1
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Silva-Pereira TT, Soler-Camargo NC, Guimarães AMS. Diversification of gene content in the Mycobacterium tuberculosis complex is determined by phylogenetic and ecological signatures. Microbiol Spectr 2024; 12:e0228923. [PMID: 38230932 PMCID: PMC10871547 DOI: 10.1128/spectrum.02289-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024] Open
Abstract
We analyzed the pan-genome and gene content modulation of the most diverse genome data set of the Mycobacterium tuberculosis complex (MTBC) gathered to date. The closed pan-genome of the MTBC was characterized by reduced accessory and strain-specific genomes, compatible with its clonal nature. However, significantly fewer gene families were shared between MTBC genomes as their phylogenetic distance increased. This effect was only observed in inter-species comparisons, not within-species, which suggests that species-specific ecological characteristics are associated with changes in gene content. Gene loss, resulting from genomic deletions and pseudogenization, was found to drive the variation in gene content. This gene erosion differed among MTBC species and lineages, even within M. tuberculosis, where L2 showed more gene loss than L4. We also show that phylogenetic proximity is not always a good proxy for gene content relatedness in the MTBC, as the gene repertoire of Mycobacterium africanum L6 deviated from its expected phylogenetic niche conservatism. Gene disruptions of virulence factors, represented by pseudogene annotations, are mostly not conserved, being poor predictors of MTBC ecotypes. Each MTBC ecotype carries its own accessory genome, likely influenced by distinct selective pressures such as host and geography. It is important to investigate how gene loss confer new adaptive traits to MTBC strains; the detected heterogeneous gene loss poses a significant challenge in elucidating genetic factors responsible for the diverse phenotypes observed in the MTBC. By detailing specific gene losses, our study serves as a resource for researchers studying the MTBC phenotypes and their immune evasion strategies.IMPORTANCEIn this study, we analyzed the gene content of different ecotypes of the Mycobacterium tuberculosis complex (MTBC), the pathogens of tuberculosis. We found that changes in their gene content are associated with their ecological features, such as host preference. Gene loss was identified as the primary driver of these changes, which can vary even among different strains of the same ecotype. Our study also revealed that the gene content relatedness of these bacteria does not always mirror their evolutionary relationships. In addition, some genes of virulence can be variably lost among strains of the same MTBC ecotype, likely helping them to evade the immune system. Overall, our study highlights the importance of understanding how gene loss can lead to new adaptations in these bacteria and how different selective pressures may influence their genetic makeup.
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Affiliation(s)
- Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Naila Cristina Soler-Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana Marcia Sá Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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2
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Abstract
The genus Mycobacterium contains several slow-growing human pathogens, including Mycobacterium tuberculosis, Mycobacterium leprae, and Mycobacterium avium. Mycobacterium smegmatis is a nonpathogenic and fast growing species within this genus. In 1990, a mutant of M. smegmatis, designated mc2155, that could be transformed with episomal plasmids was isolated, elevating M. smegmatis to model status as the ideal surrogate for mycobacterial research. Classical bacterial models, such as Escherichia coli, were inadequate for mycobacteria research because they have low genetic conservation, different physiology, and lack the novel envelope structure that distinguishes the Mycobacterium genus. By contrast, M. smegmatis encodes thousands of conserved mycobacterial gene orthologs and has the same cell architecture and physiology. Dissection and characterization of conserved genes, structures, and processes in genetically tractable M. smegmatis mc2155 have since provided previously unattainable insights on these same features in its slow-growing relatives. Notably, tuberculosis (TB) drugs, including the first-line drugs isoniazid and ethambutol, are active against M. smegmatis, but not against E. coli, allowing the identification of their physiological targets. Furthermore, Bedaquiline, the first new TB drug in 40 years, was discovered through an M. smegmatis screen. M. smegmatis has become a model bacterium, not only for M. tuberculosis, but for all other Mycobacterium species and related genera. With a repertoire of bioinformatic and physical resources, including the recently established Mycobacterial Systems Resource, M. smegmatis will continue to accelerate mycobacterial research and advance the field of microbiology.
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3
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Liu Z, Jiang Z, Wu W, Xu X, Ma Y, Guo X, Zhang S, Sun Q. Identification of region of difference and H37Rv-related deletion in Mycobacterium tuberculosis complex by structural variant detection and genome assembly. Front Microbiol 2022; 13:984582. [PMID: 36160240 PMCID: PMC9493256 DOI: 10.3389/fmicb.2022.984582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 08/15/2022] [Indexed: 11/21/2022] Open
Abstract
Mycobacterium tuberculosis complex (MTBC), the main cause of TB in humans and animals, is an extreme example of genetic homogeneity, whereas it is still nevertheless separated into various lineages by numerous typing methods, which differ in phenotype, virulence, geographic distribution, and host preference. The large sequence polymorphism (LSP), incorporating region of difference (RD) and H37Rv-related deletion (RvD), is considered to be a powerful means of constructing phylogenetic relationships within MTBC. Although there have been many studies on LSP already, focusing on the distribution of RDs in MTBC and their impact on MTB phenotypes, a crumb of new lineages or sub-lineages have been excluded and RvDs have received less attention. We, therefore, sampled a dataset of 1,495 strains, containing 113 lineages from the laboratory collection, to screen for RDs and RvDs by structural variant detection and genome assembly, and examined the distribution of RvDs in MTBC, including RvD2, RvD5, and cobF region. Consistent with genealogical delineation by single nucleotide polymorphism (SNP), we identified 125 RDs and 5 RvDs at the species, lineage, or sub-lineage levels. The specificities of RDs and RvDs were further investigated in the remaining 10,218 strains, suggesting that most of them were highly specific to distinct phylogenetic groups, could be used as stable genetic markers in genotyping. More importantly, we identified 34 new lineage or evolutionary branch specific RDs and 2 RvDs, also demonstrated the distribution of known RDs and RvDs in MTBC. This study provides novel details about deletion events that have occurred in distinct phylogenetic groups and may help to understand the genealogical differentiation.
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Affiliation(s)
- Zhuochong Liu
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhonghua Jiang
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Wei Wu
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xinyi Xu
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yudong Ma
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiaomei Guo
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Senlin Zhang
- College of Biomass Science and Engineering, Sichuan University, Chengdu, China
| | - Qun Sun
- Key Laboratory of Bio-Resources and Eco-Environment of the Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- *Correspondence: Qun Sun,
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4
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Surolia R, Antony VB. Pathophysiological Role of Vimentin Intermediate Filaments in Lung Diseases. Front Cell Dev Biol 2022; 10:872759. [PMID: 35573702 PMCID: PMC9096236 DOI: 10.3389/fcell.2022.872759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/13/2022] [Indexed: 11/17/2022] Open
Abstract
Vimentin intermediate filaments, a type III intermediate filament, are among the most widely studied IFs and are found abundantly in mesenchymal cells. Vimentin intermediate filaments localize primarily in the cytoplasm but can also be found on the cell surface and extracellular space. The cytoplasmic vimentin is well-recognized for its role in providing mechanical strength and regulating cell migration, adhesion, and division. The post-translationally modified forms of Vimentin intermediate filaments have several implications in host-pathogen interactions, cancers, and non-malignant lung diseases. This review will analyze the role of vimentin beyond just the epithelial to mesenchymal transition (EMT) marker highlighting its role as a regulator of host-pathogen interactions and signaling pathways for the pathophysiology of various lung diseases. In addition, we will also examine the clinically relevant anti-vimentin compounds and antibodies that could potentially interfere with the pathogenic role of Vimentin intermediate filaments in lung disease.
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5
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Comín J, Otal I, Samper S. In-depth Analysis of IS 6110 Genomic Variability in the Mycobacterium tuberculosis Complex. Front Microbiol 2022; 13:767912. [PMID: 35283840 PMCID: PMC8912993 DOI: 10.3389/fmicb.2022.767912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/04/2022] [Indexed: 11/13/2022] Open
Abstract
The insertion sequence (IS) 6110 is a repetitive mobile element specific for the Mycobacterium tuberculosis complex (MTBC) used for years to diagnose and genotype this pathogen. It contains the overlapping reading frames orfA and orfB that encode a transposase. Its genetic variability is difficult to study because multiple copies are present in the genome. IS6110 is randomly located, nevertheless some preferential locations have been reported, which could be related to the behaviour of the strains. The aim of this work was to determine the intra- and inter-strain genetic conservation of this element in the MTBC. For this purpose, we analysed 158 sequences of IS6110 copies from 55 strains. Eighty-four copies were from 17 strains for which we knew all the locations in their genome. In addition, we studied 74 IS6110 copies in 38 different MTBC strains in which the location was characteristic of different families including Haarlem, LAM, S, and L6 strains. We observed mutation in 13.3% of the copies studied and we found 10 IS6110 variants in 21 copies belonging to 16 strains. The high copy number strains showed 6.2% of their IS6110 copies mutated, in contrast with the 31.1% in the low-copy-number strains. The apparently more ancient copy localised in the DR region was that with more variant copies, probably because this was the most studied location. Notably, all Haarlem and X family strains studied have an IS6110 in Rv0403c, suggesting a common origin for both families. Nevertheless, we detected a variant specific for the X family that would have occurred in this location after the phylogenetic separation. This variant does not prevent transposition although it may occur at a lower frequency, as X strains remain with low copy number (LCN) of IS6110.
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Affiliation(s)
- Jessica Comín
- Unidad de Investigación Traslacional, Hospital Universitario Miguel Servet, Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain.,Fundación IIS Aragón, Zaragoza, Spain
| | - Isabel Otal
- Fundación IIS Aragón, Zaragoza, Spain.,Facultad de Medicina, Universidad de Zaragoza, Zaragoza, Spain.,CIBER de Enfermedades Respiratorias, Madrid, Spain
| | - Sofía Samper
- Unidad de Investigación Traslacional, Hospital Universitario Miguel Servet, Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain.,Fundación IIS Aragón, Zaragoza, Spain.,CIBER de Enfermedades Respiratorias, Madrid, Spain
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6
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Singh S, Nirban R, Dutta T. MTS1338 in Mycobacterium tuberculosis promotes detoxification of reactive oxygen species under oxidative stress. Tuberculosis (Edinb) 2021; 131:102142. [PMID: 34773773 DOI: 10.1016/j.tube.2021.102142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 09/22/2021] [Accepted: 10/31/2021] [Indexed: 11/29/2022]
Abstract
Diverse mechanisms exist in Mycobacterium tuberculosis for adaptation to stresses leading to its persistence in the hostile environment of macrophages. Small RNA (sRNA)-mediated regulatory mechanisms have been scarcely explored in M. tuberculosis. MTS1338, a sRNA present only in pathogenic mycobacteria, was discovered to be highly abundant during infection and significantly contributes to host-pathogen interaction. A variety of stresses have been implicated for its accumulation. Herein, we showed that MTS1338 is an oxidative stress induced sRNA, which promotes the detoxification of reactive oxygen species (ROS) under oxidative stress. Current study identified a new role of MTS1338 in M. tuberculosis under oxidative stress.
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Affiliation(s)
- Saumya Singh
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Reena Nirban
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India; School of Interdisciplinary Research, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India
| | - Tanmay Dutta
- RNA Biology Laboratory, Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India; School of Interdisciplinary Research, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, 110016, India.
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7
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Mori M, Stelitano G, Gelain A, Pini E, Chiarelli LR, Sammartino JC, Poli G, Tuccinardi T, Beretta G, Porta A, Bellinzoni M, Villa S, Meneghetti F. Shedding X-ray Light on the Role of Magnesium in the Activity of Mycobacterium tuberculosis Salicylate Synthase (MbtI) for Drug Design. J Med Chem 2020; 63:7066-7080. [PMID: 32530281 PMCID: PMC8008425 DOI: 10.1021/acs.jmedchem.0c00373] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
![]()
The
Mg2+-dependent Mycobacterium tuberculosis salicylate synthase (MbtI) is a key enzyme involved in the biosynthesis
of siderophores. Because iron is essential for the survival and pathogenicity
of the microorganism, this protein constitutes an attractive target
for antitubercular therapy, also considering the absence of homologous
enzymes in mammals. An extension of the structure–activity
relationships of our furan-based candidates allowed us to disclose
the most potent competitive inhibitor known to date (10, Ki = 4 μM), which also proved
effective on mycobacterial cultures. By structural studies, we characterized
its unexpected Mg2+-independent binding mode. We also investigated
the role of the Mg2+ cofactor in catalysis, analyzing the
first crystal structure of the MbtI–Mg2+–salicylate
ternary complex. Overall, these results pave the way for the development
of novel antituberculars through the rational design of improved MbtI
inhibitors.
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Affiliation(s)
- Matteo Mori
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Giovanni Stelitano
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - Arianna Gelain
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Elena Pini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Laurent R Chiarelli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - José C Sammartino
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via A. Ferrata 9, 27100 Pavia, Italy
| | - Giulio Poli
- Dipartimento di Farmacia, Università di Pisa, via Bonanno Pisano 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Dipartimento di Farmacia, Università di Pisa, via Bonanno Pisano 6, 56126 Pisa, Italy.,Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Giangiacomo Beretta
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, via G. Celoria 2, 20133 Milano, Italy
| | - Alessio Porta
- Dipartimento di Chimica, Università degli Studi di Pavia, via T. Taramelli 12, 27100 Pavia, Italy
| | - Marco Bellinzoni
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS, Université de Paris, F-75015 Paris, France
| | - Stefania Villa
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
| | - Fiorella Meneghetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, via L. Mangiagalli 25, 20133 Milano,Italy
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8
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A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nat Commun 2020; 11:2917. [PMID: 32518235 PMCID: PMC7283319 DOI: 10.1038/s41467-020-16626-6] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/13/2020] [Indexed: 02/03/2023] Open
Abstract
The human- and animal-adapted lineages of the Mycobacterium tuberculosis complex (MTBC) are thought to have expanded from a common progenitor in Africa. However, the molecular events that accompanied this emergence remain largely unknown. Here, we describe two MTBC strains isolated from patients with multidrug resistant tuberculosis, representing an as-yet-unknown lineage, named Lineage 8 (L8), seemingly restricted to the African Great Lakes region. Using genome-based phylogenetic reconstruction, we show that L8 is a sister clade to the known MTBC lineages. Comparison with other complete mycobacterial genomes indicate that the divergence of L8 preceded the loss of the cobF genome region - involved in the cobalamin/vitamin B12 synthesis - and gene interruptions in a subsequent common ancestor shared by all other known MTBC lineages. This discovery further supports an East African origin for the MTBC and provides additional molecular clues on the ancestral genome reduction associated with adaptation to a pathogenic lifestyle. The human- and animal-adapted lineages of the Mycobacterium tuberculosis complex (MTBC) are thought to be evolved from a common progenitor in Africa. Here, the authors identify two MTBC strains isolated from patients with multidrug-resistant tuberculosis, representing an as-yet-unknown lineage further supporting an East African origin for the MTBC.
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9
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An ancestral genomic locus in Mycobacterium tuberculosis clinical isolates from India hints the genetic link with Mycobacterium canettii. Int Microbiol 2020; 23:397-404. [PMID: 31898033 DOI: 10.1007/s10123-019-00113-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 11/06/2019] [Accepted: 12/05/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND Tuberculosis remains a worldwide public health emergency. To better understand M. tuberculosis and to identify genomic variations characteristic to the Indian clinical isolates by a low-cost method, a genomic subtractive hybridization between M. tuberculosis H37Rv and a clinical isolate from South India was performed. RESULTS This revealed a novel 0.4-kb subtractive fragment which was used as a handle to pull out a 4.5-kb genomic region characteristic to the clinical isolate and was absent in H37Rv. On further studies, this 4.5-kb region was found to be present in 91% of the M. tuberculosis clinical isolates screened from Kerala, a state in South India. Interestingly, this novel region has 99% identity (with 100% query coverage) with genomic regions of M. canettii. DISCUSSION The present study hypothesizes that this locus was present in the recent common environmental ancestor of mycobacteria, retained to the maximum extent in M. canettii and ancestral isolates of M. tuberculosis, and later deleted in other modern lineages of M. tuberculosis. Thus, this region may serve as one of the links between the pathogenic mycobacteria and the environmental species. We also propose that the Indian isolates of M. tuberculosis might be closely related to the putative progenitor M. prototuberculosis with respect to this locus. More studies on other genomic loci from different strains of M. tuberculosis are required to establish more links in this direction.
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10
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Fieweger RA, Wilburn KM, VanderVen BC. Comparing the Metabolic Capabilities of Bacteria in the Mycobacterium tuberculosis Complex. Microorganisms 2019; 7:E177. [PMID: 31216777 PMCID: PMC6617402 DOI: 10.3390/microorganisms7060177] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/10/2019] [Accepted: 06/15/2019] [Indexed: 02/06/2023] Open
Abstract
Pathogenic mycobacteria are known for their ability to maintain persistent infections in various mammals. The canonical pathogen in this genus is Mycobacterium tuberculosis and this bacterium is particularly successful at surviving and replicating within macrophages. Here, we will highlight the metabolic processes that M. tuberculosis employs during infection in macrophages and compare these findings with what is understood for other pathogens in the M. tuberculosis complex.
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Affiliation(s)
- Rachael A Fieweger
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA.
| | - Kaley M Wilburn
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA.
| | - Brian C VanderVen
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA.
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11
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Chiarelli LR, Mori M, Beretta G, Gelain A, Pini E, Sammartino JC, Stelitano G, Barlocco D, Costantino L, Lapillo M, Poli G, Caligiuri I, Rizzolio F, Bellinzoni M, Tuccinardi T, Villa S, Meneghetti F. New insight into structure-activity of furan-based salicylate synthase (MbtI) inhibitors as potential antitubercular agents. J Enzyme Inhib Med Chem 2019; 34:823-828. [PMID: 30889995 PMCID: PMC6427685 DOI: 10.1080/14756366.2019.1589462] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Starting from the analysis of the hypothetical binding mode of our previous furan-based hit (I), we successfully achieved our objective to replace the nitro moiety, leading to the disclosure of a new lead exhibiting a strong activity against MbtI. Our best candidate 1 h displayed a Ki of 8.8 µM and its antimycobacterial activity (MIC99 = 250 µM) is conceivably related to mycobactin biosynthesis inhibition. These results support the hypothesis that 5-phenylfuran-2-carboxylic derivatives are a promising class of MbtI inhibitors.
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Affiliation(s)
- Laurent R Chiarelli
- a Department of Biology and Biotechnology "L Spallanzani" , University of Pavia , Pavia , Italy
| | - Matteo Mori
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
| | - Giangiacomo Beretta
- c Department of Environmental Science and Policy , University of Milano , Milano , Italy
| | - Arianna Gelain
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
| | - Elena Pini
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
| | - Josè Camilla Sammartino
- a Department of Biology and Biotechnology "L Spallanzani" , University of Pavia , Pavia , Italy
| | - Giovanni Stelitano
- a Department of Biology and Biotechnology "L Spallanzani" , University of Pavia , Pavia , Italy
| | - Daniela Barlocco
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
| | - Luca Costantino
- d Department of Life Sciences , University of Modena e Reggio Emilia , Modena , Italy
| | | | - Giulio Poli
- e Department of Pharmacy , University of Pisa , Pisa , Italy
| | - Isabella Caligiuri
- f Pathology Unit, Department of Molecular Biology and Translational Research , National Cancer Institute and Center for Molecular Biomedicine , Aviano , Italy
| | - Flavio Rizzolio
- f Pathology Unit, Department of Molecular Biology and Translational Research , National Cancer Institute and Center for Molecular Biomedicine , Aviano , Italy.,g Department of Molecular Science and Nanosystems , Ca' Foscari University of Venezia , Venezia-Mestre , Italy
| | | | | | - Stefania Villa
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
| | - Fiorella Meneghetti
- b Department of Pharmaceutical Sciences , University of Milano , Milano , Italy
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12
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Characterisation of genes differentially expressed in macrophages by virulent and attenuated Mycobacterium tuberculosis through RNA-Seq analysis. Sci Rep 2019; 9:4027. [PMID: 30858471 PMCID: PMC6411972 DOI: 10.1038/s41598-019-40814-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 02/21/2019] [Indexed: 11/09/2022] Open
Abstract
Tuberculosis (TB) remains a global healthcare issue. Understanding the host-pathogen interactions in TB is vital to develop strategies and therapeutic tools for the control of Mycobacterium tuberculosis (Mtb). In this study, transcriptome analyses of macrophages infected with either the virulent Mtb strain H37Rv (Rv) or the avirulent Mtb strain H37Ra (Ra) were carried out and 750 differentially expressed genes (DEGs) were identified. As expected, the DEGs were mainly involved in the induction of innate immune responses against mycobacterial infections. Among the DEGs, solute carrier family 7 member 2 (Slc7a2) was more strongly expressed in Ra-infected macrophages. Induction of SLC7A2 was important for macrophages to control the intracellular survival of Mtb. Our results imply that SLC7A2 plays an important role in macrophages during Mtb infection. Our findings could prove useful for the development of new therapeutic strategies to control TB infection.
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13
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Bespyatykh J, Smolyakov A, Guliaev A, Shitikov E, Arapidi G, Butenko I, Dogonadze M, Manicheva O, Ilina E, Zgoda V, Govorun V. Proteogenomic analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster strains. J Proteomics 2019; 192:18-26. [DOI: 10.1016/j.jprot.2018.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 10/28/2022]
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14
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Pinto SM, Verma R, Advani J, Chatterjee O, Patil AH, Kapoor S, Subbannayya Y, Raja R, Gandotra S, Prasad TSK. Integrated Multi-Omic Analysis of Mycobacterium tuberculosis H37Ra Redefines Virulence Attributes. Front Microbiol 2018; 9:1314. [PMID: 29971057 PMCID: PMC6018540 DOI: 10.3389/fmicb.2018.01314] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 05/30/2018] [Indexed: 12/18/2022] Open
Abstract
H37Ra is a virulence attenuated strain of Mycobacterium tuberculosis widely employed as a model to investigate virulence mechanisms. Comparative high-throughput studies have earlier correlated its avirulence to the presence of specific mutations or absence of certain proteins. However, a recent sequencing study of H37Ra, has disproved several genomic differences earlier reported to be associated with virulence. This warrants further investigations on the H37Ra proteome as well. In this study, we carried out an integrated analysis of the genome, transcriptome, and proteome of H37Ra. In addition to confirming single nucleotide variations (SNVs) and insertion-deletions that were reported earlier, our study provides novel insights into the mutation spectrum in the promoter regions of 7 genes. We also provide transcriptional and proteomic evidence for 3,900 genes representing ~80% of the total predicted gene count including 408 proteins that have not been identified previously. We identified 9 genes whose coding potential was hitherto reported to be absent in H37Ra. These include 2 putative virulence factors belonging to ESAT-6 like family of proteins. Furthermore, proteogenomic analysis enabled us to identify 63 novel proteins coding genes and correct 25 existing gene models in H37Ra genome. A majority of these were found to be conserved in the virulent strain H37Rv as well as in other mycobacterial species suggesting that the differences in the virulent and avirulent strains of M. tuberculosis are not entirely dependent on the expression of certain proteins or their absence but may possibly be ascertained to functional changes.
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Affiliation(s)
- Sneha M Pinto
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
| | - Renu Verma
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Oishi Chatterjee
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India.,Institute of Bioinformatics, International Technology Park, Bangalore, India.,School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Arun H Patil
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India.,Institute of Bioinformatics, International Technology Park, Bangalore, India.,School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Saketh Kapoor
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
| | - Yashwanth Subbannayya
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India
| | - Remya Raja
- Institute of Bioinformatics, International Technology Park, Bangalore, India
| | - Sheetal Gandotra
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore, India.,Institute of Bioinformatics, International Technology Park, Bangalore, India
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15
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Chiarelli LR, Mori M, Barlocco D, Beretta G, Gelain A, Pini E, Porcino M, Mori G, Stelitano G, Costantino L, Lapillo M, Bonanni D, Poli G, Tuccinardi T, Villa S, Meneghetti F. Discovery and development of novel salicylate synthase (MbtI) furanic inhibitors as antitubercular agents. Eur J Med Chem 2018; 155:754-763. [PMID: 29940465 DOI: 10.1016/j.ejmech.2018.06.033] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/05/2018] [Accepted: 06/13/2018] [Indexed: 01/10/2023]
Abstract
We report on the virtual screening, synthesis, and biological evaluation of new furan derivatives targeting Mycobacterium tuberculosis salicylate synthase (MbtI). A receptor-based virtual screening procedure was applied to screen the Enamine database, identifying two compounds, I and III, endowed with a good enzyme inhibitory activity. Considering the most active compound I as starting point for the development of novel MbtI inhibitors, we obtained new derivatives based on the furan scaffold. Among the SAR performed on this class, compound 1a emerged as the most potent MbtI inhibitor reported to date (Ki = 5.3 μM). Moreover, compound 1a showed a promising antimycobacterial activity (MIC99 = 156 μM), which is conceivably related to mycobactin biosynthesis inhibition.
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Affiliation(s)
- Laurent R Chiarelli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Matteo Mori
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Daniela Barlocco
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Giangiacomo Beretta
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy
| | - Arianna Gelain
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Elena Pini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Marianna Porcino
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
| | - Giorgia Mori
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Giovanni Stelitano
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università degli Studi di Pavia, via Ferrata 9, 27100, Pavia, Italy
| | - Luca Costantino
- Dipartimento Scienze della Vita, Università degli Studi di Modena e Reggio Emilia, via Campi 103, 41121, Modena, Italy
| | - Margherita Lapillo
- Dipartimento di Farmacia, Università di Pisa, via Bonanno 6, 56126, Pisa, Italy
| | - Davide Bonanni
- Dipartimento di Farmacia, Università di Pisa, via Bonanno 6, 56126, Pisa, Italy
| | - Giulio Poli
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università di Siena, via A. Moro 2, 53100, Siena, Italy
| | - Tiziano Tuccinardi
- Dipartimento di Farmacia, Università di Pisa, via Bonanno 6, 56126, Pisa, Italy.
| | - Stefania Villa
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy.
| | - Fiorella Meneghetti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via L. Mangiagalli 25, 20133, Milano, Italy
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16
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Horizontal acquisition of a hypoxia-responsive molybdenum cofactor biosynthesis pathway contributed to Mycobacterium tuberculosis pathoadaptation. PLoS Pathog 2017; 13:e1006752. [PMID: 29176894 PMCID: PMC5720804 DOI: 10.1371/journal.ppat.1006752] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 12/07/2017] [Accepted: 11/13/2017] [Indexed: 12/16/2022] Open
Abstract
The unique ability of the tuberculosis (TB) bacillus, Mycobacterium tuberculosis, to persist for long periods of time in lung hypoxic lesions chiefly contributes to the global burden of latent TB. We and others previously reported that the M. tuberculosis ancestor underwent massive episodes of horizontal gene transfer (HGT), mostly from environmental species. Here, we sought to explore whether such ancient HGT played a part in M. tuberculosis evolution towards pathogenicity. We were interested by a HGT-acquired M. tuberculosis-specific gene set, namely moaA1-D1, which is involved in the biosynthesis of the molybdenum cofactor. Horizontal acquisition of this gene set was striking because homologues of these moa genes are present all across the Mycobacterium genus, including in M. tuberculosis. Here, we discovered that, unlike their paralogues, the moaA1-D1 genes are strongly induced under hypoxia. In vitro, a M. tuberculosis moaA1-D1-null mutant has an impaired ability to respire nitrate, to enter dormancy and to survive in oxygen-limiting conditions. Conversely, heterologous expression of moaA1-D1 in the phylogenetically closest non-TB mycobacterium, Mycobacterium kansasii, which lacks these genes, improves its capacity to respire nitrate and grants it with a marked ability to survive oxygen depletion. In vivo, the M. tuberculosis moaA1-D1-null mutant shows impaired survival in hypoxic granulomas in C3HeB/FeJ mice, but not in normoxic lesions in C57BL/6 animals. Collectively, our results identify a novel pathway required for M. tuberculosis resistance to host-imposed stress, namely hypoxia, and provide evidence that ancient HGT bolstered M. tuberculosis evolution from an environmental species towards a pervasive human-adapted pathogen. Mycobacterium tuberculosis, the etiological agent of tuberculosis (TB), can persist for years and even decades in the lungs of its human host. Here we report that a unique M. tuberculosis gene cluster involved in the synthesis of the molybdenum cofactor, a cofactor for several oxidoreductases including the nitrate reductase, allows this major pathogen to respire nitrate and to persist in a dormant state under hypoxia, a stress condition encountered in lung TB lesions. Strikingly the M. tuberculosis ancestor, which most likely was an environmental harmless bacterium, acquired this gene cluster, together with its hypoxia-responsive transcriptional regulator, horizontally from neighboring bacteria. Our results uncover a key step in M. tuberculosis evolution towards pathogenicity.
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17
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O'Toole RF, Gautam SS. Limitations of the Mycobacterium tuberculosis reference genome H37Rv in the detection of virulence-related loci. Genomics 2017; 109:471-474. [DOI: 10.1016/j.ygeno.2017.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 07/17/2017] [Accepted: 07/18/2017] [Indexed: 10/19/2022]
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18
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Abstract
Tuberculosis (TB) remains the most deadly bacterial infectious disease worldwide. Its treatment and control are threatened by increasing numbers of multidrug-resistant (MDR) or nearly untreatable extensively drug-resistant (XDR) strains. New concepts are therefore urgently needed to understand the factors driving the TB epidemics and the spread of different strain populations, especially in association with drug resistance. Classical genotyping and, more recently, whole-genome sequencing (WGS) revealed that the world population of tubercle bacilli is more diverse than previously thought. Several major phylogenetic lineages can be distinguished, which are associated with their sympatric host population. Distinct clonal (sub)populations can even coexist within infected patients. WGS is now used as the ultimate approach for differentiating clinical isolates and for linking phenotypic to genomic variation from lineage to strain levels. Multiple lines of evidence indicate that the genetic diversity of TB strains translates into pathobiological consequences, and key molecular mechanisms probably involved in differential pathoadaptation of some main lineages have recently been identified. Evidence also accumulates on molecular mechanisms putatively fostering the emergence and rapid expansion of particular MDR and XDR strain groups in some world regions. However, further integrative studies will be needed for complete elucidation of the mechanisms that allow the pathogen to infect its host, acquire multidrug resistance, and transmit so efficiently. Such knowledge will be key for the development of the most effective new diagnostics, drugs, and vaccination strategies.
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19
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Ru H, Liu X, Lin C, Yang J, Chen F, Sun R, Zhang L, Liu J. The Impact of Genome Region of Difference 4 (RD4) on Mycobacterial Virulence and BCG Efficacy. Front Cell Infect Microbiol 2017. [PMID: 28642843 PMCID: PMC5462905 DOI: 10.3389/fcimb.2017.00239] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Comparative genome analyses have revealed a number of regions of difference (RD) among mycobacterial species. The functional consequences of most of these genome variations have not been studied. RD4, which encompasses Rv1506c-Rv1516c of Mycobacterium tuberculosis (M. tb) H37Rv, is absent in the closely related Mycobacterium bovis and M. bovis Bacille Calmette-Guérin (BCG). On the other hand, we previously found that Mycobacterium marinum has an extended RD4 which includes a number of genes involved in the biosynthesis of lipooligosaccharides (LOSs). As such, there appears to be a gradual decay of RD4 in mycobacterial genomes in the order of M. marinum, M. tb, and M. bovis (including BCG). To understand the potential effect of RD4 on mycobacterial virulence, in this study, we cloned the entire (Rv1501-1516c) and partial (Rv1501-1508c) RD4 into an integrating vector. These constructs were introduced to M. bovis BCG and M. marinum and the virulence of the RD4 knock-in strains were evaluated in the SCID mice and zebrafish infection models, respectively. BCG containing the entire RD4 exhibited similar levels of virulence to the parental strain but BCG containing partial RD4 (Rv1501-Rv1508c) was more attenuated. Similarly, zebrafish infection experiments showed that addition of partial RD4 also appeared to attenuate the virulence of M. marinum. However, M. marinum containing entire RD4 was more virulent than the wild type strain. Interestingly, BCG strains containing the entire or partial RD4 exhibited better protection of zebrafish against M. marinum challenge than the parental BCG. Taken together, our data suggest that RD4 plays a role in mycobacterial virulence and that RD4 knock-in BCG strains confer improved protection. Our study has provided new insights into the biological function of RD4 and evolution of mycobacterial genomes.
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Affiliation(s)
- Huanwei Ru
- State Key Laboratory of Genetic Engineering, School of Life Science, Institute of Genetics, Fudan UniversityShanghai, China
| | - Xiaojia Liu
- State Key Laboratory of Genetic Engineering, School of Life Science, Institute of Genetics, Fudan UniversityShanghai, China
| | - Chen Lin
- State Key Laboratory of Genetic Engineering, School of Life Science, Institute of Genetics, Fudan UniversityShanghai, China
| | - Jingyan Yang
- State Key Laboratory of Genetic Engineering, School of Life Science, Institute of Genetics, Fudan UniversityShanghai, China
| | - Fuzeng Chen
- State Key Laboratory of Genetic Engineering, School of Life Science, Institute of Genetics, Fudan UniversityShanghai, China
| | - Ruifeng Sun
- State Key Laboratory of Genetic Engineering, School of Life Science, Institute of Genetics, Fudan UniversityShanghai, China
| | - Lu Zhang
- State Key Laboratory of Genetic Engineering, School of Life Science, Institute of Genetics, Fudan UniversityShanghai, China.,Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Fudan UniversityShanghai, China.,Shanghai Engineering Research Center of Industrial MicroorganismsShanghai, China
| | - Jun Liu
- State Key Laboratory of Genetic Engineering, School of Life Science, Institute of Genetics, Fudan UniversityShanghai, China.,Department of Molecular Genetics, University of TorontoToronto, ON, Canada
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20
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The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:43-78. [PMID: 29116629 DOI: 10.1007/978-3-319-64371-7_3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) is a contagious disease with a complex epidemiology. Therefore, molecular typing (genotyping) of Mycobacterium tuberculosis complex (MTBC) strains is of primary importance to effectively guide outbreak investigations, define transmission dynamics and assist global epidemiological surveillance of the disease. Large-scale genotyping is also needed to get better insights into the biological diversity and the evolution of the pathogen. Thanks to its shorter turnaround and simple numerical nomenclature system, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing, based on 24 standardized plus 4 hypervariable loci, optionally combined with spoligotyping, has replaced IS6110 DNA fingerprinting over the last decade as a gold standard among classical strain typing methods for many applications. With the continuous progress and decreasing costs of next-generation sequencing (NGS) technologies, typing based on whole genome sequencing (WGS) is now increasingly performed for near complete exploitation of the available genetic information. However, some important challenges remain such as the lack of standardization of WGS analysis pipelines, the need of databases for sharing WGS data at a global level, and a better understanding of the relevant genomic distances for defining clusters of recent TB transmission in different epidemiological contexts. This chapter provides an overview of the evolution of genotyping methods over the last three decades, which culminated with the development of WGS-based methods. It addresses the relative advantages and limitations of these techniques, indicates current challenges and potential directions for facilitating standardization of WGS-based typing, and provides suggestions on what method to use depending on the specific research question.
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21
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Transposition mechanism, molecular characterization and evolution of IS6110, the specific evolutionary marker of Mycobacterium tuberculosis complex. Mol Biol Rep 2016; 44:25-34. [DOI: 10.1007/s11033-016-4084-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 09/16/2016] [Indexed: 10/20/2022]
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22
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Slama N, Jamet S, Frigui W, Pawlik A, Bottai D, Laval F, Constant P, Lemassu A, Cam K, Daffé M, Brosch R, Eynard N, Quémard A. The changes in mycolic acid structures caused byhadCmutation have a dramatic effect on the virulence ofMycobacterium tuberculosis. Mol Microbiol 2015; 99:794-807. [DOI: 10.1111/mmi.13266] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Nawel Slama
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
- Institut de Pharmacologie et de Biologie Structurale; Université de Toulouse; Université Paul Sabatier; Toulouse France
| | - Stevie Jamet
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
- Institut de Pharmacologie et de Biologie Structurale; Université de Toulouse; Université Paul Sabatier; Toulouse France
| | - Wafa Frigui
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics; Paris France
| | - Alexandre Pawlik
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics; Paris France
| | - Daria Bottai
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics; Paris France
| | - Françoise Laval
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
- Institut de Pharmacologie et de Biologie Structurale; Université de Toulouse; Université Paul Sabatier; Toulouse France
| | - Patricia Constant
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
- Institut de Pharmacologie et de Biologie Structurale; Université de Toulouse; Université Paul Sabatier; Toulouse France
| | - Anne Lemassu
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
- Institut de Pharmacologie et de Biologie Structurale; Université de Toulouse; Université Paul Sabatier; Toulouse France
| | - Kaymeuang Cam
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
- Institut de Pharmacologie et de Biologie Structurale; Université de Toulouse; Université Paul Sabatier; Toulouse France
| | - Mamadou Daffé
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
- Institut de Pharmacologie et de Biologie Structurale; Université de Toulouse; Université Paul Sabatier; Toulouse France
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics; Paris France
| | - Nathalie Eynard
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
| | - Annaïk Quémard
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
- Institut de Pharmacologie et de Biologie Structurale; Université de Toulouse; Université Paul Sabatier; Toulouse France
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23
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Revisiting the role of phospholipases C in virulence and the lifecycle of Mycobacterium tuberculosis. Sci Rep 2015; 5:16918. [PMID: 26603639 PMCID: PMC4658479 DOI: 10.1038/srep16918] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/22/2015] [Indexed: 12/02/2022] Open
Abstract
Mycobacterium tuberculosis, the agent of human tuberculosis has developed
different virulence mechanisms and virulence-associated tools during its evolution
to survive and multiply inside the host. Based on previous reports and by analogy
with other bacteria, phospholipases C (PLC) of M. tuberculosis were thought
to be among these tools. To get deeper insights into the function of PLCs, we
investigated their putative involvement in the intracellular lifestyle of M.
tuberculosis, with emphasis on phagosomal rupture and virulence, thereby
re-visiting a research theme of longstanding interest. Through the construction and
use of an M. tuberculosis H37Rv PLC-null mutant (ΔPLC) and
control strains, we found that PLCs of M. tuberculosis were not required for
induction of phagosomal rupture and only showed marginal, if any, impact on
virulence of M. tuberculosis in the cellular and mouse infection models used
in this study. In contrast, we found that PLC-encoding genes were strongly
upregulated under phosphate starvation and that PLC-proficient M.
tuberculosis strains survived better than ΔPLC mutants under
conditions where phosphatidylcholine served as sole phosphate source, opening new
perspectives for studies on the role of PLCs in the lifecycle of M.
tuberculosis.
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24
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RD-1 encoded EspJ protein gets phosphorylated prior to affect the growth and intracellular survival of mycobacteria. Sci Rep 2015; 5:12717. [PMID: 26228622 PMCID: PMC4521147 DOI: 10.1038/srep12717] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 07/02/2015] [Indexed: 01/12/2023] Open
Abstract
Mycobacterium tuberculosis (MTB) synchronizes a number of processes and controls a series of events to subvert host defense mechanisms for the sake of residing inside macrophages. Besides these, MTB also possesses a wide range of signal enzyme systems, including eleven serine threonine protein kinases (STPKs). The present study describes STPK modulated modification in one of the hypothetical proteins of the RD1 region; EspJ (ESX-1 secretion associated protein), which is predicted to be involved in virulence of MTB. We have employed knock-out MTB, and M. bovis BCG as a surrogate strain to elaborate the consequence of the phosphorylation of EspJ. The molecular and mass spectrometric analyses in this study, confirmed EspJ as one of the substrates of STPKs. The ectopic expression of phosphoablative mutants of espJ in M. bovis BCG also articulated the effect of phosphorylation on the growth and in survival of mycobacteria. Importantly, the level of phosphorylation of EspJ also differed between pathogenic H37 Rv (Rv) and non pathogenic H37 Ra (Ra) strains of MTB. This further suggested that to a certain extent, the STPKs mediated phosphorylation may be accountable, in determining the growth and in intra-cellular survival of mycobacteria.
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25
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Thabet S, Namouchi A, Mardassi H. Evolutionary Trends of the Transposase-Encoding Open Reading Frames A and B (orfA and orfB) of the Mycobacterial IS6110 Insertion Sequence. PLoS One 2015; 10:e0130161. [PMID: 26087177 PMCID: PMC4473070 DOI: 10.1371/journal.pone.0130161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 05/17/2015] [Indexed: 12/25/2022] Open
Abstract
Background The IS6110 insertion sequence, a member of the IS3 family of insertion sequences, was found to be specific to the Mycobacterium tuberculosis complex (MTBC). Although IS6110 has been extensively characterized as a transposable genetic marker, the evolutionary history of its own transposase-encoding sequence has not, to the best of our knowledge, been investigated. Methodology/Principal Findings Here we explored the evolution of the IS6110 sequence by analysing the genetic variability and the selective forces acting on its transposase-encoding open reading frames (ORFs) A and B (orfA and orfB). For this purpose, we used a strain collection consisting of smooth tubercle bacilli (STB), an early branching lineage of the MTBC, and present-day M. tuberculosis strains representing the full breadth of genetic diversity in Tunisia. In each ORF, we found a major haplotype that dominated over a flat distribution of rare descendent haplotypes, consisting mainly of single- and double-nucleotide variant singletons. The predominant haplotypes consisted of both ancestral and present-day strains, suggesting that IS6110 acquisition predated the emergence of the MTBC. There was no evidence of recombination and both ORFs were subjected to strict purifying selection, as demonstrated by their dN/dS ratios (0.29 and 0.51, respectively), as well as their significantly negative Tajima’s D statistics. Strikingly, the purifying selection acting on orfA proved much more stringent, suggesting its critical role in regulating the transpositional process. Maximum likelihood analyses further excluded any possibility of positive selection acting on single amino acid residues. Conclusions/Significance Taken together our data fit with an evolutionary scenario according to which the observed variability pattern of the IS6110 transposase-encoding ORFs is generated mainly through random point mutations that accrued on a functionally optimal IS6110 copy, whose acquisition predated the emergence of the MTBC complex. Background selection acting against deleterious mutations led to an excess of low-frequency variants.
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Affiliation(s)
- Sara Thabet
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development; Institut Pasteur de Tunis, Tunis, Tunisia
| | - Amine Namouchi
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development; Institut Pasteur de Tunis, Tunis, Tunisia
| | - Helmi Mardassi
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development; Institut Pasteur de Tunis, Tunis, Tunisia
- * E-mail:
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26
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Desikan S, Narayanan S. Genetic markers, genotyping methods & next generation sequencing in Mycobacterium tuberculosis. Indian J Med Res 2015; 141:761-74. [PMID: 26205019 PMCID: PMC4525401 DOI: 10.4103/0971-5916.160695] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Indexed: 11/26/2022] Open
Abstract
Molecular epidemiology (ME) is one of the main areas in tuberculosis research which is widely used to study the transmission epidemics and outbreaks of tubercle bacilli. It exploits the presence of various polymorphisms in the genome of the bacteria that can be widely used as genetic markers. Many DNA typing methods apply these genetic markers to differentiate various strains and to study the evolutionary relationships between them. The three widely used genotyping tools to differentiate Mycobacterium tuberculosis strains are IS6110 restriction fragment length polymorphism (RFLP), spacer oligotyping (Spoligotyping), and mycobacterial interspersed repeat units - variable number of tandem repeats (MIRU-VNTR). A new prospect towards ME was introduced with the development of whole genome sequencing (WGS) and the next generation sequencing (NGS) methods, where the entire genome is sequenced that not only helps in pointing out minute differences between the various sequences but also saves time and the cost. NGS is also found to be useful in identifying single nucleotide polymorphisms (SNPs), comparative genomics and also various aspects about transmission dynamics. These techniques enable the identification of mycobacterial strains and also facilitate the study of their phylogenetic and evolutionary traits.
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Affiliation(s)
- Srinidhi Desikan
- Department of Immunology, National Institute of Research in Tuberculosis (ICMR), Chennai, India
| | - Sujatha Narayanan
- Department of Immunology, National Institute of Research in Tuberculosis (ICMR), Chennai, India
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Pouseele H, Supply P. Accurate Whole-Genome Sequencing-Based Epidemiological Surveillance of Mycobacterium Tuberculosis. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Dunn EA, Roxburgh M, Larsen L, Smith RAJ, McLellan AD, Heikal A, Murphy MP, Cook GM. Incorporation of triphenylphosphonium functionality improves the inhibitory properties of phenothiazine derivatives in Mycobacterium tuberculosis. Bioorg Med Chem 2014; 22:5320-8. [PMID: 25150092 DOI: 10.1016/j.bmc.2014.07.050] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 07/21/2014] [Accepted: 07/30/2014] [Indexed: 10/24/2022]
Abstract
Tuberculosis (TB) is a difficult to treat disease caused by the bacterium Mycobacterium tuberculosis. The need for improved therapies is required to kill different M. tuberculosis populations present during infection and to kill drug resistant strains. Protein complexes associated with energy generation, required for the survival of all M. tuberculosis populations, have shown promise as targets for novel therapies (e.g., phenothiazines that target type II NADH dehydrogenase (NDH-2) in the electron transport chain). However, the low efficacy of these compounds and their off-target effects has made the development of phenothiazines as a therapeutic agent for TB limited. This study reports that a series of alkyltriphenylphosphonium (alkylTPP) cations, a known intracellular delivery functionality, improves the localization and effective concentration of phenothiazines at the mycobacterial membrane. AlkylTPP cations were shown to accumulate at biological membranes in a range of bacteria and lipophilicity was revealed as an important feature of the structure-function relationship. Incorporation of the alkylTPP cationic function significantly increased the concentration and potency of a series of phenothiazine derivatives at the mycobacterial membrane (the site of NDH-2), where the lead compound 3a showed inhibition of M. tuberculosis growth at 0.5μg/mL. Compound 3a was shown to act in a similar manner to that previously published for other active phenothiazines by targeting energetic processes (i.e., NADH oxidation and oxygen consumption), occurring in the mycobacterial membrane. This shows the enormous potential of alkylTPP cations to improve the delivery and therefore efficacy of bioactive agents targeting oxidative phosphorylation in the mycobacterial membrane.
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Affiliation(s)
- Elyse A Dunn
- Department of Microbiology & Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Marina Roxburgh
- Department of Chemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Lesley Larsen
- Department of Chemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Robin A J Smith
- Department of Chemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Alexander D McLellan
- Department of Microbiology & Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Adam Heikal
- Department of Microbiology & Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Michael P Murphy
- MRC Mitochondrial Biology Unit, Hills Road, Cambridge CB2 0XY, UK
| | - Gregory M Cook
- Department of Microbiology & Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand.
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Sales ML, Fonseca AA, Sales EB, Cottorello ACP, Issa MA, Hodon MA, Soares Filho PM, Ramalho AK, Silva MR, Lage AP, Heinemann MB. Evaluation of molecular markers for the diagnosis of Mycobacterium bovis. Folia Microbiol (Praha) 2014; 59:433-8. [PMID: 24744007 DOI: 10.1007/s12223-014-0317-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 04/08/2014] [Indexed: 11/24/2022]
Abstract
Mycobacterium tuberculosis complex (MTC) comprises a group of bacteria that have a high degree of genetic similarity. Two species in this group, Mycobacterium tuberculosis and Mycobacterium bovis, are the main cause of human and bovine tuberculosis, respectively. M. bovis has a broader host range that includes humans; thus, the differentiation of mycobacterium is of great importance for epidemiological and public health considerations and to optimize treatment. The current study aimed to evaluate primers and molecular markers described in the literature to differentiate M. bovis and M. tuberculosis by PCR. Primers JB21/22, frequently cited in scientific literature, presented in our study the highest number of errors to identify M. bovis or M. tuberculosis (73%) and primers Mb.400, designed to flank region of difference 4 (RD4), were considered the most efficient (detected all M. bovis tested and did not detect any M. tuberculosis tested). Although also designed to flank RD4, primers Mb.115 misidentified eight samples due to primer design problems. The results showed that RD4 is the ideal region to differentiate M. bovis from other bacteria classified in MTC, but primer design should be considered carefully.
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Shitikov EA, Bespyatykh JA, Ischenko DS, Alexeev DG, Karpova IY, Kostryukova ES, Isaeva YD, Nosova EY, Mokrousov IV, Vyazovaya AA, Narvskaya OV, Vishnevsky BI, Otten TF, Zhuravlev VY, Yablonsky PK, Ilina EN, Govorun VM. Unusual large-scale chromosomal rearrangements in Mycobacterium tuberculosis Beijing B0/W148 cluster isolates. PLoS One 2014; 9:e84971. [PMID: 24416324 PMCID: PMC3885621 DOI: 10.1371/journal.pone.0084971] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 11/28/2013] [Indexed: 11/18/2022] Open
Abstract
The Mycobacterium tuberculosis (MTB) Beijing family isolates are geographically widespread, and there are examples of Beijing isolates that are hypervirulent and associated with drug resistance. One-fourth of Beijing genotype isolates found in Russia belong to the B0/W148 group. The aim of the present study was to investigate features of these endemic strains on a genomic level. Four Russian clinical isolates of this group were sequenced, and the data obtained was compared with published sequences of various MTB strain genomes, including genome of strain W-148 of the same B0/W148 group. The comparison of the W-148 and H37Rv genomes revealed two independent inversions of large segments of the chromosome. The same inversions were found in one of the studied strains after deep sequencing using both the fragment and mate-paired libraries. Additionally, inversions were confirmed by RFLP hybridization analysis. The discovered rearrangements were verified by PCR in all four newly sequenced strains in the study and in four additional strains of the same Beijing B0/W148 group. The other 32 MTB strains from different phylogenetic lineages were tested and revealed no inversions. We suggest that the initial largest inversion changed the orientation of the three megabase (Mb) segment of the chromosome, and the second one occurred in the previously inverted region and partly restored the orientation of the 2.1 Mb inner segment of the region. This is another remarkable example of genomic rearrangements in the MTB in addition to the recently published of large-scale duplications. The described cases suggest that large-scale genomic rearrangements in the currently circulating MTB isolates may occur more frequently than previously considered, and we hope that further studies will help to determine the exact mechanism of such events.
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MESH Headings
- Antitubercular Agents/therapeutic use
- China/epidemiology
- Chromosome Inversion
- Chromosome Mapping
- Chromosomes, Bacterial
- DNA, Bacterial/classification
- DNA, Bacterial/genetics
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Genome, Bacterial
- High-Throughput Nucleotide Sequencing
- Humans
- Mycobacterium tuberculosis/classification
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Phylogeny
- Russia/epidemiology
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/epidemiology
- Tuberculosis, Pulmonary/microbiology
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Affiliation(s)
- Egor A. Shitikov
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
- * E-mail:
| | - Julia A. Bespyatykh
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
| | - Dmitry S. Ischenko
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Dmitry G. Alexeev
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Irina Y. Karpova
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
| | | | - Yulia D. Isaeva
- Moscow Scientific-Practical Center of Treatment of Tuberculosis of Moscow Healthcare, Moscow, Russian Federation
| | - Elena Y. Nosova
- Moscow Scientific-Practical Center of Treatment of Tuberculosis of Moscow Healthcare, Moscow, Russian Federation
| | - Igor V. Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Anna A. Vyazovaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Olga V. Narvskaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Boris I. Vishnevsky
- Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
| | - Tatiana F. Otten
- Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
| | - Valery Y. Zhuravlev
- Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
| | - Peter K. Yablonsky
- Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
| | - Elena N. Ilina
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
| | - Vadim M. Govorun
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
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Global study of IS6110 in a successful Mycobacterium tuberculosis strain: clues for deciphering its behavior and for its rapid detection. J Clin Microbiol 2013; 51:3631-7. [PMID: 23985924 DOI: 10.1128/jcm.00970-13] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Mycobacterium tuberculosis insertion sequence IS6110, besides being a very useful tool in molecular epidemiology, seems to have an impact on the biology of bacilli. In the present work, we mapped the 12 points of insertion of IS6110 in the genome of a successful strain named M. tuberculosis Zaragoza (which has been referred to as the MTZ strain). This strain, belonging to principal genetic group 3, caused a large unsuspected tuberculosis outbreak involving 85 patients in Zaragoza, Spain, in 2001 to 2004. The mapping of the points of insertion of IS6110 in the genome of the Zaragoza strain offers clues for a better understanding of the adaptability and virulence of M. tuberculosis. Surprisingly, the presence of one copy of IS6110 was found in Rv2286c, as was recently described for a successful Beijing sublineage. As a result of this analysis, a rapid method for detecting this particular M. tuberculosis strain has been designed.
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Williams M, Mizrahi V, Kana BD. Molybdenum cofactor: a key component of Mycobacterium tuberculosis pathogenesis? Crit Rev Microbiol 2013; 40:18-29. [PMID: 23317461 DOI: 10.3109/1040841x.2012.749211] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mycobacterium tuberculosis (Mtb) and other members of the Mtb complex possess an expanded complement of genes for the biosynthesis of molybdenum cofactor (MoCo), a tricyclic pterin molecule that is covalently attached to molybdate. This cofactor allows the redox properties of molybdenum to be harnessed by enzymes in order to catalyze redox reactions in carbon, nitrogen and sulfur metabolism. In this article, we summarize recent advances in elucidating the MoCo biosynthetic pathway in Mtb and highlight the evidence implicating the biosynthesis of this cofactor, as well as the enzymes that depend upon it for activity, in Mtb pathogenesis.
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Affiliation(s)
- Monique Williams
- MRC/NHLS/UCT Molecular Mycobacteriology Research Unit, Division of Medical Microbiology, Faculty of Health Sciences , University of Cape Town
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Giovannini D, Cappelli G, Jiang L, Castilletti C, Colone A, Serafino A, Wannenes F, Giacò L, Quintiliani G, Fraziano M, Nepravishta R, Colizzi V, Mariani F. A new Mycobacterium tuberculosis smooth colony reduces growth inside human macrophages and represses PDIM Operon gene expression. Does an heterogeneous population exist in intracellular mycobacteria? Microb Pathog 2012; 53:135-46. [DOI: 10.1016/j.micpath.2012.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 06/18/2012] [Accepted: 06/26/2012] [Indexed: 11/30/2022]
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Youm J, Saier MH. Comparative analyses of transport proteins encoded within the genomes of Mycobacterium tuberculosis and Mycobacterium leprae. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1818:776-97. [PMID: 22179038 DOI: 10.1016/j.bbamem.2011.11.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 11/18/2011] [Accepted: 11/18/2011] [Indexed: 10/15/2022]
Abstract
The co-emergence of multidrug resistant pathogenic bacterial strains and the Human Immunodeficiency Virus pandemic has made tuberculosis a leading public health threat. The causative agent is Mycobacterium tuberculosis (Mtu), a facultative intracellular parasite. Mycobacterium leprae (Mle), a related organism that causes leprosy, is an obligate intracellular parasite. Given that different transporters are required for bacterial growth and persistence under a variety of growth conditions, we conducted comparative analyses of transport proteins encoded within the genomes of these two organisms. A minimal set of genes required for intracellular and extracellular life was identified. Drug efflux systems utilizing primary active transport mechanisms have been preferentially retained in Mle and still others preferentially lost. Transporters associated with environmental adaptation found in Mtu were mostly lost in Mle. These findings provide starting points for experimental studies that may elucidate the dependencies of pathogenesis on transport for these two pathogenic mycobacteria. They also lead to suggestions regarding transporters that function in intra- versus extra-cellular growth.
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Affiliation(s)
- Jiwon Youm
- University of California, La Jolla, CA, USA
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Karim AF, Chandra P, Chopra A, Siddiqui Z, Bhaskar A, Singh A, Kumar D. Express path analysis identifies a tyrosine kinase Src-centric network regulating divergent host responses to Mycobacterium tuberculosis infection. J Biol Chem 2011; 286:40307-19. [PMID: 21953458 PMCID: PMC3220550 DOI: 10.1074/jbc.m111.266239] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Global gene expression profiling has emerged as a major tool in understanding complex response patterns of biological systems to perturbations. However, a lack of unbiased analytical approaches has restricted the utility of complex microarray data to gain novel system level insights. Here we report a strategy, express path analysis (EPA), that helps to establish various pathways differentially recruited to achieve specific cellular responses under contrasting environmental conditions in an unbiased manner. The analysis superimposes differentially regulated genes between contrasting environments onto the network of functional protein associations followed by a series of iterative enrichments and network analysis. To test the utility of the approach, we infected THP1 macrophage cells with a virulent Mycobacterium tuberculosis strain (H37Rv) or the attenuated non-virulent strain H37Ra as contrasting perturbations and generated the temporal global expression profiles. EPA of the results provided details of response-specific and time-dependent host molecular network perturbations. Further analysis identified tyrosine kinase Src as the major regulatory hub discriminating the responses between wild-type and attenuated Mtb infection. We were then able to verify this novel role of Src experimentally and show that Src executes its role through regulating two vital antimicrobial processes of the host cells (i.e. autophagy and acidification of phagolysosome). These results bear significant potential for developing novel anti-tuberculosis therapy. We propose that EPA could prove extremely useful in understanding complex cellular responses for a variety of perturbations, including pathogenic infections.
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Affiliation(s)
- Ahmad Faisal Karim
- Immunology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
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Zhang Y, Zhang H, Zhou T, Zhong Y, Jin Q. Genes under positive selection in Mycobacterium tuberculosis. Comput Biol Chem 2011; 35:319-22. [PMID: 22000803 DOI: 10.1016/j.compbiolchem.2011.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 07/20/2011] [Accepted: 08/11/2011] [Indexed: 12/29/2022]
Abstract
We employed an evolutionary genomics approach to detect genes under lineage-specific positive selection for the two closely related Mycobacterium tuberculosis strains, the virulent H37Rv and the avirulent H37Ra, with the clinical isolate CDC1551 as the outgroup. We found six H37Rv-specific and six H37Ra-specific positively selected genes, among which the former comprised a flavoprotein, a RNA polymerase sigma factor SigM, two PPE family proteins, as well as two hypothetical proteins, while the latter consisted of a dehydrogenase, a (3R)-hydroxyacyl-ACP dehydratase subunit HadA, a PPE family protein, and three PE-PGRS family proteins. Obviously, the PE/PPE/PE-PGRS family proteins were the main targets of positive selection. The functional discussion of our findings implied that those positively selected genes were highly involved in antigen variations and immune evasions of Mycobacterium tuberculosis.
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Affiliation(s)
- Yuan Zhang
- State Key Laboratory for Molecular Virology and Genetic Engineering, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China.
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Alonso H, Aguilo JI, Samper S, Caminero JA, Campos-Herrero MI, Gicquel B, Brosch R, Martín C, Otal I. Deciphering the role of IS6110 in a highly transmissible Mycobacterium tuberculosis Beijing strain, GC1237. Tuberculosis (Edinb) 2011; 91:117-26. [DOI: 10.1016/j.tube.2010.12.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 12/20/2010] [Accepted: 12/28/2010] [Indexed: 10/18/2022]
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40
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Målen H, De Souza GA, Pathak S, Søfteland T, Wiker HG. Comparison of membrane proteins of Mycobacterium tuberculosis H37Rv and H37Ra strains. BMC Microbiol 2011; 11:18. [PMID: 21261938 PMCID: PMC3033788 DOI: 10.1186/1471-2180-11-18] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Accepted: 01/24/2011] [Indexed: 01/24/2023] Open
Abstract
Background The potential causes for variation in virulence between distinct M. tuberculosis strains are still not fully known. However, differences in protein expression are probably an important factor. In this study we used a label-free quantitative proteomic approach to estimate differences in protein abundance between two closely related M. tuberculosis strains; the virulent H37Rv strain and its attenuated counterpart H37Ra. Results We were able to identify more than 1700 proteins from both strains. As expected, the majority of the identified proteins had similar relative abundance in the two strains. However, 29 membrane-associated proteins were observed with a 5 or more fold difference in their relative abundance in one strain compared to the other. Of note, 19 membrane- and lipo-proteins had higher abundance in H37Rv, while another 10 proteins had a higher abundance in H37Ra. Interestingly, the possible protein-export membrane protein SecF (Rv2586c), and three ABC-transporter proteins (Rv0933, Rv1273c and Rv1819c) were among the more abundant proteins in M. tuberculosis H37Rv. Conclusion Our data suggests that the bacterial secretion system and the transmembrane transport system may be important determinants of the ability of distinct M. tuberculosis strains to cause disease.
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Affiliation(s)
- Hiwa Målen
- Section for Microbiology and Immunology, the Gade Institute, University of Bergen, Bergen, Norway
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Vishnoi A, Roy R, Prasad HK, Bhattacharya A. Anchor-based whole genome phylogeny (ABWGP): a tool for inferring evolutionary relationship among closely related microorganisms [corrected]. PLoS One 2010; 5:e14159. [PMID: 21152403 PMCID: PMC2994773 DOI: 10.1371/journal.pone.0014159] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Accepted: 10/21/2010] [Indexed: 12/03/2022] Open
Abstract
Phenotypic behavior of a group of organisms can be studied using a range of molecular evolutionary tools that help to determine evolutionary relationships. Traditionally a gene or a set of gene sequences was used for generating phylogenetic trees. Incomplete evolutionary information in few selected genes causes problems in phylogenetic tree construction. Whole genomes are used as remedy. Now, the task is to identify the suitable parameters to extract the hidden information from whole genome sequences that truly represent evolutionary information. In this study we explored a random anchor (a stretch of 100 nucleotides) based approach (ABWGP) for finding distance between any two genomes, and used the distance estimates to compute evolutionary trees. A number of strains and species of Mycobacteria were used for this study. Anchor-derived parameters, such as cumulative normalized score, anchor order and indels were computed in a pair-wise manner, and the scores were used to compute distance/phylogenetic trees. The strength of branching was determined by bootstrap analysis. The terminal branches are clearly discernable using the distance estimates described here. In general, different measures gave similar trees except the trees based on indels. Overall the tree topology reflected the known biology of the organisms. This was also true for different strains of Escherichia coli. A new whole genome-based approach has been described here for studying evolutionary relationships among bacterial strains and species.
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Affiliation(s)
- Anchal Vishnoi
- School of Information Technology, Center for Computational Biology and Bioinformatics, Jawaharlal Nehru University, New Delhi, India
| | - Rahul Roy
- Indian Statistical Institute, New Delhi, India
| | - Hanumanthappa K. Prasad
- Department of Biotechnology, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Alok Bhattacharya
- School of Information Technology, Center for Computational Biology and Bioinformatics, Jawaharlal Nehru University, New Delhi, India
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
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Functional analysis of molybdopterin biosynthesis in mycobacteria identifies a fused molybdopterin synthase in Mycobacterium tuberculosis. J Bacteriol 2010; 193:98-106. [PMID: 20971904 DOI: 10.1128/jb.00774-10] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Most mycobacterial species possess a full complement of genes for the biosynthesis of molybdenum cofactor (MoCo). However, a distinguishing feature of members of the Mycobacterium tuberculosis complex is their possession of multiple homologs associated with the first two steps of the MoCo biosynthetic pathway. A mutant of M. tuberculosis lacking the moaA1-moaD1 gene cluster and a derivative in which moaD2 was also deleted were significantly impaired for growth in media containing nitrate as a sole nitrogen source, indicating a reduced availability of MoCo to support the assimilatory function of the MoCo-dependent nitrate reductase, NarGHI. However, the double mutant displayed residual respiratory nitrate reductase activity, suggesting that it retains the capacity to produce MoCo. The M. tuberculosis moaD and moaE homologs were further analyzed by expressing these genes in mutant strains of M. smegmatis that lacked one or both of the sole molybdopterin (MPT) synthase-encoding genes, moaD2 and moaE2, and were unable to grow on nitrate, presumably as a result of the loss of MoCo-dependent nitrate assimilatory activity. Expression of M. tuberculosis moaD2 in the M. smegmatis moaD2 mutant and of M. tuberculosis moaE1 or moaE2 in the M. smegmatis moaE2 mutant restored nitrate assimilation, confirming the functionality of these genes in MPT synthesis. Expression of M. tuberculosis moaX also restored MoCo biosynthesis in M. smegmatis mutants lacking moaD2, moaE2, or both, thus identifying MoaX as a fused MPT synthase. By implicating multiple synthase-encoding homologs in MoCo biosynthesis, these results suggest that important cellular functions may be served by their expansion in M. tuberculosis.
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Li AH, Waddell SJ, Hinds J, Malloff CA, Bains M, Hancock RE, Lam WL, Butcher PD, Stokes RW. Contrasting transcriptional responses of a virulent and an attenuated strain of Mycobacterium tuberculosis infecting macrophages. PLoS One 2010; 5:e11066. [PMID: 20548782 PMCID: PMC2883559 DOI: 10.1371/journal.pone.0011066] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Accepted: 04/29/2010] [Indexed: 02/02/2023] Open
Abstract
Background H37Rv and H37Ra are well-described laboratory strains of Mycobacterium tuberculosis derived from the same parental strain, H37, that show dramatically different pathogenic phenotypes. Methodology/Principal Findings In this study, the transcriptomes of the two strains during axenic growth in broth and during intracellular growth within murine bone-marrow macrophages were compared by whole genome expression profiling. We identified and compared adaptations of either strain upon encountering an intracellular environment, and also contrasted the transcriptomes of the two strains while inside macrophages. In the former comparison, both strains induced genes that would facilitate intracellular survival including those involved in mycobactin synthesis and fatty acid metabolism. However, this response was stronger and more extensive for H37Rv than for H37Ra. This was manifested as the differential expression of a greater number of genes and an increased magnitude of expression for these genes in H37Rv. In comparing intracellular transcriptional signatures, fifty genes were found to be differentially expressed between the strains. Of these fifty, twelve were under control of the PhoPR regulon. Further differences between strains included genes whose products were members of the ESAT-6 family of proteins, or were associated with their secretion. Conclusions/Significance Along with the recent identification of single nucleotide polymorphisms in H37Ra when compared to H37Rv, our demonstration of differential expression of PhoP-regulated and ESX-1 region-related genes during macrophage infection further highlights the significance of these genes in the attenuation of H37Ra.
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Affiliation(s)
- Alice H. Li
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Simon J. Waddell
- Division of Cellular & Molecular Medicine, Department of Medical Microbiology, Centre for Infection, St. George's University of London, London, United Kingdom
| | - Jason Hinds
- Division of Cellular & Molecular Medicine, Department of Medical Microbiology, Centre for Infection, St. George's University of London, London, United Kingdom
| | - Chad A. Malloff
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Manjeet Bains
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Robert E. Hancock
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
| | - Wan L. Lam
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Philip D. Butcher
- Division of Cellular & Molecular Medicine, Department of Medical Microbiology, Centre for Infection, St. George's University of London, London, United Kingdom
| | - Richard W. Stokes
- Department of Paediatrics, University of British Columbia, Vancouver, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Division of Infectious Diseases, British Columbia's Children's Hospital, Vancouver, Canada
- * E-mail:
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Lu LD, Sun Q, Fan XY, Zhong Y, Yao YF, Zhao GP. Mycobacterial MazG is a novel NTP pyrophosphohydrolase involved in oxidative stress response. J Biol Chem 2010; 285:28076-85. [PMID: 20529853 DOI: 10.1074/jbc.m109.088872] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
MazG nucleoside triphosphate pyrophosphohydrolase (NTP-PPase, EC 3.6.1.8) from the avirulent Mycobacterium tuberculosis H37Ra contains a spontaneous mutation on a highly conserved residue, resulting in an A219E substitution (MtMazG[A219E]). In this work, we show that mycobacterial MazG from either the virulent M. tuberculosis H37Rv (MtMazG) or the fast-growing Mycobacterium smegmatis (MsMazG) is a potent NTP-PPase capable of hydrolyzing all canonical (d)NTPs, as well as the mutagenic dUTP and 8-oxo-7,8-dihydro-2'-dGTP. However, this hydrolysis activity is diminished by the MtMazG[A219E] mutation. Moreover, deletion of mazG in M. smegmatis rendered the mycobacteria defective in response to oxidative stress. Importantly, expression of the wild-type MtMazG, but not the A219E mutant, restored cell viability under oxidative stress. Intriguingly, under oxidative stress, both the mazG-null and MtMazG[A219E]-expressing M. smegmatis strains failed to elevate relA, while retaining their ability to up-regulate sigE, suggesting a specific role for the MazG NTP-PPase activity in oxidative stress-triggered, transcriptional activation of relA. The MtMazG is a homotetramer with each subunit containing a single MazG core domain flanked by two regions, both of which are essential for NTP-PPase activity. Taken together, these results demonstrate that the mycobacterial MazG is a potent NTP-PPase and that this activity is required to maintain the full capacity of the mycobacteria to respond to oxidative stress. Our work implicates a role for the MazG activity in the virulence of M. tuberculosis.
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Affiliation(s)
- Liang-dong Lu
- State Key Laboratory of Genetic Engineering, Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China
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Målen H, Pathak S, Søfteland T, de Souza GA, Wiker HG. Definition of novel cell envelope associated proteins in Triton X-114 extracts of Mycobacterium tuberculosis H37Rv. BMC Microbiol 2010; 10:132. [PMID: 20429878 PMCID: PMC2874799 DOI: 10.1186/1471-2180-10-132] [Citation(s) in RCA: 118] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2009] [Accepted: 04/29/2010] [Indexed: 12/04/2022] Open
Abstract
Background Membrane- and membrane-associated proteins are important for the pathogenicity of bacteria. We have analysed the content of these proteins in virulent Mycobacterium tuberculosis H37Rv using Triton X-114 detergent-phase separation for extraction of lipophilic proteins, followed by their identification with high resolution mass spectrometry. Results In total, 1417 different proteins were identified. In silico analysis of the identified proteins revealed that 248 proteins had at least one predicted trans-membrane region. Also, 64 of the identified proteins were predicted lipoproteins, and 54 proteins were predicted as outer membrane proteins. Three-hundred-and-ninety-five of the observed proteins, including 91 integral membrane proteins were described for the first time. Comparison of abundance levels of the identified proteins was performed using the exponentially modified protein abundance index (emPAI) which takes into account the number of the observable peptides to the number of experimentally observed peptide ions for a given protein. The outcome showed that among the membrane-and membrane-associated proteins several proteins are present with high relative abundance. Further, a close examination of the lipoprotein LpqG (Rv3623) which is only detected in the membrane fractions of M. tuberculosis but not in M. bovis, revealed that the homologous gene in M. bovis lack the signal peptide and lipobox motif, suggesting impaired export to the membrane. Conclusions Altogether, we have identified a substantial proportion of membrane- and membrane-associated proteins of M. tuberculosis H37Rv, compared the relative abundance of the identified proteins and also revealed subtle differences between the different members of the M. tuberculosis complex.
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Affiliation(s)
- Hiwa Målen
- Section for Microbiology and Immunology, the Gade Institute, University of Bergen, Bergen, Norway
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Stokes RW, Waddell SJ. Adjusting to a new home: Mycobacterium tuberculosis gene expression in response to an intracellular lifestyle. Future Microbiol 2010; 4:1317-35. [PMID: 19995191 DOI: 10.2217/fmb.09.94] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mycobacterium tuberculosis remains the most significant single species of bacteria causing disease in mankind. The ability of M. tuberculosis to survive and replicate within host macrophages is a pivotal step in its pathogenesis. Understanding the microenvironments that M. tuberculosis encounters within the macrophage and the adaptations that the bacterium undergoes to facilitate its survival will lead to insights into possible therapeutic targets for improved treatment of tuberculosis. This is urgently needed with the emergence of multi- and extensively drug resistant strains of M. tuberculosis. Significant advances have been made in understanding the macrophage response on encountering M. tuberculosis. Complementary information is also accumulating regarding the counter responses of M. tuberculosis during the various stages of its interactions with the host. As such, a picture is emerging delineating the gene expression of intracellular M. tuberculosis at different stages of the interaction with macrophages.
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Affiliation(s)
- Richard W Stokes
- Department of Paediatrics, University of British Columbia, British Columbia, Canada.
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Sekar B, Arunagiri K, Selvakumar N, Preethi KS, Menaka K. Low frequency of moaA3 gene among the clinical isolates of Mycobacterium tuberculosis from Tamil Nadu and Pondicherry--south eastern coastal states of India. BMC Infect Dis 2009; 9:114. [PMID: 19630991 PMCID: PMC2721839 DOI: 10.1186/1471-2334-9-114] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Accepted: 07/25/2009] [Indexed: 11/28/2022] Open
Abstract
Background Comparative genomic analysis of M. tuberculosis H37Rv and M. bovis BCG have shown that 16 RDs (Regions of Differences) are deleted in BCG and have shown six deletion regions in M. tuberculosis H37Rv. RD1, is present in M. tuberculosis but is absent in all M. bovis BCG sub-strains. A study from Kerala, a south-western coastal state of India aimed to find out differences in RD1 region showed for the first time the presence of moaA3 gene in majority of their clinical isolates, that was absent in type strain H37Rv. We attempted to find out such polymorphism between type strains and the clinical isolates within RD1, targeting moaA3 gene among the clinical isolates of Tamil Nadu & Pondicherry, south-eastern coastal states of India Methods One hundred and sixteen clinical isolates of M. tuberculosis were included in the study. PCR using RD1DLa and RD1DRa primers was carried out to amplify a 652 bp fragment, encoding for cfp10 and esat 6 proteins of RD1. A second PCR using primers designed from the surrounding regions of moaA3 gene was done to confirm the presence of the full Open Reading Frame (ORF) in clinical isolates. Results In M. tuberculosis H37Rv the expected 652 bp band was present. In BCG it was absent as expected, but a 386 bp fragment was amplified. Around 12/116 (10.3%) of our clinical isolates showed both 652 and 386 bp fragments. The additional 386 bp amplicon is a part of the moaA3 gene which codes for molybdopterin cofactor protein A in M. bovis. The second PCR amplified the flanking sequence of moaA3 and yielded the expected amplicon of 1254 bp in all those 10.3% of clinical isolates which had the 386 bp fragment. However the earlier study carried out in Kerala, reported the presence of moaA3 gene in majority (97%) of their clinical isolates. Conclusion This finding showed that there was regional variation presenting polymorphism in moA3 gene, among the strains of M. tuberculosis and further strengthens the speculation of genetic differences among the strains of Kerala and Tamil Nadu & Pondicherry, the South Indian states
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Affiliation(s)
- Balaraman Sekar
- Division of Laboratories, Central Leprosy Teaching and Research Institute, Chengalpattu, Tamil Nadu, India.
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Silver RF, Walrath J, Lee H, Jacobson BA, Horton H, Bowman MR, Nocka K, Sypek JP. Human alveolar macrophage gene responses to Mycobacterium tuberculosis strains H37Ra and H37Rv. Am J Respir Cell Mol Biol 2009; 40:491-504. [PMID: 18787177 PMCID: PMC2660564 DOI: 10.1165/rcmb.2008-0219oc] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2008] [Accepted: 08/18/2008] [Indexed: 11/24/2022] Open
Abstract
H37Rv and H37Ra have been widely used as models of virulent and avirulent strains, respectively, of Mycobacterium tuberculosis. Since the sequencing of H37Rv, microarrays have been used to investigate gene expression of M. tuberculosis strains under various conditions, and to compare gene expression of specific isolates of the organism. Because differences in the virulence of these organisms could also be manifest via their differential induction of host genes, we used Affymetrix Human Genome Arrays U133A and U133B to evaluate human alveolar macrophage (AM) responses to infection with H37Rv and H37Ra. H37Rv altered expression of far more genes than did H37Ra. Moreover, the genes induced by H37Rv to a greater extent than by H37Ra were predominantly associated with the development of effective immunity. H37Rv markedly increased expression of IL-23 p19, whereas neither organism significantly induced IL-12 p35 expression. Quantitative PCR confirmed that H37Rv induced significantly more AM p19 expression than did H37Ra. After low-level infection of both AM and peripheral blood monocytes (MN) with H37Rv, neither cell type produced IL-12 (by ELISA). In contrast, AM displayed significant IL-23 production in response to H37Rv, whereas MN did not. Our findings thus suggest an important role for IL-23 in human host responses to pulmonary infection with M. tuberculosis, and are consistent with epidemiologic and genetic studies that imply that H37Rv may not have unusual capacity to cause human disease.
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Affiliation(s)
- Richard F Silver
- Division of Pulmonary, Critical Care, and Sleep Medicine, Biomedical Research Building, Rm. 1030, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106-4984, USA.
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Sharma D, Tyagi JS. The value of comparative genomics in understanding mycobacterial virulence: Mycobacterium tuberculosis H37Ra genome sequencing - a worthwhile endeavour. J Biosci 2008; 32:185-9. [PMID: 17435310 DOI: 10.1007/s12038-007-0018-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Deepak Sharma
- National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India
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Li AH, Lam WL, Stokes RW. Characterization of genes differentially expressed within macrophages by virulent and attenuated Mycobacterium tuberculosis identifies candidate genes involved in intracellular growth. MICROBIOLOGY-SGM 2008; 154:2291-2303. [PMID: 18667562 DOI: 10.1099/mic.0.2008/019661-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
To identify genes involved in the intracellular survival of Mycobacterium tuberculosis we compared the transcriptomes of virulent (H37Rv) and attenuated (H37Ra) strains during their interaction with murine bone-marrow-derived macrophages. Expression profiling was accomplished via the bacterial artificial chromosome fingerprint array (BACFA) technique. Genes identified with BACFA, and confirmed via qPCR to be upregulated in the attenuated H37Ra at 168 h post-infection, were frdB, frdC and frdD. Genes upregulated in the virulent H37Rv were pks2, aceE and Rv1571. Further qPCR analysis of these genes at 4 and 96 h post-infection revealed that the frd operon (encoding the fumarate reductase enzyme complex) is expressed at higher levels in the virulent H37Rv at earlier time points while the expression of aceE and pks2 is higher in the virulent strain throughout the course of infection. Assessment of frd transcripts in oxygen-limited cultures of M. tuberculosis H37Ra and H37Rv showed that the attenuated strain displayed a lag in frdA and frdB expression at the onset of microaerophilic culture, when compared to microaerophilic cultures of H37Rv and aerated cultures of H37Ra. Lastly, treatment of intracellular bacteria with a putative inhibitor of fumarate reductase resulted in a significant reduction of bacterial growth.
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Affiliation(s)
- Alice H Li
- Department of Pathology and Laboratory Medicine, University of British Columbia, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada
| | - Wan L Lam
- Department of Pathology and Laboratory Medicine, University of British Columbia, Department of Cancer Genetics, BC Cancer Research Centre, 601 West 10th Avenue, Vancouver, BC V5Z 1L3, Canada
| | - Richard W Stokes
- Departments of Paediatrics and Pathology and Laboratory Medicine, University of British Columbia, Division of Infectious and Immunological Diseases, BC Children's Hospital, 950 West 28th Avenue, Vancouver, BC V5Z 4H4, Canada
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