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Mvubu NE, Jacoby K. Mycobacterium tuberculosis complex molecular networks and their regulation: Implications of strain heterogeneity on epigenetic diversity and transcriptome regulation. Heliyon 2023; 9:e22611. [PMID: 38046135 PMCID: PMC10686871 DOI: 10.1016/j.heliyon.2023.e22611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 12/05/2023] Open
Abstract
Tuberculosis has been a public health crisis since the 1900, which has caused the highest mortalities due to a single bacterial infection worldwide, that was recently further complicated by the Coronavirus disease 2019 pandemic. The causative agent of Tuberculosis, Mycobacterium tuberculosis, belongs to a genetically well-characterized family of strains known as the Mycobacterium tuberculosis complex, which has complicated progress made towards eradicating Tuberculosis due to pathogen-specific phenotypic differences in the members of this complex. Mycobacterium tuberculosis complex strains are genetically diverse human- and animal-adapted pathogens belonging to 7 lineages (Indo-Oceanic, East-Asian, East-African Indian, Euro-American, M. africanum West Africa 1, M. africanum West Africa 2 and Ethopia), respectively and the recently identified Lineage 8 and M. africanum Lineage 9. Genomic studies have revealed that Mycobacterium tuberculosis complex members are ∼99 % similar, however, due to selective pressure and adaptation to human host, they are prone to mutations that have resulted in development of drug resistance and phenotypic heterogeneity that impact strain virulence. Furthermore, members of the Mycobacterium tuberculosis complex have preferred geographic locations and possess unique phenotypic characteristics that is linked to their pathogenicity. Due to the recent advances in development next generation sequencing platforms, several studies have revealed epigenetic changes in genomic regions combined with "unique" gene regulatory mechanisms through non-coding RNAs that are responsible for strain-specific behaviour on in vitro and in vivo infection models. The current review provides up to date epigenetic patterns, gene regulation through non-coding RNAs, together with implications of these mechanisms in down-stream proteome and metabolome, which may be responsible for "unique" responses to infection by members of the Mycobacterium tuberculosis complex. Understanding lineage-specific molecular mechanisms during infection may provide novel drug targets and disease control measures towards World Health organization END-TB strategy.
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Affiliation(s)
- Nontobeko Eunice Mvubu
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
| | - Kieran Jacoby
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, 4000, South Africa
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2
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Gómez-González PJ, Grabowska AD, Tientcheu LD, Tsolaki AG, Hibberd ML, Campino S, Phelan JE, Clark TG. Functional genetic variation in pe/ ppe genes contributes to diversity in Mycobacterium tuberculosis lineages and potential interactions with the human host. Front Microbiol 2023; 14:1244319. [PMID: 37876785 PMCID: PMC10591178 DOI: 10.3389/fmicb.2023.1244319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/21/2023] [Indexed: 10/26/2023] Open
Abstract
Introduction Around 10% of the coding potential of Mycobacterium tuberculosisis constituted by two poorly understood gene families, the pe and ppe loci, thought to be involved in host-pathogen interactions. Their repetitive nature and high GC content have hindered sequence analysis, leading to exclusion from whole-genome studies. Understanding the genetic diversity of pe/ppe families is essential to facilitate their potential translation into tools for tuberculosis prevention and treatment. Methods To investigate the genetic diversity of the 169 pe/ppe genes, we performed a sequence analysis across 73 long-read assemblies representing seven different lineages of M. tuberculosis and M. bovis BCG. Individual pe/ppe gene alignments were extracted and diversity and conservation across the different lineages studied. Results The pe/ppe genes were classified into three groups based on the level of protein sequence conservation relative to H37Rv, finding that >50% were conserved, with indels in pe_pgrs and ppe_mptr sub-families being major drivers of structural variation. Gene rearrangements, such as duplications and gene fusions, were observed between pe and pe_pgrs genes. Inter-lineage diversity revealed lineage-specific SNPs and indels. Discussion The high level of pe/ppe genes conservation, together with the lineage-specific findings, suggest their phylogenetic informativeness. However, structural variants and gene rearrangements differing from the reference were also identified, with potential implications for pathogenicity. Overall, improving our knowledge of these complex gene families may have insights into pathogenicity and inform the development of much-needed tools for tuberculosis control.
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Affiliation(s)
| | - Anna D. Grabowska
- Department of Biophysics, Physiology and Pathophysiology, Medical University of Warsaw, Warsaw, Poland
| | - Leopold D. Tientcheu
- MRC Unit, The Gambia at the London School of Hygiene and Tropical Medicine, Vaccines and Immunity Theme, Fajara, The Gambia
| | - Anthony G. Tsolaki
- Department of Life Sciences, Brunel University London, Uxbridge, United Kingdom
| | - Martin L. Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Jody E. Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
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3
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Gómez-González PJ, Campino S, Phelan JE, Clark TG. Portable sequencing of Mycobacterium tuberculosis for clinical and epidemiological applications. Brief Bioinform 2022; 23:6650479. [PMID: 35894606 PMCID: PMC9487601 DOI: 10.1093/bib/bbac256] [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: 02/21/2022] [Revised: 05/23/2022] [Accepted: 06/01/2022] [Indexed: 11/14/2022] Open
Abstract
With >1 million associated deaths in 2020, human tuberculosis (TB) caused by the bacteria Mycobacterium tuberculosis remains one of the deadliest infectious diseases. A plethora of genomic tools and bioinformatics pipelines have become available in recent years to assist the whole genome sequencing of M. tuberculosis. The Oxford Nanopore Technologies (ONT) portable sequencer is a promising platform for cost-effective application in clinics, including personalizing treatment through detection of drug resistance-associated mutations, or in the field, to assist epidemiological and transmission investigations. In this study, we performed a comparison of 10 clinical isolates with DNA sequenced on both long-read ONT and (gold standard) short-read Illumina HiSeq platforms. Our analysis demonstrates the robustness of the ONT variant calling for single nucleotide polymorphisms, despite the high error rate. Moreover, because of improved coverage in repetitive regions where short sequencing reads fail to align accurately, ONT data analysis can incorporate additional regions of the genome usually excluded (e.g. pe/ppe genes). The resulting extra resolution can improve the characterization of transmission clusters and dynamics based on inferring closely related isolates. High concordance in variants in loci associated with drug resistance supports its use for the rapid detection of resistant mutations. Overall, ONT sequencing is a promising tool for TB genomic investigations, particularly to inform clinical and surveillance decision-making to reduce the disease burden.
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Affiliation(s)
- Paula J Gómez-González
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Jody E Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK.,Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, WC1E 7HT London, UK
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Smith TM, Youngblom MA, Kernien JF, Mohamed MA, Fry SS, Bohr LL, Mortimer TD, O'Neill MB, Pepperell CS. Rapid adaptation of a complex trait during experimental evolution of Mycobacterium tuberculosis. eLife 2022; 11:e78454. [PMID: 35726854 PMCID: PMC9213004 DOI: 10.7554/elife.78454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/15/2022] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tb), is a leading cause of death due to infectious disease. TB is not traditionally associated with biofilms, but M. tb biofilms are linked with drug and immune tolerance and there is increasing recognition of their contribution to the recalcitrance of TB infections. Here, we used M. tb experimental evolution to investigate this complex phenotype and identify candidate loci controlling biofilm formation. We identified novel candidate loci, adding to our understanding of the genetic architecture underlying M. tb biofilm development. Under selective pressure to grow as a biofilm, regulatory mutations rapidly swept to fixation and were associated with changes in multiple traits, including extracellular matrix production, cell size, and growth rate. Genetic and phenotypic paths to enhanced biofilm growth varied according to the genetic background of the parent strain, suggesting that epistatic interactions are important in M. tb adaptation to changing environments.
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Affiliation(s)
| | - Madison A Youngblom
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
- Microbiology Doctoral Training Program, University of Wisconsin-MadisonMadisonUnited States
| | - John F Kernien
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
| | - Mohamed A Mohamed
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
| | - Sydney S Fry
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
| | - Lindsey L Bohr
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
- Microbiology Doctoral Training Program, University of Wisconsin-MadisonMadisonUnited States
| | - Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Mary B O'Neill
- Laboratoire de Biochimie (LBC), Chimie Biologie et Innovation, ESPCI Paris, PSL UniversitéParisFrance
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
- Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
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Swargam S, Kumari I, Kumar A, Pradhan D, Alam A, Singh H, Jain A, Devi KR, Trivedi V, Sarma J, Hanif M, Narain K, Ehtesham NZ, Hasnain SE, Ahmad S. MycoVarP: Mycobacterium Variant and Drug Resistance Prediction Pipeline for Whole-Genome Sequence Data Analysis. FRONTIERS IN BIOINFORMATICS 2022; 1:805338. [PMID: 36303799 PMCID: PMC9580932 DOI: 10.3389/fbinf.2021.805338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
Whole-genome sequencing (WGS) provides a comprehensive tool to analyze the bacterial genomes for genotype–phenotype correlations, diversity of single-nucleotide variant (SNV), and their evolution and transmission. Several online pipelines and standalone tools are available for WGS analysis of Mycobacterium tuberculosis (Mtb) complex (MTBC). While they facilitate the processing of WGS data with minimal user expertise, they are either too general, providing little insights into bacterium-specific issues such as gene variations, INDEL/synonymous/PE-PPE (IDP family), and drug resistance from sample data, or are limited to specific objectives, such as drug resistance. It is understood that drug resistance and lineage-specific issues require an elaborate prioritization of identified variants to choose the best target for subsequent therapeutic intervention. Mycobacterium variant pipeline (MycoVarP) addresses these specific issues with a flexible battery of user-defined and default filters. It provides an end-to-end solution for WGS analysis of Mtb variants from the raw reads and performs two quality checks, viz, before trimming and after alignments of reads to the reference genome. MycoVarP maps the annotated variants to the drug-susceptible (DS) database and removes the false-positive variants, provides lineage identification, and predicts potential drug resistance. We have re-analyzed the WGS data reported by Advani et al. (2019) using MycoVarP and identified some additional variants not reported so far. We conclude that MycoVarP will help in identifying nonsynonymous, true-positive, drug resistance–associated variants more effectively and comprehensively, including those within the IDP of the PE-PPE/PGRS family, than possible from the currently available pipelines.
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Affiliation(s)
- Sandeep Swargam
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, India
- Department of Molecular Medicine, School of Interdisciplinary Sciences, Jamia Hamdard, New Delhi, India
| | - Indu Kumari
- Inflammation Biology and Cell Signalling Lab, Safdarjung Hospital Campus, ICMR National Institute of Pathology, New Delhi, India
| | - Amit Kumar
- ICMR Computational Genomics Centre, Informatics Systems and Research Management (ISRM) Division, Indian Council of Medical Research (ICMR), New Delhi, India
| | - Dibyabhaba Pradhan
- ICMR Computational Genomics Centre, Informatics Systems and Research Management (ISRM) Division, Indian Council of Medical Research (ICMR), New Delhi, India
| | - Anwar Alam
- Inflammation Biology and Cell Signalling Lab, Safdarjung Hospital Campus, ICMR National Institute of Pathology, New Delhi, India
| | - Harpreet Singh
- ICMR Computational Genomics Centre, Informatics Systems and Research Management (ISRM) Division, Indian Council of Medical Research (ICMR), New Delhi, India
| | - Anuja Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - Vishal Trivedi
- Department of Biosciences and Bioengineering, Indian Institute of Technology-Guwahati, Guwahati, India
| | - Jogesh Sarma
- Department of Pulmonary Medicine, Guwahati, India
| | | | - Kanwar Narain
- ICMR-Regional Medical Research Centre, Dibrugarh, India
| | - Nasreen Zafar Ehtesham
- Inflammation Biology and Cell Signalling Lab, Safdarjung Hospital Campus, ICMR National Institute of Pathology, New Delhi, India
| | - Seyed Ehtesham Hasnain
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, India
- Department of Life Sciences, Sharda University, Greater NOIDA, India
| | - Shandar Ahmad
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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Martínez-Pérez A, Estévez O, González-Fernández Á. Contribution and Future of High-Throughput Transcriptomics in Battling Tuberculosis. Front Microbiol 2022; 13:835620. [PMID: 35283833 PMCID: PMC8908424 DOI: 10.3389/fmicb.2022.835620] [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: 12/14/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022] Open
Abstract
While Tuberculosis (TB) infection remains a serious challenge worldwide, big data and “omic” approaches have greatly contributed to the understanding of the disease. Transcriptomics have been used to tackle a wide variety of queries including diagnosis, treatment evolution, latency and reactivation, novel target discovery, vaccine response or biomarkers of protection. Although a powerful tool, the elevated cost and difficulties in data interpretation may hinder transcriptomics complete potential. Technology evolution and collaborative efforts among multidisciplinary groups might be key in its exploitation. Here, we discuss the main fields explored in TB using transcriptomics, and identify the challenges that need to be addressed for a real implementation in TB diagnosis, prevention and therapy.
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Affiliation(s)
- Amparo Martínez-Pérez
- Biomedical Research Center (CINBIO), Universidade de Vigo, Vigo, Spain.,Hospital Álvaro Cunqueiro, Galicia Sur Health Research Institute (IIS-GS), Vigo, Spain
| | - Olivia Estévez
- Biomedical Research Center (CINBIO), Universidade de Vigo, Vigo, Spain.,Hospital Álvaro Cunqueiro, Galicia Sur Health Research Institute (IIS-GS), Vigo, Spain
| | - África González-Fernández
- Biomedical Research Center (CINBIO), Universidade de Vigo, Vigo, Spain.,Hospital Álvaro Cunqueiro, Galicia Sur Health Research Institute (IIS-GS), Vigo, Spain
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Early alveolar macrophage response and IL-1R-dependent T cell priming determine transmissibility of Mycobacterium tuberculosis strains. Nat Commun 2022; 13:884. [PMID: 35173157 PMCID: PMC8850437 DOI: 10.1038/s41467-022-28506-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 01/28/2022] [Indexed: 12/15/2022] Open
Abstract
Mechanisms underlying variability in transmission of Mycobacterium tuberculosis strains remain undefined. By characterizing high and low transmission strains of M.tuberculosis in mice, we show here that high transmission M.tuberculosis strain induce rapid IL-1R-dependent alveolar macrophage migration from the alveolar space into the interstitium and that this action is key to subsequent temporal events of early dissemination of bacteria to the lymph nodes, Th1 priming, granulomatous response and bacterial control. In contrast, IL-1R-dependent alveolar macrophage migration and early dissemination of bacteria to lymph nodes is significantly impeded in infection with low transmission M.tuberculosis strain; these events promote the development of Th17 immunity, fostering neutrophilic inflammation and increased bacterial replication. Our results suggest that by inducing granulomas with the potential to develop into cavitary lesions that aids bacterial escape into the airways, high transmission M.tuberculosis strain is poised for greater transmissibility. These findings implicate bacterial heterogeneity as an important modifier of TB disease manifestations and transmission.
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8
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Dippenaar A, Goossens SN, Grobbelaar M, Oostvogels S, Cuypers B, Laukens K, Meehan CJ, Warren RM, van Rie A. Nanopore Sequencing for Mycobacterium tuberculosis: a Critical Review of the Literature, New Developments, and Future Opportunities. J Clin Microbiol 2022; 60:e0064621. [PMID: 34133895 PMCID: PMC8769739 DOI: 10.1128/jcm.00646-21] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The next-generation, short-read sequencing technologies that generate comprehensive, whole-genome data with single nucleotide resolution have already advanced tuberculosis diagnosis, treatment, surveillance, and source investigation. Their high costs, tedious and lengthy processes, and large equipment remain major hurdles for research use in high tuberculosis burden countries and implementation into routine care. The portable next-generation sequencing devices developed by Oxford Nanopore Technologies (ONT) are attractive alternatives due to their long-read sequence capability, compact low-cost hardware, and continued improvements in accuracy and throughput. A systematic review of the published literature demonstrated limited uptake of ONT sequencing in tuberculosis research and clinical care. Of the 12 eligible articles presenting ONT sequencing data on at least one Mycobacterium tuberculosis sample, four addressed software development for long-read ONT sequencing data with potential applications for M. tuberculosis. Only eight studies presented results of ONT sequencing of M. tuberculosis, of which five performed whole-genome and three did targeted sequencing. Based on these findings, we summarize the standard processes, reflect on the current limitations of ONT sequencing technology, and the research needed to overcome the main hurdles. The low capital cost, portable nature and continued improvement in the performance of ONT sequencing make it an attractive option for sequencing for research and clinical care, but limited data are available on its application in the tuberculosis field. Important research investment is needed to unleash the full potential of ONT sequencing for tuberculosis research and care.
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Affiliation(s)
- Anzaan Dippenaar
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sander N. Goossens
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Melanie Grobbelaar
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Selien Oostvogels
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Bart Cuypers
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
- Molecular Parasitology Group, Institute of Tropical Medicine, Antwerp, Belgium
| | - Kris Laukens
- Molecular Parasitology Group, Institute of Tropical Medicine, Antwerp, Belgium
| | - Conor J. Meehan
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
- School of Chemistry and Bioscience, Faculty of Life Science, University of Bradford, Bradford, West Yorkshire, United Kingdom
| | - Robin M. Warren
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Annelies van Rie
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
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Differences in the Accessory Genomes and Methylomes of Strains of Streptococcus equi subsp. equi and of Streptococcus equi subsp. zooepidemicus Obtained from the Respiratory Tract of Horses from Texas. Microbiol Spectr 2022; 10:e0076421. [PMID: 35019696 PMCID: PMC8754150 DOI: 10.1128/spectrum.00764-21] [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] [Indexed: 11/20/2022] Open
Abstract
Streptococcus equi subsp. equi (SEE) is a host-restricted equine pathogen considered to have evolved from Streptococcus equi subsp. zooepidemicus (SEZ). SEZ is promiscuous in host range and is commonly recovered from horses as a commensal. Comparison of a single strain each of SEE and SEZ using whole-genome sequencing, supplemented by PCR of selected genes in additional SEE and SEZ strains, was used to characterize the evolution of SEE. But the known genetic variability of SEZ warrants comparison of the whole genomes of multiple SEE and SEZ strains. To fill this knowledge gap, we utilized whole-genome sequencing to characterize the accessory genome elements (AGEs; i.e., elements present in some SEE strains but absent in SEZ or vice versa) and methylomes of 50 SEE and 50 SEZ isolates from Texas. Consistent with previous findings, AGEs consistently found in all SEE isolates were primarily from mobile genetic elements that might contribute to host restriction or pathogenesis of SEE. Fewer AGEs were identified in SEZ because of the greater genomic variability among these isolates. The global methylation patterns of SEE isolates were more consistent than those of the SEZ isolates. Among homologous genes of SEE and SEZ, differential methylation was identified only in genes of SEE encoding proteins with functions of quorum sensing, exopeptidase activity, and transitional metal ion binding. Our results indicate that effects of genetic mobile elements in SEE and differential methylation of genes shared by SEE and SEZ might contribute to the host specificity of SEE. IMPORTANCE Strangles, caused by the host-specific bacterium Streptococcus equi subsp. equi (SEE), is the most commonly diagnosed infectious disease of horses worldwide. Its ancestor, Streptococcus equi subsp. zooepidemicus (SEZ), is frequently isolated from a wide array of hosts, including horses and humans. A comparison of the genomes of a single strain of SEE and SEZ has been reported, but sequencing of further isolates has revealed variability among SEZ strains. Thus, the importance of this study is that it characterizes genomic and methylomic differences of multiple SEE and SEZ isolates from a common geographic region (viz., Texas). Our results affirm many of the previously described differences between the genomes of SEE and SEZ, including the role of mobile genetic elements in contributing to host restriction. We also provide the first characterization of the global methylome of Streptococcus equi and evidence that differential methylation might contribute to the host restriction of SEE.
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Goossens SN, Heupink TH, De Vos E, Dippenaar A, De Vos M, Warren R, Van Rie A. Detection of minor variants in Mycobacterium tuberculosis whole genome sequencing data. Brief Bioinform 2021; 23:6484510. [PMID: 34962257 PMCID: PMC8769888 DOI: 10.1093/bib/bbab541] [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: 09/14/2021] [Revised: 11/05/2021] [Accepted: 11/24/2021] [Indexed: 11/25/2022] Open
Abstract
The study of genetic minority variants is fundamental to the understanding of complex processes such as evolution, fitness, transmission, virulence, heteroresistance and drug tolerance in Mycobacterium tuberculosis (Mtb). We evaluated the performance of the variant calling tool LoFreq to detect de novo as well as drug resistance conferring minor variants in both in silico and clinical Mtb next generation sequencing (NGS) data. The in silico simulations demonstrated that LoFreq is a conservative variant caller with very high precision (≥96.7%) over the entire range of depth of coverage tested (30x to1000x), independent of the type and frequency of the minor variant. Sensitivity increased with increasing depth of coverage and increasing frequency of the variant, and was higher for calling insertion and deletion (indel) variants than for single nucleotide polymorphisms (SNP). The variant frequency limit of detection was 0.5% and 3% for indel and SNP minor variants, respectively. For serial isolates from a patient with DR-TB; LoFreq successfully identified all minor Mtb variants in the Rv0678 gene (allele frequency as low as 3.22% according to targeted deep sequencing) in whole genome sequencing data (median coverage of 62X). In conclusion, LoFreq can successfully detect minor variant populations in Mtb NGS data, thus limiting the need for filtering of possible false positive variants due to sequencing error. The observed performance statistics can be used to determine the limit of detection in existing whole genome sequencing Mtb data and guide the required depth of future studies that aim to investigate the presence of minor variants.
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Affiliation(s)
- Sander N Goossens
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Tim H Heupink
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Elise De Vos
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | - Anzaan Dippenaar
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
| | | | - Rob Warren
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Annelies Van Rie
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Wilrijk, Belgium
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11
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Chu H, Hu Y, Zhang B, Sun Z, Zhu B. DNA Methyltransferase HsdM Induce Drug Resistance on Mycobacterium tuberculosis via Multiple Effects. Antibiotics (Basel) 2021; 10:antibiotics10121544. [PMID: 34943756 PMCID: PMC8698436 DOI: 10.3390/antibiotics10121544] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/12/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
Besides the genomic variants, epigenetic mechanisms such as DNA methylation also have an effect on drug resistance. This study aimed to investigate the methylomes of totally/extensively drug-resistant M. tuberculosis clinical isolates using the PacBio single-molecule real-time technology. The results showed they were almost the same as the pan-susceptible ones. Genetics and bioinformatics analysis confirmed three DNA methyltransferases-MamA, MamB, and HsdM. Moreover, anti-tuberculosis drug treatment did not change the methylomes. In addition, the knockout of the DNA methyltransferase hsdM gene in the extensively drug-resistant clinical isolate 11826 revealed that the motifs of GTAYN4ATC modified by HsdM were completely demethylated. Furthermore, the results of the methylated DNA target analysis found that HsdM was mainly involved in redox-related pathways, especially the prodrug isoniazid active protein KatG. HsdM also targeted three drug-targeted genes, eis, embB, and gyrA, and three drug transporters (Rv0194, Rv1410, and Rv1877), which mildly affected the drug susceptibility. The overexpression of HsdM in M. smegmatis increased the basal mutation rate. Our results suggested that DNA methyltransferase HsdM affected the drug resistance of M. tuberculosis by modulating the gene expression of redox, drug targets and transporters, and gene mutation.
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Affiliation(s)
- Hongqian Chu
- Translational Medicine Center Beijing Chest Hospital, Capital Medical University, Beijing 101149, China;
- Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing 101149, China
| | - Yongfei Hu
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Bing Zhang
- Core Genomic Facility, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China;
| | - Zhaogang Sun
- Translational Medicine Center Beijing Chest Hospital, Capital Medical University, Beijing 101149, China;
- Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing 101149, China
- Correspondence: (Z.S.); (B.Z.)
| | - Baoli Zhu
- CAS Key Laboratory of Pathogenic Microbiology & Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
- Correspondence: (Z.S.); (B.Z.)
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12
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Borah K, Xu Y, McFadden J. Dissecting Host-Pathogen Interactions in TB Using Systems-Based Omic Approaches. Front Immunol 2021; 12:762315. [PMID: 34795672 PMCID: PMC8593131 DOI: 10.3389/fimmu.2021.762315] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 10/18/2021] [Indexed: 01/10/2023] Open
Abstract
Tuberculosis (TB) is a devastating infectious disease that kills over a million people every year. There is an increasing burden of multi drug resistance (MDR) and extensively drug resistance (XDR) TB. New and improved therapies are urgently needed to overcome the limitations of current treatment. The causative agent, Mycobacterium tuberculosis (Mtb) is one of the most successful pathogens that can manipulate host cell environment for adaptation, evading immune defences, virulence, and pathogenesis of TB infection. Host-pathogen interaction is important to establish infection and it involves a complex set of processes. Metabolic cross talk between the host and pathogen is a facet of TB infection and has been an important topic of research where there is growing interest in developing therapies and drugs that target these interactions and metabolism of the pathogen in the host. Mtb scavenges multiple nutrient sources from the host and has adapted its metabolism to survive in the intracellular niche. Advancements in systems-based omic technologies have been successful to unravel host-pathogen interactions in TB. In this review we discuss the application and usefulness of omics in TB research that provides promising interventions for developing anti-TB therapies.
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Affiliation(s)
- Khushboo Borah
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | | | - Johnjoe McFadden
- School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
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13
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Differences in the genome, methylome, and transcriptome do not differentiate isolates of Streptococcus equi subsp. equi from horses with acute clinical signs from isolates of inapparent carriers. PLoS One 2021; 16:e0252804. [PMID: 34125848 PMCID: PMC8202921 DOI: 10.1371/journal.pone.0252804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/21/2021] [Indexed: 12/13/2022] Open
Abstract
Streptococcus equi subsp. equi (SEE) is a host-restricted bacterium that causes the common infectious upper respiratory disease known as strangles in horses. Perpetuation of SEE infection appears attributable to inapparent carrier horses because it neither persists long-term in the environment nor infects other host mammals or vectors, and infection results in short-lived immunity. Whether pathogen factors enable SEE to remain in horses without causing clinical signs remains poorly understood. Thus, our objective was to use next-generation sequencing technologies to characterize the genome, methylome, and transcriptome of isolates of SEE from horses with acute clinical strangles and inapparent carrier horses—including isolates recovered from individual horses sampled repeatedly—to assess pathogen-associated changes that might reflect specific adaptions of SEE to the host that contribute to inapparent carriage. The accessory genome elements and methylome of SEE isolates from Sweden and Pennsylvania revealed no significant or consistent differences between acute clinical and inapparent carrier isolates of SEE. RNA sequencing of SEE isolates from Pennsylvania demonstrated no genes that were differentially expressed between acute clinical and inapparent carrier isolates of SEE. The absence of specific, consistent changes in the accessory genomes, methylomes, and transcriptomes of acute clinical and inapparent carrier isolates of SEE indicates that adaptations of SEE to the host are unlikely to explain the carrier state of SEE. Efforts to understand the carrier state of SEE should instead focus on host factors.
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14
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Leiva F, Bravo S, Garcia KK, Moya J, Guzman O, Bascuñan N, Vidal R. Temporal genome-wide DNA methylation signature of post-smolt Pacific salmon challenged with Piscirickettsia salmonis. Epigenetics 2020; 16:1335-1346. [PMID: 33319647 DOI: 10.1080/15592294.2020.1864166] [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] [Indexed: 01/01/2023] Open
Abstract
Piscirickettsiosis is the most important bacterial disease in the Chilean salmon industry, which has sorted several efforts to its control, generating enormous economic losses. Epigenetic alterations, such as DNA methylation, can play a relevant role in the modulation of the metazoans response to pathogens. Bacterial disease may activate global and local immune responses generating intricate responses with significant biological impact in the host. However, it is scarcely understood how bacterial infections influence fish epigenetic alterations. In the present study, we utilized Pacific salmon and Piscirickettsiosis as model, to gain understanding into the dynamics of DNA methylation among fish-bacterial infection interactions. A genome-wide analysis of DNA methylation patterns in female spleen tissue of Pacific salmon was achieved by reduced representation bisulphite sequencing from a time course design. We determined 2,251, 1,918, and 2,516 differentially methylated regions DMRs among infected and control Pacific salmon in 1 dpi, 5 dpi, and 15 dpi, respectively. The mean methylation difference per DMR among control and infected groups was of ~35%, with an oscillatory pattern of hypo, hyper, and hypomethylation across the disease. DMCs, among the control and infected group, showed that they were statistically enriched in intergenic regions and depleted in exons. Functional annotation of the DMR genes demonstrated three KEGG principal categories, associated directly with the host response to pathogens infections. Our results provide the first evidence of epigenetic variation in fish provoked by bacterial infection and demonstrate that this variation can be modulated across the disease.
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Affiliation(s)
- Francisco Leiva
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Universidad de Santiago de Chile, Santiago, Chile
| | - Scarlet Bravo
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Universidad de Santiago de Chile, Santiago, Chile
| | - Killen Ko Garcia
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Universidad de Santiago de Chile, Santiago, Chile
| | | | | | - Nicolás Bascuñan
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Universidad de Santiago de Chile, Santiago, Chile
| | - Rodrigo Vidal
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Universidad de Santiago de Chile, Santiago, Chile
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15
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Rodríguez-Hernández E, Quintas-Granados LI, Flores-Villalva S, Cantó-Alarcón JG, Milián-Suazo F. Application of antigenic biomarkers for Mycobacterium tuberculosis. J Zhejiang Univ Sci B 2020; 21:856-870. [PMID: 33150770 PMCID: PMC7670104 DOI: 10.1631/jzus.b2000325] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/19/2020] [Indexed: 01/12/2023]
Abstract
The study and characterization of biomolecules involved in the interaction between mycobacteria and their hosts are crucial to determine their roles in the invasion process and provide basic knowledge about the biology and pathogenesis of disease. Promising new biomarkers for diagnosis and immunotherapy have emerged recently. Mycobacterium is an ancient pathogen that has developed complex strategies for its persistence in the host and environment, likely based on the complexity of the network of interactions between the molecules involved in infection. Several biomarkers have received recent attention in the process of developing rapid and reliable detection techniques for tuberculosis. Among the most widely investigated antigens are CFP-10 (10-kDa culture filtrate protein), ESAT-6 (6-kDa early secretory antigenic target), Ag85A, Ag85B, CFP-7, and PPE18. Some of these antigens have been proposed as biomarkers to assess the key elements of the response to infection of both the pathogen and host. The design of novel and accurate diagnostic methods is essential for the control of tuberculosis worldwide. Presently, the diagnostic methods are based on the identification of molecules in the humoral response in infected individuals. Therefore, these tests depend on the capacity of the host to develop an immune response, which usually is heterogeneous. In the last 20 years, special attention has been given to the design of multiantigenic diagnostic methods to improve the levels of sensitivity and specificity. In this review, we summarize the state of the art in the study and use of mycobacterium biomolecules with the potential to support novel tuberculosis control strategies.
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Affiliation(s)
- Elba Rodríguez-Hernández
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, Km. 1 Carretera a Colón, Ajuchitlán Colón, 76280, Colón, Querétaro, México
| | - Laura Itzel Quintas-Granados
- Universidad Mexiquense del Bicentenario, Unidad de Estudios Superiores de Tultitlán, Avenida Ex-Hacienda de Portales s/n, Villa Esmeralda, Tultitlán Estado de México, 54910, Tultitlán, México
| | - Susana Flores-Villalva
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal, Km. 1 Carretera a Colón, Ajuchitlán Colón, 76280, Colón, Querétaro, México
| | - Jorge Germinal Cantó-Alarcón
- Universidad Autónoma de Querétaro, Facultad de Ciencias Naturales, Avenida de las Ciencias s/n, Juriquilla, Delegación Santa Rosa Jáuregui, 76230, Querétaro, México
| | - Feliciano Milián-Suazo
- Universidad Autónoma de Querétaro, Facultad de Ciencias Naturales, Avenida de las Ciencias s/n, Juriquilla, Delegación Santa Rosa Jáuregui, 76230, Querétaro, México
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16
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Modlin SJ, Conkle-Gutierrez D, Kim C, Mitchell SN, Morrissey C, Weinrick BC, Jacobs WR, Ramirez-Busby SM, Hoffner SE, Valafar F. Drivers and sites of diversity in the DNA adenine methylomes of 93 Mycobacterium tuberculosis complex clinical isolates. eLife 2020; 9:58542. [PMID: 33107429 PMCID: PMC7591249 DOI: 10.7554/elife.58542] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022] Open
Abstract
This study assembles DNA adenine methylomes for 93 Mycobacterium tuberculosis complex (MTBC) isolates from seven lineages paired with fully-annotated, finished, de novo assembled genomes. Integrative analysis yielded four key results. First, methyltransferase allele-methylome mapping corrected methyltransferase variant effects previously obscured by reference-based variant calling. Second, heterogeneity analysis of partially active methyltransferase alleles revealed that intracellular stochastic methylation generates a mosaic of methylomes within isogenic cultures, which we formalize as ‘intercellular mosaic methylation’ (IMM). Mutation-driven IMM was nearly ubiquitous in the globally prominent Beijing sublineage. Third, promoter methylation is widespread and associated with differential expression in the ΔhsdM transcriptome, suggesting promoter HsdM-methylation directly influences transcription. Finally, comparative and functional analyses identified 351 sites hypervariable across isolates and numerous putative regulatory interactions. This multi-omic integration revealed features of methylomic variability in clinical isolates and provides a rational basis for hypothesizing the functions of DNA adenine methylation in MTBC physiology and adaptive evolution.
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Affiliation(s)
- Samuel J Modlin
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Derek Conkle-Gutierrez
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Calvin Kim
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Scott N Mitchell
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Christopher Morrissey
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | | | - William R Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, United States
| | - Sarah M Ramirez-Busby
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
| | - Sven E Hoffner
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States.,Department of Public Health Sciences, Karolinska Institute, Stockholm, Sweden
| | - Faramarz Valafar
- Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence, San Diego State University, San Diego, United States
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17
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Marimani M, Ahmad A, Stacey S, Duse A. Examining the levels of acetylation, DNA methylation and phosphorylation in HIV-1 positive and multidrug-resistant TB-HIV patients. J Glob Antimicrob Resist 2020; 23:232-242. [PMID: 33045438 DOI: 10.1016/j.jgar.2020.09.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 08/30/2020] [Accepted: 09/27/2020] [Indexed: 01/03/2023] Open
Abstract
OBJECTIVES In this study, we examined the impact of epigenetic modifications on host gene functioning by assessing the expression of seven candidate genes in three separate groups including healthy, multidrug-resistant (MDR) TB-HIV co-infected and HIV-1 positive individuals. METHODS Ten patients with MDR TB and HIV-1 co-infection on TB and HIV therapy and a cohort comprised of 10 newly diagnosed individuals with HIV-1 infection were recruited from the TB and HIV clinics at the Charlotte Maxeke Johannesburg Academic Hospital. Notably, the HIV-1 positive individuals were not placed on antiretroviral therapy (ART) at the time of recruitment and blood collection. A third group consisting of 10 healthy participants without MDR TB or HIV infection was recruited from the University of the Witwatersrand. Blood samples collected from all three cohorts were employed for extraction of plasma, total RNA and genomic DNA. RESULTS Our data indicated that the expression of DNA methyltransferase 1 (DNMT1) and Ten-eleven translocation methylcytosine dioxygenase 1 (TET1) genes was significantly increased in HIV-1 positive patients and was lowest in MDR TB-HIV co-infected patients. By contrast, histone acetyltransferase (HAT), histone deacetylase (HDAC), protein tyrosine kinase (PtkA) and protein tyrosine phosphatase (PtpA) mRNA expression levels were substantially enhanced in HIV-1 infected and were lowest in healthy individuals. Conversely, Dicer expression levels were comparable among all three study groups. CONCLUSION Promising preliminary data emanating from this investigation may potentially be used for generation of novel vaccines and therapeutic compounds capable of neutralising MDR TB-HIV and HIV-1 infection.
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Affiliation(s)
- Musa Marimani
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Aijaz Ahmad
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, South Africa.
| | - Sarah Stacey
- Division of Pulmonology, Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Adriano Duse
- Clinical Microbiology and Infectious Diseases, School of Pathology, Health Sciences, University of the Witwatersrand, Johannesburg, South Africa; Infection Control, Charlotte Maxeke Johannesburg Academic Hospital, National Health Laboratory Service, Johannesburg, South Africa
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18
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Randall SE, Martini MC, Zhou Y, Joubran SR, Shell SS. MamA essentiality in Mycobacterium smegmatis is explained by the presence of an apparent cognate restriction endonuclease. BMC Res Notes 2020; 13:462. [PMID: 32993774 PMCID: PMC7526240 DOI: 10.1186/s13104-020-05302-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/22/2020] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Restriction-Modification (R-M) systems are ubiquitous in bacteria and were considered for years as rudimentary immune systems that protect bacterial cells from foreign DNA. Currently, these R-M systems are recognized as important players in global gene expression and other cellular processes such us virulence and evolution of genomes. Here, we report the role of the unique DNA methyltransferase in Mycobacterium smegmatis, which shows a moderate degree of sequence similarity to MamA, a previously characterized methyltransferase that affects gene expression in Mycobacterium tuberculosis and is important for survival under hypoxic conditions. RESULTS We found that depletion of mamA levels impairs growth and produces elongated cell bodies. Microscopy revealed irregular septation and unevenly distributed DNA, with large areas devoid of DNA and small DNA-free cells. Deletion of MSMEG_3214, a predicted endonuclease-encoding gene co-transcribed with mamA, restored the WT growth phenotype in a mamA-depleted background. Our results suggest that the mamA-depletion phenotype can be explained by DNA cleavage by the apparent cognate restriction endonuclease MSMEG_3214. In addition, in silico analysis predicts that both MamA methyltransferase and MSMEG_3214 endonuclease recognize the same palindromic DNA sequence. We propose that MamA and MSMEG_3214 constitute a previously undescribed R-M system in M. smegmatis.
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Affiliation(s)
- Samantha E Randall
- Department of Biology & Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Maria Carla Martini
- Department of Biology & Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Ying Zhou
- Department of Biology & Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Samantha R Joubran
- Department of Biology & Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Scarlet S Shell
- Department of Biology & Biotechnology, Worcester Polytechnic Institute, Worcester, MA, USA. .,Program in Bioinformatics & Computational Biology, Worcester Polytechnic Institute, Worcester, MA, USA.
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Peters JS, Ismail N, Dippenaar A, Ma S, Sherman DR, Warren RM, Kana BD. Genetic Diversity in Mycobacterium tuberculosis Clinical Isolates and Resulting Outcomes of Tuberculosis Infection and Disease. Annu Rev Genet 2020; 54:511-537. [PMID: 32926793 DOI: 10.1146/annurev-genet-022820-085940] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Tuberculosis claims more human lives than any other bacterial infectious disease and represents a clear and present danger to global health as new tools for vaccination, treatment, and interruption of transmission have been slow to emerge. Additionally, tuberculosis presents with notable clinical heterogeneity, which complicates diagnosis, treatment, and the establishment of nonrelapsing cure. How this heterogeneity is driven by the diversity ofclinical isolates of the causative agent, Mycobacterium tuberculosis, has recently garnered attention. Herein, we review advances in the understanding of how naturally occurring variation in clinical isolates affects transmissibility, pathogenesis, immune modulation, and drug resistance. We also summarize how specific changes in transcriptional responses can modulate infection or disease outcome, together with strain-specific effects on gene essentiality. Further understanding of how this diversity of M. tuberculosis isolates affects disease and treatment outcomes will enable the development of more effective therapeutic options and vaccines for this dreaded disease.
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Affiliation(s)
- Julian S Peters
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa; ,
| | - Nabila Ismail
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa; ,
| | - Anzaan Dippenaar
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa; , .,Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, 2000, Belgium;
| | - Shuyi Ma
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98109, USA; ,
| | - David R Sherman
- Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98109, USA; ,
| | - Robin M Warren
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa; ,
| | - Bavesh D Kana
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa; ,
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20
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Infection of pulmonary epithelial cells by clinical strains of M. tuberculosis induces alternate splicing events. Gene 2020; 750:144755. [PMID: 32380040 DOI: 10.1016/j.gene.2020.144755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/29/2020] [Accepted: 05/01/2020] [Indexed: 11/21/2022]
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