1
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Craske MW, Wilson JS, Fogg PCM. Gene transfer agents: structural and functional properties of domesticated viruses. Trends Microbiol 2024:S0966-842X(24)00133-1. [PMID: 38806321 DOI: 10.1016/j.tim.2024.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/30/2024]
Abstract
Horizontal exchange of DNA between bacteria and archaea is prevalent and has major potential implications for genome evolution, plasticity, and population fitness. Several transfer mechanisms have been identified, including gene transfer agents (GTAs). GTAs are intricately regulated domesticated viruses that package host DNA into virus-like capsids and transfer this DNA throughout the bacterial community. Several important advances have recently been made in our understanding of these unusual particles. In this review, we highlight some of these findings, primarily for the model GTA produced by Rhodobacter capsulatus but also for newly identified GTA producers. We provide key insights into these important genetic elements, including the differences between GTAs from their ancestral bacteriophages, their regulation and control, and their elusive evolutionary function.
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Affiliation(s)
| | - Jason S Wilson
- Biology Department, University of York, York YO10 5DD, UK; York Structural Biology Laboratory (YSBL), University of York, York YO10 5DD, UK
| | - Paul C M Fogg
- Biology Department, University of York, York YO10 5DD, UK; York Biomedical Research Institute (YBRI), University of York, York YO10 5NG, UK.
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2
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Fogg PCM. Gene transfer agents: The ambiguous role of selfless viruses in genetic exchange and bacterial evolution. Mol Microbiol 2024. [PMID: 38511257 DOI: 10.1111/mmi.15251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024]
Abstract
Gene transfer agents (GTAs) are genetic elements derived from ancestral bacteriophages that have become domesticated by the host. GTAs are present in diverse prokaryotic organisms, where they can facilitate horizontal gene transfer under certain conditions. Unlike typical bacteriophages, GTAs do not exhibit any preference for the replication or transfer of the genes encoding them; instead, they exhibit a remarkable capacity to package chromosomal, and sometimes extrachromosomal, DNA into virus-like capsids and disseminate it to neighboring cells. Because GTAs resemble defective prophages, identification of novel GTAs is not trivial. The detection of candidates relies on the genetic similarity to known GTAs, which has been fruitful in α-proteobacterial lineages but challenging in more distant bacteria. Here we consider several fundamental questions: What is the true prevalence of GTAs in prokaryote genomes? Given there are high costs for GTA production, what advantage do GTAs provide to the bacterial host to justify their maintenance? How is the bacterial chromosome recognized and processed for inclusion in GTA particles? This article highlights the challenges in comprehensively understanding GTAs' prevalence, function and DNA packaging method. Going forward, broad study of atypical GTAs and use of ecologically relevant conditions are required to uncover their true impact on bacterial chromosome evolution.
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3
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Abstract
Prokaryotes commonly undergo genome reduction, particularly in the case of symbiotic bacteria. Genome reductions tend toward the energetically favorable removal of unnecessary, redundant, or nonfunctional genes. However, without mechanisms to compensate for these losses, deleterious mutation and genetic drift might otherwise overwhelm a population. Among the mechanisms employed to counter gene loss and share evolutionary success within a population, gene transfer agents (GTAs) are increasingly becoming recognized as important contributors. Although viral in origin, GTA particles package fragments of their "host" genome for distribution within a population of cells, often in a synchronized manner, rather than selfishly packaging genes necessary for their spread. Microbes as diverse as archaea and alpha-proteobacteria have been known to produce GTA particles, which are capable of transferring selective advantages such as virulence factors and antibiotic resistance. In this review, we discuss the various types of GTAs identified thus far, focusing on a defined set of symbiotic alpha-proteobacteria known to carry them. Drawing attention to the predicted presence of these genes, we discuss their potential within the selective marine and terrestrial environments occupied by mutualistic, parasitic, and endosymbiotic microbes.
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Affiliation(s)
- Steen Christensen
- Department of Biological Sciences, Florida International University, Miami, FL, USA.,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
| | - Laura R Serbus
- Department of Biological Sciences, Florida International University, Miami, FL, USA. .,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA.
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4
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Grüll MP, Mulligan ME, Lang AS. Small extracellular particles with big potential for horizontal gene transfer: membrane vesicles and gene transfer agents. FEMS Microbiol Lett 2019; 365:5067299. [PMID: 30085064 DOI: 10.1093/femsle/fny192] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 08/04/2018] [Indexed: 12/18/2022] Open
Abstract
Bacteria are known to release different types of particles that serve various purposes such as the processing of metabolites, communication, and the transfer of genetic material. One of the most interesting aspects of the production of such particles is the biogenesis and trafficking of complex particles that can carry DNA, RNA, proteins or toxins into the surrounding environment to aid in bacterial survival or lead to gene transfer. Two important bacterial extracellular complexes are membrane vesicles and gene transfer agents. In this review, we will discuss the production, contents and functions of these two types of particles as related to their abilities to facilitate horizontal gene transfer.
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Affiliation(s)
| | - M E Mulligan
- Biochemistry, Memorial University of Newfoundland, St John's, NL, Canada
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5
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Redfield RJ, Soucy SM. Evolution of Bacterial Gene Transfer Agents. Front Microbiol 2018; 9:2527. [PMID: 30410473 PMCID: PMC6209664 DOI: 10.3389/fmicb.2018.02527] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 10/03/2018] [Indexed: 01/30/2023] Open
Abstract
Bacterial gene transfer agents (GTAs) are small virus-like particles that package DNA fragments and inject them into cells. They are encoded by gene clusters resembling defective prophages, with genes for capsid head and tail components. These gene clusters are usually assumed to be maintained by selection for the benefits of GTA-mediated recombination, but this has never been tested. We rigorously examined the potential benefits of GTA-mediated recombination, considering separately transmission of GTA-encoding genes and recombination of all chromosomal genes. In principle GTA genes could be directly maintained if GTA particles spread them to GTA- cells often enough to compensate for the loss of GTA-producing cells. However, careful bookkeeping showed that losses inevitably exceed gains for two reasons. First, cells must lyse to release particles to the environment. Second, GTA genes are not preferentially replicated before DNA is packaged. A simulation model was then used to search for conditions where recombination of chromosomal genes makes GTA+ populations fitter than GTA- populations. Although the model showed that both synergistic epistasis and some modes of regulation could generate fitness benefits large enough to overcome the cost of lysis, these benefits neither allowed GTA+ cells to invade GTA- populations, nor allowed GTA+ populations to resist invasion by GTA- cells. Importantly, the benefits depended on highly improbable assumptions about the efficiencies of GTA production and recombination. Thus, the selective benefits that maintain GTA gene clusters over many millions of years must arise from consequences other than transfer of GTA genes or recombination of chromosomal genes.
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Affiliation(s)
- Rosemary J Redfield
- Department of Zoology, University of British Columbia, Vancouver, BC, Canada
| | - Shannon M Soucy
- Department of Biological Sciences, Dartmouth College, Hanover, NH, United States
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6
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Lang AS, Westbye AB, Beatty JT. The Distribution, Evolution, and Roles of Gene Transfer Agents in Prokaryotic Genetic Exchange. Annu Rev Virol 2017; 4:87-104. [DOI: 10.1146/annurev-virology-101416-041624] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andrew S. Lang
- Department of Biology, Memorial University of Newfoundland, St. John's, A1B 3X9, Canada
| | - Alexander B. Westbye
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, Canada
| | - J. Thomas Beatty
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, V6T 1Z3, Canada
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7
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Xu F, Cheng G, Hao H, Wang Y, Wang X, Chen D, Peng D, Liu Z, Yuan Z, Dai M. Mechanisms of Antibacterial Action of Quinoxaline 1,4-di- N-oxides against Clostridium perfringens and Brachyspira hyodysenteriae. Front Microbiol 2016; 7:1948. [PMID: 28018297 PMCID: PMC5147047 DOI: 10.3389/fmicb.2016.01948] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 11/21/2016] [Indexed: 11/24/2022] Open
Abstract
Quinoxaline 1,4-di-N-oxides (QdNOs) are a class of bioreductive compounds, however, their antibacterial mechanisms are still unclarified. The aim of this study was to assess the ability of two representative QdNO drugs, cyadox (CYA) and olaquindox (OLA), to produce reactive oxide species (ROS) in Gram-positive anaerobe Clostridium perfringens CVCC1125 and Gram-negative anaerobe Brachyspira hyodysenteriae B204. In addition, the effects of QdNOs on the integrity of bacterial cell walls and membranes as well as the morphological alterations and DNA oxidative damage in C. perfringens and B. hyodysenteriae were analyzed. It was demonstrated that under anaerobic conditions, QdNOs were metabolized into the reduced products which did not show any antibacterial activity. A significant dose-related increase of intracellular ROS level and intracellular hydroxyl radicals were evident in bacteria exposed to QdNOs. The result of biochemical assay showed that the cell walls and membranes of the bacteria treated with QdNOs were damaged. After exposure to 1/2MIC to 4MIC of CYA and OLA, C. perfringens and B. hyodysenteriae became elongated and filamentous. Morphological observation with scanning and transmission electron microscopes revealed rupture, loss of cytoplasmic material and cell lysis in QdNO-treated bacteria, indicating serious damage of cells. There was an increase of 8-OHdG in the two strains treated by QdNOs, but it was lower in C. perfringens CVCC1125 than in B. hyodysenteriae B204. Agarose gel electrophoresis showed the degradation of chromosomal DNA in both of the two anaerobes treated by QdNOs. The results suggest that QdNOs may kill C. perfringens and B. hyodysenteriae via the generation of ROS and hydroxyl radicals from the bacterial metabolism of QdNOs, which cause oxidative damage in bacteria under anaerobic conditions.
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Affiliation(s)
- Fanfan Xu
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Ministry of Agriculture Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University Wuhan, China
| | - Guyue Cheng
- Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University Wuhan, China
| | - Haihong Hao
- Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University Wuhan, China
| | - Yulian Wang
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Ministry of Agriculture Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China; Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China
| | - Xu Wang
- Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University Wuhan, China
| | - Dongmei Chen
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Ministry of Agriculture Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China; Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China
| | - Dapeng Peng
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Ministry of Agriculture Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China; Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China
| | - Zhenli Liu
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Ministry of Agriculture Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China; Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China
| | - Zonghui Yuan
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Ministry of Agriculture Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural UniversityWuhan, China; Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural UniversityWuhan, China
| | - Menghong Dai
- Ministry of Agriculture Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University Wuhan, China
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Hynes AP, Shakya M, Mercer RG, Grüll MP, Bown L, Davidson F, Steffen E, Matchem H, Peach ME, Berger T, Grebe K, Zhaxybayeva O, Lang AS. Functional and Evolutionary Characterization of a Gene Transfer Agent's Multilocus "Genome". Mol Biol Evol 2016; 33:2530-43. [PMID: 27343288 PMCID: PMC5026251 DOI: 10.1093/molbev/msw125] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Gene transfer agents (GTAs) are phage-like particles that can package and transfer a random piece of the producing cell’s genome, but are unable to transfer all the genes required for their own production. As such, GTAs represent an evolutionary conundrum: are they selfish genetic elements propagating through an unknown mechanism, defective viruses, or viral structures “repurposed” by cells for gene exchange, as their name implies? In Rhodobacter capsulatus, production of the R. capsulatus GTA (RcGTA) particles is associated with a cluster of genes resembling a small prophage. Utilizing transcriptomic, genetic and biochemical approaches, we report that the RcGTA “genome” consists of at least 24 genes distributed across five distinct loci. We demonstrate that, of these additional loci, two are involved in cell recognition and binding and one in the production and maturation of RcGTA particles. The five RcGTA “genome” loci are widespread within Rhodobacterales, but not all loci have the same evolutionary histories. Specifically, two of the loci have been subject to frequent, probably virus-mediated, gene transfer events. We argue that it is unlikely that RcGTA is a selfish genetic element. Instead, our findings are compatible with the scenario that RcGTA is a virus-derived element maintained by the producing organism due to a selective advantage of within-population gene exchange. The modularity of the RcGTA “genome” is presumably a result of selection on the host organism to retain GTA functionality.
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Affiliation(s)
- Alexander P Hynes
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Migun Shakya
- Department of Biological Sciences, Dartmouth College
| | - Ryan G Mercer
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Marc P Grüll
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Luke Bown
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Fraser Davidson
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Ekaterina Steffen
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Heidi Matchem
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Mandy E Peach
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Tim Berger
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Katherine Grebe
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College Department of Computer Science, Dartmouth College
| | - Andrew S Lang
- Department of Biology, Memorial University of Newfoundland, St John's, NL, Canada
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9
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Jansen G, Barbosa C, Schulenburg H. Experimental evolution as an efficient tool to dissect adaptive paths to antibiotic resistance. Drug Resist Updat 2014; 16:96-107. [PMID: 24594007 DOI: 10.1016/j.drup.2014.02.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Antibiotic treatments increasingly fail due to rapid dissemination of drug resistance. Comparative genomics of clinical isolates highlights the role of de novo adaptive mutations and horizontal gene transfer (HGT) in the acquisition of resistance. Yet it cannot fully describe the selective pressures and evolutionary trajectories that yielded today's problematic strains. Experimental evolution offers a compelling addition to such studies because the combination of replicated experiments under tightly controlled conditions with genomics of intermediate time points allows real-time reconstruction of evolutionary trajectories. Recent studies thus established causal links between antibiotic deployment therapies and the course and timing of mutations, the cost of resistance and the likelihood of compensating mutations. They particularly underscored the importance of long-term effects. Similar investigations incorporating horizontal gene transfer (HGT) are wanting, likely because of difficulties associated with its integration into experiments. In this review, we describe current advances in experimental evolution of antibiotic resistance and reflect on ways to incorporate horizontal gene transfer into the approach. We contend it provides a powerful tool for systematic and highly controlled dissection of evolutionary paths to antibiotic resistance that needs to be taken into account for the development of sustainable anti-bacterial treatment strategies.
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Affiliation(s)
- Gunther Jansen
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Germany.
| | - Camilo Barbosa
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Germany
| | - Hinrich Schulenburg
- Department of Evolutionary Ecology and Genetics, Zoological Institute, Christian-Albrechts University of Kiel, Germany
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10
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Mappley LJ, La Ragione RM, Woodward MJ. Brachyspira and its role in avian intestinal spirochaetosis. Vet Microbiol 2013; 168:245-60. [PMID: 24355534 DOI: 10.1016/j.vetmic.2013.11.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 11/17/2013] [Accepted: 11/18/2013] [Indexed: 10/26/2022]
Abstract
The fastidious, anaerobic spirochaete Brachyspira is capable of causing enteric disease in avian, porcine and human hosts, amongst others, with a potential for zoonotic transmission. Avian intestinal spirochaetosis (AIS), the resulting disease from colonisation of the caeca and colon of poultry by Brachyspira leads to production losses, with an estimated annual cost of circa £ 18 million to the commercial layer industry in the United Kingdom. Of seven known and several proposed species of Brachyspira, three are currently considered pathogenic to poultry; B. alvinipulli, B. intermedia and B. pilosicoli. Currently, AIS is primarily prevented by strict biosecurity controls and is treated using antimicrobials, including tiamulin. Other treatment strategies have been explored, including vaccination and probiotics, but such developments have been hindered by a limited understanding of the pathobiology of Brachyspira. A lack of knowledge of the metabolic capabilities and little genomic information for Brachyspira has resulted in a limited understanding of the pathobiology. In addition to an emergence of antibiotic resistance amongst Brachyspira, bans on the prophylactic use of antimicrobials in livestock are driving an urgent requirement for alternative treatment strategies for Brachyspira-related diseases, such as AIS. Advances in the molecular biology and genomics of Brachyspira heralds the potential for the development of tools for genetic manipulation to gain an improved understanding of the pathogenesis of Brachyspira.
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Affiliation(s)
- Luke J Mappley
- Department of Bacteriology, Animal Health and Veterinary Laboratories Agency, Addlestone, Surrey KT15 3NB, UK; Department of Food and Nutritional Sciences, University of Reading, Reading, Berkshire RG6 6AP, UK.
| | - Roberto M La Ragione
- Department of Bacteriology, Animal Health and Veterinary Laboratories Agency, Addlestone, Surrey KT15 3NB, UK; School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
| | - Martin J Woodward
- Department of Food and Nutritional Sciences, University of Reading, Reading, Berkshire RG6 6AP, UK
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Wisniewski-Dyé F, Lozano L, Acosta-Cruz E, Borland S, Drogue B, Prigent-Combaret C, Rouy Z, Barbe V, Herrera AM, González V, Mavingui P. Genome Sequence of Azospirillum brasilense CBG497 and Comparative Analyses of Azospirillum Core and Accessory Genomes provide Insight into Niche Adaptation. Genes (Basel) 2012; 3:576-602. [PMID: 24705077 PMCID: PMC3899980 DOI: 10.3390/genes3040576] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2012] [Revised: 08/24/2012] [Accepted: 09/13/2012] [Indexed: 11/29/2022] Open
Abstract
Bacteria of the genus Azospirillum colonize roots of important cereals and grasses, and promote plant growth by several mechanisms, notably phytohormone synthesis. The genomes of several Azospirillum strains belonging to different species, isolated from various host plants and locations, were recently sequenced and published. In this study, an additional genome of an A. brasilense strain, isolated from maize grown on an alkaline soil in the northeast of Mexico, strain CBG497, was obtained. Comparative genomic analyses were performed on this new genome and three other genomes (A. brasilense Sp245, A. lipoferum 4B and Azospirillum sp. B510). The Azospirillum core genome was established and consists of 2,328 proteins, representing between 30% to 38% of the total encoded proteins within a genome. It is mainly chromosomally-encoded and contains 74% of genes of ancestral origin shared with some aquatic relatives. The non-ancestral part of the core genome is enriched in genes involved in signal transduction, in transport and in metabolism of carbohydrates and amino-acids, and in surface properties features linked to adaptation in fluctuating environments, such as soil and rhizosphere. Many genes involved in colonization of plant roots, plant-growth promotion (such as those involved in phytohormone biosynthesis), and properties involved in rhizosphere adaptation (such as catabolism of phenolic compounds, uptake of iron) are restricted to a particular strain and/or species, strongly suggesting niche-specific adaptation.
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Affiliation(s)
- Florence Wisniewski-Dyé
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
| | - Luis Lozano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, AP565-A Cuernavaca, Morelos 62210, México.
| | - Erika Acosta-Cruz
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
| | - Stéphanie Borland
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
| | - Benoît Drogue
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
| | - Claire Prigent-Combaret
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
| | - Zoé Rouy
- Laboratoire d'Analyse Bioinformatique en Génomique et Métabolisme CNRS UMR8030, France.
| | - Valérie Barbe
- Institut de Génomique, CEA, Génoscope, 2 rue Gaston Crémieux, 91057 Evry, France.
| | - Alberto Mendoza Herrera
- Centro de Biotecnología Genómica, Instituto politécnico Nacional, 88710 Reynosa, Tamaulipas, México.
| | - Victor González
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, AP565-A Cuernavaca, Morelos 62210, México.
| | - Patrick Mavingui
- Université de Lyon, UMR 5557 CNRS, USC 1193 INRA, VetAgro Sup Ecologie Microbienne, Villeurbanne 69622, France.
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12
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Abstract
The spirochetes in the Borrelia burgdorferi sensu lato genospecies group cycle in nature between tick vectors and vertebrate hosts. The current assemblage of B. burgdorferi sensu lato, of which three species cause Lyme disease in humans, originated from a rapid species radiation that occurred near the origin of the clade. All of these species share a unique genome structure that is highly segmented and predominantly composed of linear replicons. One of the circular plasmids is a prophage that exists as several isoforms in each cell and can be transduced to other cells, likely contributing to an otherwise relatively anemic level of horizontal gene transfer, which nevertheless appears to be adequate to permit strong natural selection and adaptation in populations of B. burgdorferi. Although the molecular genetic toolbox is meager, several antibiotic-resistant mutants have been isolated, and the resistance alleles, as well as some exogenous genes, have been fashioned into markers to dissect gene function. Genetic studies have probed the role of the outer membrane lipoprotein OspC, which is maintained in nature by multiple niche polymorphisms and negative frequency-dependent selection. One of the most intriguing genetic systems in B. burgdorferi is vls recombination, which generates antigenic variation during infection of mammalian hosts.
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MESH Headings
- Alleles
- Animals
- Antigenic Variation
- Antigens, Bacterial/genetics
- Antigens, Bacterial/immunology
- Antigens, Bacterial/metabolism
- Bacterial Outer Membrane Proteins/genetics
- Bacterial Outer Membrane Proteins/metabolism
- Bacterial Proteins/genetics
- Bacterial Proteins/immunology
- Bacterial Proteins/metabolism
- Bacteriophages/genetics
- Bacteriophages/metabolism
- Bacteriophages/pathogenicity
- Borrelia burgdorferi/genetics
- Borrelia burgdorferi/immunology
- Borrelia burgdorferi/pathogenicity
- Borrelia burgdorferi/virology
- DNA, Bacterial/genetics
- DNA, Bacterial/metabolism
- Electroporation
- Evolution, Molecular
- Genes, Bacterial
- Genetic Variation
- Humans
- Ixodes/microbiology
- Linkage Disequilibrium
- Lipoproteins/genetics
- Lipoproteins/immunology
- Lipoproteins/metabolism
- Lyme Disease/microbiology
- Plasmids/genetics
- Plasmids/metabolism
- Prophages/genetics
- Prophages/metabolism
- Recombination, Genetic
- Selection, Genetic
- Species Specificity
- Transduction, Genetic
- Transformation, Genetic
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Affiliation(s)
- Dustin Brisson
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Dan Drecktrah
- Division of Biological Sciences, The University of Montana, Missoula, Montana 59812
| | - Christian H. Eggers
- Department of Biomedical Sciences, Quinnipiac University, Hamden, Connecticut 06518
| | - D. Scott Samuels
- Division of Biological Sciences, The University of Montana, Missoula, Montana 59812
- Center for Biomolecular Structure and Dynamics, The University of Montana, Missoula, Montana 59812
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13
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Lang AS, Zhaxybayeva O, Beatty JT. Gene transfer agents: phage-like elements of genetic exchange. Nat Rev Microbiol 2012; 10:472-82. [PMID: 22683880 DOI: 10.1038/nrmicro2802] [Citation(s) in RCA: 255] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Horizontal gene transfer is important in the evolution of bacterial and archaeal genomes. An interesting genetic exchange process is carried out by diverse phage-like gene transfer agents (GTAs) that are found in a wide range of prokaryotes. Although GTAs resemble phages, they lack the hallmark capabilities that define typical phages, and they package random pieces of the producing cell's genome. In this Review, we discuss the defining characteristics of the GTAs that have been identified to date, along with potential functions for these agents and the possible evolutionary forces that act on the genes involved in their production.
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Affiliation(s)
- Andrew S Lang
- Department of Biology, Memorial University, St. John's, Newfoundland and Labrador A1B 3X9, Canada.
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Håfström T, Jansson DS, Segerman B. Complete genome sequence of Brachyspira intermedia reveals unique genomic features in Brachyspira species and phage-mediated horizontal gene transfer. BMC Genomics 2011; 12:395. [PMID: 21816042 PMCID: PMC3163572 DOI: 10.1186/1471-2164-12-395] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 08/04/2011] [Indexed: 11/10/2022] Open
Abstract
Background Brachyspira spp. colonize the intestines of some mammalian and avian species and show different degrees of enteropathogenicity. Brachyspira intermedia can cause production losses in chickens and strain PWS/AT now becomes the fourth genome to be completed in the genus Brachyspira. Results 15 classes of unique and shared genes were analyzed in B. intermedia, B. murdochii, B. hyodysenteriae and B. pilosicoli. The largest number of unique genes was found in B. intermedia and B. murdochii. This indicates the presence of larger pan-genomes. In general, hypothetical protein annotations are overrepresented among the unique genes. A 3.2 kb plasmid was found in B. intermedia strain PWS/AT. The plasmid was also present in the B. murdochii strain but not in nine other Brachyspira isolates. Within the Brachyspira genomes, genes had been translocated and also frequently switched between leading and lagging strands, a process that can be followed by different AT-skews in the third positions of synonymous codons. We also found evidence that bacteriophages were being remodeled and genes incorporated into them. Conclusions The accessory gene pool shapes species-specific traits. It is also influenced by reductive genome evolution and horizontal gene transfer. Gene-transfer events can cross both species and genus boundaries and bacteriophages appear to play an important role in this process. A mechanism for horizontal gene transfer appears to be gene translocations leading to remodeling of bacteriophages in combination with broad tropism.
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Affiliation(s)
- Therese Håfström
- Department of Bacteriology, National Veterinary Institute (SVA), SE 751 89 Uppsala, Sweden
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