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Refaya AK, Vetrivel U, Palaniyandi K. Genomic Characterization of IS 6110 Insertions in Mycobacterium orygis. Evol Bioinform Online 2024; 20:11769343241240558. [PMID: 38586439 PMCID: PMC10996354 DOI: 10.1177/11769343241240558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 03/04/2024] [Indexed: 04/09/2024] Open
Abstract
Mycobacterium orygis, a subspecies of the Mycobacterium tuberculosis complex (MTBC), has emerged as a significant concern in the context of One Health, with implications for zoonosis or zooanthroponosis or both. MTBC strains are characterized by the unique insertion element IS6110, which is widely used as a diagnostic marker. IS6110 transposition drives genetic modifications in MTBC, imparting genome plasticity and profound biological consequences. While IS6110 insertions are customarily found in the MTBC genomes, the evolutionary trajectory of strains seems to correlate with the number of IS6110 copies, indicating enhanced adaptability with increasing copy numbers. Here, we present a comprehensive analysis of IS6110 insertions in the M. orygis genome, utilizing ISMapper, and elucidate their genetic consequences in promoting successful host adaptation. Our study encompasses a panel of 67 paired-end reads, comprising 11 isolates from our laboratory and 56 sequences downloaded from public databases. Among these sequences, 91% exhibited high-copy, 4.5% low-copy, and 4.5% lacked IS6110 insertions. We identified 255 insertion loci, including 141 intragenic and 114 intergenic insertions. Most of these loci were either unique or shared among a limited number of isolates, potentially influencing strain behavior. Furthermore, we conducted gene ontology and pathway analysis, using eggNOG-mapper 5.0, on the protein sequences disrupted by IS6110 insertions, revealing 63 genes involved in diverse functions of Gene Ontology and 45 genes participating in various KEGG pathways. Our findings offer novel insights into IS6110 insertions, their preferential insertion regions, and their impact on metabolic processes and pathways, providing valuable knowledge on the genetic changes underpinning IS6110 transposition in M. orygis.
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Affiliation(s)
- Ahmed Kabir Refaya
- Department of Immunology, ICMR-National Institute for Research in Tuberculosis, Chetpet, Chennai, India
| | - Umashankar Vetrivel
- Department of Virology & Biotechnology/Bioinformatics Division, ICMR-National Institute for Research in Tuberculosis, Chetpet, Chennai, India
| | - Kannan Palaniyandi
- Department of Immunology, ICMR-National Institute for Research in Tuberculosis, Chetpet, Chennai, India
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Shitikov E, Guliaev A, Bespyatykh J, Malakhova M, Kolchenko S, Smirnov G, Merker M, Niemann S, Mokrousov I, Ilina E, Govorun V. The role of IS6110 in micro- and macroevolution of Mycobacterium tuberculosis lineage 2. Mol Phylogenet Evol 2019; 139:106559. [PMID: 31302224 DOI: 10.1016/j.ympev.2019.106559] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 05/16/2019] [Accepted: 07/10/2019] [Indexed: 11/29/2022]
Abstract
The insertion sequence 6110 (IS6110) is the most studied transposable element in the Mycobacterium tuberculosis complex species. The element plays a significant role in genome plasticity of this important human pathogen, but still many causes and consequences of its transposition have not been fully studied. Here, we analyzed insertion sites for 902 Mycobacterium tuberculosis lineage 2 strains using whole-genome sequencing data. In total, 17,972 insertions were found, corresponding to 827 independent positions in the genome of the reference strain H37Rv. To trace the history of IS6110 expansion since proto-Beijing strains up to modern sublineages, we looked at the distribution of IS6110 across the genome-wide SNP-based phylogenetic tree. This analysis demonstrated a stepwise transposition of IS6110 that occurs by «copy-and-paste» mechanism. Additionally, we detected evolutionary-scale and sublineage-specific integration sites, which can be used for typing and for understanding the reasons for the success of the lineage. A significant part of such insertions affected the genes that are essential for the pathogen. Finally, we identified and confirmed deletions that occurred between differently oriented elements, which is uncommon for this family of insertion elements and appears to be another mechanism of genome variability.
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Affiliation(s)
- Egor Shitikov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation.
| | - Andrei Guliaev
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Julia Bespyatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Maja Malakhova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Sergey Kolchenko
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Georgy Smirnov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Germany
| | - Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Elena Ilina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Vadim Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
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Gonzalo-Asensio J, Pérez I, Aguiló N, Uranga S, Picó A, Lampreave C, Cebollada A, Otal I, Samper S, Martín C. New insights into the transposition mechanisms of IS6110 and its dynamic distribution between Mycobacterium tuberculosis Complex lineages. PLoS Genet 2018; 14:e1007282. [PMID: 29649213 PMCID: PMC5896891 DOI: 10.1371/journal.pgen.1007282] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 02/28/2018] [Indexed: 11/19/2022] Open
Abstract
The insertion Sequence IS6110, only present in the pathogens of the Mycobacterium tuberculosis Complex (MTBC), has been the gold-standard epidemiological marker for TB for more than 25 years, but biological implications of IS6110 transposition during MTBC adaptation to humans remain elusive. By studying 2,236 clinical isolates typed by IS6110-RFLP and covering the MTBC, we remarked a lineage-specific content of IS6110 being higher in modern globally distributed strains. Once observed the IS6110 distribution in the MTBC, we selected representative isolates and found a correlation between the normalized expression of IS6110 and its abundance in MTBC chromosomes. We also studied the molecular regulation of IS6110 transposition and we found a synergistic action of two post-transcriptional mechanisms: a -1 ribosomal frameshift and a RNA pseudoknot which interferes translation. The construction of a transcriptionally active transposase resulted in 20-fold increase of the transposition frequency. Finally, we examined transposition in M. bovis and M. tuberculosis during laboratory starvation and in a mouse infection model of TB. Our results shown a higher transposition in M. tuberculosis, that preferably happens during TB infection in mice and after one year of laboratory culture, suggesting that IS6110 transposition is dynamically adapted to the host and to adverse growth conditions. Since the pioneering discovery of transposition by Barbara McClintock in eukaryotes and later in prokaryotes by Robert W. Hedges and Alan E. Jacob, it has become clear the key role of mobile genetics elements in chromosome remodelling, microbial evolution and host adaptation. The insertion sequence IS6110 is widely recognized for its utility in TB diagnosis and epidemiology because it is only present in the M. tuberculosis Complex (MTBC) and its transposition provides an excellent chromosomal polymorphic variability allowing the study of recent TB transmission. This inherent feature of IS6110 leads us to hypothesize that IS6110 plays a crucial role during the TB infectious cycle. However, the biological significance of IS6110 has been hindered by its almost exclusive use as an epidemiological marker. Here, we study the regulatory mechanisms and the distribution of IS6110 in the different MTBC lineages. We discuss the potential biological implications of IS6110, that is much more than an excellent TB epidemiological tool. Since IS6110 could play an important role in the adaptation of MTBC to the host, this study opens new avenues to decipher the biological roles of IS6110 in TB pathogenesis.
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Affiliation(s)
- Jesús Gonzalo-Asensio
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Zaragoza, Spain
- * E-mail: (JGA); (CM)
| | - Irene Pérez
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Nacho Aguiló
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Santiago Uranga
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Picó
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Lampreave
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Alberto Cebollada
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Isabel Otal
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Sofía Samper
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Unidad de Investigación Translacional, Hospital Universitario Miguel Servet, Instituto de Investigación Sanitaria Aragón. Zaragoza, Spain
| | - Carlos Martín
- Grupo de Genética de Micobacterias, Departamento de Microbiología y Medicina Preventiva. Facultad de Medicina, Universidad de Zaragoza, IIS Aragón, Zaragoza, Spain
- CIBER Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Miguel Servet, Zaragoza, Spain
- * E-mail: (JGA); (CM)
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Vandecraen J, Chandler M, Aertsen A, Van Houdt R. The impact of insertion sequences on bacterial genome plasticity and adaptability. Crit Rev Microbiol 2017; 43:709-730. [PMID: 28407717 DOI: 10.1080/1040841x.2017.1303661] [Citation(s) in RCA: 224] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Transposable elements (TE), small mobile genetic elements unable to exist independently of the host genome, were initially believed to be exclusively deleterious genomic parasites. However, it is now clear that they play an important role as bacterial mutagenic agents, enabling the host to adapt to new environmental challenges and to colonize new niches. This review focuses on the impact of insertion sequences (IS), arguably the smallest TE, on bacterial genome plasticity and concomitant adaptability of phenotypic traits, including resistance to antibacterial agents, virulence, pathogenicity and catabolism. The direct consequence of IS transposition is the insertion of one DNA sequence into another. This event can result in gene inactivation as well as in modulation of neighbouring gene expression. The latter is usually mediated by de-repression or by the introduction of a complete or partial promoter located within the element. Furthermore, transcription and transposition of IS are affected by host factors and in some cases by environmental signals offering the host an adaptive strategy and promoting genetic variability to withstand the environmental challenges.
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Affiliation(s)
- Joachim Vandecraen
- a Microbiology Unit, Interdisciplinary Biosciences , Belgian Nuclear Research Centre (SCK•CEN) , Mol , Belgium.,b Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre , Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering , KU Leuven , Leuven , Belgium
| | - Michael Chandler
- c Laboratoire de Microbiologie et Génétique Moléculaires, Centre national de la recherche scientifique , Toulouse , France
| | - Abram Aertsen
- b Laboratory of Food Microbiology and Leuven Food Science and Nutrition Research Centre , Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering , KU Leuven , Leuven , Belgium
| | - Rob Van Houdt
- a Microbiology Unit, Interdisciplinary Biosciences , Belgian Nuclear Research Centre (SCK•CEN) , Mol , Belgium
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5
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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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Ioerger TR, O’Malley T, Liao R, Guinn KM, Hickey MJ, Mohaideen N, Murphy KC, Boshoff HIM, Mizrahi V, Rubin EJ, Sassetti CM, Barry CE, Sherman DR, Parish T, Sacchettini JC. Identification of new drug targets and resistance mechanisms in Mycobacterium tuberculosis. PLoS One 2013; 8:e75245. [PMID: 24086479 PMCID: PMC3781026 DOI: 10.1371/journal.pone.0075245] [Citation(s) in RCA: 185] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2013] [Accepted: 08/12/2013] [Indexed: 11/18/2022] Open
Abstract
Identification of new drug targets is vital for the advancement of drug discovery against Mycobacterium tuberculosis, especially given the increase of resistance worldwide to first- and second-line drugs. Because traditional target-based screening has largely proven unsuccessful for antibiotic discovery, we have developed a scalable platform for target identification in M. tuberculosis that is based on whole-cell screening, coupled with whole-genome sequencing of resistant mutants and recombineering to confirm. The method yields targets paired with whole-cell active compounds, which can serve as novel scaffolds for drug development, molecular tools for validation, and/or as ligands for co-crystallization. It may also reveal other information about mechanisms of action, such as activation or efflux. Using this method, we identified resistance-linked genes for eight compounds with anti-tubercular activity. Four of the genes have previously been shown to be essential: AspS, aspartyl-tRNA synthetase, Pks13, a polyketide synthase involved in mycolic acid biosynthesis, MmpL3, a membrane transporter, and EccB3, a component of the ESX-3 type VII secretion system. AspS and Pks13 represent novel targets in protein translation and cell-wall biosynthesis. Both MmpL3 and EccB3 are involved in membrane transport. Pks13, AspS, and EccB3 represent novel candidates not targeted by existing TB drugs, and the availability of whole-cell active inhibitors greatly increases their potential for drug discovery.
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Affiliation(s)
- Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Theresa O’Malley
- Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - Reiling Liao
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Kristine M. Guinn
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Mark J. Hickey
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Nilofar Mohaideen
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
| | - Kenan C. Murphy
- University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Helena I. M. Boshoff
- Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Valerie Mizrahi
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Eric J. Rubin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Christopher M. Sassetti
- University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| | - Clifton E. Barry
- Tuberculosis Research Section, Laboratory of Clinical Infectious Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - David R. Sherman
- Seattle Biomedical Research Institute, Seattle, Washington, United States of America
| | - Tanya Parish
- Infectious Disease Research Institute, Seattle, Washington, United States of America
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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Reyes A, Sandoval A, Cubillos-Ruiz A, Varley KE, Hernández-Neuta I, Samper S, Martín C, García MJ, Ritacco V, López L, Robledo J, Zambrano MM, Mitra RD, Del Portillo P. IS-seq: a novel high throughput survey of in vivo IS6110 transposition in multiple Mycobacterium tuberculosis genomes. BMC Genomics 2012; 13:249. [PMID: 22703188 PMCID: PMC3443423 DOI: 10.1186/1471-2164-13-249] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 05/30/2012] [Indexed: 11/10/2022] Open
Abstract
Background The insertion element IS6110 is one of the main sources of genomic variability in Mycobacterium tuberculosis, the etiological agent of human tuberculosis. Although IS 6110 has been used extensively as an epidemiological marker, the identification of the precise chromosomal insertion sites has been limited by technical challenges. Here, we present IS-seq, a novel method that combines high-throughput sequencing using Illumina technology with efficient combinatorial sample multiplexing to simultaneously probe 519 clinical isolates, identifying almost all the flanking regions of the element in a single experiment. Results We identified a total of 6,976 IS6110 flanking regions on the different isolates. When validated using reference strains, the method had 100% specificity and 98% positive predictive value. The insertions mapped to both coding and non-coding regions, and in some cases interrupted genes thought to be essential for virulence or in vitro growth. Strains were classified into families using insertion sites, and high agreement with previous studies was observed. Conclusions This high-throughput IS-seq method, which can also be used to map insertions in other organisms, extends previous surveys of in vivo interrupted loci and provides a baseline for probing the consequences of disruptions in M. tuberculosis strains.
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Affiliation(s)
- Alejandro Reyes
- Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St, Louis, MO 63108, USA
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Karpinets T, Greenwood D, Pogribny I, Samatova N. Bacterial stationary-state mutagenesis and Mammalian tumorigenesis as stress-induced cellular adaptations and the role of epigenetics. Curr Genomics 2011; 7:481-96. [PMID: 18369407 DOI: 10.2174/138920206779315764] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Revised: 11/11/2006] [Accepted: 11/23/2006] [Indexed: 01/16/2023] Open
Abstract
Mechanisms of cellular adaptation may have some commonalities across different organisms. Revealing these common mechanisms may provide insight in the organismal level of adaptation and suggest solutions to important problems related to the adaptation. An increased rate of mutations, referred as the mutator phenotype, and beneficial nature of these mutations are common features of the bacterial stationary-state mutagenesis and of the tumorigenic transformations in mammalian cells. We argue that these commonalities of mammalian and bacterial cells result from their stress-induced adaptation that may be described in terms of a common model. Specifically, in both organisms the mutator phenotype is activated in a subpopulation of proliferating stressed cells as a strategy to survival. This strategy is an alternative to other survival strategies, such as senescence and programmed cell death, which are also activated in the stressed cells by different subpopulations. Sustained stress-related proliferative signalling and epigenetic mechanisms play a decisive role in the choice of the mutator phenotype survival strategy in the cells. They reprogram cellular functions by epigenetic silencing of cell-cycle inhibitors, DNA repair, programmed cell death, and by activation of repetitive DNA elements. This reprogramming leads to the mutator phenotype that is implemented by error-prone cell divisions with the involvement of Y family polymerases. Studies supporting the proposed model of stress-induced cellular adaptation are discussed. Cellular mechanisms involved in the bacterial stress-induced adaptation are considered in more detail.
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Affiliation(s)
- Tv Karpinets
- Computational Biology Institute, Computer Science and Mathematics Division, Oak Ridge National Laboratory, P.O. Box 2008, MS6164, Oak Ridge, TN 37831, USA
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Conjugative interaction induces transposition of ISPst9 in Pseudomonas stutzeri AN10. J Bacteriol 2008; 191:1239-47. [PMID: 19060139 DOI: 10.1128/jb.01071-08] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
ISPst9 is an ISL3-like insertion sequence (IS) that was recently described in the naphthalene-degrading organism Pseudomonas stutzeri strain AN10. In this paper we describe a novel strong IS regulation stimulus; transposition of ISPst9 is induced in all P. stutzeri AN10 cells after conjugative interaction with Escherichia coli. Thus, we observed that in all P. stutzeri AN10 cells that received genetic material by conjugation the ISPst9 genomic dose and/or distribution was changed. Furthermore, ISPst9 transposition was also observed when P. stutzeri AN10 cells were put in contact with the plasmidless conjugative strain E. coli S17-1lambda(pir), but not when they were put in contact with E. coli DH5alpha (a nonconjugative strain). The mechanism of ISPst9 transposition was analyzed, and transposition was shown to proceed by excision from the donor DNA using a conservative mechanism, which generated 3- to 10-bp deletions of the flanking DNA. Our results indicate that ISPst9 transposes, forming double-stranded DNA circular intermediates consisting of the IS and a 5-bp intervening DNA sequence probably derived from the ISPst9 flanking regions. The kinetics of IS circle formation are also described.
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10
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McEvoy CRE, Falmer AA, Gey van Pittius NC, Victor TC, van Helden PD, Warren RM. The role of IS6110 in the evolution of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2007; 87:393-404. [PMID: 17627889 DOI: 10.1016/j.tube.2007.05.010] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 05/15/2007] [Accepted: 05/22/2007] [Indexed: 10/23/2022]
Abstract
Members of the Mycobacterium tuberculosis complex contain the transposable element IS6110 which, due to its high numerical and positional polymorphism, has become a widely used marker in epidemiological studies. Here, we review the evidence that IS6110 is not simply a passive or 'junk' DNA sequence, but that, through its transposable activity, it is able to generate genotypic variation that translates into strain-specific phenotypic variation. We also speculate on the role that this variation has played in the evolution of M. tuberculosis and conclude that the presence of a moderate IS6110 copy number within the genome may provide the pathogen with a selective advantage that has aided its virulence.
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Affiliation(s)
- Christopher R E McEvoy
- DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa.
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11
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Ullrich S, Kube M, Schübbe S, Reinhardt R, Schüler D. A hypervariable 130-kilobase genomic region of Magnetospirillum gryphiswaldense comprises a magnetosome island which undergoes frequent rearrangements during stationary growth. J Bacteriol 2005; 187:7176-84. [PMID: 16237001 PMCID: PMC1272989 DOI: 10.1128/jb.187.21.7176-7184.2005] [Citation(s) in RCA: 164] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genes involved in magnetite biomineralization are clustered in the genome of the magnetotactic bacterium Magnetospirillum gryphiswaldense. We analyzed a 482-kb genomic fragment, in which we identified an approximately 130-kb region representing a putative genomic "magnetosome island" (MAI). In addition to all known magnetosome genes, the MAI contains genes putatively involved in magnetosome biomineralization and numerous genes with unknown functions, as well as pseudogenes, and it is particularly rich in insertion elements. Substantial sequence polymorphism of clones from different subcultures indicated that this region undergoes frequent rearrangements during serial subcultivation in the laboratory. Spontaneous mutants affected in magnetosome formation arise at a frequency of up to 10(-2) after prolonged storage of cells at 4 degrees C or exposure to oxidative stress. All nonmagnetic mutants exhibited extended and multiple deletions in the MAI and had lost either parts of or the entire mms and mam gene clusters encoding magnetosome proteins. The mutations were polymorphic with respect to the sites and extents of deletions, but all mutations were found to be associated with the loss of various copies of insertion elements, as revealed by Southern hybridization and PCR analysis. Insertions and deletions in the MAI were also found in different magnetosome-producing clones, indicating that parts of this region are not essential for the magnetic phenotype. Our data suggest that the genomic MAI undergoes frequent transposition events, which lead to subsequent deletion by homologous recombination under physiological stress conditions. This can be interpreted in terms of adaptation to physiological stress and might contribute to the genetic plasticity and mobilization of the magnetosome island.
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Affiliation(s)
- Susanne Ullrich
- MPI für Marine Mikrobiologie, Celsiusstr. 1, 28359 Bremen, Germany
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12
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Suokko A, Savijoki K, Malinen E, Palva A, Varmanen P. Characterization of a mobile clpL gene from Lactobacillus rhamnosus. Appl Environ Microbiol 2005; 71:2061-9. [PMID: 15812039 PMCID: PMC1082546 DOI: 10.1128/aem.71.4.2061-2069.2005] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two genes encoding ClpL ATPase proteins were identified in a probiotic Lactobacillus rhamnosus strain, E-97800. Sequence analyses revealed that the genes, designated clpL1 and clpL2, share 80% identity. The clpL2 gene showed the highest degree of identity (98.5%) to a clpL gene from Lactobacillus plantarum WCFSI, while it was not detected in three other L. rhamnosus strains studied. According to Northern analyses, the expression of clpL1 and the clpL2 were induced during heat shock by > 20- and 3-fold, respectively. The functional promoter regions were determined by primer extension analyses, and the clpL1 promoter was found to be overlapped by an inverted repeat structure identical to the conserved CIRCE element, indicating that clpL1 belongs to the HrcA regulon in L. rhamnosus. No consensus binding sites for HrcA or CtsR could be identified in the clpL2 promoter region. Interestingly, the clpL2 gene was found to be surrounded by truncated transposase genes and flanked by inverted repeat structures nearly identical to the terminal repeats of the ISLpl1 from L. plantarum HN38. Furthermore, clpL2 was shown to be mobilized during prolonged cultivation at elevated temperature. The presence of a gene almost identical to clpL2 in L. plantarum and its absence in other L. rhamnosus strains suggest that the L. rhamnosus E-97800 has acquired the clpL2 gene via horizontal transfer. No change in the stress tolerance of the ClpL2-deficient derivative of E-97800 compared to the parental strain was observed.
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Affiliation(s)
- Aki Suokko
- Division of Microbiology and Epidemiology, Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine, University of Helsinki, University of Helsinki, Helsinki, Finland
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13
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Stragier P, Ablordey A, Meyers WM, Portaels F. Genotyping Mycobacterium ulcerans and Mycobacterium marinum by using mycobacterial interspersed repetitive units. J Bacteriol 2005; 187:1639-47. [PMID: 15716434 PMCID: PMC1064023 DOI: 10.1128/jb.187.5.1639-1647.2005] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel category of variable tandem repeats (VNTR) called mycobacterial interspersed repetitive units (MIRUs) has been identified for Mycobacterium ulcerans (n = 39), M. marinum (n = 27), and one related organism. Fifteen MIRU loci were identified in the genome of M. marinum and were used to genotype M. ulcerans, M. marinum, and an M. marinum-like organism that is considered a possible missing link between M. marinum and M. ulcerans. Seven MIRU loci were polymorphic, and locus-specific PCRs for four of these loci differentiated seven M. ulcerans genotypes, four M. marinum genotypes, and a unique genotype for the missing link organism. The seven M. ulcerans genotypes were related to six different geographic origins of isolates. All isolates from West and Central Africa, including old and recent isolates, belonged to the same genotype, emphasizing the great spatiotemporal homogeneity among African isolates. Unlike the M. ulcerans genotypes, the four M. marinum genotypes could not be clearly related to the geographic origins of the isolates. According to MIRU-VNTR typing, all M. ulcerans and M. marinum isolates of American origin were closely related, suggesting a common American ancestor for these two pathogenic species on the American continents. MIRU typing has significant potential value for discriminating between reoccurrence and reinfection for M. ulcerans disease.
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Affiliation(s)
- Pieter Stragier
- Department of Microbiology, Mycobacteriology Unit, Institute of Tropical Medicine, Nationalestraat 155, B-2000 Antwerp, Belgium
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14
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Del Re B, Bersani F, Agostini C, Mesirca P, Giorgi G. Various effects on transposition activity and survival of Escherichia coli cells due to different ELF-MF signals. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2004; 43:265-270. [PMID: 15645314 DOI: 10.1007/s00411-004-0260-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2004] [Accepted: 09/20/2004] [Indexed: 05/24/2023]
Abstract
Previous assays with weak sinusoidal magnetic fields (SMF) have shown that bacteria that had been exposed to a 50 Hz magnetic field (0.1-1 mT) gave colonies with significantly lower transposition activity as compared to sham-exposed bacteria. These experiments have now been extended by using a pulsed-square wave magnetic field (PMF) and, unexpectedly, it was found that bacteria exposed to PMF showed a higher transposition activity compared to the controls. The increase of the transposition activity was positively correlated with the intensity of the magnetic fields (linear dose-effect relation). This phenomenon was not affected by any bacterial cell proliferation, since no significant difference was observed in number and size of PMF-exposed and sham-exposed colonies. In addition, the cell viability of E. coli was significantly higher than that of the controls when exposed to SMF, and lower than that of the controls when exposed to PMF. Under our experimental conditions it was shown that exposure to PMF stimulates the transposition activity and reduces cell viability of bacteria, whereas exposure to SMF reduces the transposition mobility and enhances cell viability. These results suggest that the biological effects of magnetic fields may critically depend on the physical characteristics of the magnetic signal, in particular the wave shape.
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Affiliation(s)
- B Del Re
- Department of Evolutionary Experimental Biology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
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15
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Garbe TR, Suzuki N, Inui M, Yukawa H. Inhibitor-associated transposition events in Corynebacterium glutamicum. Mol Genet Genomics 2004; 271:729-41. [PMID: 15221457 DOI: 10.1007/s00438-004-1026-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2004] [Accepted: 05/06/2004] [Indexed: 11/30/2022]
Abstract
In up to 100% of all bacteria grown in the presence of initially inhibitory concentrations of five diverse inhibitors, an extra copy of the resident insertion element IS 31831 was found in specific chromosomal regions, the sites of which apparently depended on the inhibitor used. Thus, in nine out of nine independently isolated cyanide-associated transpositions, the acquired copy was located within an ORF encoding a protein related to the hypothetical but conserved protein YeiH of Escherichia coli. A putative Sox box upstream of the yeiH gene implicates superoxide as a potential regulator of the gene, a possibility further supported by the finding that superoxide dismutase (SodA) is overexpressed in cells cultured in cyanide-containing medium. Neither the cyanide-associated nor any of the other transposition mutations appeared to confer any discernible phenotypic advantage upon cells grown in the presence or absence of the inhibitors, as revealed most stringently by mixed-cell experiments. An alternative, albeit heterodox, explanation for the emergence of the mutants postulates a very high rate of transpositional activity in the presence of inhibitors. The initial emergence of the mutants was found to depend crucially upon the cell density. Thus, when growth medium was supplemented with 50 mM fluoropyruvate and inoculated to a density of 2 x 10(7) cfu/ml, single colonies with heterogeneous restriction fragment length polymorphisms (RFLPs) were routinely isolated at a frequency of 6 to 16% after 1-2 days of incubation. After 3 days, 10-36% of the colonies showed RFLPs, but the type was now dominated by the fluoropyruvate-specific RFLP, which, at higher resolution, invariably proved to be heterogeneous. This heterogeneity proved that these specific mutants were of multiple origin, indicating that clonal enrichment was irrelevant to their emergence. It is suggested that the presence of the inhibitor induces the development of hyper-transpositional activity, which is regulated by a soluble bacterial product.
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Affiliation(s)
- T R Garbe
- Research Institute of Innovative Technology for the Earth (RITE), 9-2, Kizugawadai, 619-0292, Kizu-cho, Kyoto, Japan
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16
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Safi H, Barnes PF, Lakey DL, Shams H, Samten B, Vankayalapati R, Howard ST. IS6110 functions as a mobile, monocyte-activated promoter in Mycobacterium tuberculosis. Mol Microbiol 2004; 52:999-1012. [PMID: 15130120 DOI: 10.1111/j.1365-2958.2004.04037.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The mobile insertion sequence, IS6110, is an important marker in tracking of Mycobacterium tuberculosis strains. Here, we demonstrate that IS6110 can upregulate downstream genes through an outward-directed promoter in its 3' end, thus adding to the significance of this element. Promoter activity was orientation dependent and was localized within a 110 bp fragment adjacent to the right terminal inverted repeat. Transcripts from this promoter, named OP6110, begin approximately 85 bp upstream of the 3' end of IS6110. Use of green fluorescent protein (GFP) expression constructs showed that OP6110 was upregulated in M. tuberculosis during growth in human monocytes and in late growth phases in broth. Analysis of natural insertion sites in M. tuberculosis showed that IS6110 upregulated expression of several downstream genes during growth in human monocytes, including Rv2280 in H37Rv and the PE-PGRS gene, Rv1468c, in the clinical strain 210, which is a member of the Beijing family. Transcription between IS6110 and downstream genes was confirmed by reverse transcription polymerase chain reaction. The ability to activate genes during infection suggests that IS6110 has the potential to influence growth characteristics of different strains, and indicates another mechanism by which IS6110 can impact M. tuberculosis evolution.
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Affiliation(s)
- Hassan Safi
- Department of Microbiology, Center for Pulmonary and Infectious Disease Control, University of Texas Health Center at Tyler, 11937 US Highway 271, Tyler, TX 75708-3154, USA
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17
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Kana BD, Weinstein EA, Avarbock D, Dawes SS, Rubin H, Mizrahi V. Characterization of the cydAB-encoded cytochrome bd oxidase from Mycobacterium smegmatis. J Bacteriol 2001; 183:7076-86. [PMID: 11717265 PMCID: PMC95555 DOI: 10.1128/jb.183.24.7076-7086.2001] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The cydAB genes from Mycobacterium smegmatis have been cloned and characterized. The cydA and cydB genes encode the two subunits of a cytochrome bd oxidase belonging to the widely distributed family of quinol oxidases found in prokaryotes. The cydD and cydC genes located immediately downstream of cydB encode a putative ATP-binding cassette-type transporter. At room temperature, reduced minus oxidized difference spectra of membranes purified from wild-type M. smegmatis displayed spectral features that are characteristic of the gamma-proteobacterial type cytochrome bd oxidase. Inactivation of cydA or cydB by insertion of a kanamycin resistance marker resulted in loss of d-heme absorbance at 631 nm. The d-heme could be restored by transformation of the M. smegmatis cyd mutants with a replicating plasmid carrying the highly homologous cydABDC gene cluster from Mycobacterium tuberculosis. Inactivation of cydA had no effect on the ability of M. smegmatis to exit from stationary phase at 37 or 42 degrees C. The growth rate of the cydA mutant was tested under oxystatic conditions. Although no discernible growth defect was observed under moderately aerobic conditions (9.2 to 37.5 x 10(2) Pa of pO(2) or 5 to 21% air saturation), the mutant displayed a significant growth disadvantage when cocultured with the wild type under extreme microaerophilia (0.8 to 1.7 x 10(2) Pa of pO(2) or 0.5 to 1% air saturation). These observations were in accordance with the two- to threefold increase in cydAB gene expression observed upon reduction of the pO(2) of the growth medium from 21 to 0.5% air saturation and with the concomitant increase in d-heme absorbance in spectra of membranes isolated from wild-type M. smegmatis cultured at 1% air saturation. Finally, the cydA mutant displayed a competitive growth disadvantage in the presence of the terminal oxidase inhibitor, cyanide, when cocultured with wild type at 21% air saturation in an oxystat. In conjunction with these findings, our results suggest that cytochrome bd is an important terminal oxidase in M. smegmatis.
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Affiliation(s)
- B D Kana
- MRC/SAIMR/WITS Molecular Mycobacteriology Research Unit, South African Institute for Medical Research, Johannesburg, South Africa
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18
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Vera-Cabrera L, Hernández-Vera MA, Welsh O, Johnson WM, Castro-Garza J. Phospholipase region of Mycobacterium tuberculosis is a preferential locus for IS6110 transposition. J Clin Microbiol 2001; 39:3499-504. [PMID: 11574563 PMCID: PMC88379 DOI: 10.1128/jcm.39.10.3499-3504.2001] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Enzymes with phospholipase C activity in Mycobacterium tuberculosis have been recently described. The three genes encoding these proteins, plcA, plcB, and plcC, are located at position 2351 of the genomic map of M. tuberculosis H37Rv and are arranged in tandem. We have previously described the presence of variations in the restriction fragment length polymorphism patterns of the plcA and plcB genes in M. tuberculosis clinical isolates. In the present work we investigated the origin of this polymorphism by sequence analysis of the phospholipase-encoding regions of 11 polymorphic M. tuberculosis clinical isolates. To do so, a long-PCR assay was used to amplify a 5,131-bp fragment that contains the plcA and plcB genes and part of the plcC gene. In the M. tuberculosis strains studied the production of an amplicon approximately 1,400 bp larger than anticipated was observed. Sequence analysis of the PCR products indicated the presence of a foreign sequence that corresponded to an IS6110 element. We observed insertion elements in the plcA, plcB, and plcC genes. One site in plcB had the highest incidence of transposition (5 out of 11 strains). In two strains the insertion element was found in plcA in the same nucleotide position. In all the cases, IS6110 was transposed in the same direction. The high level of transposition in the phospholipase region can lead to the excision of fragments of genomic DNA by recombination of neighboring IS6110 elements, as demonstrated by finding the deletion, in two strains, of a 2,837-bp fragment that included plcA and most of plcB. This can explain the negative results obtained by some authors when detecting the mtp40 sequence (plcA) by PCR. Given the high polymorphism in this region, the use of the mtp40 sequence as a genetic marker for M. tuberculosis sensu stricto is very restricted.
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Affiliation(s)
- L Vera-Cabrera
- Servicio de Dermatología, Hospital Universitario José E. González, Madero y Gonzalitos, Col Mitras Centro, Monterrey, México.
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19
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Chemlal K, Huys G, Fonteyne PA, Vincent V, Lopez AG, Rigouts L, Swings J, Meyers WM, Portaels F. Evaluation of PCR-restriction profile analysis and IS2404 restriction fragment length polymorphism and amplified fragment length polymorphism fingerprinting for identification and typing of Mycobacterium ulcerans and M. marinum. J Clin Microbiol 2001; 39:3272-8. [PMID: 11526162 PMCID: PMC88330 DOI: 10.1128/jcm.39.9.3272-3278.2001] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2000] [Accepted: 05/29/2001] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium ulcerans and M. marinum are emerging necrotizing mycobacterial pathogens that reside in common reservoirs of infection and exhibit striking pathophysiological similarities. Furthermore, the interspecific taxonomic relationship between the two species is not clear as a result of the very high phylogenetic relatedness (i.e., >99.8% 16S rRNA sequence similarity), in contrast to only 25 to 47% DNA relatedness. To help understand the genotypic affiliation between these two closely related species, we performed a comparative analysis including PCR restriction profile analysis (PRPA), IS2404 restriction fragment length polymorphism (RFLP), and amplified fragment length polymorphism (AFLP) on a set of M. ulcerans (n = 29) and M. marinum (n = 28) strains recovered from different geographic origins. PRPA was based on a triple restriction of the 3' end region of 16S rRNA, which differentiated M. ulcerans into three types; however, the technique could not distinguish M. marinum from M. ulcerans isolates originating from South America and Southeast Asia. RFLP based on IS2404 produced six M. ulcerans types related to six geographic regions and did not produce any band with M. marinum, confirming the previous findings of Chemlal et al. (K. Chemlal, K. DeRidder, P. A. Fonteyne, W. M. Meyers, J. Swings, and F. Portaels, Am. J. Trop. Med. Hyg. 64:270-273, 2001). AFLP analysis resulted in profiles which grouped M. ulcerans and M. marinum into two separate clusters. The numerical analysis also revealed subgroups among the M. marinum and M. ulcerans isolates. In conclusion, PRPA appears to provide a rapid method for differentiating the African M. ulcerans type from other geographical types but is unsuitable for interspecific differentiation of M. marinum and M. ulcerans. In comparison, whole- genome techniques such as IS 2404-RFLP and AFLP appear to be far more useful in discriminating between M. marinum and M. ulcerans, and may thus be promising molecular tools for the differential diagnosis of infections caused by these two species.
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Affiliation(s)
- K Chemlal
- Department of Microbiology, Mycobacteriology Unit, Institute of Tropical Medicine, B-2000 Antwerp, Belgium.
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20
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Fodor B, Rákhely G, Kovács KL. Transposon mutagenesis in purple sulfur photosynthetic bacteria: identification of hypF, encoding a protein capable of processing [NiFe] hydrogenases in alpha, beta, and gamma subdivisions of the proteobacteria. Appl Environ Microbiol 2001; 67:2476-83. [PMID: 11375153 PMCID: PMC92897 DOI: 10.1128/aem.67.6.2476-2483.2001] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A random transposon-based mutagenesis system was optimized for the purple sulfur phototrophic bacterium Thiocapsa roseopersicina BBS. Screening for hydrogenase-deficient phenotypes resulted in the isolation of six independent mutants in a mini-Tn5 library. One of the mutations was in a gene showing high amino acid sequence similarity to HypF proteins in other organisms. Inactivation of hydrogen uptake activity in the hypF-deficient mutant resulted in a dramatic increase in the hydrogen evolution capacity of T. roseopersicina under nitrogen-fixing conditions. This mutant is therefore a promising candidate for use in practical biohydrogen-producing systems. The reconstructed hypF gene was able to complement the hypF-deficient mutant of T. roseopersicina BBS. Heterologous complementation experiments, using hypF mutant strains of T. roseopersicina, Escherichia coli, and Ralstonia eutropha and various hypF genes, were performed. They were successful in all of the cases tested, although for E. coli, the regulatory region of the foreign gene had to be replaced in order to achieve partial complementation. RT-PCR data suggested that HypF has no effect on the transcriptional regulation of the structural genes of hydrogenases in this organism.
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Affiliation(s)
- B Fodor
- Institute of Biophysics, Biological Research Center, Hungarian Academy of Sciences, and Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary
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21
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Lim A, Dick T. Plate-based dormancy culture system for Mycobacterium smegmatis and isolation of metronidazole-resistant mutants. FEMS Microbiol Lett 2001; 200:215-9. [PMID: 11425478 DOI: 10.1111/j.1574-6968.2001.tb10718.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Mycobacterium smegmatis is an obligate aerobe. However, growth analyses in oxygen-limited liquid cultures have shown that the bacillus is able to survive anoxia with a half-life of 4 days by shifting down to a drug-resistant, dormant state. Metronidazole is the first lead against dormant bacilli and shows selective toxicity for this physiological state. Here, we report a plate-based dormancy culture system employing anoxic jars for M. smegmatis. Its usefulness for the genetic analysis of dormancy was demonstrated by isolating the first metronidazole-resistant mutants. Highly resistant mutants formed slightly yellow (as opposed to creamy) colonies. Furthermore, high-level metronidazole resistance correlated with an increased half-life of 12 days under anoxic conditions. This suggests a link between metronidazole susceptibility and anaerobic survival.
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Affiliation(s)
- A Lim
- Institute of Molecular and Cell Biology, 30 Medical Drive, 117609, Singapore, Singapore
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22
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de Boer AS, Kremer K, Borgdorff MW, de Haas PE, Heersma HF, van Soolingen D. Genetic heterogeneity in Mycobacterium tuberculosis isolates reflected in IS6110 restriction fragment length polymorphism patterns as low-intensity bands. J Clin Microbiol 2000; 38:4478-84. [PMID: 11101583 PMCID: PMC87624 DOI: 10.1128/jcm.38.12.4478-4484.2000] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis isolates with identical IS6110 restriction fragment length polymorphism (RFLP) patterns are considered to originate from the same ancestral strain and thus to reflect ongoing transmission. In this study, we investigated 1,277 IS6110 RFLP patterns for the presence of multiple low-intensity bands (LIBs), which may indicate infections with multiple M. tuberculosis strains. We did not find any multiple LIBs, suggesting that multiple infections are rare in the Netherlands. However, we did observe a few LIBs in 94 patterns (7.4%) and examined the nature of this phenomenon. With single-colony cultures it was found that LIBs mostly represent mixed bacterial populations with slightly different RFLP patterns. Mixtures were expressed in RFLP patterns as LIBs when 10 to 30% of the DNA analyzed originated from a bacterial population with another RFLP pattern. Presumably, a part of the LIBs did not represent mixed bacterial populations, as in some clusters all strains exhibited LIBs in their RFLP patterns. The occurrence of LIBs was associated with increased age in patients. This may reflect either a gradual change of the bacterial population in the human body over time or IS6110-mediated genetic adaptation of M. tuberculosis to changes in the environmental conditions during the dormant state or reactivation thereafter.
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Affiliation(s)
- A S de Boer
- Department of Infectious Disease Epidemiology, National Institute of Public Health and the Environment (RIVM), 3720 BA Bilthoven, The Netherlands.
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Machowski EE, McAdam RA, Derbyshire KM, Mizrahi V. Construction and application of mycobacterial reporter transposons. Gene 2000; 253:67-75. [PMID: 10925203 DOI: 10.1016/s0378-1119(00)00238-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The transposon Tn5367, which is a derivative of the mycobacterial insertion sequence IS1096, was modified by introducing novel genes to produce reporter transposons which can be used to generate transposon insertion libraries containing mycobacterial gene or operon fusions. A plasmid that is temperature-sensitive for replication in mycobacteria was used to deliver promoterless lacZ or aph reporter genes to Mycobacterium smegmatis as transcriptional (lacZ), or translational ('aph) fusions. Mutants containing lacZ produced varying intensities of blue colour on indicator media. This reporter activity could be used as a quantitative measure of promoter strength. Mutants displaying varying levels of resistance to kanamycin were obtained by transpositional insertion of the 'aph reporter lacking a promoter, ribosome binding site and start codon to form functionally active translational fusions. Finally, inclusion of the R6Kgamma origin within Tn5367 allowed transposon insertions to be rescued in an Escherichia coli host strain permissive for the replication of this origin. This study demonstrates that transcriptional and translational reporter derivatives of Tn5367 are functional, and they supplement the growing range of molecular tools available for the study of mycobacteria.
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Affiliation(s)
- E E Machowski
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa
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24
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Wall S, Ghanekar K, McFadden J, Dale JW. Context-sensitive transposition of IS6110 in mycobacteria. MICROBIOLOGY (READING, ENGLAND) 1999; 145 ( Pt 11):3169-3176. [PMID: 10589725 DOI: 10.1099/00221287-145-11-3169] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The rational use of IS6110 fingerprinting for studies of the molecular epidemiology and evolution of Mycobacterium tuberculosis requires understanding of the dynamics of transposition. In laboratory model systems, it has been shown that transposition is context-sensitive, i.e. it is influenced by the nature of the site in which the insertion sequence is presented. Stimulation of transposition by activation of an adjacent promoter supports the hypothesis that transposition occurs more readily from transcriptionally active locations. In addition, it has been shown that transposition can be enhanced by the expression of the transposase in trans. These findings imply that the frequency of transposition will vary substantially between different strains of M. tuberculosis, and furthermore that a hitherto stable strain may develop more rapid variation due to transposition into an active site. The use of IS6110 fingerprinting for the analysis of longer-range relationships between M. tuberculosis isolates therefore needs to be interpreted with care.
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Affiliation(s)
- Sue Wall
- Molecular Microbiology Group, School of Biological Sciences, University of Surrey, Guildford GU2 5XH, UK1
| | - Kiran Ghanekar
- Molecular Microbiology Group, School of Biological Sciences, University of Surrey, Guildford GU2 5XH, UK1
| | - Johnjoe McFadden
- Molecular Microbiology Group, School of Biological Sciences, University of Surrey, Guildford GU2 5XH, UK1
| | - Jeremy W Dale
- Molecular Microbiology Group, School of Biological Sciences, University of Surrey, Guildford GU2 5XH, UK1
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