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Xu G, Wang J, Gao GF, Liu CH. Insights into battles between Mycobacterium tuberculosis and macrophages. Protein Cell 2014; 5:728-36. [PMID: 24938416 PMCID: PMC4180456 DOI: 10.1007/s13238-014-0077-5] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 05/07/2014] [Indexed: 01/11/2023] Open
Abstract
As the first line of immune defense for Mycobacterium tuberculosis (Mtb), macrophages also provide a major habitat for Mtb to reside in the host for years. The battles between Mtb and macrophages have been constant since ancient times. Triggered upon Mtb infection, multiple cellular pathways in macrophages are activated to initiate a tailored immune response toward the invading pathogen and regulate the cellular fates of the host as well. Toll-like receptors (TLRs) expressed on macrophages can recognize pathogen-associated-molecular patterns (PAMPs) on Mtb and mediate the production of immune-regulatory cytokines such as tumor necrosis factor (TNF) and type I Interferons (IFNs). In addition, Vitamin D receptor (VDR) and Vitamin D-1-hydroxylase are up-regulated in Mtb-infected macrophages, by which Vitamin D participates in innate immune responses. The signaling pathways that involve TNF, type I IFNs and Vitamin D are inter-connected, which play critical roles in the regulation of necroptosis, apoptosis, and autophagy of the infected macrophages. This review article summarizes current knowledge about the interactions between Mtb and macrophages, focusing on cellular fates of the Mtb-infected macrophages and the regulatory molecules and cellular pathways involved in those processes.
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Affiliation(s)
- Guanghua Xu
- CAS key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
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52
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Liu F, Hu Y, Wang Q, Li HM, Gao GF, Liu CH, Zhu B. Comparative genomic analysis of Mycobacterium tuberculosis clinical isolates. BMC Genomics 2014; 15:469. [PMID: 24923884 PMCID: PMC4070564 DOI: 10.1186/1471-2164-15-469] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2013] [Accepted: 06/10/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Due to excessive antibiotic use, drug-resistant Mycobacterium tuberculosis has become a serious public health threat and a major obstacle to disease control in many countries. To better understand the evolution of drug-resistant M. tuberculosis strains, we performed whole genome sequencing for 7 M. tuberculosis clinical isolates with different antibiotic resistance profiles and conducted comparative genomic analysis of gene variations among them. RESULTS We observed that all 7 M. tuberculosis clinical isolates with different levels of drug resistance harbored similar numbers of SNPs, ranging from 1409-1464. The numbers of insertion/deletions (Indels) identified in the 7 isolates were also similar, ranging from 56 to 101. A total of 39 types of mutations were identified in drug resistance-associated loci, including 14 previously reported ones and 25 newly identified ones. Sixteen of the identified large Indels spanned PE-PPE-PGRS genes, which represents a major source of antigenic variability. Aside from SNPs and Indels, a CRISPR locus with varied spacers was observed in all 7 clinical isolates, suggesting that they might play an important role in plasticity of the M. tuberculosis genome. The nucleotide diversity (Л value) and selection intensity (dN/dS value) of the whole genome sequences of the 7 isolates were similar. The dN/dS values were less than 1 for all 7 isolates (range from 0.608885 to 0.637365), supporting the notion that M. tuberculosis genomes undergo purifying selection. The Л values and dN/dS values were comparable between drug-susceptible and drug-resistant strains. CONCLUSIONS In this study, we show that clinical M. tuberculosis isolates exhibit distinct variations in terms of the distribution of SNP, Indels, CRISPR-cas locus, as well as the nucleotide diversity and selection intensity, but there are no generalizable differences between drug-susceptible and drug-resistant isolates on the genomic scale. Our study provides evidence strengthening the notion that the evolution of drug resistance among clinical M. tuberculosis isolates is clearly a complex and diversified process.
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Affiliation(s)
| | | | | | | | | | - Cui Hua Liu
- CAS key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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Wang J, Pritchard JR, Kreitmann L, Montpetit A, Behr MA. Disruption of Mycobacterium avium subsp. paratuberculosis-specific genes impairs in vivo fitness. BMC Genomics 2014; 15:415. [PMID: 24885784 PMCID: PMC4058006 DOI: 10.1186/1471-2164-15-415] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 05/27/2014] [Indexed: 01/08/2023] Open
Abstract
Background Mycobacterium avium subsp. paratuberculosis (MAP) is an obligate intracellular pathogen that infects many ruminant species. The acquisition of foreign genes via horizontal gene transfer has been postulated to contribute to its pathogenesis, as these genetic elements are absent from its putative ancestor, M. avium subsp. hominissuis (MAH), an environmental organism with lesser pathogenicity. In this study, high-throughput sequencing of MAP transposon libraries were analyzed to qualitatively and quantitatively determine the contribution of individual genes to bacterial survival during infection. Results Out of 52384 TA dinucleotides present in the MAP K-10 genome, 12607 had a MycoMarT7 transposon in the input pool, interrupting 2443 of the 4350 genes in the MAP genome (56%). Of 96 genes situated in MAP-specific genomic islands, 82 were disrupted in the input pool, indicating that MAP-specific genomic regions are dispensable for in vitro growth (odds ratio = 0.21). Following 5 independent in vivo infections with this pool of mutants, the correlation between output pools was high for 4 of 5 (R = 0.49 to 0.61) enabling us to define genes whose disruption reproducibly reduced bacterial fitness in vivo. At three different thresholds for reduced fitness in vivo, MAP-specific genes were over-represented in the list of predicted essential genes. We also identified additional genes that were severely depleted after infection, and several of them have orthologues that are essential genes in M. tuberculosis. Conclusions This work indicates that the genetic elements required for the in vivo survival of MAP represent a combination of conserved mycobacterial virulence genes and MAP-specific genes acquired via horizontal gene transfer. In addition, the in vitro and in vivo essential genes identified in this study may be further characterized to offer a better understanding of MAP pathogenesis, and potentially contribute to the discovery of novel therapeutic and vaccine targets. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-415) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, QC H3A 2B4, Canada.
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Wang J, Behr MA. Building a better bacillus: the emergence of Mycobacterium tuberculosis. Front Microbiol 2014; 5:139. [PMID: 24765091 PMCID: PMC3982062 DOI: 10.3389/fmicb.2014.00139] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 03/18/2014] [Indexed: 11/29/2022] Open
Abstract
The genus Mycobacterium is comprised of more than 150 species that reside in a wide variety of habitats. Most mycobacteria are environmental organisms that are either not associated with disease or are opportunistic pathogens that cause non-transmissible disease in immunocompromised individuals. In contrast, a small number of species, such as the tubercle bacillus, Mycobacterium tuberculosis, are host-adapted pathogens for which there is no known environmental reservoir. In recent years, gene disruption studies using the host-adapted pathogen have uncovered a number of “virulence factors,” yet genomic data indicate that many of these elements are present in non-pathogenic mycobacteria. This suggests that much of the genetic make-up that enables virulence in the host-adapted pathogen is already present in environmental members of the genus. In addition to these generic factors, we hypothesize that molecules elaborated exclusively by professional pathogens may be particularly implicated in the ability of M. tuberculosis to infect, persist, and cause transmissible pathology in its host species, Homo sapiens. One approach to identify these molecules is to employ comparative analysis of mycobacterial genomes, to define evolutionary events such as horizontal gene transfer (HGT) that contributed M. tuberculosis-specific genetic elements. Independent studies have now revealed the presence of HGT genes in the M. tuberculosis genome and their role in the pathogenesis of disease is the subject of ongoing investigations. Here we review these studies, focusing on the hypothesized role played by HGT loci in the emergence of M. tuberculosis from a related environmental species into a highly specialized human-adapted pathogen.
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Affiliation(s)
- Joyce Wang
- Department of Microbiology and Immunology, McGill University Montreal, QC, Canada
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University Montreal, QC, Canada ; Department of Medicine, McGill University Montreal, QC, Canada ; McGill International TB Centre Montreal, QC, Canada
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Macheras E, Konjek J, Roux AL, Thiberge JM, Bastian S, Leão SC, Palaci M, Sivadon-Tardy V, Gutierrez C, Richter E, Rüsch-Gerdes S, Pfyffer GE, Bodmer T, Jarlier V, Cambau E, Brisse S, Caro V, Rastogi N, Gaillard JL, Heym B. Multilocus sequence typing scheme for the Mycobacterium abscessus complex. Res Microbiol 2013; 165:82-90. [PMID: 24384536 DOI: 10.1016/j.resmic.2013.12.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 12/19/2013] [Indexed: 11/29/2022]
Abstract
We developed a multilocus sequence typing (MLST) scheme for Mycobacterium abscessus sensu lato, based on the partial sequencing of seven housekeeping genes: argH, cya, glpK, gnd, murC, pta and purH. This scheme was used to characterize a collection of 227 isolates recovered between 1994 and 2010 in France, Germany, Switzerland and Brazil. We identified 100 different sequence types (STs), which were distributed into three groups on the tree obtained by concatenating the sequences of the seven housekeeping gene fragments (3576bp): the M. abscessus sensu stricto group (44 STs), the "M. massiliense" group (31 STs) and the "M. bolletii" group (25 STs). SplitTree analysis showed a degree of intergroup lateral transfers. There was also evidence of lateral transfer events involving rpoB. The most prevalent STs in our collection were ST1 (CC5; 20 isolates) and ST23 (CC3; 31 isolates). Both STs were found in Europe and Brazil, and the latter was implicated in a large post-surgical procedure outbreak in Brazil. Respiratory isolates from patients with cystic fibrosis belonged to a large variety of STs; however, ST2 was predominant in this group of patients. Our MLST scheme, publicly available at www.pasteur.fr/mlst, offers investigators a valuable typing tool for M. abscessus sensu lato in future epidemiological studies throughout the world.
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Affiliation(s)
- Edouard Macheras
- APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Service de Microbiologie, Hôpital Ambroise Paré, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France; EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Bièvre, 78180 Montigny-le-Bretonneux, France.
| | - Julie Konjek
- EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Bièvre, 78180 Montigny-le-Bretonneux, France.
| | - Anne-Laure Roux
- APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Laboratoire de Microbiologie, Hôpital Raymond Poincaré, AP-HP, Garches, France; EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Bièvre, 78180 Montigny-le-Bretonneux, France.
| | - Jean-Michel Thiberge
- Institut Pasteur, Genotyping of Pathogens and Public Health, 25 rue du Docteur Roux, 75015 Paris, France.
| | - Sylvaine Bastian
- Centre national de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, 47-83 Boulevard de l'Hôpital, 75013 Paris, France; APHP, Groupe Hospitalier Pitié-Salpêtrière, Laboratoire de Bactériologie - Hygiène, 47-83 Boulevard de l'Hôpital, 75013 Paris, France.
| | - Sylvia Cardoso Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo, Rua Botucatu, 862, Vila Clementino, São Paulo SP CEP 04023-062, Brazil.
| | - Moises Palaci
- Nucleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Av. Fernando Ferrari, 514, Goiabeiras Vitória - ES, CEP 29075-910, Brazil.
| | - Valérie Sivadon-Tardy
- APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Service de Microbiologie, Hôpital Ambroise Paré, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France.
| | - Cristina Gutierrez
- Caribbean Public Health Agency (CARPHA), 16-18 Jamaica Boulevard, Federation Park, Port of Spain, Trinidad and Tobago.
| | - Elvira Richter
- National Reference Center for Mycobacteria, Forschungszentrum Borstel, Parkalle 18, 23845 Borstel, Germany.
| | - Sabine Rüsch-Gerdes
- National Reference Center for Mycobacteria, Forschungszentrum Borstel, Parkalle 18, 23845 Borstel, Germany.
| | - Gaby E Pfyffer
- Institut für Medizinische Mikrobiologie, Zentrum für LaborMedizin, Luzerner Kantonsspital, Spitalstrasse, 6004 Luzern, Switzerland.
| | - Thomas Bodmer
- Institut für Infektionskrankheiten, Universität Bern, Hochschulstrasse 4, 3010 Bern, Switzerland.
| | - Vincent Jarlier
- Centre national de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, 47-83 Boulevard de l'Hôpital, 75013 Paris, France; APHP, Groupe Hospitalier Pitié-Salpêtrière, Laboratoire de Bactériologie - Hygiène, 47-83 Boulevard de l'Hôpital, 75013 Paris, France.
| | - Emmanuelle Cambau
- APHP, Groupe hospitalier Lariboisière-Fernand Widal, Laboratoire de Microbiologie, 2 rue Ambroise Paré, 75010 Paris, France.
| | - Sylvain Brisse
- Institut Pasteur, Genotyping of Pathogens and Public Health, 25 rue du Docteur Roux, 75015 Paris, France.
| | - Valérie Caro
- Institut Pasteur, Genotyping of Pathogens and Public Health, 25 rue du Docteur Roux, 75015 Paris, France.
| | - Nalin Rastogi
- Institut Pasteur, Laboratoire de Recherche et de Référence sur la Tuberculose et les Mycobactéries, BP 484 Morne Jolivière, Les Abymes 97183 Cedex, Guadeloupe, France.
| | - Jean-Louis Gaillard
- APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Service de Microbiologie, Hôpital Ambroise Paré, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France; APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Laboratoire de Microbiologie, Hôpital Raymond Poincaré, AP-HP, Garches, France; EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Bièvre, 78180 Montigny-le-Bretonneux, France.
| | - Beate Heym
- APHP Hôpitaux universitaires Paris Ile-de-France Ouest, Service de Microbiologie, Hôpital Ambroise Paré, 9 avenue Charles de Gaulle, 92100 Boulogne-Billancourt, France; EA 3647, Université de Versailles Saint-Quentin-en-Yvelines, 2 avenue de la Source de la Bièvre, 78180 Montigny-le-Bretonneux, France.
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Radomski N, Roguet A, Lucas FS, Veyrier FJ, Cambau E, Accrombessi H, Moilleron R, Behr MA, Moulin L. atpE gene as a new useful specific molecular target to quantify Mycobacterium in environmental samples. BMC Microbiol 2013; 13:277. [PMID: 24299240 PMCID: PMC4219376 DOI: 10.1186/1471-2180-13-277] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 11/26/2013] [Indexed: 11/10/2022] Open
Abstract
Background The environment is the likely source of many pathogenic mycobacterial species but detection of mycobacteria by bacteriological tools is generally difficult and time-consuming. Consequently, several molecular targets based on the sequences of housekeeping genes, non-functional RNA and structural ribosomal RNAs have been proposed for the detection and identification of mycobacteria in clinical or environmental samples. While certain of these targets were proposed as specific for this genus, most are prone to false positive results in complex environmental samples that include related, but distinct, bacterial genera. Nowadays the increased number of sequenced genomes and the availability of software for genomic comparison provide tools to develop novel, mycobacteria-specific targets, and the associated molecular probes and primers. Consequently, we conducted an in silico search for proteins exclusive to Mycobacterium spp. genomes in order to design sensitive and specific molecular targets. Results Among the 3989 predicted proteins from M. tuberculosis H37Rv, only 11 proteins showed 80% to 100% of similarity with Mycobacterium spp. genomes, and less than 50% of similarity with genomes of closely related Corynebacterium, Nocardia and Rhodococcus genera. Based on DNA sequence alignments, we designed primer pairs and a probe that specifically detect the atpE gene of mycobacteria, as verified by quantitative real-time PCR on a collection of mycobacteria and non-mycobacterial species. The real-time PCR method we developed was successfully used to detect mycobacteria in tap water and lake samples. Conclusions The results indicate that this real-time PCR method targeting the atpE gene can serve for highly specific detection and precise quantification of Mycobacterium spp. in environmental samples.
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Affiliation(s)
- Nicolas Radomski
- Laboratoire Eau Environnement Systèmes Urbains (Leesu) UMR MA 102-AgroParisTech, Université Paris-Est, 6-8 avenue Blaise Pascal Cité, Descartes, FR 77455, Champs sur Marne, France.
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Prasanna AN, Mehra S. Comparative phylogenomics of pathogenic and non-pathogenic mycobacterium. PLoS One 2013; 8:e71248. [PMID: 24015186 PMCID: PMC3756022 DOI: 10.1371/journal.pone.0071248] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 06/26/2013] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium species are the source of a variety of infectious diseases in a range of hosts. Genome based methods are used to understand the adaptation of each pathogenic species to its unique niche. In this work, we report the comparison of pathogenic and non-pathogenic Mycobacterium genomes. Phylogenetic trees were constructed using sequence of core orthologs, gene content and gene order. It is found that the genome based methods can better resolve the inter-species evolutionary distances compared to the conventional 16S based tree. Phylogeny based on gene order highlights distinct evolutionary characteristics as compared to the methods based on sequence, as illustrated by the shift in the relative position of M. abscessus. This difference in gene order among the Mycobacterium species is further investigated using a detailed synteny analysis. It is found that while rearrangements between some Mycobacterium genomes are local within synteny blocks, few possess global rearrangements across the genomes. The study illustrates how a combination of different genome based methods is essential to build a robust phylogenetic relationship between closely related organisms.
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Affiliation(s)
- Arun N. Prasanna
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sarika Mehra
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- * E-mail:
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58
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Pepperell CS, Casto AM, Kitchen A, Granka JM, Cornejo OE, Holmes EC, Holmes EC, Birren B, Galagan J, Feldman MW. The role of selection in shaping diversity of natural M. tuberculosis populations. PLoS Pathog 2013; 9:e1003543. [PMID: 23966858 PMCID: PMC3744410 DOI: 10.1371/journal.ppat.1003543] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Accepted: 06/24/2013] [Indexed: 12/26/2022] Open
Abstract
Mycobacterium tuberculosis (M.tb), the cause of tuberculosis (TB), is estimated to infect a new host every second. While analyses of genetic data from natural populations of M.tb have emphasized the role of genetic drift in shaping patterns of diversity, the influence of natural selection on this successful pathogen is less well understood. We investigated the effects of natural selection on patterns of diversity in 63 globally extant genomes of M.tb and related pathogenic mycobacteria. We found evidence of strong purifying selection, with an estimated genome-wide selection coefficient equal to -9.5 × 10(-4) (95% CI -1.1 × 10(-3) to -6.8 × 10(-4)); this is several orders of magnitude higher than recent estimates for eukaryotic and prokaryotic organisms. We also identified different patterns of variation across categories of gene function. Genes involved in transport and metabolism of inorganic ions exhibited very low levels of non-synonymous polymorphism, equivalent to categories under strong purifying selection (essential and translation-associated genes). The highest levels of non-synonymous variation were seen in a group of transporter genes, likely due to either diversifying selection or local selective sweeps. In addition to selection, we identified other important influences on M.tb genetic diversity, such as a 25-fold expansion of global M.tb populations coincident with explosive growth in human populations (estimated timing 1684 C.E., 95% CI 1620-1713 C.E.). These results emphasize the parallel demographic histories of this obligate pathogen and its human host, and suggest that the dominant effect of selection on M.tb is removal of novel variants, with exceptions in an interesting group of genes involved in transportation and defense. We speculate that the hostile environment within a host imposes strict demands on M.tb physiology, and thus a substantial fitness cost for most new mutations. In this respect, obligate bacterial pathogens may differ from other host-associated microbes such as symbionts.
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Affiliation(s)
- Caitlin S Pepperell
- Departments of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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Evolution of Mycobacterium tuberculosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013; 783:81-91. [DOI: 10.1007/978-1-4614-6111-1_4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Abstract
Recent years have witnessed an increased appreciation of the extent and relevance of strain-to-strain variation in Mycobacterium tuberculosis. This paradigm shift can largely be attributed to an improved understanding of the global population structure of this organism, and to the realisation that the various members of the M. tuberculosis complex (MTBC) harbour more genetic diversity than previously realised. Moreover, many studies using experimental models of infection have demonstrated that MTBC diversity translates into significant differences in immunogenecity and virulence . However, linking these experimental phenotypes to relevant clinical phenotypes has been difficult, and to date, largely unsuccessful. Nevertheless, emerging high-throughput technologies, in particular next-generation sequencing , offer new opportunities, and have already lead to important new insights. Given the complexity of the host-pathogen interaction in tuberculosis, systems approaches will be key to define the role of MTBC diversity in the fight against one of humankind's most important pathogens.
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61
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Wang TC, Chen FC. The evolutionary landscape of the Mycobacterium tuberculosis genome. Gene 2012; 518:187-93. [PMID: 23219994 DOI: 10.1016/j.gene.2012.11.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 11/27/2012] [Indexed: 10/27/2022]
Abstract
Mycobacterium tuberculosis is one of the most deadly human pathogens. The major mechanism for the adaptations of M. tuberculosis is nucleotide substitution. Previous studies have relied on the nonsynonymous-to-synonymous substitution rate (dN/dS) ratio as a measurement of selective constraint based on the assumed selective neutrality of synonymous substitutions. However, this assumption has been shown to be untrue in many cases. In this study, we used the substitution rate in intergenic regions (di) of the M. tuberculosis genome as the neutral reference, and conducted a genome-wide profiling for di, dS, and the rate of insertions/deletions (indel rate) as compared with the genome of M. canettii using a 50kb sliding window. We demonstrate significant variations in all of the three evolutionary measurements across the M. tuberculosis genome, even for regions in close vicinity. Furthermore, we identified a total of 233 genes with their dS deviating significantly from di within the same window. Interestingly, dS also varies significantly in some of the windows, indicating drastic changes in mutation rate and/or selection pressure within relatively short distances in the M. tuberculosis genome. Importantly, our results indicate that selection on synonymous substitutions is common in the M. tuberculosis genome. Therefore, the dN/dS ratio test must be applied carefully for measuring selection pressure on M. tuberculosis genes.
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Affiliation(s)
- Tai-Chun Wang
- Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, 35 Keyen Road, Zhunan, Miaoli County, 350 Taiwan.
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Zakham F, Aouane O, Ussery D, Benjouad A, Ennaji MM. Computational genomics-proteomics and Phylogeny analysis of twenty one mycobacterial genomes (Tuberculosis & non Tuberculosis strains). MICROBIAL INFORMATICS AND EXPERIMENTATION 2012; 2:7. [PMID: 22929624 PMCID: PMC3504576 DOI: 10.1186/2042-5783-2-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 08/02/2012] [Indexed: 12/04/2022]
Abstract
Background The genus Mycobacterium comprises different species, among them the most contagious and infectious bacteria. The members of the complex Mycobacterium tuberculosis are the most virulent microorganisms that have killed human and other mammals since millennia. Additionally, with the many different mycobacterial sequences available, there is a crucial need for the visualization and the simplification of their data. In this present study, we aim to highlight a comparative genome, proteome and phylogeny analysis between twenty-one mycobacterial (Tuberculosis and non tuberculosis) strains using a set of computational and bioinformatics tools (Pan and Core genome plotting, BLAST matrix and phylogeny analysis). Results Considerably the result of pan and core genome Plotting demonstrated that less than 1250 Mycobacterium gene families are conserved across all species, and a total set of about 20,000 gene families within the Mycobacterium pan-genome of twenty one mycobacterial genomes. Viewing the BLAST matrix a high similarity was found among the species of the complex Mycobacterium tuberculosis and less conservation is found with other slow growing pathogenic mycobacteria. Phylogeny analysis based on both protein conservation, as well as rRNA clearly resolve known relationships between slow growing mycobacteria. Conclusion Mycobacteria include important pathogenic species for human and animals and the Mycobacterium tuberculosis complex is the most cause of death of the humankind. The comparative genome analysis could provide a new insight for better controlling and preventing these diseases.
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Affiliation(s)
- Fathiah Zakham
- Laboratoire de Virologie et Hygiène & Microbiologie, Faculté des Sciences et Techniques, BP 146, Mohammedia, 20650, Morocco.
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Soto ME, Del Carmen Ávila-Casado M, Huesca-Gómez C, Alarcon GV, Castrejon V, Soto V, Hernandez S, Espinola-Zavaleta N, Vallejo M, Reyes PA, Gamboa R. Detection of IS6110 and HupB gene sequences of Mycobacterium tuberculosis and bovis in the aortic tissue of patients with Takayasu's arteritis. BMC Infect Dis 2012; 12:194. [PMID: 22905864 PMCID: PMC3552787 DOI: 10.1186/1471-2334-12-194] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 05/09/2012] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Takayasu's arteritis (TA) is a chronic inflammatory disease affecting the large arteries and their branches; its etiology is still unknown. In individuals suffering from TA, arterial inflammation progresses to stenosis and/or occlusion, leading to organ damage and affecting survival. Relation of TA with Mycobacterium tuberculosis has been known, but there have been only a few systematic studies focusing on this association. The IS6110 sequence identifies the Mycobacterium tuberculosis complex and the HupB establishes the differences between M. tuberculosis and M. bovis. Our objective was to search the presence of IS6110 and HupB genes in aorta of patients with TA. METHODS We analyzed aorta tissues embedded in paraffin from 5760 autopsies obtained from our institution, we divided the selected samples as cases and controls; CASES aortic tissues of individuals with Takayasu's arteritis. Control positive: aortic tissues (with tuberculosis disease confirmed) and control negative with other disease aortic (atherosclerosis). RESULTS Of 181 selected aorta tissues, 119 fulfilled the corresponding criteria for TA, TB or atherosclerosis. Thus 33 corresponded to TA, 33 to tuberculosis (TB) and 53 to atherosclerosis. The mean age was 22 ± 13, 41 ± 19, and 57 ± 10, respectively. IS6110 and HupB sequences were detected in 70% of TA tissues, 82% in tuberculosis, and in 32% with atherosclerosis. Important statistical differences between groups with TA, tuberculosis versus atherosclerosis (p = 0.004 and 0.0001, respectively) were found. CONCLUSION We identified a higher frequency of IS6110 and HupB genes in aortic tissues of TA patients. This data suggests that arterial damage could occur due to previous infection with M. tuberculosis.
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Affiliation(s)
- María Elena Soto
- Department of Physiology, National Institute of Cardiology Ignacio Chavez, Juan Badiano No 1, Colonia Sección XVI, 14080 México DF, Mexico
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Lamrabet O, Drancourt M. Genetic engineering of Mycobacterium tuberculosis: a review. Tuberculosis (Edinb) 2012; 92:365-76. [PMID: 22789498 DOI: 10.1016/j.tube.2012.06.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 06/06/2012] [Indexed: 01/01/2023]
Abstract
Genetic engineering has been used for decades to mutate and delete genes in the Mycobacterium tuberculosis genome with the translational goal of producing attenuated mutants with conserved susceptibility to antituberculous antibiotics. The development of plasmids and mycobacteriophages that can transfer DNA into the M. tuberculosis chromosome has effectively overcome M. tuberculosis slow growth rate and the capsule and mycolic acid wall, which limit DNA uptake. The use of genetic engineering techniques has shed light on many aspects of pathogenesis mechanisms, including cellular growth, mycolic acid biosynthesis, metabolism, drug resistance and virulence. Moreover, such research gave clues to the development of new vaccines or new drugs for routine clinical practice. The use of genetic engineering tools is mainly based on the underlying concept that altering or reducing the M. tuberculosis genome could decrease its virulence. A contrario, recent post-genomic analyses indicated that reduced bacterial genomes are often associated with increased bacterial virulence and that M. tuberculosis acquired genes by lateral genetic exchange during its evolution. Therefore, ancestors utilizing genetic engineering to add genes to the M. tuberculosis genome may lead to new vaccines and the availability of M. tuberculosis isolates with increased susceptibility to antituberculous antibiotics.
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Affiliation(s)
- Otmane Lamrabet
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 6236 IRD 3R198, Méditerranée Infection, FRIDMM, Aix-Marseille Université, Marseille, France.
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Lamrabet O, Merhej V, Pontarotti P, Raoult D, Drancourt M. The genealogic tree of mycobacteria reveals a long-standing sympatric life into free-living protozoa. PLoS One 2012; 7:e34754. [PMID: 22511965 PMCID: PMC3325273 DOI: 10.1371/journal.pone.0034754] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Accepted: 03/08/2012] [Indexed: 02/07/2023] Open
Abstract
Free-living protozoa allow horizontal gene transfer with and between the microorganisms that they host. They host mycobacteria for which the sources of transferred genes remain unknown. Using BLASTp, we searched within the genomes of 15 mycobacteria for homologous genes with 34 amoeba-resistant bacteria and the free-living protozoa Dictyostelium discoideum. Subsequent phylogenetic analysis of these sequences revealed that eight mycobacterial open-reading frames (ORFs) were probably acquired via horizontal transfer from beta- and gamma-Proteobacteria and from Firmicutes, but the transfer histories could not be reliably established in details. One further ORF encoding a pyridine nucleotide disulfide oxidoreductase (pyr-redox) placed non-tuberculous mycobacteria in a clade with Legionella spp., Francisella spp., Coxiella burnetii, the ciliate Tetrahymena thermophila and D. discoideum with a high reliability. Co-culturing Mycobacterium avium and Legionella pneumophila with the amoeba Acanthamoeba polyphaga demonstrated that these two bacteria could live together in amoebae for five days, indicating the biological relevance of intra-amoebal transfer of the pyr-redox gene. In conclusion, the results of this study support the hypothesis that protists can serve as a source and a place for gene transfer in mycobacteria.
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Affiliation(s)
- Otmane Lamrabet
- URMITE CNRS-IRD UMR 6236, IFR48, Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Vicky Merhej
- URMITE CNRS-IRD UMR 6236, IFR48, Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Pierre Pontarotti
- Equipe Evolution Biologique et Modélisation UMR 6632, IRF48, Aix-Marseille Université/CNRS, Marseille, France
| | - Didier Raoult
- URMITE CNRS-IRD UMR 6236, IFR48, Méditerranée Infection, Aix-Marseille Université, Marseille, France
| | - Michel Drancourt
- URMITE CNRS-IRD UMR 6236, IFR48, Méditerranée Infection, Aix-Marseille Université, Marseille, France
- * E-mail:
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McGuire AM, Weiner B, Park ST, Wapinski I, Raman S, Dolganov G, Peterson M, Riley R, Zucker J, Abeel T, White J, Sisk P, Stolte C, Koehrsen M, Yamamoto RT, Iacobelli-Martinez M, Kidd MJ, Maer AM, Schoolnik GK, Regev A, Galagan J. Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis. BMC Genomics 2012; 13:120. [PMID: 22452820 PMCID: PMC3388012 DOI: 10.1186/1471-2164-13-120] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 03/28/2012] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The sequence of the pathogen Mycobacterium tuberculosis (Mtb) strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to understand the evolution of Mtb pathogenesis. We conducted a comparative analysis using 31 genomes from the Tuberculosis Database (TBDB.org), including 8 strains of Mtb and M. bovis, 11 additional Mycobacteria, 4 Corynebacteria, 2 Streptomyces, Rhodococcus jostii RHA1, Nocardia farcinia, Acidothermus cellulolyticus, Rhodobacter sphaeroides, Propionibacterium acnes, and Bifidobacterium longum. RESULTS Our results highlight the functional importance of lipid metabolism and its regulation, and reveal variation between the evolutionary profiles of genes implicated in saturated and unsaturated fatty acid metabolism. It also suggests that DNA repair and molybdopterin cofactors are important in pathogenic Mycobacteria. By analyzing sequence conservation and gene expression data, we identify nearly 400 conserved noncoding regions. These include 37 predicted promoter regulatory motifs, of which 14 correspond to previously validated motifs, as well as 50 potential noncoding RNAs, of which we experimentally confirm the expression of four. CONCLUSIONS Our analysis of protein evolution highlights gene families that are associated with the adaptation of environmental Mycobacteria to obligate pathogenesis. These families include fatty acid metabolism, DNA repair, and molybdopterin biosynthesis. Our analysis reinforces recent findings suggesting that small noncoding RNAs are more common in Mycobacteria than previously expected. Our data provide a foundation for understanding the genome and biology of Mtb in a comparative context, and are available online and through TBDB.org.
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Namouchi A, Didelot X, Schöck U, Gicquel B, Rocha EPC. After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection. Genome Res 2012; 22:721-34. [PMID: 22377718 DOI: 10.1101/gr.129544.111] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Many of the most virulent bacterial pathogens show low genetic diversity and sexual isolation. Accordingly, Mycobacterium tuberculosis, the deadliest human pathogen, is thought to be clonal and evolve by genetic drift. Yet, its genome shows few of the concomitant signs of genome degradation. We analyzed 24 genomes and found an excess of genetic diversity in regions encoding key adaptive functions including the type VII secretion system and the ancient horizontally transferred virulence-related regions. Four different approaches showed evident signs of recombination in M. tuberculosis. Recombination tracts add a high density of polymorphisms, and many are thus predicted to arise from outside the clade. Some of these tracts match Mycobacterium canettii sequences. Recombination introduced an excess of non-synonymous diversity in general and even more in genes expected to be under positive or diversifying selection, e.g., cell wall component genes. Mutations leading to non-synonymous SNPs are effectively purged in MTBC, which shows dominance of purifying selection. MTBC mutation bias toward AT nucleotides is not compensated by biased gene conversion, suggesting the action of natural selection also on synonymous changes. Together, all of these observations point to a strong imprint of recombination and selection in the genome affecting both non-synonymous and synonymous positions. Hence, contrary to some other pathogens and previous proposals concerning M. tuberculosis, this lineage may have come out of its ancestral bottleneck as a very successful pathogen that is rapidly diversifying by the action of mutation, recombination, and natural selection.
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Affiliation(s)
- Amine Namouchi
- Unité de Génétique Mycobactérienne, Institut Pasteur, 75015 Paris, France.
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68
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Skippington E, Ragan MA. Lateral genetic transfer and the construction of genetic exchange communities. FEMS Microbiol Rev 2011; 35:707-35. [DOI: 10.1111/j.1574-6976.2010.00261.x] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
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de Souza GA, Wiker HG. A proteomic view of mycobacteria. Proteomics 2011; 11:3118-27. [PMID: 21726049 DOI: 10.1002/pmic.201100043] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 03/25/2011] [Accepted: 04/19/2011] [Indexed: 01/23/2023]
Abstract
Tuberculosis, the disease caused by Mycobacterium tuberculosis, remains a relevant public health issue. This is due mostly to the coepidemiology with HIV/AIDS, the appearance of multidrug-resistant strains globally, and failure of BCG (bacillus Calmette-Guerin) vaccination to confer complete protection. This bacterium was one of the first to have its genome sequenced, yet over a decade after the release of the genomic information, the characterization of its phylogenetic tree and of different strain variants inside this species revealed that much is still needed to be done for a full understanding of the M. tuberculosis genome and proteome. Current methods using LC-MS/MS and hybrid high-resolution mass spectrometers can identify 2400-2800 proteins of the 4000 predicted genes in M. tuberculosis. In this article, we review relevant details of this bacterium's pathology and immunology, describing articles where proteomics helped the community to tackle some of the organism biology, from understanding strain diversity, cellular structure composition, immunogenicity, and host-pathogen interactions. Finally, we will discuss the challenges yet to be fulfilled in order to better characterize M. tuberculosis by proteomics.
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Affiliation(s)
- Gustavo A de Souza
- The Gade Institute, Section for Microbiology and Immunology, University of Bergen, Bergen, Norway
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Veyrier FJ, Dufort A, Behr MA. The rise and fall of the Mycobacterium tuberculosis genome. Trends Microbiol 2011; 19:156-61. [PMID: 21277778 DOI: 10.1016/j.tim.2010.12.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 12/21/2010] [Accepted: 12/30/2010] [Indexed: 12/17/2022]
Abstract
When studied from the perspective of non-tuberculous mycobacteria (NTM) it is apparent that Mycobacterium tuberculosis has undergone a biphasic evolutionary process involving genome expansion (gene acquisition and duplication) and reductive evolution (deletions). This scheme can instruct descriptive and experimental studies that determine the importance of ancestral events (including horizontal gene transfer) in shaping the present-day pathogen. For example, heterologous complementation in an NTM can test the functional importance of M. tuberculosis-specific genetic insertions. An appreciation of both phases of M. tuberculosis evolution is expected to improve our fundamental understanding of its pathogenicity and facilitate the evaluation of novel diagnostics and vaccines.
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Affiliation(s)
- Frédéric J Veyrier
- Unité des Infections Bactériennes Invasives, Département Infection et Epidémiologie, Pasteur Institute, Paris, France
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Multiple-genome comparison reveals new loci for Mycobacterium species identification. J Clin Microbiol 2010; 49:144-53. [PMID: 21048007 DOI: 10.1128/jcm.00957-10] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To identify loci useful for species identification and to enhance our understanding of the population structure and genetic variability of the genus Mycobacterium, we conducted a multiple-genome comparison of a total of 27 sequenced genomes in the suborder of Corynebacterineae (18 from the Mycobacterium genus, 7 from the Corynebacterium genus, 1 each from the Nocardia and Rhodococcus genera). Our study revealed 26 informative loci for species identification in Mycobacterium. The sequences from these loci were used in a phylogenetic analysis to infer the evolutionary relations of the 18 mycobacterial genomes. Among the loci that we identified, rpoBC, dnaK, and hsp65 were amplified from 29 ATCC reference strains and 17 clinical isolates and sequenced. The phylogenetic trees generated from these loci show similar topologies. The newly identified dnaK locus is more discriminatory and more robust than the widely used hsp65 locus. The length-variable rpoBC locus is the first intergenic locus between two protein-encoding genes being used for mycobacterial species identification. A multilocus sequence analysis system including the rpoBC, dnaK, and hsp65 loci is a robust tool for accurate identification of Mycobacterium species.
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Novel tuberculosis vaccines on the horizon. Curr Opin Immunol 2010; 22:374-84. [DOI: 10.1016/j.coi.2010.04.006] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2010] [Revised: 04/15/2010] [Accepted: 04/15/2010] [Indexed: 01/20/2023]
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Wang G, Zhou F, Olman V, Li F, Xu Y. Prediction of pathogenicity islands in enterohemorrhagic Escherichia coli O157:H7 using genomic barcodes. FEBS Lett 2010; 584:194-8. [PMID: 19941858 DOI: 10.1016/j.febslet.2009.11.067] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Revised: 11/16/2009] [Accepted: 11/19/2009] [Indexed: 12/14/2022]
Abstract
The genome of lethal animal pathogenic bacterium Enterohemorrhagic Escherichia coli (EHEC) O157:H7 is characterized by the presence of multiple pathogenicity islands (PAIs). Computational methods have been developed to identify PAIs based on the distinguishing G+C levels in some PAI versus non-PAI regions. We observed that PAIs can have a very similar G+C level to that of the host chromosome, which may have led to false negative predictions using these methods. We have applied a novel method of genomic barcodes to identify PAIs. Using this technique, we have successfully identified both known and novel PAIs in the genomes of three strains of EHEC O157:H7.
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Affiliation(s)
- Guoqing Wang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602 7229, USA
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Ramage HR, Connolly LE, Cox JS. Comprehensive functional analysis of Mycobacterium tuberculosis toxin-antitoxin systems: implications for pathogenesis, stress responses, and evolution. PLoS Genet 2009; 5:e1000767. [PMID: 20011113 PMCID: PMC2781298 DOI: 10.1371/journal.pgen.1000767] [Citation(s) in RCA: 356] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Accepted: 11/12/2009] [Indexed: 12/16/2022] Open
Abstract
Toxin-antitoxin (TA) systems, stress-responsive genetic elements ubiquitous in microbial genomes, are unusually abundant in the major human pathogen Mycobacterium tuberculosis. Why M. tuberculosis has so many TA systems and what role they play in the unique biology of the pathogen is unknown. To address these questions, we have taken a comprehensive approach to identify and functionally characterize all the TA systems encoded in the M. tuberculosis genome. Here we show that 88 putative TA system candidates are present in M. tuberculosis, considerably more than previously thought. Comparative genomic analysis revealed that the vast majority of these systems are conserved in the M. tuberculosis complex (MTBC), but largely absent from other mycobacteria, including close relatives of M. tuberculosis. We found that many of the M. tuberculosis TA systems are located within discernable genomic islands and were thus likely acquired recently via horizontal gene transfer. We discovered a novel TA system located in the core genome that is conserved across the genus, suggesting that it may fulfill a role common to all mycobacteria. By expressing each of the putative TA systems in M. smegmatis, we demonstrate that 30 encode a functional toxin and its cognate antitoxin. We show that the toxins of the largest family of TA systems, VapBC, act by inhibiting translation via mRNA cleavage. Expression profiling demonstrated that four systems are specifically activated during stresses likely encountered in vivo, including hypoxia and phagocytosis by macrophages. The expansion and maintenance of TA genes in the MTBC, coupled with the finding that a subset is transcriptionally activated by stress, suggests that TA systems are important for M. tuberculosis pathogenesis. Tuberculosis (TB) continues to be a major global health problem, causing 2 million deaths every year. A hallmark of TB pathogenesis is that the bacilli can enter into a slow or non-growing state in response to the host immune system. Because these persistent bacteria are resistant to antibiotic treatment, efforts to eliminate TB from the human population must include therapies to target dormant organisms as they can eventually resume replication to cause active disease. How Mycobacterium tuberculosis, the causative agent of TB, alters its replication dynamics in response to host cues is not understood. Toxin-antitoxin (TA) systems, which may control persistence in other bacteria, are massively expanded in M. tuberculosis, suggesting that they are important for TB pathogenesis. Surprisingly, the vast majority of these numerous TA systems are conserved only in pathogenic mycobacteria, suggesting their acquisition was important in M. tuberculosis evolution. Of the 88 putative TA systems identified, we show that 30 are functional in mycobacteria. A subset of these systems is activated upon exposure to stresses encountered during infection, indicating that specific TA systems are involved in adapting to environmental cues in the host. These genes are promising candidates for the development of novel therapies to target persistent bacteria.
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Affiliation(s)
- Holly R. Ramage
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
- Program in Microbial Pathogenesis and Host Defense, University of California San Francisco, San Francisco, California, United States of America
| | - Lynn E. Connolly
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
- Program in Microbial Pathogenesis and Host Defense, University of California San Francisco, San Francisco, California, United States of America
- Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, California, United States of America
| | - Jeffery S. Cox
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, California, United States of America
- Program in Microbial Pathogenesis and Host Defense, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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