ratios, and massive expansion of toxin–antitoxin systems. Consistently, analysis of predicted horizontal gene transfer regions suggests that putative functions acquired by MTBAP members were markedly associated with changes in microbial ecology, for example adaption to intracellular stress resistance. Our study thus considerably deepens our view on MTB evolutionary history, unveiling a decisive shift that promoted conversion to host-adaptation among ancestral founders of the MTBAP lineage long before Mycobacterium tuberculosis has adapted to the human host.
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Affiliation(s)
- Guillaume Sapriel
- UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France.,Atelier de Bioinformatique, ISYEB, UMR 7205, Paris, France
| | - Roland Brosch
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, CNRS UMR 3525, Paris, France
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Iron Supplementation Therapy, A Friend and Foe of Mycobacterial Infections? Pharmaceuticals (Basel) 2019; 12:ph12020075. [PMID: 31108902 PMCID: PMC6630247 DOI: 10.3390/ph12020075] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/21/2022] Open
Abstract
Iron is an essential element that is required for oxygen transfer, redox, and metabolic activities in mammals and bacteria. Mycobacteria, some of the most prevalent infectious agents in the world, require iron as growth factor. Mycobacterial-infected hosts set up a series of defense mechanisms, including systemic iron restriction and cellular iron distribution, whereas mycobacteria have developed sophisticated strategies to acquire iron from their hosts and to protect themselves from iron’s harmful effects. Therefore, it is assumed that host iron and iron-binding proteins, and natural or synthetic chelators would be keys targets to inhibit mycobacterial proliferation and may have a therapeutic potential. Beyond this hypothesis, recent evidence indicates a host protective effect of iron against mycobacterial infections likely through promoting remodeled immune response. In this review, we discuss experimental procedures and clinical observations that highlight the role of the immune response against mycobacteria under various iron availability conditions. In addition, we discuss the clinical relevance of our knowledge regarding host susceptibility to mycobacteria in the context of iron availability and suggest future directions for research on the relationship between host iron and the immune response and the use of iron as a therapeutic agent.
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8
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Saelens JW, Viswanathan G, Tobin DM. Mycobacterial Evolution Intersects With Host Tolerance. Front Immunol 2019; 10:528. [PMID: 30967867 PMCID: PMC6438904 DOI: 10.3389/fimmu.2019.00528] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/27/2019] [Indexed: 12/12/2022] Open
Abstract
Over the past 200 years, tuberculosis (TB) has caused more deaths than any other infectious disease, likely infecting more people than it has at any other time in human history. Mycobacterium tuberculosis (Mtb), the etiologic agent of TB, is an obligate human pathogen that has evolved through the millennia to become an archetypal human-adapted pathogen. This review focuses on the evolutionary framework by which Mtb emerged as a specialized human pathogen and applies this perspective to the emergence of specific lineages that drive global TB burden. We consider how evolutionary pressures, including transmission dynamics, host tolerance, and human population patterns, may have shaped the evolution of diverse mycobacterial genomes.
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Affiliation(s)
- Joseph W. Saelens
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - Gopinath Viswanathan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - David M. Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
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9
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Schwenk S, Moores A, Nobeli I, McHugh TD, Arnvig KB. Cell-wall synthesis and ribosome maturation are co-regulated by an RNA switch in Mycobacterium tuberculosis. Nucleic Acids Res 2018; 46:5837-5849. [PMID: 29618088 PMCID: PMC6009663 DOI: 10.1093/nar/gky226] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/11/2018] [Accepted: 03/15/2018] [Indexed: 01/16/2023] Open
Abstract
The success of Mycobacterium tuberculosis relies on the ability to switch between active growth and non-replicating persistence, associated with latent TB infection. Resuscitation promoting factors (Rpfs) are essential for the transition between these states. Rpf expression is tightly regulated as these enzymes are able to degrade the cell wall, and hence potentially lethal to the bacterium itself. We have identified a regulatory element in the 5' untranslated region (UTR) of rpfB. We demonstrate that this element is a transcriptionally regulated RNA switch/riboswitch candidate, which appears to be restricted to pathogenic mycobacteria, suggesting a role in virulence. We have used translation start site mapping to re-annotate the RpfB start codon and identified and validated a ribosome binding site that is likely to be targeted by an rpfB antisense RNA. Finally, we show that rpfB is co-transcribed with ksgA and ispE downstream. ksgA encodes a universally conserved methyltransferase involved in ribosome maturation and ispE encodes an essential kinase involved in cell wall synthesis. This arrangement implies co-regulation of resuscitation, cell wall synthesis and ribosome maturation via the RNA switch.
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Affiliation(s)
- Stefan Schwenk
- Institute for Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Alexandra Moores
- Institute for Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Irene Nobeli
- Institute for Structural and Molecular Biology, Birkbeck, London WC1E 7HX, UK
| | - Timothy D McHugh
- Centre for Clinical Microbiology, Royal Free Campus, University College London, London NW3 2QG, UK
| | - Kristine B Arnvig
- Institute for Structural and Molecular Biology, University College London, London WC1E 6BT, UK
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10
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Allen AR. One bacillus to rule them all? - Investigating broad range host adaptation in Mycobacterium bovis. INFECTION GENETICS AND EVOLUTION 2017; 53:68-76. [PMID: 28434972 DOI: 10.1016/j.meegid.2017.04.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 04/11/2017] [Accepted: 04/19/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Adrian R Allen
- Agri-Food and Biosciences Institute, AFBI Stormont, Department of Bacteriology, Lamont Building, Stoney Road, Belfast BT4 3SD, United Kingdom.
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11
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Thirunavukkarasu S, Plain KM, de Silva K, Marais BJ, Whittington RJ. Applying the One Health Concept to Mycobacterial Research - Overcoming Parochialism. Zoonoses Public Health 2017; 64:401-422. [PMID: 28084673 DOI: 10.1111/zph.12334] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Indexed: 12/27/2022]
Abstract
Mycobacterial infections remain a public health problem. Historically important, globally ubiquitous and with a wide host range, we are still struggling to control mycobacterial infections in humans and animals. While previous reviews have focused on individual mycobacterial infections in either humans or animals, a comprehensive review of the zoonotic aspect of mycobacteria in the context of the One Health initiative is lacking. With the purpose of providing a concise and comprehensive resource, we have collated literature to address the zoonotic potential of different mycobacterial species and elaborate on the necessity for an inter-sectorial approach to attain a new vision to combat mycobacterial infections.
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Affiliation(s)
- S Thirunavukkarasu
- Faculty of Veterinary Science, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia.,Boise Veterans Affairs Medical Center, Boise, ID, USA
| | - K M Plain
- Faculty of Veterinary Science, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - K de Silva
- Faculty of Veterinary Science, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - B J Marais
- Marie Bashir Institute for Infectious Diseases and Biosecurity and the Centre for Research Excellence in Emerging Infections, University of Sydney, Sydney, NSW, Australia
| | - R J Whittington
- Faculty of Veterinary Science, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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Peters JS, Calder B, Gonnelli G, Degroeve S, Rajaonarifara E, Mulder N, Soares NC, Martens L, Blackburn JM. Identification of Quantitative Proteomic Differences between Mycobacterium tuberculosis Lineages with Altered Virulence. Front Microbiol 2016; 7:813. [PMID: 27303394 PMCID: PMC4885829 DOI: 10.3389/fmicb.2016.00813] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 05/12/2016] [Indexed: 11/22/2022] Open
Abstract
Evidence currently suggests that as a species Mycobacterium tuberculosis exhibits very little genomic sequence diversity. Despite limited genetic variability, members of the M. tuberculosis complex (MTBC) have been shown to exhibit vast discrepancies in phenotypic presentation in terms of virulence, elicited immune response and transmissibility. Here, we used qualitative and quantitative mass spectrometry tools to investigate the proteomes of seven clinically-relevant mycobacterial strains—four M. tuberculosis strains, M. bovis, M. bovis BCG, and M. avium—that show varying degrees of pathogenicity and virulence, in an effort to rationalize the observed phenotypic differences. Following protein preparation, liquid chromatography mass spectrometry (LC MS/MS) and data capture were carried out using an LTQ Orbitrap Velos. Data analysis was carried out using a novel bioinformatics strategy, which yielded high protein coverage and was based on high confidence peptides. Through this approach, we directly identified a total of 3788 unique M. tuberculosis proteins out of a theoretical proteome of 4023 proteins and identified an average of 3290 unique proteins for each of the MTBC organisms (representing 82% of the theoretical proteomes), as well as 4250 unique M. avium proteins (80% of the theoretical proteome). Data analysis showed that all major classes of proteins are represented in every strain, but that there are significant quantitative differences between strains. Targeted selected reaction monitoring (SRM) assays were used to quantify the observed differential expression of a subset of 23 proteins identified by comparison to gene expression data as being of particular relevance to virulence. This analysis revealed differences in relative protein abundance between strains for proteins which may promote bacterial fitness in the more virulent W. Beijing strain. These differences may contribute to this strain's capacity for surviving within the host and resisting treatment, which has contributed to its rapid spread. Through this approach, we have begun to describe the proteomic portrait of a successful mycobacterial pathogen. Data are available via ProteomeXchange with identifier PXD004165.
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Affiliation(s)
- Julian S Peters
- Centre of Excellence for Biomedical TB Research, Witwatersrand University Johannesburg, South Africa
| | - Bridget Calder
- Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | | | | | - Elinambinina Rajaonarifara
- Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Nicola Mulder
- Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | - Nelson C Soares
- Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
| | | | - Jonathan M Blackburn
- Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town Cape Town, South Africa
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Aboubaker Osman D, Bouzid F, Canaan S, Drancourt M. Smooth Tubercle Bacilli: Neglected Opportunistic Tropical Pathogens. Front Public Health 2016; 3:283. [PMID: 26793699 PMCID: PMC4707939 DOI: 10.3389/fpubh.2015.00283] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 12/18/2015] [Indexed: 11/23/2022] Open
Abstract
Smooth tubercle bacilli (STB) including “Mycobacterium canettii” are members of the Mycobacterium tuberculosis complex (MTBC), which cause non-contagious tuberculosis in human. This group comprises <100 isolates characterized by smooth colonies and cordless organisms. Most STB isolates have been obtained from patients exposed to the Republic of Djibouti but seven isolates, including the three seminal ones obtained by Georges Canetti between 1968 and 1970, were recovered from patients in France, Madagascar, Sub-Sahara East Africa, and French Polynesia. STB form a genetically heterogeneous group of MTBC organisms with large 4.48 ± 0.05 Mb genomes, which may link Mycobacterium kansasii to MTBC organisms. Lack of inter-human transmission suggested a yet unknown environmental reservoir. Clinical data indicate a respiratory tract route of contamination and the digestive tract as an alternative route of contamination. Further epidemiological and clinical studies are warranted to elucidate areas of uncertainty regarding these unusual mycobacteria and the tuberculosis they cause.
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Affiliation(s)
- Djaltou Aboubaker Osman
- Aix-Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, Marseille, France; Centre d'Études et de Recherche de Djibouti (CERD), Institut de Recherche Médicinale (IRM), Djibouti, Republic of Djibouti
| | - Feriel Bouzid
- Aix-Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, Marseille, France; Enzymologie Interfaciale et Physiologie de la Lipolyse UMR7282, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, Marseille, France
| | - Stéphane Canaan
- Enzymologie Interfaciale et Physiologie de la Lipolyse UMR7282, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université , Marseille , France
| | - Michel Drancourt
- Aix-Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095 , Marseille , France
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15
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Young DB, Comas I, de Carvalho LPS. Phylogenetic analysis of vitamin B12-related metabolism in Mycobacterium tuberculosis. Front Mol Biosci 2015; 2:6. [PMID: 25988174 PMCID: PMC4428469 DOI: 10.3389/fmolb.2015.00006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 02/09/2015] [Indexed: 11/13/2022] Open
Abstract
Comparison of genome sequences from clinical isolates of Mycobacterium tuberculosis with phylogenetically-related pathogens Mycobacterium marinum, Mycobacterium kansasii, and Mycobacterium leprae reveals diversity amongst genes associated with vitamin B12-related metabolism. Diversity is generated by gene deletion events, differential acquisition of genes by horizontal transfer, and single nucleotide polymorphisms (SNPs) with predicted impact on protein function and transcriptional regulation. Differences in the B12 synthesis pathway, methionine biosynthesis, fatty acid catabolism, and DNA repair and replication are consistent with adaptations to different environmental niches and pathogenic lifestyles. While there is no evidence of further gene acquisition during expansion of the M. tuberculosis complex, the emergence of other forms of genetic diversity provides insights into continuing host-pathogen co-evolution and has the potential to identify novel targets for disease intervention.
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Affiliation(s)
- Douglas B Young
- Division of Mycobacterial Research, MRC National Institute for Medical Research London, UK
| | | | - Luiz P S de Carvalho
- Division of Mycobacterial Research, MRC National Institute for Medical Research London, UK
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16
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Narrandes NC, Machowski EE, Mizrahi V, Kana BD. Cleavage of the moaX-encoded fused molybdopterin synthase from Mycobacterium tuberculosis is necessary for activity. BMC Microbiol 2015; 15:22. [PMID: 25651977 PMCID: PMC4326299 DOI: 10.1186/s12866-015-0355-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 01/19/2015] [Indexed: 11/21/2022] Open
Abstract
Background Molybdopterin cofactor (MoCo) biosynthesis in Mycobacterium tuberculosis is associated with a multiplicity of genes encoding several enzymes in the pathway, including the molybdopterin (MPT) synthase, a hetero tetramer comprising two MoaD and two MoaE subunits. In addition to moaD1, moaD2, moaE1, moaE2, the M. tuberculosis genome also contains a moaX gene which encodes an MPT-synthase in which the MoaD and MoaE domains are located on a single polypeptide. In this study, we assessed the requirement for post-translational cleavage of MoaX for functionality of this novel, fused MPT synthase and attempted to establish a functional hierarchy for the various MPT-synthase encoding genes in M. tuberculosis. Results Using a heterologous Mycobacterium smegmatis host and the activity of the MoCo-dependent nitrate reductase, we confirmed that moaD2 and moaE2 from M. tuberculosis together encode a functional MPT synthase. In contrast, moaD1 displayed no functionality in this system, even in the presence of the MoeBR sulphurtransferase, which contains the rhodansese-like domain, predicted to activate MoaD subunits. We demonstrated that cleavage of MoaX into its constituent MoaD and MoaE subunits was required for MPT synthase activity and confirmed that cleavage occurs between the Gly82 and Ser83 residues in MoaX. Further analysis of the Gly81-Gly82 motif confirmed that both of these residues are necessary for catalysis and that the Gly81 was required for recognition/cleavage of MoaX by an as yet unidentified protease. In addition, the MoaE component of MoaX was able to function in conjunction with M. smegmatis MoaD2 suggesting that cleavage of MoaX renders functionally interchangeable subunits. Expression of MoaX in E. coli revealed that incorrect post-translational processing is responsible for the lack of activity of MoaX in this heterologous host. Conclusions There is a degree of functional interchangeability between the MPT synthase subunits of M. tuberculosis. In the case of MoaX, post-translational cleavage at the Gly82 residue is required for function. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0355-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicole C Narrandes
- DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, University of the Witwatersrand, National Health Laboratory Service, P.O. Box 1038, Johannesburg, 2000, South Africa.
| | - Edith Erika Machowski
- DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, University of the Witwatersrand, National Health Laboratory Service, P.O. Box 1038, Johannesburg, 2000, South Africa.
| | - Valerie Mizrahi
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit and DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease & Molecular Medicine and Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa.
| | - Bavesh D Kana
- DST/NRF Centre of Excellence for Biomedical TB Research, Faculty of Health Sciences, University of the Witwatersrand, National Health Laboratory Service, P.O. Box 1038, Johannesburg, 2000, South Africa.
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17
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Host Evasion and Exploitation Schemes of Mycobacterium tuberculosis. Cell 2014; 159:1497-509. [DOI: 10.1016/j.cell.2014.11.024] [Citation(s) in RCA: 269] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Indexed: 12/20/2022]
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18
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bis-Molybdopterin guanine dinucleotide is required for persistence of Mycobacterium tuberculosis in guinea pigs. Infect Immun 2014; 83:544-50. [PMID: 25404027 DOI: 10.1128/iai.02722-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Mycobacterium tuberculosis is able to synthesize molybdopterin cofactor (MoCo), which is utilized by numerous enzymes that catalyze redox reactions in carbon, nitrogen, and sulfur metabolism. In bacteria, MoCo is further modified through the activity of a guanylyltransferase, MobA, which converts MoCo to bis-molybdopterin guanine dinucleotide (bis-MGD), a form of the cofactor that is required by the dimethylsulfoxide (DMSO) reductase family of enzymes, which includes the nitrate reductase NarGHI. In this study, the functionality of the mobA homolog in M. tuberculosis was confirmed by demonstrating the loss of assimilatory and respiratory nitrate reductase activity in a mobA deletion mutant. This mutant displayed no survival defects in human monocytes or mouse lungs but failed to persist in the lungs of guinea pigs. These results implicate one or more bis-MGD-dependent enzymes in the persistence of M. tuberculosis in guinea pig lungs and underscore the applicability of this animal model for assessing the role of molybdoenzymes in this pathogen.
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19
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Behr MA. Comparative genomics of mycobacteria: some answers, yet more new questions. Cold Spring Harb Perspect Med 2014; 5:a021204. [PMID: 25395374 DOI: 10.1101/cshperspect.a021204] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Comparative genomic studies permit a genus-level perspective on the distinction between environmental mycobacteria and Mycobacterium tuberculosis, as well as a species-level assessment of genetic variability within M. tuberculosis. Both of these strata of evolutionary analysis serve to generate hypotheses regarding the genomic basis of M. tuberculosis virulence. In contrasting lessons from macroevolutionary study and microevolutionary study, one can form predictions about which segments of the genome are likely to be essential for or dispensable for the pathogenesis of tuberculosis. Although some of these predictions have been experimentally verified, notable exceptions challenge the direct link between these virulence factors and the capacity of M. tuberculosis to successfully cause disease and propagate between human hosts. These unexpected findings serve as the stimulus for further studies, using genomic comparisons and other approaches, to better define the remarkable success of this recalcitrant pathogen.
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Affiliation(s)
- Marcel A Behr
- McGill International Tuberculosis Centre, McGill University, Montreal, Quebec H3G 1A4, Canada Research Institute of the McGill University Health Centre, Montreal, Quebec H3G 1A4, Canada
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20
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Lamrabet O, Ghigo E, Mège JL, Lepidi H, Nappez C, Raoult D, Drancourt M. MspA-Mycobacterium tuberculosis-transformant with reduced virulence: The “unbirthday paradigm”. Microb Pathog 2014; 76:10-8. [DOI: 10.1016/j.micpath.2014.08.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 08/07/2014] [Accepted: 08/18/2014] [Indexed: 11/27/2022]
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21
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Costa P, Botelho A, Couto I, Viveiros M, Inácio J. Standing of nucleic acid testing strategies in veterinary diagnosis laboratories to uncover Mycobacterium tuberculosis complex members. Front Mol Biosci 2014; 1:16. [PMID: 25988157 PMCID: PMC4428369 DOI: 10.3389/fmolb.2014.00016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Accepted: 09/25/2014] [Indexed: 12/03/2022] Open
Abstract
Nucleic acid testing (NAT) designate any molecular approach used for the detection, identification, and characterization of pathogenic microorganisms, enabling the rapid, specific, and sensitive diagnostic of infectious diseases, such as tuberculosis. These assays have been widely used since the 90s of the last century in human clinical laboratories and, subsequently, also in veterinary diagnostics. Most NAT strategies are based in the polymerase chain reaction (PCR) and its several enhancements and variations. From the conventional PCR, real-time PCR and its combinations, isothermal DNA amplification, to the nanotechnologies, here we review how the NAT assays have been applied to decipher if and which member of the Mycobacterium tuberculosis complex is present in a clinical sample. Recent advances in DNA sequencing also brought new challenges and have made possible to generate rapidly and at a low cost, large amounts of sequence data. This revolution with the high-throughput sequencing (HTS) technologies makes whole genome sequencing (WGS) and metagenomics the trendiest NAT strategies, today. The ranking of NAT techniques in the field of clinical diagnostics is rising, and we provide a SWOT (Strengths, Weaknesses, Opportunities, and Threats) analysis with our view of the use of molecular diagnostics for detecting tuberculosis in veterinary laboratories, notwithstanding the gold standard being still the classical culture of the agent. The complementary use of both classical and molecular diagnostics approaches is recommended to speed the diagnostic, enabling a fast decision by competent authorities and rapid tackling of the disease.
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Affiliation(s)
- Pedro Costa
- Instituto Nacional de Investigação Agrária e Veterinária IPLisboa, Portugal
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical da Universidade Nova de LisboaLisboa, Portugal
| | - Ana Botelho
- Instituto Nacional de Investigação Agrária e Veterinária IPLisboa, Portugal
| | - Isabel Couto
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical da Universidade Nova de LisboaLisboa, Portugal
- Centro de Recursos Microbiológicos (CREM), Universidade Nova de LisboaCaparica, Portugal
| | - Miguel Viveiros
- Grupo de Micobactérias, Unidade de Microbiologia Médica, Instituto de Higiene e Medicina Tropical da Universidade Nova de LisboaLisboa, Portugal
- Centro de Malária e Outras Doenças Tropicais, Instituto de Higiene e Medicina Tropical da Universidade Nova de LisboaLisboa, Portugal
| | - João Inácio
- School of Pharmacy and Biomolecular Sciences, University of BrightonBrighton, UK
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22
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Mulder NJ, Akinola RO, Mazandu GK, Rapanoel H. Using biological networks to improve our understanding of infectious diseases. Comput Struct Biotechnol J 2014; 11:1-10. [PMID: 25379138 PMCID: PMC4212278 DOI: 10.1016/j.csbj.2014.08.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Infectious diseases are the leading cause of death, particularly in developing countries. Although many drugs are available for treating the most common infectious diseases, in many cases the mechanism of action of these drugs or even their targets in the pathogen remain unknown. In addition, the key factors or processes in pathogens that facilitate infection and disease progression are often not well understood. Since proteins do not work in isolation, understanding biological systems requires a better understanding of the interconnectivity between proteins in different pathways and processes, which includes both physical and other functional interactions. Such biological networks can be generated within organisms or between organisms sharing a common environment using experimental data and computational predictions. Though different data sources provide different levels of accuracy, confidence in interactions can be measured using interaction scores. Connections between interacting proteins in biological networks can be represented as graphs and edges, and thus studied using existing algorithms and tools from graph theory. There are many different applications of biological networks, and here we discuss three such applications, specifically applied to the infectious disease tuberculosis, with its causative agent Mycobacterium tuberculosis and host, Homo sapiens. The applications include the use of the networks for function prediction, comparison of networks for evolutionary studies, and the generation and use of host–pathogen interaction networks.
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Affiliation(s)
- Nicola J Mulder
- Computational Biology Group, Department of Clinical Laboratory Sciences, IDM, University of Cape Town Faculty of Health Sciences, Anzio Road, Observatory, Cape Town, South Africa
| | - Richard O Akinola
- Computational Biology Group, Department of Clinical Laboratory Sciences, IDM, University of Cape Town Faculty of Health Sciences, Anzio Road, Observatory, Cape Town, South Africa
| | - Gaston K Mazandu
- Computational Biology Group, Department of Clinical Laboratory Sciences, IDM, University of Cape Town Faculty of Health Sciences, Anzio Road, Observatory, Cape Town, South Africa
| | - Holifidy Rapanoel
- Computational Biology Group, Department of Clinical Laboratory Sciences, IDM, University of Cape Town Faculty of Health Sciences, Anzio Road, Observatory, Cape Town, South Africa
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