1
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Santin YG, Sogues A, Bourigault Y, Remaut HK, Laloux G. Lifecycle of a predatory bacterium vampirizing its prey through the cell envelope and S-layer. Nat Commun 2024; 15:3590. [PMID: 38678033 PMCID: PMC11055950 DOI: 10.1038/s41467-024-48042-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/16/2024] [Indexed: 04/29/2024] Open
Abstract
Predatory bacteria feed upon other bacteria in various environments. Bdellovibrio exovorus is an obligate epibiotic predator that attaches on the prey cell surface, where it grows and proliferates. Although the mechanisms allowing feeding through the prey cell envelope are unknown, it has been proposed that the prey's proteinaceous S-layer may act as a defensive structure against predation. Here, we use time-lapse and cryo-electron microscopy to image the lifecycle of B. exovorus feeding on Caulobacter crescentus. We show that B. exovorus proliferates by non-binary division, primarily generating three daughter cells. Moreover, the predator feeds on C. crescentus regardless of the presence of an S-layer, challenging its assumed protective role against predators. Finally, we show that apparently secure junctions are established between prey and predator outer membranes.
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Affiliation(s)
- Yoann G Santin
- de Duve Institute, UCLouvain, 75 avenue Hippocrate, 1200, Brussels, Belgium
| | - Adrià Sogues
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Yvann Bourigault
- de Duve Institute, UCLouvain, 75 avenue Hippocrate, 1200, Brussels, Belgium
| | - Han K Remaut
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Géraldine Laloux
- de Duve Institute, UCLouvain, 75 avenue Hippocrate, 1200, Brussels, Belgium.
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2
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Tyson J, Radford P, Lambert C, Till R, Huwiler SG, Lovering AL, Elizabeth Sockett R. Prey killing without invasion by Bdellovibrio bacteriovorus defective for a MIDAS-family adhesin. Nat Commun 2024; 15:3078. [PMID: 38594280 PMCID: PMC11003981 DOI: 10.1038/s41467-024-47412-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 03/27/2024] [Indexed: 04/11/2024] Open
Abstract
The bacterium Bdellovibrio bacteriovorus is a predator of other Gram-negative bacteria. The predator invades the prey's periplasm and modifies the prey's cell wall, forming a rounded killed prey, or bdelloplast, containing a live B. bacteriovorus. Redundancy in adhesive processes makes invasive mutants rare. Here, we identify a MIDAS adhesin family protein, Bd0875, that is expressed at the predator-prey invasive junction and is important for successful invasion of prey. A mutant strain lacking bd0875 is still able to form round, dead bdelloplasts; however, 10% of the bdelloplasts do not contain B. bacteriovorus, indicative of an invasion defect. Bd0875 activity requires the conserved MIDAS motif, which is linked to catch-and-release activity of MIDAS proteins in other organisms. A proteomic analysis shows that the uninvaded bdelloplasts contain B. bacteriovorus proteins, which are likely secreted into the prey by the Δbd0875 predator during an abortive invasion period. Thus, secretion of proteins into the prey seems to be sufficient for prey killing, even in the absence of a live predator inside the prey periplasm.
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Affiliation(s)
- Jess Tyson
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, NG7 2UH, UK
- Chain Biotechnology Ltd, MediCity, D6 Thane Road, Nottingham, NG90 6BH, UK
| | - Paul Radford
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Carey Lambert
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, NG7 2UH, UK
- Biodiscovery Institute, University of Nottingham, Coates Road, Nottingham, NG7 2RD, UK
| | - Rob Till
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, NG7 2UH, UK
- Biodiscovery Institute, University of Nottingham, Coates Road, Nottingham, NG7 2RD, UK
| | - Simona G Huwiler
- Department of Plant & Microbial Biology, University of Zurich, CH-, 8057, Zurich, Switzerland
| | - Andrew L Lovering
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - R Elizabeth Sockett
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, NG7 2UH, UK.
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3
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Kaplan M, Chang YW, Oikonomou CM, Nicolas WJ, Jewett AI, Kreida S, Dutka P, Rettberg LA, Maggi S, Jensen GJ. Bdellovibrio predation cycle characterized at nanometre-scale resolution with cryo-electron tomography. Nat Microbiol 2023; 8:1267-1279. [PMID: 37349588 PMCID: PMC11061892 DOI: 10.1038/s41564-023-01401-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/27/2023] [Indexed: 06/24/2023]
Abstract
Bdellovibrio bacteriovorus is a microbial predator that offers promise as a living antibiotic for its ability to kill Gram-negative bacteria, including human pathogens. Even after six decades of study, fundamental details of its predation cycle remain mysterious. Here we used cryo-electron tomography to comprehensively image the lifecycle of B. bacteriovorus at nanometre-scale resolution. With high-resolution images of predation in a native (hydrated, unstained) state, we discover several surprising features of the process, including macromolecular complexes involved in prey attachment/invasion and a flexible portal structure lining a hole in the prey peptidoglycan that tightly seals the prey outer membrane around the predator during entry. Unexpectedly, we find that B. bacteriovorus does not shed its flagellum during invasion, but rather resorbs it into its periplasm for degradation. Finally, following growth and division in the bdelloplast, we observe a transient and extensive ribosomal lattice on the condensed B. bacteriovorus nucleoid.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Microbiology, University of Chicago, Chicago, IL, USA.
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - William J Nicolas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andrew I Jewett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Stefan Kreida
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - Przemysław Dutka
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Stefano Maggi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
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4
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Lai TF, Ford RM, Huwiler SG. Advances in cellular and molecular predatory biology of Bdellovibrio bacteriovorus six decades after discovery. Front Microbiol 2023; 14:1168709. [PMID: 37256055 PMCID: PMC10225642 DOI: 10.3389/fmicb.2023.1168709] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/14/2023] [Indexed: 06/01/2023] Open
Abstract
Since its discovery six decades ago, the predatory bacterium Bdellovibrio bacteriovorus has sparked recent interest as a potential remedy to the antibiotic resistance crisis. Here we give a comprehensive historical overview from discovery to progressive developments in microscopy and molecular mechanisms. Research on B. bacteriovorus has moved from curiosity to a new model organism, revealing over time more details on its physiology and fascinating predatory life cycle with the help of a variety of methods. Based on recent findings in cryo-electron tomography, we recapitulate on the intricate molecular details known in the predatory life cycle including how this predator searches for its prey bacterium, to how it attaches, grows, and divides all from within the prey cell. Finally, the newly developed B. bacteriovorus progeny leave the prey cell remnants in the exit phase. While we end with some unanswered questions remaining in the field, new imaging technologies and quantitative, systematic advances will likely help to unravel them in the next decades.
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Affiliation(s)
- Ting F. Lai
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Rhian M. Ford
- School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Simona G. Huwiler
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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5
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Rasmussen T. The Potassium Efflux System Kef: Bacterial Protection against Toxic Electrophilic Compounds. MEMBRANES 2023; 13:membranes13050465. [PMID: 37233526 DOI: 10.3390/membranes13050465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
Abstract
Kef couples the potassium efflux with proton influx in gram-negative bacteria. The resulting acidification of the cytosol efficiently prevents the killing of the bacteria by reactive electrophilic compounds. While other degradation pathways for electrophiles exist, Kef is a short-term response that is crucial for survival. It requires tight regulation since its activation comes with the burden of disturbed homeostasis. Electrophiles, entering the cell, react spontaneously or catalytically with glutathione, which is present at high concentrations in the cytosol. The resulting glutathione conjugates bind to the cytosolic regulatory domain of Kef and trigger activation while the binding of glutathione keeps the system closed. Furthermore, nucleotides can bind to this domain for stabilization or inhibition. The binding of an additional ancillary subunit, called KefF or KefG, to the cytosolic domain is required for full activation. The regulatory domain is termed K+ transport-nucleotide binding (KTN) or regulator of potassium conductance (RCK) domain, and it is also found in potassium uptake systems or channels in other oligomeric arrangements. Bacterial RosB-like transporters and K+ efflux antiporters (KEA) of plants are homologs of Kef but fulfill different functions. In summary, Kef provides an interesting and well-studied example of a highly regulated bacterial transport system.
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Affiliation(s)
- Tim Rasmussen
- Rudolf Virchow Center and Biocenter, Institute of Biochemistry II, Julius-Maximilians-Universität Würzburg, Josef-Schneider-Str. 2, 97080 Würzburg, Germany
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6
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Pita T, Feliciano JR, Leitão JH. Identification of Burkholderia cenocepacia non-coding RNAs expressed during Caenorhabditis elegans infection. Appl Microbiol Biotechnol 2023; 107:3653-3671. [PMID: 37097504 PMCID: PMC10175445 DOI: 10.1007/s00253-023-12530-3] [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: 01/24/2023] [Revised: 04/03/2023] [Accepted: 04/10/2023] [Indexed: 04/26/2023]
Abstract
Small non-coding RNAs (sRNAs) are key regulators of post-transcriptional gene expression in bacteria. Despite the identification of hundreds of bacterial sRNAs, their roles on bacterial physiology and virulence remain largely unknown, as is the case of bacteria of the Burkholderia cepacia complex (Bcc). Bcc is a group of opportunistic pathogens with relatively large genomes that can cause lethal lung infections amongst cystic fibrosis (CF) patients. To characterise sRNAs expressed by Bcc bacteria when infecting a host, the nematode Caenorhabditis elegans was used as an infection model by the epidemic CF strain B. cenocepacia J2315. A total of 108 new and 31 previously described sRNAs with a predicted Rho independent terminator were identified, most of them located on chromosome 1. RIT11b, a sRNA downregulated under C. elegans infection conditions, was shown to directly affect B. cenocepacia virulence, biofilm formation, and swimming motility. RIT11b overexpression reduced the expression of the direct targets dusA and pyrC, involved in biofilm formation, epithelial cell adherence, and chronic infections in other organisms. The in vitro direct interaction of RIT11b with the dusA and pyrC messengers was demonstrated by electrophoretic mobility shift assays. To the best of our knowledge this is the first report on the functional characterization of a sRNA directly involved in B. cenocepacia virulence. KEY POINTS: • 139 sRNAs expressed by B. cenocepacia during C. elegans infection were identified • The sRNA RIT11b affects B. cenocepacia virulence, biofilm formation, and motility • RIT11b directly binds to and regulates dusA and pyrC mRNAs.
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Affiliation(s)
- Tiago Pita
- Department of Bioengineering, iBB-Institute for Bioengineering and Biosciences, and Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal
| | - Joana R Feliciano
- Department of Bioengineering, iBB-Institute for Bioengineering and Biosciences, and Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal.
| | - Jorge H Leitão
- Department of Bioengineering, iBB-Institute for Bioengineering and Biosciences, and Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Instituto Superior Técnico, Universidade de Lisboa, 1049-001, Lisbon, Portugal.
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7
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Smith WPJ, Wucher BR, Nadell CD, Foster KR. Bacterial defences: mechanisms, evolution and antimicrobial resistance. Nat Rev Microbiol 2023:10.1038/s41579-023-00877-3. [PMID: 37095190 DOI: 10.1038/s41579-023-00877-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 04/26/2023]
Abstract
Throughout their evolutionary history, bacteria have faced diverse threats from other microorganisms, including competing bacteria, bacteriophages and predators. In response to these threats, they have evolved sophisticated defence mechanisms that today also protect bacteria against antibiotics and other therapies. In this Review, we explore the protective strategies of bacteria, including the mechanisms, evolution and clinical implications of these ancient defences. We also review the countermeasures that attackers have evolved to overcome bacterial defences. We argue that understanding how bacteria defend themselves in nature is important for the development of new therapies and for minimizing resistance evolution.
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Affiliation(s)
- William P J Smith
- Division of Genomics, Infection and Evolution, University of Manchester, Manchester, UK.
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Benjamin R Wucher
- Department of Biological sciences, Dartmouth College, Hanover, NH, USA
| | - Carey D Nadell
- Department of Biological sciences, Dartmouth College, Hanover, NH, USA
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
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8
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Atterbury RJ, Tyson J. Predatory bacteria as living antibiotics - where are we now? MICROBIOLOGY-SGM 2021; 167. [PMID: 33465024 DOI: 10.1099/mic.0.001025] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Antimicrobial resistance (AMR) is a global health and economic crisis. With too few antibiotics in development to meet current and anticipated needs, there is a critical need for new therapies to treat Gram-negative infections. One potential approach is the use of living predatory bacteria, such as Bdellovibrio bacteriovorus (small Gram-negative bacteria that naturally invade and kill Gram-negative pathogens of humans, animals and plants). Moving toward the use of Bdellovibrio as a 'living antibiotic' demands the investigation and characterization of these bacterial predators in biologically relevant systems. We review the fundamental science supporting the feasibility of predatory bacteria as alternatives to antibiotics.
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Affiliation(s)
- Robert J Atterbury
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, UK
| | - Jess Tyson
- School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, NG7 2UH, UK
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9
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Assessment of predatory bacteria and prey interactions using culture-based methods and EMA-qPCR. Microbiol Res 2019; 228:126305. [DOI: 10.1016/j.micres.2019.126305] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 07/19/2019] [Accepted: 07/20/2019] [Indexed: 10/26/2022]
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10
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Negus D, Moore C, Baker M, Raghunathan D, Tyson J, Sockett RE. Predator Versus Pathogen: How Does Predatory Bdellovibrio bacteriovorus Interface with the Challenges of Killing Gram-Negative Pathogens in a Host Setting? Annu Rev Microbiol 2018; 71:441-457. [PMID: 28886689 DOI: 10.1146/annurev-micro-090816-093618] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bdellovibrio bacteriovorus is a small deltaproteobacterial predator that has evolved to invade, reseal, kill, and digest other gram-negative bacteria in soils and water environments. It has a broad host range and kills many antibiotic-resistant, clinical pathogens in vitro, a potentially useful capability if it could be translated to a clinical setting. We review relevant mechanisms of B. bacteriovorus predation and the physiological properties that would influence its survival in a mammalian host. Bacterial pathogens increasingly display conventional antibiotic resistance by expressing and varying surface and soluble biomolecules. Predators coevolved alongside prey bacteria and so encode diverse predatory enzymes that are hard for pathogens to resist by simple mutation. Predators do not replicate outside pathogens and thus express few transport proteins and thus few surface epitopes for host immune recognition. We explain these features, relating them to the potential of predatory bacteria as cellular medicines.
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Affiliation(s)
- David Negus
- School of Life Science, University of Nottingham, University Park, Nottingham NG7 2UH, United Kingdom; , , , , ,
| | - Chris Moore
- School of Life Science, University of Nottingham, University Park, Nottingham NG7 2UH, United Kingdom; , , , , ,
| | - Michelle Baker
- School of Life Science, University of Nottingham, University Park, Nottingham NG7 2UH, United Kingdom; , , , , , .,School of Computer Science, University of Nottingham, University Park, Nottingham NG7 2UH, United Kingdom
| | - Dhaarini Raghunathan
- School of Life Science, University of Nottingham, University Park, Nottingham NG7 2UH, United Kingdom; , , , , ,
| | - Jess Tyson
- School of Life Science, University of Nottingham, University Park, Nottingham NG7 2UH, United Kingdom; , , , , ,
| | - R Elizabeth Sockett
- School of Life Science, University of Nottingham, University Park, Nottingham NG7 2UH, United Kingdom; , , , , ,
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11
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Mavridou DAI, Gonzalez D, Kim W, West SA, Foster KR. Bacteria Use Collective Behavior to Generate Diverse Combat Strategies. Curr Biol 2018; 28:345-355.e4. [PMID: 29395918 DOI: 10.1016/j.cub.2017.12.030] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/06/2017] [Accepted: 12/14/2017] [Indexed: 01/06/2023]
Abstract
Animals have evolved a wide diversity of aggressive behavior often based upon the careful monitoring of other individuals. Bacteria are also capable of aggression, with many species using toxins to kill or inhibit their competitors. Like animals, bacteria also have systems to monitor others during antagonistic encounters, but how this translates into behavior remains poorly understood. Here, we use colonies of Escherichia coli carrying colicin-encoding plasmids as a model for studying antagonistic behavior. We show that in the absence of threat, dispersed cells with low reproductive value produce colicin toxins spontaneously, generating efficient pre-emptive attacks. Cells can also respond conditionally to toxins released by clonemates via autoinduction or other genotypes via competition sensing. The strength of both pre-emptive and responsive attacks varies widely between strains. We demonstrate that this variability occurs easily through mutation by rationally engineering strains to recapitulate the diversity in naturally occurring strategies. Finally, we discover that strains that can detect both competitors and clonemates are capable of massive coordinated attacks on competing colonies. This collective behavior protects established colonies from competitors, mirroring the evolution of alarm calling in the animal world.
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Affiliation(s)
- Despoina A I Mavridou
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK; Calleva Research Centre for Evolution and Human Sciences, Magdalen College, Oxford OX1 4AU, UK; MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, Kensington, London SW7 2DD, UK
| | - Diego Gonzalez
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK; Calleva Research Centre for Evolution and Human Sciences, Magdalen College, Oxford OX1 4AU, UK
| | - Wook Kim
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK; Calleva Research Centre for Evolution and Human Sciences, Magdalen College, Oxford OX1 4AU, UK
| | - Kevin R Foster
- Department of Zoology, University of Oxford, Oxford OX1 3PS, UK; Calleva Research Centre for Evolution and Human Sciences, Magdalen College, Oxford OX1 4AU, UK.
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12
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Pérez J, Moraleda-Muñoz A, Marcos-Torres FJ, Muñoz-Dorado J. Bacterial predation: 75 years and counting! Environ Microbiol 2016; 18:766-79. [PMID: 26663201 DOI: 10.1111/1462-2920.13171] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 11/23/2015] [Accepted: 12/01/2015] [Indexed: 11/30/2022]
Abstract
The first documented study on bacterial predation was carried out using myxobacteria three quarters of a century ago. Since then, many predatory strains, diverse hunting strategies, environmental consequences and potential applications have been reported by groups all over the world. Now we know that predatory bacteria are distributed in a wide variety of environments and that interactions between predatory and non-predatory populations seem to be the most important factor in bacterial selection and mortality in some ecosystems. Bacterial predation has now been proposed as an evolutionary driving force. The structure and diversity of the predatory bacterial community is beginning to be recognized as an important factor in biodiversity due to its potential role in controlling and modelling bacterial populations in the environment. In this paper, we review the current understanding of bacterial predation, going over the strategies used by the main predatory bacteria to kill their prey. We have also reviewed and integrated the accumulated advances of the last 75 years with the interesting new insights that are provided by the analyses of genomes, predatomes, predatosomes and other comparative genomics studies, focusing on potential applications that derive from all of these areas of study.
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Affiliation(s)
- Juana Pérez
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, E-18071, Granada, Spain
| | - Aurelio Moraleda-Muñoz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, E-18071, Granada, Spain
| | - Francisco Javier Marcos-Torres
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, E-18071, Granada, Spain
| | - José Muñoz-Dorado
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Avda. Fuentenueva s/n, E-18071, Granada, Spain
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13
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de la Peña AH, Suarez A, Duong-ly KC, Schoeffield AJ, Pizarro-Dupuy MA, Zarr M, Pineiro SA, Amzel LM, Gabelli SB. Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus. PLoS One 2015; 10:e0141716. [PMID: 26524597 PMCID: PMC4629899 DOI: 10.1371/journal.pone.0141716] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 10/12/2015] [Indexed: 11/18/2022] Open
Abstract
Given the broad range of substrates hydrolyzed by Nudix (nucleoside diphosphate linked to X) enzymes, identification of sequence and structural elements that correctly predict a Nudix substrate or characterize a family is key to correctly annotate the myriad of Nudix enzymes. Here, we present the structure determination and characterization of Bd3179 -- a Nudix hydrolase from Bdellovibrio bacteriovorus-that we show localized in the periplasmic space of this obligate Gram-negative predator. We demonstrate that the enzyme is a nucleoside diphosphate sugar hydrolase (NDPSase) and has a high degree of sequence and structural similarity to a canonical ADP-ribose hydrolase and to a nucleoside diphosphate sugar hydrolase (1.4 and 1.3 Å Cα RMSD respectively). Examination of the structural elements conserved in both types of enzymes confirms that an aspartate-X-lysine motif on the C-terminal helix of the α-β-α NDPSase fold differentiates NDPSases from ADPRases.
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Affiliation(s)
- Andres H. de la Peña
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Allison Suarez
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Krisna C. Duong-ly
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Andrew J. Schoeffield
- Biology Department, Loyola University Maryland, Baltimore, Maryland, United States of America
| | - Mario A. Pizarro-Dupuy
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Melissa Zarr
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Silvia A. Pineiro
- Department of Medical and Research Technology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - L. Mario Amzel
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sandra B. Gabelli
- Structural Enzymology and Thermodynamics Group, Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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14
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Farrugia DN, Elbourne LDH, Mabbutt BC, Paulsen IT. A novel family of integrases associated with prophages and genomic islands integrated within the tRNA-dihydrouridine synthase A (dusA) gene. Nucleic Acids Res 2015; 43:4547-57. [PMID: 25883135 PMCID: PMC4482086 DOI: 10.1093/nar/gkv337] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 04/01/2015] [Indexed: 12/12/2022] Open
Abstract
Genomic islands play a key role in prokaryotic genome plasticity. Genomic islands integrate into chromosomal loci such as transfer RNA genes and protein coding genes, whilst retaining various cargo genes that potentially bestow novel functions on the host organism. A gene encoding a putative integrase was identified at a single site within the 5′ end of the dusA gene in the genomes of over 200 bacteria. This integrase was discovered to be a component of numerous genomic islands, which appear to share a target site within the dusA gene. dusA encodes the tRNA-dihydrouridine synthase A enzyme, which catalyses the post-transcriptional reduction of uridine to dihydrouridine in tRNA. Genomic islands encoding homologous dusA-associated integrases were found at a much lower frequency within the related dusB and dusC genes, and non-dus genes. Excision of these dusA-associated islands from the chromosome as circularized intermediates was confirmed by polymerase chain reaction. Analysis of the dusA-associated islands indicated that they were highly diverse, with the integrase gene representing the only universal common feature.
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Affiliation(s)
- Daniel N Farrugia
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Liam D H Elbourne
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Bridget C Mabbutt
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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15
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Capeness MJ, Lambert C, Lovering AL, Till R, Uchida K, Chaudhuri R, Alderwick LJ, Lee DJ, Swarbreck D, Liddell S, Aizawa SI, Sockett RE. Activity of Bdellovibrio hit locus proteins, Bd0108 and Bd0109, links Type IVa pilus extrusion/retraction status to prey-independent growth signalling. PLoS One 2013; 8:e79759. [PMID: 24224002 PMCID: PMC3818213 DOI: 10.1371/journal.pone.0079759] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 09/22/2013] [Indexed: 11/18/2022] Open
Abstract
Bdellovibrio bacteriovorus are facultatively predatory bacteria that grow within gram-negative prey, using pili to invade their periplasmic niche. They also grow prey-independently on organic nutrients after undergoing a reversible switch. The nature of the growth switching mechanism has been elusive, but several independent reports suggested mutations in the hit (host-interaction) locus on the Bdellovibrio genome were associated with the transition to prey-independent growth. Pili are essential for prey entry by Bdellovibrio and sequence analysis of the hit locus predicted that it was part of a cluster of Type IVb pilus-associated genes, containing bd0108 and bd0109. In this study we have deleted the whole bd0108 gene, which is unique to Bdellovibrio, and compared its phenotype to strains containing spontaneous mutations in bd0108 and the common natural 42 bp deletion variant of bd0108. We find that deletion of the whole bd0108 gene greatly reduced the extrusion of pili, whereas the 42 bp deletion caused greater pilus extrusion than wild-type. The pili isolated from these strains were comprised of the Type IVa pilin protein; PilA. Attempts to similarly delete gene bd0109, which like bd0108 encodes a periplasmic/secreted protein, were not successful, suggesting that it is likely to be essential for Bdellovibrio viability in any growth mode. Bd0109 has a sugar binding YD- repeat motif and an N-terminus with a putative pilin-like fold and was found to interact directly with Bd0108. These results lead us to propose that the Bd0109/Bd0108 interaction regulates pilus production in Bdellovibrio (possibly by interaction with the pilus fibre at the cell wall), and that the presence (and possibly retraction state) of the pilus feeds back to alter the growth state of the Bdellovibrio cell. We further identify a novel small RNA encoded by the hit locus, the transcription of which is altered in different bd0108 mutation backgrounds.
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Affiliation(s)
- Michael J. Capeness
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Carey Lambert
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Andrew L. Lovering
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Rob Till
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Kaoru Uchida
- Department of Life Sciences, Prefectural University of Hiroshima, Shobara, Japan
| | - Roy Chaudhuri
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Luke J. Alderwick
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - David J. Lee
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | | | - Susan Liddell
- Division of Animal Sciences Proteomics Laboratory, University of Nottingham, Nottingham, United Kingdom
| | - Shin-Ichi Aizawa
- Department of Life Sciences, Prefectural University of Hiroshima, Shobara, Japan
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16
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Jurkevitch E. Isolation and classification of Bdellovibrio and like organisms. CURRENT PROTOCOLS IN MICROBIOLOGY 2012; Chapter 7:Unit7B.1. [PMID: 22875568 DOI: 10.1007/978-3-642-39044-9_379] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Bdellovibrio and like organisms (BALOs) are obligate predators of Gram-negative bacteria. BALOs are isolated as plaques growing at the expense of their prey and are cultivated as two-member cultures. The growth cycle is composed of an extracellular attack phase and an intraperiplasmic elongation and replication phase. However, there are methods for obtaining host-independent (HI) mutants that grow without prey on rich media. BALOs are commonly found in the environment but generally constitute small populations; therefore, their isolation may require enrichment steps. Contamination by other bacteria during isolation necessitates efficient separation between the smaller BALO cells from the majority of larger bacteria. BALOs can also be directly detected and quantified in environmental samples using specific PCR. Synchronous cultures of both wild-type and HI derivatives can be obtained to study the different growth phases. These can be further separated by centrifugation. Classification is based on 16S rDNA analysis. Protocols relevant to these aspects of BALO detection, isolation, growth, classification, and quantitation are presented in this unit.
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Affiliation(s)
- Edouard Jurkevitch
- Plant Pathology and Microbiology, The Hebrew University of Jerusalem, Rehovot, Israel
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17
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Chang CY, Hobley L, Till R, Capeness M, Kanna M, Burtt W, Jagtap P, Aizawa SI, Sockett RE. The Bdellovibrio bacteriovorus twin-arginine transport system has roles in predatory and prey-independent growth. MICROBIOLOGY-SGM 2011; 157:3079-3093. [PMID: 21903758 DOI: 10.1099/mic.0.052449-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bdellovibrio bacteriovorus grows in one of two ways: either (i) predatorily [in a host-dependent (HD) manner], when it invades the periplasm of another Gram-negative bacterium, exporting into the prey co-ordinated waves of soluble enzymes using the prey cell contents for growth; or (ii) in a host-independent (HI) manner, when it grows (slowly) axenically in rich media. Periplasmic invasion potentially exposes B. bacteriovorus to extremes of pH and exposes the need to scavenge electron donors from prey electron transport components by synthesis of metalloenzymes. The twin-arginine transport system (Tat) in other bacteria transports folded metalloenzymes and the B. bacteriovorus genome encodes 21 potential Tat-transported substrates and Tat transporter proteins TatA1, TatA2 and TatBC. GFP tagging of the Tat signal peptide from Bd1802, a high-potential iron-sulfur protein (HiPIP), revealed it to be exported into the prey bacterium during predatory growth. Mutagenesis showed that the B. bacteriovorus tatA2 and tatC gene products are essential for both HI and HD growth, despite the fact that they partially complement (in SDS resistance assays) the corresponding mutations in Escherichia coli where neither TatA nor TatC are essential for life. The essentiality of B. bacteriovorus TatA2 was surprising given that the B. bacteriovorus genome encodes a second tatA homologue, tatA1. Transcription of tatA1 was found to be induced upon entry to the bdelloplast, and insertional inactivation of tatA1 showed that it significantly slowed the rates of both HI and HD growth. B. bacteriovorus is one of a few bacterial species that are reliant on a functional Tat system and where deletion of a single tatA1 gene causes a significant growth defect(s), despite the presence of its tatA2 homologue.
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Affiliation(s)
- Chien-Yi Chang
- Institute of Genetics, School of Biology, University of Nottingham Medical School, Nottingham NG7 2UH, UK
| | - Laura Hobley
- Institute of Genetics, School of Biology, University of Nottingham Medical School, Nottingham NG7 2UH, UK
| | - Rob Till
- Institute of Genetics, School of Biology, University of Nottingham Medical School, Nottingham NG7 2UH, UK
| | - Michael Capeness
- Institute of Genetics, School of Biology, University of Nottingham Medical School, Nottingham NG7 2UH, UK
| | - Machi Kanna
- Prefectural University of Hiroshima, 562 Nanatsuka, Shobara, Hiroshima 727-0023, Japan
| | - William Burtt
- Institute of Genetics, School of Biology, University of Nottingham Medical School, Nottingham NG7 2UH, UK
| | - Pratik Jagtap
- Max-Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Shin-Ichi Aizawa
- Prefectural University of Hiroshima, 562 Nanatsuka, Shobara, Hiroshima 727-0023, Japan
| | - R Elizabeth Sockett
- Institute of Genetics, School of Biology, University of Nottingham Medical School, Nottingham NG7 2UH, UK
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18
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Atterbury RJ, Hobley L, Till R, Lambert C, Capeness MJ, Lerner TR, Fenton AK, Barrow P, Sockett RE. Effects of orally administered Bdellovibrio bacteriovorus on the well-being and Salmonella colonization of young chicks. Appl Environ Microbiol 2011; 77:5794-803. [PMID: 21705523 PMCID: PMC3165243 DOI: 10.1128/aem.00426-11] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 06/14/2011] [Indexed: 11/20/2022] Open
Abstract
Bdellovibrio bacteriovorus is a bacterium which preys upon and kills Gram-negative bacteria, including the zoonotic pathogens Escherichia coli and Salmonella. Bdellovibrio has potential as a biocontrol agent, but no reports of it being tested in living animals have been published, and no data on whether Bdellovibrio might spread between animals are available. In this study, we tried to fill this knowledge gap, using B. bacteriovorus HD100 doses in poultry with a normal gut microbiota or predosed with a colonizing Salmonella strain. In both cases, Bdellovibrio was dosed orally along with antacids. After dosing non-Salmonella-infected birds with Bdellovibrio, we measured the health and well-being of the birds and any changes in their gut pathology and culturable microbiota, finding that although a Bdellovibrio dose at 2 days of age altered the overall diversity of the natural gut microbiota in 28-day-old birds, there were no adverse effects on their growth and well-being. Drinking water and fecal matter from the pens in which the birds were housed as groups showed no contamination by Bdellovibrio after dosing. Predatory Bdellovibrio orally administered to birds that had been predosed with a gut-colonizing Salmonella enterica serovar Enteritidis phage type 4 strain (an important zoonotic pathogen) significantly reduced Salmonella numbers in bird gut cecal contents and reduced abnormal cecal morphology, indicating reduced cecal inflammation, compared to the ceca of the untreated controls or a nonpredatory ΔpilA strain, suggesting that these effects were due to predatory action. This work is a first step to applying Bdellovibrio therapeutically for other animal, and possibly human, infections.
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Affiliation(s)
- Robert J. Atterbury
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Laura Hobley
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Robert Till
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Carey Lambert
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Michael J. Capeness
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Thomas R. Lerner
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Andrew K. Fenton
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Paul Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - R. Elizabeth Sockett
- Centre for Genetics and Genomics, School of Biology, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, United Kingdom
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