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Herencias C, Rivero-Buceta V, Salgado S, Hernández-Herreros N, Baquero F, Del Campo R, Nogales J, Prieto MA. Bdellovibrio's prey-independent lifestyle is fueled by amino acids as a carbon source. Appl Microbiol Biotechnol 2024; 108:422. [PMID: 39031211 PMCID: PMC11271337 DOI: 10.1007/s00253-024-13250-y] [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: 01/19/2024] [Revised: 06/18/2024] [Accepted: 07/01/2024] [Indexed: 07/22/2024]
Abstract
Identifying the nutritional requirements and growth conditions of microorganisms is crucial for determining their applicability in industry and understanding their role in clinical ecology. Predatory bacteria such as Bdellovibrio bacteriovorus have emerged as promising tools for combating infections by human bacterial pathogens due to their natural killing features. Bdellovibrio's lifecycle occurs inside prey cells, using the cytoplasm as a source of nutrients and energy. However, this lifecycle supposes a challenge when determining the specific uptake of metabolites from the prey to complete the growth inside cells, a process that has not been completely elucidated. Here, following a model-based approach, we illuminate the ability of B. bacteriovorus to replicate DNA, increase biomass, and generate adenosine triphosphate (ATP) in an amino acid-based rich media in the absence of prey, keeping intact its predatory capacity. In this culture, we determined the main carbon sources used and their preference, being glutamate, serine, aspartate, isoleucine, and threonine. This study offers new insights into the role of predatory bacteria in natural environments and establishes the basis for developing new Bdellovibrio applications using appropriate metabolic and physiological methodologies. KEY POINTS: • Amino acids support axenic lifestyle of Bdellovibrio bacteriovorus. • B. bacteriovorus preserves its predatory ability when growing in the absence of prey.
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Affiliation(s)
- Cristina Herencias
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigacion Sanitaria (IRYCIS), Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas-CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain.
| | - Virginia Rivero-Buceta
- Polymer Biotechnology Laboratory, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain
| | - Sergio Salgado
- Polymer Biotechnology Laboratory, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain
| | - Natalia Hernández-Herreros
- Polymer Biotechnology Laboratory, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain
| | - Fernando Baquero
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigacion Sanitaria (IRYCIS), Madrid, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública-CIBERESP, Instituto Carlos III, Madrid, Spain
| | - Rosa Del Campo
- Department of Microbiology, Hospital Universitario Ramón y Cajal, Instituto Ramón y Cajal de Investigacion Sanitaria (IRYCIS), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Infecciosas-CIBERINFEC, Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Nogales
- Systems Biotechnology GroupDepartment of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain
| | - M Auxiliadora Prieto
- Polymer Biotechnology Laboratory, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain.
- Interdisciplinary Platform for Sustainable Plastics Towards a Circular Economy-CSIC (SusPlast-CSIC), Madrid, Spain.
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2
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Remy O, Santin YG, Jonckheere V, Tesseur C, Kaljević J, Van Damme P, Laloux G. Distinct dynamics and proximity networks of hub proteins at the prey-invading cell pole in a predatory bacterium. J Bacteriol 2024; 206:e0001424. [PMID: 38470120 PMCID: PMC11025332 DOI: 10.1128/jb.00014-24] [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: 02/15/2024] [Accepted: 02/23/2024] [Indexed: 03/13/2024] Open
Abstract
In bacteria, cell poles function as subcellular compartments where proteins localize during specific lifecycle stages, orchestrated by polar "hub" proteins. Whereas most described bacteria inherit an "old" pole from the mother cell and a "new" pole from cell division, generating cell asymmetry at birth, non-binary division poses challenges for establishing cell polarity, particularly for daughter cells inheriting only new poles. We investigated polarity dynamics in the obligate predatory bacterium Bdellovibrio bacteriovorus, proliferating through filamentous growth followed by non-binary division within prey bacteria. Monitoring the subcellular localization of two proteins known as polar hubs in other species, RomR and DivIVA, revealed RomR as an early polarity marker in B. bacteriovorus. RomR already marks the future anterior poles of the progeny during the predator's growth phase, during a precise period closely following the onset of divisome assembly and the end of chromosome segregation. In contrast to RomR's stable unipolar localization in the progeny, DivIVA exhibits a dynamic pole-to-pole localization. This behavior changes shortly before the division of the elongated predator cell, where DivIVA accumulates at all septa and both poles. In vivo protein interaction networks for DivIVA and RomR, mapped through endogenous miniTurbo-based proximity labeling, further underscore their distinct roles in cell polarization and reinforce the importance of the anterior "invasive" cell pole in prey-predator interactions. Our work also emphasizes the precise spatiotemporal order of cellular processes underlying B. bacteriovorus proliferation, offering insights into the subcellular organization of bacteria with filamentous growth and non-binary division.IMPORTANCEIn bacteria, cell poles are crucial areas where "hub" proteins orchestrate lifecycle events through interactions with multiple partners at specific times. While most bacteria exhibit one "old" and one "new" pole, inherited from the previous division event, setting polar identity poses challenges in bacteria with non-binary division. This study explores polar proteins in the predatory bacterium Bdellovibrio bacteriovorus, which undergoes filamentous growth followed by non-binary division inside another bacterium. Our research reveals distinct localization dynamics of the polar proteins RomR and DivIVA, highlighting RomR as an early "hub" marking polar identity in the filamentous mother cell. Using miniTurbo-based proximity labeling, we uncovered their unique protein networks. Overall, our work provides new insights into the cell polarity in non-binary dividing bacteria.
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Affiliation(s)
- Ophélie Remy
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Yoann G. Santin
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Veronique Jonckheere
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Coralie Tesseur
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Jovana Kaljević
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Géraldine Laloux
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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3
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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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4
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Pląskowska K, Zakrzewska-Czerwińska J. Chromosome structure and DNA replication dynamics during the life cycle of the predatory bacterium Bdellovibrio bacteriovorus. FEMS Microbiol Rev 2023; 47:fuad057. [PMID: 37791401 PMCID: PMC11318664 DOI: 10.1093/femsre/fuad057] [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: 09/07/2023] [Revised: 09/27/2023] [Accepted: 10/02/2023] [Indexed: 10/05/2023] Open
Abstract
Bdellovibrio bacteriovorus, an obligate predatory Gram-negative bacterium that proliferates inside and kills other Gram-negative bacteria, was discovered more than 60 years ago. However, we have only recently begun to understand the detailed cell biology of this proficient bacterial killer. Bdellovibrio bacteriovorus exhibits a peculiar life cycle and bimodal proliferation, and thus represents an attractive model for studying novel aspects of bacterial cell biology. The life cycle of B. bacteriovorus consists of two phases: a free-living nonreplicative attack phase and an intracellular reproductive phase. During the reproductive phase, B. bacteriovorus grows as an elongated cell and undergoes binary or nonbinary fission, depending on the prey size. In this review, we discuss: (1) how the chromosome structure of B. bacteriovorus is remodeled during its life cycle; (2) how its chromosome replication dynamics depends on the proliferation mode; (3) how the initiation of chromosome replication is controlled during the life cycle, and (4) how chromosome replication is spatiotemporally coordinated with the proliferation program.
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Affiliation(s)
- Karolina Pląskowska
- Department of Molecular Microbiology, Faculty of Biotechnology, University
of Wrocław, ul. Joliot-Curie 14A, Wrocław,
Poland
| | - Jolanta Zakrzewska-Czerwińska
- Department of Molecular Microbiology, Faculty of Biotechnology, University
of Wrocław, ul. Joliot-Curie 14A, Wrocław,
Poland
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5
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Caulton SG, Lovering AL. Moving toward a better understanding of the model bacterial predator Bdellovibrio bacteriovorus. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001380. [PMID: 37535060 PMCID: PMC10482364 DOI: 10.1099/mic.0.001380] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/27/2023] [Indexed: 08/04/2023]
Abstract
The bacterial predator Bdellovibrio bacteriovorus is a model for the wider phenomenon of bacteria:bacteria predation, and the specialization required to achieve a lifestyle dependent on prey consumption. Bdellovibrio bacteriovorus is able to recognize, enter and ultimately consume fellow Gram-negative bacteria, killing these prey from within their periplasmic space, and lysing the host at the end of the cycle. The classic phenotype-driven characterization (and observation of predation) has benefitted from an increased focus on molecular mechanisms and fluorescence microscopy and tomography, revealing new features of several of the lifecycle stages. Herein we summarize a selection of these advances and describe likely areas for exploration that will push the field toward a more complete understanding of this fascinating 'two-cell' system.
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Affiliation(s)
- Simon G. Caulton
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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6
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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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7
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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: 9] [Impact Index Per Article: 9.0] [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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8
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Volle C, Núñez ME, Spain EM, Hart BC, Wengen MB, Lane S, Criollo A, Mahoney CA, Ferguson MA. AFM Force Mapping Elucidates Pilus Deployment and Key Lifestyle-Dependent Surface Properties in Bdellovibrio bacteriovorus. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:4233-4244. [PMID: 36926913 PMCID: PMC10062353 DOI: 10.1021/acs.langmuir.2c03134] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Bdellovibrio bacteriovorus is known for predation of a wide variety of Gram-negative bacteria, making it of interest as an alternative or supplement to chemical antibiotics. However, a fraction of B. bacteriovorus follows a nonpredatory, "host-independent" (HI) life cycle. In this study, live predatory and HI B. bacteriovorus were captured on a surface and examined, in buffer, by collecting force maps using atomic force microscopy (AFM). The approach curves obtained on HI cells are similar to those on other Gram-negative cells, with a short nonlinear region followed by a linear region. In contrast, the approach curves obtained on predatory cells have a large nonlinear region, reflecting the unusual flexibility of the predatory cell. As the AFM tip is retracted, it shows virtually no adhesion to predatory B. bacteriovorus but has multiple adhesion events on HI cells and the 200-500+ nm region immediately surrounding them. Measured pull-off forces, pull-off distances, and effective spring constants are consistent with the multiple stretching events of Type IV pili, both on and especially adjacent to the cells. Exposure of the HI B. bacteriovorus to a pH-neutral 10% cranberry juice solution, which contains type A proanthocyanidins that are known to interfere with the adhesion of multiple types of pili, results in a substantial reduction in adhesion. Type IV pili are required for successful predation by B. bacteriovorus, but pili used in the predation process are located at the non-flagellated pole of the cell and can retract when not in use. Such pili are rarely observed under the conditions of this study, where the predator has not encountered a prey cell. In contrast, HI cells appear to have many pili distributed on and around the whole cell, presumably ready to be utilized for a variety of HI cell activities including attachment to surfaces.
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Affiliation(s)
- Catherine
B. Volle
- Departments
of Chemistry and Biology, Cornell College, Mount Vernon, Iowa 52314, United States
| | - Megan E. Núñez
- Department
of Chemistry, Wellesley College, Wellesley, Massachusetts 02481, United States
| | - Eileen M. Spain
- Department
of Chemistry, Occidental College, Los Angeles, California 90041, United States
| | - Bridget C. Hart
- Department
of Chemistry, State University of New York, New Paltz, New York 12561, United States
| | - Michael B. Wengen
- Department
of Chemistry, State University of New York, New Paltz, New York 12561, United States
| | - Sophia Lane
- Department
of Chemistry, State University of New York, New Paltz, New York 12561, United States
| | - Alexa Criollo
- Department
of Chemistry, State University of New York, New Paltz, New York 12561, United States
| | - Catherine A. Mahoney
- Department
of Chemistry, State University of New York, New Paltz, New York 12561, United States
| | - Megan A. Ferguson
- Department
of Chemistry, State University of New York, New Paltz, New York 12561, United States
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9
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Breakdown of clonal cooperative architecture in multispecies biofilms and the spatial ecology of predation. Proc Natl Acad Sci U S A 2023; 120:e2212650120. [PMID: 36730197 PMCID: PMC9963355 DOI: 10.1073/pnas.2212650120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Biofilm formation, including adherence to surfaces and secretion of extracellular matrix, is common in the microbial world, but we often do not know how interaction at the cellular spatial scale translates to higher-order biofilm community ecology. Here we explore an especially understudied element of biofilm ecology, namely predation by the bacterium Bdellovibrio bacteriovorus. This predator can kill and consume many different Gram-negative bacteria, including Vibrio cholerae and Escherichia coli. V. cholerae can protect itself from predation within densely packed biofilm structures that it creates, whereas E. coli biofilms are highly susceptible to B. bacteriovorus. We explore how predator-prey dynamics change when V. cholerae and E. coli are growing in biofilms together. We find that in dual-species prey biofilms, E. coli survival under B. bacteriovorus predation increases, whereas V. cholerae survival decreases. E. coli benefits from predator protection when it becomes embedded within expanding groups of highly packed V. cholerae. But we also find that the ordered, highly packed, and clonal biofilm structure of V. cholerae can be disrupted if V. cholerae cells are directly adjacent to E. coli cells at the start of biofilm growth. When this occurs, the two species become intermixed, and the resulting disordered cell groups do not block predator entry. Because biofilm cell group structure depends on initial cell distributions at the start of prey biofilm growth, the surface colonization dynamics have a dramatic impact on the eventual multispecies biofilm architecture, which in turn determines to what extent both species survive exposure to B. bacteriovorus.
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10
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A noncanonical cytochrome c stimulates calcium binding by PilY1 for type IVa pili formation. Proc Natl Acad Sci U S A 2022; 119:2115061119. [PMID: 35121662 PMCID: PMC8833165 DOI: 10.1073/pnas.2115061119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/28/2021] [Indexed: 12/23/2022] Open
Abstract
Type IVa pili (T4aP) are versatile bacterial cell surface structures that undergo extension/adhesion/retraction cycles powered by the cell envelope-spanning T4aP machine. In this machine, a complex composed of four minor pilins and PilY1 primes T4aP extension and is also present at the pilus tip mediating adhesion. Similar to many several other bacteria, Myxococcus xanthus contains multiple minor pilins/PilY1 sets that are incompletely understood. Here, we report that minor pilins and PilY1 (PilY1.1) of cluster_1 form priming and tip complexes contingent on calcium and a noncanonical cytochrome c (TfcP) with an unusual His/Cys heme ligation. We provide evidence that TfcP is unlikely to participate in electron transport and instead stimulates calcium binding by PilY1.1 at low-calcium concentrations, thereby stabilizing PilY1.1 and enabling T4aP function in a broader range of calcium concentrations. These results not only identify a previously undescribed function of cytochromes c but also illustrate how incorporation of an accessory factor expands the environmental range under which the T4aP system functions.
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11
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Ooi MC, Goulden EF, Smith GG, Bridle AR. Predatory bacteria in the haemolymph of the cultured spiny lobster Panulirus ornatus. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34846286 PMCID: PMC8743626 DOI: 10.1099/mic.0.001113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bdellovibrio and like organisms (BALOs) are Gram-negative obligate predators of other bacteria in a range of environments. The recent discovery of BALOs in the circulatory system of cultured spiny lobster P. ornatus warrants more investigation. We used a combination of co-culture agar and broth assays and transmission electron microscopy to show a Halobacteriovorax sp. strain Hbv preyed upon the model prey bacterium Vibrio sp. strain Vib. The haemolymph microbiome of juvenile P. ornatus was characterised following injection of phosphate buffered saline (control) or prey and/or predator bacteria for 3 d. The predator Hbv had no effect on survival compared to the control after 3 d. However, when compared to the prey only treatment group, lobsters injected with both prey and predator showed significantly lower abundance of genus Vibrio in the haemolymph bacterial community composition. This study indicates that predatory bacteria are not pathogenic and may assist in controlling microbial population growth in the haemolymph of lobsters.
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Affiliation(s)
- Mei C. Ooi
- Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Australia
- *Correspondence: Mei C. Ooi,
| | - Evan F. Goulden
- Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Australia
- Bribie Island Research Centre, Department of Agriculture and Fisheries, QLD, Australia
| | - Gregory G. Smith
- Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Australia
| | - Andrew R. Bridle
- Institute for Marine and Antarctic Studies, University of Tasmania, TAS, Australia
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12
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Ezzedine JA, Desdevises Y, Jacquet S. Bdellovibrio and like organisms: current understanding and knowledge gaps of the smallest cellular hunters of the microbial world. Crit Rev Microbiol 2021; 48:428-449. [PMID: 34595998 DOI: 10.1080/1040841x.2021.1979464] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Almost sixty years ago, Bdellovibrio and like organisms (BALOs) were discovered as the first obligate bacterial predators of other bacteria known to science. Since then, they were shown to be diverse and ubiquitous in the environment, and to bear astonishing ecological, physiological, and metabolic capabilities. The last decade has seen important strides made in understanding the mechanistic basis of their life cycle, the dynamics of their interactions with prey, along with significant developments towards their use in medicine, agriculture, and industry. This review details these achievements, identify current understanding and knowledge gaps to encourage and guide future BALO research.
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Affiliation(s)
- Jade A Ezzedine
- Université Savoie Mont-Blanc, INRAE, CARRTEL, Thonon-les-Bains, France.,Laboratoire de Physiologie Cellulaire et Végétale, CNRS, CEA, INRAE, IRIG, Université Grenoble Alpes, Grenoble, France
| | - Yves Desdevises
- CNRS, Biologie Intégrative des Organismes Marins, Observatoire Océanologique, Sorbonne Université, Banyuls-sur-Mer, France
| | - Stéphan Jacquet
- Université Savoie Mont-Blanc, INRAE, CARRTEL, Thonon-les-Bains, France
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13
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Hoshiko Y, Nishiyama Y, Moriya T, Kadokami K, López-Jácome LE, Hirano R, García-Contreras R, Maeda T. Quinolone Signals Related to Pseudomonas Quinolone Signal-Quorum Sensing Inhibits the Predatory Activity of Bdellovibrio bacteriovorus. Front Microbiol 2021; 12:722579. [PMID: 34566925 PMCID: PMC8461301 DOI: 10.3389/fmicb.2021.722579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022] Open
Abstract
Bdellovibrio bacteriovorus is one of the predatory bacteria; therefore, it can act as a novel “living antibiotic,” unlike the current antibiotics. Here the predation of Escherichia coli by B. bacteriovorus was inhibited in the presence of Pseudomonas aeruginosa. This study investigated whether P. aeruginosa-induced predation inhibition is associated with bacterial quorum sensing (QS). Each las, rhl, or pqs QS mutant in P. aeruginosa was used to check the predatory activity of E. coli cells using B. bacteriovorus. As a result, the predatory activity of B. bacteriovorus increased in a mutant pqs QS system, whereas wild-type PA14 inhibited the predatory activity. Moreover, the addition of 4-hydroxy-2-heptylquinoline (HHQ) or the analog triggered the low predatory activity of B. bacteriovorus and killed B. bacteriovorus cells. Therefore, a defensive action of P. aeruginosa against B. bacteriovorus is activated by the pqs QS system, which produces some quinolone compounds such as HHQ.
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Affiliation(s)
- Yuki Hoshiko
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Yoshito Nishiyama
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Tae Moriya
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | - Kiwao Kadokami
- Institute of Environmental Science and Technology, The University of Kitakyushu, Kitakyushu, Japan
| | - Luis Esaú López-Jácome
- Department of Microbiology and Parasitology, Faculty of Medicine, UNAM, Mexico City, Mexico.,Laboratory of Infectology, National Institute of Rehabilitation Luis Guillermo Ibarra Ibarra, Mexico City, Mexico
| | - Ryutaro Hirano
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
| | | | - Toshinari Maeda
- Department of Biological Functions Engineering, Graduate School of Life Science and Systems Engineering, Kyushu Institute of Technology, Kitakyushu, Japan
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14
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Abstract
Bacteria have developed a large array of motility mechanisms to exploit available resources and environments. These mechanisms can be broadly classified into swimming in aqueous media and movement over solid surfaces. Swimming motility involves either the rotation of rigid helical filaments through the external medium or gyration of the cell body in response to the rotation of internal filaments. On surfaces, bacteria swarm collectively in a thin layer of fluid powered by the rotation of rigid helical filaments, they twitch by assembling and disassembling type IV pili, they glide by driving adhesins along tracks fixed to the cell surface and, finally, non-motile cells slide over surfaces in response to outward forces due to colony growth. Recent technological advances, especially in cryo-electron microscopy, have greatly improved our knowledge of the molecular machinery that powers the various forms of bacterial motility. In this Review, we describe the current understanding of the physical and molecular mechanisms that allow bacteria to move around.
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15
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Aharon E, Mookherjee A, Pérez-Montaño F, Mateus da Silva G, Sathyamoorthy R, Burdman S, Jurkevitch E. Secretion systems play a critical role in resistance to predation by Bdellovibrio bacteriovorus. Res Microbiol 2021; 172:103878. [PMID: 34492337 DOI: 10.1016/j.resmic.2021.103878] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/02/2021] [Accepted: 08/07/2021] [Indexed: 11/28/2022]
Abstract
Bdellovibrio bacteriovorus, a Gram-negative predatory bacterium belonging to the Bdellovibrio and like organisms (BALOs), predate on Gram-negative bacteria. BALO strains differ in prey range but so far, the genetic basis of resistance against BALO predation is hardly understood. We developed a loss-of-function approach to screen for sensitive mutants in a library of strain M6, a predation-resistant strain of the plant pathogen Acidovorax citrulli. The screen is based on tracking the growth of a B. bacteriovorus strain expressing the fluorescent reporter Tdtomato in mutant pools to reveal predation-sensitive variants. Two independent loci were identified in mutant strains exhibiting significant levels of susceptibility to the predator. Genes in the two loci were analysed using both protein sequence homology and protein structure modeling. Both were secretion-related proteins and thus associated to the bacterial cell wall. Successful complementation of gspK, a gene encoding for a minor pseudopilin protein confirmed the involvement of the type II secretion system in A. citrulli M6 resistance. This proof of concept study shows that our approach can identify key elements of the BALO-prey interaction, and it validates the hypothesis that mutational changes in a single gene can drastically impact prey resistance to BALO predation.
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Affiliation(s)
- Einav Aharon
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Abhirup Mookherjee
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Francisco Pérez-Montaño
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel; Department of Microbiology, University of Seville, Seville, Spain.
| | - Gustavo Mateus da Silva
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Rajesh Sathyamoorthy
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Saul Burdman
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Institute of Environmental Sciences, The Hebrew University of Jerusalem, Rehovot, Israel.
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16
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Kaljević J, Saaki TNV, Govers SK, Remy O, van Raaphorst R, Lamot T, Laloux G. Chromosome choreography during the non-binary cell cycle of a predatory bacterium. Curr Biol 2021; 31:3707-3720.e5. [PMID: 34256020 PMCID: PMC8445325 DOI: 10.1016/j.cub.2021.06.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 05/13/2021] [Accepted: 06/09/2021] [Indexed: 12/03/2022]
Abstract
In bacteria, the dynamics of chromosome replication and segregation are tightly coordinated with cell-cycle progression and largely rely on specific spatiotemporal arrangement of the chromosome. Whereas these key processes are mostly investigated in species that divide by binary fission, they remain mysterious in bacteria producing larger number of descendants. Here, we establish the predatory bacterium Bdellovibrio bacteriovorus as a model to investigate the non-binary processing of a circular chromosome. We found that its single chromosome is highly compacted in a polarized nucleoid that excludes freely diffusing proteins during the non-proliferative stage of the cell cycle. A binary-like cycle of DNA replication and asymmetric segregation is followed by multiple asynchronous rounds of replication and progressive ParABS-dependent partitioning, uncoupled from cell division. Finally, we provide the first evidence for an on-off behavior of the ParB protein, which localizes at the centromere in a cell-cycle-regulated manner. Altogether, our findings support a model of complex chromosome choreography leading to the generation of variable, odd, or even numbers of offspring and highlight the adaptation of conserved mechanisms to achieve non-binary reproduction. The Bdellovibrio chromosome is polarized, with ori located near the invasive pole The highly compacted nucleoid excludes cytosolic proteins in non-replicative cells Replication and segregation of chromosomes are uncoupled from cell division The centromeric protein ParB localizes at parS in a cell-cycle-dependent manner
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Affiliation(s)
- Jovana Kaljević
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
| | - Terrens N V Saaki
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
| | - Sander K Govers
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Ophélie Remy
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
| | | | - Thomas Lamot
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium
| | - Géraldine Laloux
- de Duve Institute, UCLouvain, 75 Avenue Hippocrate, 1200 Brussels, Belgium.
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17
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Batinovic S, Rose JJA, Ratcliffe J, Seviour RJ, Petrovski S. Cocultivation of an ultrasmall environmental parasitic bacterium with lytic ability against bacteria associated with wastewater foams. Nat Microbiol 2021; 6:703-711. [PMID: 33927381 DOI: 10.1038/s41564-021-00892-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 03/22/2021] [Indexed: 02/02/2023]
Abstract
Many wastewater treatment plants around the world suffer from the operational problem of foaming. This is characterized by a persistent stable foam that forms on the aeration basin, which reduces effluent quality. The foam is often stabilized by a highly hydrophobic group of Actinobacteria known as the Mycolata1. Gordonia amarae is one of the most frequently reported foaming members1. With no currently reliable method for treating foams, phage biocontrol has been suggested as an attractive treatment strategy2. Phages isolated from related foaming bacteria can destabilize foams at the laboratory scale3,4; however, no phage has been isolated that lyses G. amarae. Here, we assemble the complete genomes of G. amarae and a previously undescribed species, Gordonia pseudoamarae, to examine mechanisms that encourage stable foam production. We show that both of these species are recalcitrant to phage infection via a number of antiviral mechanisms including restriction, CRISPR-Cas and bacteriophage exclusion. Instead, we isolate and cocultivate an environmental ultrasmall epiparasitic bacterium from the phylum Saccharibacteria that lyses G. amarae and G. pseudoamarae and several other Mycolata commonly associated with wastewater foams. The application of this parasitic bacterium, 'Candidatus Mycosynbacter amalyticus', may represent a promising strategy for the biocontrol of bacteria responsible for stabilizing wastewater foams.
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Affiliation(s)
- Steven Batinovic
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Jayson J A Rose
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Julian Ratcliffe
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Robert J Seviour
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, Victoria, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, Victoria, Australia.
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18
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Bauer A, Forchhammer K. Bacterial Predation on Cyanobacteria. Microb Physiol 2021; 31:99-108. [PMID: 34010833 DOI: 10.1159/000516427] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/07/2021] [Indexed: 11/19/2022]
Abstract
Predatory bacteria gained interest in the last 20 years. Nevertheless, only a few species are well characterized. The endobiotic predator Bdellovibrio bacteriovorus invades its prey to consume it from the inside, whereas Myxococcus xanthus hunts as a whole group to overcome its prey. Both species were described to prey on cyanobacteria as well. This minireview summarizes the findings of the last 20 years of predatory bacteria of cyanobacteria and is supplemented by new findings from a screening experiment for bacterial predators of the model organism Anabaena variabilis PCC 7937. Known predatory bacteria of cyanobacteria belong to the phyla Proteobacteria, Bacteroidetes, and Firmicutes and follow different hunting strategies. The underlying mechanisms are in most cases not known in much detail. Isolates from the screening experiment were clustered after predation behaviour and analyzed with respect to their size. The effect of predation in high nitrate levels and the occurrence of nitrogen-fixing cells, called heterocysts, are addressed.
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Affiliation(s)
- Antje Bauer
- Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls Universität, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, Eberhard Karls Universität, Tübingen, Germany
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19
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Cavallo FM, Jordana L, Friedrich AW, Glasner C, van Dijl JM. Bdellovibrio bacteriovorus: a potential 'living antibiotic' to control bacterial pathogens. Crit Rev Microbiol 2021; 47:630-646. [PMID: 33934682 DOI: 10.1080/1040841x.2021.1908956] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Bdellovibrio bacteriovorus is a small Deltaproteobacterium which, since its discovery, has distinguished itself for the unique ability to prey on other Gram-negative bacteria. The studies on this particular "predatory bacterium", have gained momentum in response to the rising problem of antibiotic resistance, because it could be applied as a potential probiotic and antibiotic agent. Hereby, we present recent advances in the study of B. bacteriovorus, comprehending fundamental aspects of its biology, obligatory intracellular life cycle, predation resistance, and potential applications. Furthermore, we discuss studies that pave the road towards the use of B. bacteriovorus as a "living antibiotic" in human therapy, focussing on its interaction with biofilms, the host immune response, predation susceptibility and in vivo application models. The available data imply that it will be possible to upgrade this predator bacterium from a predominantly academic interest to an instrument that could confront antibiotic resistant infections.
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Affiliation(s)
- Francis M Cavallo
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Lorea Jordana
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Alexander W Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Corinna Glasner
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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20
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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: 29] [Impact Index Per Article: 9.7] [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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21
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Utter DR, He X, Cavanaugh CM, McLean JS, Bor B. The saccharibacterium TM7x elicits differential responses across its host range. THE ISME JOURNAL 2020; 14:3054-3067. [PMID: 32839546 PMCID: PMC7784981 DOI: 10.1038/s41396-020-00736-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 07/01/2020] [Accepted: 08/03/2020] [Indexed: 12/28/2022]
Abstract
Host range is a fundamental component of symbiotic interactions, yet it remains poorly characterized for the prevalent yet enigmatic subcategory of bacteria/bacteria symbioses. The recently characterized obligate bacterial epibiont Candidatus Nanosynbacter lyticus TM7x with its bacterial host Actinomyces odontolyticus XH001 offers an ideal system to study such a novel relationship. In this study, the host range of TM7x was investigated by coculturing TM7x with various related Actinomyces strains and characterizing their growth dynamics from initial infection through subsequent co-passages. Of the twenty-seven tested Actinomyces, thirteen strains, including XH001, could host TM7x, and further classified into "permissive" and "nonpermissive" based on their varying initial responses to TM7x. Ten permissive strains exhibited growth/crash/recovery phases following TM7x infection, with crash timing and extent dependent on initial TM7x dosage. Meanwhile, three nonpermissive strains hosted TM7x without a growth-crash phase despite high TM7x dosage. The physical association of TM7x with all hosts, including nonpermissive strains, was confirmed by microscopy. Comparative genomic analyses revealed distinguishing genomic features between permissive and nonpermissive hosts. Our results expand the concept of host range beyond a binary to a wider spectrum, and the varying susceptibility of Actinomyces strains to TM7x underscores how small genetic differences between hosts can underly divergent selective trajectories.
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Affiliation(s)
- Daniel R Utter
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Xuesong He
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, 02142, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, 02115, USA
| | - Colleen M Cavanaugh
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Jeffrey S McLean
- Department of Periodontics, University of Washington, Seattle, WA, 98119, USA
| | - Batbileg Bor
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, 02142, USA.
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, 02115, USA.
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22
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The polar Ras-like GTPase MglA activates type IV pilus via SgmX to enable twitching motility in Myxococcus xanthus. Proc Natl Acad Sci U S A 2020; 117:28366-28373. [PMID: 33093210 PMCID: PMC7668184 DOI: 10.1073/pnas.2002783117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The type IV pilus (Tfp) is a multipurpose machine found on bacterial surfaces that works by cycles of synthesis/retraction of a pilin fiber. During surface (twitching) motility, the coordinated actions of multiple Tfps at the cell pole promotes single cells and synchronized group movements. Here, directly observing polar Tfp machines in action during motility of Myxococcus xanthus, we identified the mechanism underlying pole-specific Tfps activation. In this process, the Ras-like protein MglA targets a novel essential Tfp-activator, SgmX, to the pole, ensuring both the unipolar activation of Tfps and its switching to the opposite pole when cells reverse their movement. Thus, a dynamic cascade of polar activators regulates multicellular movements, a feature that is likely conserved in other twitching bacteria. Type IV pili (Tfp) are highly conserved macromolecular structures that fulfill diverse cellular functions, such as adhesion to host cells, the import of extracellular DNA, kin recognition, and cell motility (twitching). Outstandingly, twitching motility enables a poorly understood process by which highly coordinated groups of hundreds of cells move in cooperative manner, providing a basis for multicellular behaviors, such as biofilm formation. In the social bacteria Myxococcus xanthus, we know that twitching motility is under the dependence of the small GTPase MglA, but the underlying molecular mechanisms remain elusive. Here we show that MglA complexed to GTP recruits a newly characterized Tfp regulator, termed SgmX, to activate Tfp machines at the bacterial cell pole. This mechanism also ensures spatial regulation of Tfp, explaining how MglA switching provokes directional reversals. This discovery paves the way to elucidate how polar Tfp machines are regulated to coordinate multicellular movements, a conserved feature in twitching bacteria.
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23
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Schirmacher AM, Hanamghar SS, Zedler JAZ. Function and Benefits of Natural Competence in Cyanobacteria: From Ecology to Targeted Manipulation. Life (Basel) 2020; 10:E249. [PMID: 33105681 PMCID: PMC7690421 DOI: 10.3390/life10110249] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/18/2020] [Accepted: 10/20/2020] [Indexed: 02/03/2023] Open
Abstract
Natural competence is the ability of a cell to actively take up and incorporate foreign DNA in its own genome. This trait is widespread and ecologically significant within the prokaryotic kingdom. Here we look at natural competence in cyanobacteria, a group of globally distributed oxygenic photosynthetic bacteria. Many cyanobacterial species appear to have the genetic potential to be naturally competent, however, this ability has only been demonstrated in a few species. Reasons for this might be due to a high variety of largely uncharacterised competence inducers and a lack of understanding the ecological context of natural competence in cyanobacteria. To shed light on these questions, we describe what is known about the molecular mechanisms of natural competence in cyanobacteria and analyse how widespread this trait might be based on available genomic datasets. Potential regulators of natural competence and what benefits or drawbacks may derive from taking up foreign DNA are discussed. Overall, many unknowns about natural competence in cyanobacteria remain to be unravelled. A better understanding of underlying mechanisms and how to manipulate these, can aid the implementation of cyanobacteria as sustainable production chassis.
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Affiliation(s)
| | | | - Julie A. Z. Zedler
- Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University Jena, 07743 Jena, Germany; (A.M.S.); (S.S.H.)
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24
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The small GTPase MglA together with the TPR domain protein SgmX stimulates type IV pili formation in M. xanthus. Proc Natl Acad Sci U S A 2020; 117:23859-23868. [PMID: 32900945 PMCID: PMC7519303 DOI: 10.1073/pnas.2004722117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many bacteria move across surfaces using type IV pili (T4P). The piliation pattern varies between species; however, the underlying mechanisms governing these patterns remain largely unknown. Here, we demonstrate that in the rod-shaped Myxococcus xanthus cells, the unipolar formation of T4P at the leading cell pole is the result of stimulation by the small GTPase MglA together with the effector protein SgmX, while MglB, the cognate MglA GTPase activating protein (GAP) that localizes to the lagging cell pole, blocks this stimulation at the lagging pole due to its GAP activity. During reversals, MglA/SgmX and MglB switch polarity, laying the foundation for T4P formation at the new leading cell pole and inhibition of T4P formation at the former leading cell pole. Bacteria can move across surfaces using type IV pili (T4P), which undergo cycles of extension, adhesion, and retraction. The T4P localization pattern varies between species; however, the underlying mechanisms are largely unknown. In the rod-shaped Myxococcus xanthus cells, T4P localize at the leading cell pole. As cells reverse their direction of movement, T4P are disassembled at the old leading pole and then form at the new leading pole. Thus, cells can form T4P at both poles but engage only one pole at a time in T4P formation. Here, we address how this T4P unipolarity is realized. We demonstrate that the small Ras-like GTPase MglA stimulates T4P formation in its GTP-bound state by direct interaction with the tetratricopeptide repeat (TPR) domain-containing protein SgmX. SgmX, in turn, is important for polar localization of the T4P extension ATPase PilB. The cognate MglA GTPase activating protein (GAP) MglB, which localizes mainly to the lagging cell pole, indirectly blocks T4P formation at this pole by stimulating the conversion of MglA-GTP to MglA-GDP. Based on these findings, we propose a model whereby T4P unipolarity is accomplished by stimulation of T4P formation at the leading pole by MglA-GTP and SgmX and indirect inhibition of T4P formation at the lagging pole by MglB due to its MglA GAP activity. During reversals, MglA, SgmX, and MglB switch polarity, thus laying the foundation for T4P formation at the new leading pole and inhibition of T4P formation at the new lagging pole.
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25
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Caulton SG, Lovering AL. Bacterial invasion and killing by predatory Bdellovibrio primed by predator prey cell recognition and self protection. Curr Opin Microbiol 2020; 56:74-80. [DOI: 10.1016/j.mib.2020.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/07/2020] [Accepted: 07/12/2020] [Indexed: 01/13/2023]
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26
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Bratanis E, Andersson T, Lood R, Bukowska-Faniband E. Biotechnological Potential of Bdellovibrio and Like Organisms and Their Secreted Enzymes. Front Microbiol 2020; 11:662. [PMID: 32351487 PMCID: PMC7174725 DOI: 10.3389/fmicb.2020.00662] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 03/23/2020] [Indexed: 02/01/2023] Open
Abstract
Bdellovibrio and like organisms (BALOs) are obligate predatory bacteria that selectively prey on a broad range of Gram-negative bacteria, including multidrug-resistant human pathogens. Due to their unique lifestyle, they have been long recognized as a potential therapeutic and biocontrol agent. Research on BALOs has rapidly grown over the recent decade, resulting in many publications concerning molecular details of bacterial predation as well as applications thereof in medicine and biotechnology. This review summarizes the current knowledge on biotechnological potential of obligate predatory bacteria and their secreted enzymes.
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Affiliation(s)
- Eleni Bratanis
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Tilde Andersson
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Rolf Lood
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Ewa Bukowska-Faniband
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
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27
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Hobley L, Summers JK, Till R, Milner DS, Atterbury RJ, Stroud A, Capeness MJ, Gray S, Leidenroth A, Lambert C, Connerton I, Twycross J, Baker M, Tyson J, Kreft JU, Sockett RE. Dual Predation by Bacteriophage and Bdellovibrio bacteriovorus Can Eradicate Escherichia coli Prey in Situations where Single Predation Cannot. J Bacteriol 2020; 202:e00629-19. [PMID: 31907203 PMCID: PMC7043672 DOI: 10.1128/jb.00629-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/17/2019] [Indexed: 01/05/2023] Open
Abstract
Bacteria are preyed upon by diverse microbial predators, including bacteriophage and predatory bacteria, such as Bdellovibrio bacteriovorus While bacteriophage are used as antimicrobial therapies in Eastern Europe and are being applied for compassionate use in the United States, predatory bacteria are only just beginning to reveal their potential therapeutic uses. However, predation by either predator type can falter due to different adaptations arising in the prey bacteria. When testing poultry farm wastewater for novel Bdellovibrio isolates on Escherichia coli prey lawns, individual composite plaques were isolated containing both an RTP (rosette-tailed-phage)-like-phage and a B. bacteriovorus strain and showing central prey lysis and halos of extra lysis. Combining the purified phage with a lab strain of B. bacteriovorus HD100 recapitulated haloed plaques and increased killing of the E. coli prey in liquid culture, showing an effective side-by-side action of these predators compared to their actions alone. Using approximate Bayesian computation to select the best fitting from a variety of different mathematical models demonstrated that the experimental data could be explained only by assuming the existence of three prey phenotypes: (i) sensitive to both predators, (ii) genetically resistant to phage only, and (iii) plastic resistant to B. bacteriovorus only. Although each predator reduces prey availability for the other, high phage numbers did not abolish B. bacteriovorus predation, so both predators are competent to coexist and are causing different selective pressures on the bacterial surface while, in tandem, controlling prey bacterial numbers efficiently. This suggests that combinatorial predator therapy could overcome problems of phage resistance.IMPORTANCE With increasing levels of antibiotic resistance, the development of alternative antibacterial therapies is urgently needed. Two potential alternatives are bacteriophage and predatory bacteria. Bacteriophage therapy has been used, but prey/host specificity and the rapid acquisition of bacterial resistance to bacteriophage are practical considerations. Predatory bacteria are of interest due to their broad Gram-negative bacterial prey range and the lack of simple resistance mechanisms. Here, a bacteriophage and a strain of Bdellovibrio bacteriovorus, preyed side by side on a population of E. coli, causing a significantly greater decrease in prey numbers than either alone. Such combinatorial predator therapy may have greater potential than individual predators since prey surface changes selected for by each predator do not protect prey against the other predator.
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Affiliation(s)
- Laura Hobley
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - J Kimberley Summers
- Institute of Microbiology and Infection and Centre for Computational Biology and School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - Rob Till
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - David S Milner
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Robert J Atterbury
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Amy Stroud
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Michael J Capeness
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Stephanie Gray
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Andreas Leidenroth
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Carey Lambert
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Ian Connerton
- School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Jamie Twycross
- School of Computer Science, University of Nottingham, Nottingham, United Kingdom
| | - Michelle Baker
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jess Tyson
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Jan-Ulrich Kreft
- Institute of Microbiology and Infection and Centre for Computational Biology and School of Biosciences, University of Birmingham, Birmingham, United Kingdom
| | - R Elizabeth Sockett
- School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
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28
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Expression of attack and growth phase genes of Bdellovibrio bacteriovorus in the presence of Gram-negative and Gram-positive prey. Microbiol Res 2020; 235:126437. [PMID: 32088503 DOI: 10.1016/j.micres.2020.126437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 11/21/2022]
Abstract
The expression of attack phase (AP) and growth phase (GP) genes of Bdellovibrio bacteriovorus (B. bacteriovorus) was compared in the presence of Gram-negative [Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae)] and Gram-positive [Enterococcus faecium (E. faecium)] prey, using relative quantitative polymerase chain reaction (relative qPCR) assays. The genes bd0108 (pili retraction/extrusion) and merRNA (massively expressed riboswitch RNA) were highly expressed in the AP cells [3.99- to 6.06-fold (E. coli), 3.91- to 7.05-fold (K. pneumoniae) and 2.91- to 7.30-fold (E. faecium)]. The fliC1 gene (flagella filament) was also expressed at a high level in the AP cells however, after 240 min of co-culture with E. faecium the expression of fliC1 remained low (at 0.759-fold), while in the presence of the Gram-negative prey fliC1 expression increased. Additionally, the GP genes bd0816 (peptidoglycan-modifying enzyme) and groES1 (chaperone protein) were not induced in the presence of E. faecium. However, they were expressed in the early GP and GP of B. bacteriovorus after exposure to the Gram-negative prey. It can thus be concluded that B. bacteriovorus senses the presence of potential prey when exposed to Gram-positive and Gram-negative bacteria, however the GP genes are not induced in co-culture with E. faecium. The results from this study thus indicate that B. bacteriovorus does not actively grow in the presence of E. faecium and the second predatory cue (induces active growth of B. bacteriovorus) is lacking when B. bacteriovorus is co-cultured with the Gram-positive prey.
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29
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Laloux G. Shedding Light on the Cell Biology of the Predatory Bacterium Bdellovibrio bacteriovorus. Front Microbiol 2020; 10:3136. [PMID: 32038570 PMCID: PMC6985089 DOI: 10.3389/fmicb.2019.03136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/26/2019] [Indexed: 12/25/2022] Open
Abstract
Bdellovibrio bacteriovorus is a predatory bacterium that feeds upon and proliferates inside other Gram-negative bacteria. Upon entry into the periplasmic space of the prey envelope, B. bacteriovorus initiates an exquisite developmental program in which it digests the host resources and grows as a filament, which eventually divides in a non-binary manner, releasing a variable number of daughter cells. The progeny then escape from the prey ghost to encounter new victims and resume the predation cycle. Owing to its unique biology, B. bacteriovorus undoubtedly represents an attractive model to unravel novel mechanisms of bacterial cell cycle control and cellular organization. Yet, the molecular factors behind the sophisticated lifestyle of this micro-predator are still mysterious. In particular, the spatiotemporal dynamics of proteins that control key cellular processes such as transmission of the genetic information, cell growth and division remain largely unexplored. In this Perspective article, I highlight outstanding fundamental questions related to these aspects and arising from the original biology of this bacterium. I also discuss available insights and potential cell biology approaches based on quantitative live imaging techniques, in combination with bacterial genetics and biochemistry, to shed light on the intracellular organization of B. bacteriovorus in space and time.
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Affiliation(s)
- Géraldine Laloux
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
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30
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Williams LE, Cullen N, DeGiorgis JA, Martinez KJ, Mellone J, Oser M, Wang J, Zhang Y. Variation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100. MICROBIOLOGY (READING, ENGLAND) 2019; 165:1315-1330. [PMID: 31592759 PMCID: PMC7137782 DOI: 10.1099/mic.0.000861] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/20/2019] [Indexed: 12/23/2022]
Abstract
Defining phenotypic and associated genotypic variation among Bdellovibrio may further our understanding of how this genus attacks and kills different Gram-negative bacteria. We isolated Bdellovibrio sp. NC01 from soil. Analysis of 16S rRNA gene sequences and average amino acid identity showed that NC01 belongs to a different species than the type species bacteriovorus. By clustering amino acid sequences from completely sequenced Bdellovibrio and comparing the resulting orthologue groups to a previously published analysis, we defined a 'core genome' of 778 protein-coding genes and identified four protein-coding genes that appeared to be missing only in NC01. To determine how horizontal gene transfer (HGT) may have impacted NC01 genome evolution, we performed genome-wide comparisons of Bdellovibrio nucleotide sequences, which indicated that eight NC01 genomic regions were likely acquired by HGT. To investigate how genome variation may impact predation, we compared protein-coding gene content between NC01 and the B. bacteriovorus type strain HD100, focusing on genes implicated as important in successful killing of prey. Of these, NC01 is missing ten genes that may play roles in lytic activity during predation. Compared to HD100, NC01 kills fewer tested prey strains and kills Escherichia coli ML35 less efficiently. NC01 causes a smaller log reduction in ML35, after which the prey population recovers and the NC01 population decreases. In addition, NC01 forms turbid plaques on lawns of E. coli ML35, in contrast to clear plaques formed by HD100. Linking phenotypic variation in interactions between Bdellovibrio and Gram-negative bacteria with underlying Bdellovibrio genome variation is valuable for understanding the ecological significance of predatory bacteria and evaluating their effectiveness in clinical applications.
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Affiliation(s)
| | - Nicole Cullen
- Department of Biology, Providence College, Providence, RI, USA
| | - Joseph A. DeGiorgis
- Department of Biology, Providence College, Providence, RI, USA
- Cellular Dynamics Program, Marine Biological Laboratory, Woods Hole, MA, USA
| | | | - Justina Mellone
- Department of Biology, Providence College, Providence, RI, USA
| | - Molly Oser
- Department of Biology, Providence College, Providence, RI, USA
| | - Jing Wang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI, USA
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31
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Dynamics of Chromosome Replication and Its Relationship to Predatory Attack Lifestyles in Bdellovibrio bacteriovorus. Appl Environ Microbiol 2019; 85:AEM.00730-19. [PMID: 31076424 PMCID: PMC6606864 DOI: 10.1128/aem.00730-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/04/2019] [Indexed: 12/20/2022] Open
Abstract
Bdellovibrio bacteriovorus is a small Gram-negative, obligate predatory bacterium that is largely found in wet, aerobic environments (e.g., soil). This bacterium attacks and invades other Gram-negative bacteria, including animal and plant pathogens. The intriguing life cycle of B. bacteriovorus consists of two phases: a free-living nonreplicative attack phase, in which the predatory bacterium searches for its prey, and a reproductive phase, in which B. bacteriovorus degrades a host's macromolecules and reuses them for its own growth and chromosome replication. Although the cell biology of this predatory bacterium has gained considerable interest in recent years, we know almost nothing about the dynamics of its chromosome replication. Here, we performed a real-time investigation into the subcellular localization of the replisome(s) in single cells of B. bacteriovorus Our results show that in B. bacteriovorus, chromosome replication takes place only during the reproductive phase and exhibits a novel spatiotemporal arrangement of replisomes. The replication process starts at the invasive pole of the predatory bacterium inside the prey cell and proceeds until several copies of the chromosome have been completely synthesized. Chromosome replication is not coincident with the predator cell division, and it terminates shortly before synchronous predator filament septation occurs. In addition, we demonstrate that if this B. bacteriovorus life cycle fails in some cells of Escherichia coli, they can instead use second prey cells to complete their life cycle.IMPORTANCE New strategies are needed to combat multidrug-resistant bacterial infections. Application of the predatory bacterium Bdellovibrio bacteriovorus, which kills other bacteria, including pathogens, is considered promising for combating bacterial infections. The B. bacteriovorus life cycle consists of two phases, a free-living, invasive attack phase and an intracellular reproductive phase, in which this predatory bacterium degrades the host's macromolecules and reuses them for its own growth. To understand the use of B. bacteriovorus as a "living antibiotic," it is first necessary to dissect its life cycle, including chromosome replication. Here, we present a real-time investigation into subcellular localization of chromosome replication in a single cell of B. bacteriovorus This process initiates at the invasion pole of B. bacteriovorus and proceeds until several copies of the chromosome have been completely synthesized. Interestingly, we demonstrate that some cells of B. bacteriovorus require two prey cells sequentially to complete their life cycle.
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32
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Lowry RC, Milner DS, Al-Bayati AMS, Lambert C, Francis VI, Porter SL, Sockett RE. Evolutionary diversification of the RomR protein of the invasive deltaproteobacterium, Bdellovibrio bacteriovorus. Sci Rep 2019; 9:5007. [PMID: 30899045 PMCID: PMC6428892 DOI: 10.1038/s41598-019-41263-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 02/27/2019] [Indexed: 01/19/2023] Open
Abstract
Bdellovibrio bacteriovorus is a predatory deltaproteobacterium that encounters individual Gram-negative prey bacteria with gliding or swimming motility, and then is able to invade such prey cells via type IVa pilus-dependent mechanisms. Movement control (pili or gliding) in other deltaproteobacteria, such as the pack hunting Myxococcus xanthus, uses a response regulator protein, RomRMx (which dynamically relocalises between the cell poles) and a GTPase, MglAMx, previously postulated as an interface between the FrzMx chemosensory system and gliding or pilus-motility apparatus, to produce regulated bidirectional motility. In contrast, B. bacteriovorus predation is a more singular encounter between a lone predator and prey; contact is always via the piliated, non-flagellar pole of the predator, involving MglABd, but no Frz system. In this new study, tracking fluorescent RomRBd microscopically during predatory growth shows that it does not dynamically relocalise, in contrast to the M. xanthus protein; instead having possible roles in growth events. Furthermore, transcriptional start analysis, site-directed mutagenesis and bacterial two-hybrid interaction studies, indicate an evolutionary loss of RomRBd activation (via receiver domain phosphorylation) in this lone hunting bacterium, demonstrating divergence from its bipolar role in motility in pack-hunting M. xanthus and further evolution that may differentiate lone from pack predators.
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Affiliation(s)
- Rebecca C Lowry
- School of Life Sciences, University of Nottingham, Medical School, Nottingham, United Kingdom
| | - David S Milner
- School of Life Sciences, University of Nottingham, Medical School, Nottingham, United Kingdom.,Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Asmaa M S Al-Bayati
- School of Life Sciences, University of Nottingham, Medical School, Nottingham, United Kingdom.,Northern Technical University, Mosul, Iraq
| | - Carey Lambert
- School of Life Sciences, University of Nottingham, Medical School, Nottingham, United Kingdom
| | - Vanessa I Francis
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Steven L Porter
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom.
| | - R E Sockett
- School of Life Sciences, University of Nottingham, Medical School, Nottingham, United Kingdom.
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33
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Said N, Chatzinotas A, Schmidt M. Have an Ion on It: The Life-Cycle of Bdellovibrio bacteriovorus Viewed by Helium-Ion Microscopy. ACTA ACUST UNITED AC 2018; 3:e1800250. [PMID: 32627346 DOI: 10.1002/adbi.201800250] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/11/2018] [Indexed: 11/12/2022]
Abstract
Helium-ion microscopy (HIM) has so far rarely been employed to image microbial interactions. Here, the visualization of the life-cycle of the bacterial predator Bdellovibrio bacteriovorus HD100 with Escherichia coli and Pseudomonas putida, respectively, as prey is presented. The predator is brought in contact with prey and samples are taken at selected times. The system is monitored by phase-contrast microscopy and HIM. For HIM imaging, a sample preparation protocol is established that preserves the structure of Bdellovibrio, prey, and bdelloplasts. The micrographs show the attachment of the predator to its prey, the evolution of bdelloplasts, their lysis, and the release of predator progeny. The combination of HIM with two more approaches allows for investigating predator-prey interactions from different angles: First, phase-contrast micrographs provide quantitative information for the numbers of predator, prey, and bdelloplasts. Second, a numerical model solving the retarded differential equations that describe the system's time-evolution is developed and fits the experimentally determined cell numbers. In conclusion, the high resolution, the large depth of focus, and surface sensitivity of HIM hold promise to expand future studies on so far neglected ecological interactions within the microbial food web, in particular in samples with pronounced topography such as bacterial biofilms.
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Affiliation(s)
- Nedal Said
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
| | - Antonis Chatzinotas
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103, Leipzig, Germany
| | - Matthias Schmidt
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research - UFZ, Permoserstrasse 15, 04318, Leipzig, Germany
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34
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Sharma G, Burrows LL, Singer M. Diversity and Evolution of Myxobacterial Type IV Pilus Systems. Front Microbiol 2018; 9:1630. [PMID: 30072980 PMCID: PMC6060248 DOI: 10.3389/fmicb.2018.01630] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/29/2018] [Indexed: 12/18/2022] Open
Abstract
Type IV pili (T4P) are surface-exposed protein fibers that play key roles in the bacterial life cycle via surface attachment/adhesion, biofilm formation, motility, and development. The order Myxococcales (myxobacteria) are members of the class Deltaproteobacteria and known for their large genome size and complex social behaviors, including gliding motility, fruiting body formation, biofilm production, and prey hunting. Myxococcus xanthus, the best-characterized member of the order, relies on the appropriate expression of 17 type IVa (T4aP) genes organized in a single cluster plus additional genes (distributed throughout the genome) for social motility and development. Here, we compared T4aP genes organization within the myxobacteria to understand their evolutionary origins and diversity. We found that T4aP genes are organized as large clusters in suborder Cystobacterineae, whereas in other two suborders Sorangiineae and Nannocystineae, these genes are dispersed throughout the genome. Based on the genomic organization, the phylogeny of conserved proteins, and synteny studies among 28 myxobacterial and 66 Proteobacterial genomes, we propose an evolutionary model for the origin of myxobacterial T4aP genes independently from other orders in class Deltaproteobacteria. Considering a major role for T4P, this study further proposes the origins and evolution of social motility in myxobacteria and provides a foundation for understanding how complex-behavioral traits, such as gliding motility, multicellular development, etc., might have evolved in this diverse group of complex organisms.
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Affiliation(s)
- Gaurav Sharma
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, United States
| | - Lori L Burrows
- Department of Biochemistry and Biomedical Sciences and the Michael G. DeGroote Institute for Infectious Diseases Research, McMaster University, Hamilton, ON, Canada
| | - Mitchell Singer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, United States
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35
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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: 51] [Impact Index Per Article: 8.5] [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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36
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Heidari Tajabadi F, Medrano-Soto A, Ahmadzadeh M, Salehi Jouzani G, Saier MH. Comparative Analyses of Transport Proteins Encoded within the Genomes of Bdellovibrio bacteriovorus HD100 and Bdellovibrio exovorus JSS. J Mol Microbiol Biotechnol 2017; 27:332-349. [PMID: 29212086 DOI: 10.1159/000484563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/17/2017] [Indexed: 12/21/2022] Open
Abstract
Bdellovibrio, δ-proteobacteria, including B. bacteriovorus (Bba) and B. exovorus (Bex), are obligate predators of other Gram-negative bacteria. While Bba grows in the periplasm of the prey cell, Bex grows externally. We have analyzed and compared the transport proteins of these 2 organisms based on the current contents of the Transporter Classification Database (TCDB; www.tcdb.org). Bba has 103 transporters more than Bex, 50% more secondary carriers, and 3 times as many MFS carriers. Bba has far more metabolite transporters than Bex as expected from its larger genome, but there are 2 times more carbohydrate uptake and drug efflux systems, and 3 times more lipid transporters. Bba also has polyamine and carboxylate transporters lacking in Bex. Bba has more than twice as many members of the Mot-Exb family of energizers, but both may have energizers for gliding motility. They use entirely different types of systems for iron acquisition. Both contain unexpectedly large numbers of pseudogenes and incomplete systems, suggesting that they are undergoing genome size reduction. Interestingly, all 5 outer-membrane receptors in Bba are lacking in Bex. The 2 organisms have similar numbers and types of peptide and amino acid uptake systems as well as protein and carbohydrate secretion systems. The differences observed correlate with and may account, in part, for the different lifestyles of these 2 bacterial predators.
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37
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Fluorescent D-amino-acids reveal bi-cellular cell wall modifications important for Bdellovibrio bacteriovorus predation. Nat Microbiol 2017; 2:1648-1657. [PMID: 28974693 PMCID: PMC5705579 DOI: 10.1038/s41564-017-0029-y] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 08/11/2017] [Indexed: 01/05/2023]
Abstract
Modification of essential bacterial peptidoglycan (PG) containing cell
walls can lead to antibiotic resistance, for example β-lactam resistance
by L,D-transpeptidase activities. Predatory Bdellovibrio
bacteriovorus are naturally antibacterial and combat infections by
traversing, modifying and finally destroying walls of Gram-negative prey
bacteria, modifying their own PG as they grow inside prey. Historically, these
multi-enzymatic processes on two similar PG walls have proved challenging to
elucidate. Here, with a PG labelling approach utilizing timed pulses of multiple
fluorescent D-amino acids (FDAAs), we illuminate dynamic changes that predator
and prey walls go through during the different phases of bacteria:bacteria
invasion. We show formation of a reinforced circular port-hole in the prey wall;
L,D-transpeptidaseBd mediated D-amino acid modifications
strengthening prey PG during Bdellovibrio invasion and a zonal
mode of predator-elongation. This process is followed by unconventional,
multi-point and synchronous septation of the intracellular
Bdellovibrio, accommodating odd- and even-numbered progeny
formation by non-binary division.
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38
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Jurkevitch É, Jacquet S. [Bdellovibrio and like organisms: outstanding predators!]. Med Sci (Paris) 2017; 33:519-527. [PMID: 28612728 DOI: 10.1051/medsci/20173305016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Obligate predatory bacteria, i.e. bacteria requiring a Gram negative prey cell in order to complete their cell cycle, belong to the polyphyletic group referred to as the Bdellovibrio And Like Organisms (BALO). Predatory interactions between bacteria are complex, yet their dynamics and impact on bacterial communities in the environment are becoming better understood. BALO have unique life cycles: they grow epibiotically with the predator remaining attached to the prey's envelope, dividing in a binary manner or periplasmically, i.e. by penetrating the prey's periplasm to generate a number of progeny cells. The periplasmic life cycle includes unique gene and protein patterns and unique signaling features. These ecological and cellular features, along with applications of the BALO in the medical, agricultural and environmental fields are surveyed.
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Affiliation(s)
- Édouard Jurkevitch
- Faculté d'Agriculture, de l'Alimentation et de l'Environnement, Université Hébraïque de Jérusalem, Rehovot, Israël
| | - Stéphan Jacquet
- INRA, UMR CARRTEL, 75, avenue de Corzent, 74200 Thonon-les-Bains, France
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39
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Shatzkes K, Singleton E, Tang C, Zuena M, Shukla S, Gupta S, Dharani S, Rinaggio J, Kadouri DE, Connell ND. Examining the efficacy of intravenous administration of predatory bacteria in rats. Sci Rep 2017; 7:1864. [PMID: 28500337 PMCID: PMC5431856 DOI: 10.1038/s41598-017-02041-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/06/2017] [Indexed: 12/20/2022] Open
Abstract
The proteobacteria Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus are obligate predators of Gram-negative bacteria, and have been proposed to be used to treat multidrug-resistant bacterial infections. The ability of predatory bacteria to reduce bacterial burden in vivo within the lungs of rats has been demonstrated, but it was unknown if predatory bacteria can attenuate systemic bacterial burden administered intravenously. In this study, we first assessed the safety of intravenous inoculation of predatory bacteria in rats. No rat morbidity or adverse histopathology of various organs due to predatory bacteria administration was observed. An increase in proinflammatory cytokines (TNFα and KC/GRO) was observed at two hours post-inoculation; however, cytokines returned to baseline levels by 18 hours. Furthermore, bacterial dissemination analysis demonstrated that predatory bacteria were efficiently cleared from the host by 20 days post-injection. To determine whether predatory bacteria could reduce bacterial burden in vivo, Klebsiella pneumoniae was injected into the tail veins of rats and followed with multiple doses of predatory bacteria over 16 or 24 hours. Predatory bacteria were unable to significantly reduce K. pneumoniae burden in the blood or prevent dissemination to other organs. The results suggest that predatory bacteria may not be effective for treatment of acute blood infections.
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Affiliation(s)
- Kenneth Shatzkes
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Eric Singleton
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Chi Tang
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Michael Zuena
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Sean Shukla
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Shilpi Gupta
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Sonal Dharani
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Joseph Rinaggio
- Department of Diagnostic Sciences, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, 07103, USA
| | - Nancy D Connell
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.
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Kongrueng J, Mitraparp-Arthorn P, Bangpanwimon K, Robins W, Vuddhakul V, Mekalanos J. Isolation of Bdellovibrio and like organisms and potential to reduce acute hepatopancreatic necrosis disease caused by Vibrio parahaemolyticus. DISEASES OF AQUATIC ORGANISMS 2017; 124:223-232. [PMID: 28492178 DOI: 10.3354/dao03120] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Acute hepatopancreatic necrosis disease, a severe disease of shrimp, is caused by Vibrio parahaemolyticus (AHPND Vp), a halophilic bacterium harboring a plasmid that contains toxin genes homologous to Photorhabdus insect-related toxins. We obtained 9 isolates of Bdellovibrio and like organisms (BALOs) from water and sediment samples in Thailand. Using 16S rRNA sequencing, all of the organisms were identified as Bacteriovorax spp. and were able to attack all tested AHPND Vp isolates. In addition, their various susceptible hosts, including Gram-positive and Gram-negative bacteria, were observed. The optimal ratio for interaction between the Bacteriovorax isolate BV-A and AHPND Vp was determined to be 1:10. The suitable conditions applied for co-culture between BV-A and AHPND Vp were 30°C, 2% NaCl, and pH 7.6. The capability of BV-A to reduce numbers of AHPND Vp in vitro was observed in co-culture after incubation for 2 d and continued until the end of the incubation period. In vivo, BV-A was able to reduce mortality of shrimp post-larvae infected with AHPND Vp. In addition, BV-A significantly decreased the formation of biofilm by AHPND Vp. These findings provide evidence for using Bacteriovorax as a biocontrol of AHPND Vp in shrimp aquaculture.
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Affiliation(s)
- Jetnapang Kongrueng
- Food Safety and Health Research Unit, Department of Microbiology, Faculty of Science, Prince of Songkla University, Hat Yai, Thailand
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Identification and Characterization of Differentially-Regulated Type IVb Pilin Genes Necessary for Predation in Obligate Bacterial Predators. Sci Rep 2017; 7:1013. [PMID: 28432347 PMCID: PMC5430801 DOI: 10.1038/s41598-017-00951-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/17/2017] [Indexed: 11/08/2022] Open
Abstract
Bdellovibrio bacteriovorus is an obligate predator of bacteria that grows and divides within the periplasm of its prey. Functions involved in the early steps of predation have been identified and characterized, but mediators of prey invasion are still poorly detailed. By combining omics data available for Bdellovibrio and like organisms (BALO’s), we identified 43 genes expressed in B. bacteriovorus during the early interaction with prey. These included genes in a tight adherence (TAD) operon encoding for two type IVb fimbriae-like pilin proteins (flp1 and flp2), and their processing and export machinery. Two additional flp genes (flp3 and flp4) were computationally identified at other locations along the chromosome, defining the largest and most diverse type IVb complement known in bacteria to date. Only flp1, flp2 and flp4 were expressed; their respective gene knock-outs resulted in a complete loss of the predatory ability without losing the ability to adhere to prey cells. Additionally, we further demonstrate differential regulation of the flp genes as the TAD operon of BALOs with different predatory strategies is controlled by a flagellar sigma factor FliA, while flp4 is not. Finally, we show that FliA, a known flagellar transcriptional regulator in other bacteria, is an essential Bdellovibrio gene.
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42
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Effect of predatory bacteria on the gut bacterial microbiota in rats. Sci Rep 2017; 7:43483. [PMID: 28262674 PMCID: PMC5337950 DOI: 10.1038/srep43483] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/24/2017] [Indexed: 01/14/2023] Open
Abstract
Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus are Gram-negative proteobacteria that are obligate predators of other Gram-negative bacteria and are considered potential alternatives to antibiotics. Most studies focusing on predatory bacteria have been performed in vitro, thus the effect of predatory bacteria on a live host, including the impact on the ecology of the native microbiota, has yet to be fully examined. In this study, intrarectal inoculations of Sprague-Dawley rats with predatory bacteria were performed. Additionally, feces were collected for seven days post-inoculation to determine the effect on gut bacterial diversity. Rat colonic tissue exhibited no abnormal histopathological effects due to predatory bacteria. A modest increase in pro-inflammatory cytokines was measured in the colons of rats inoculated with predatory bacteria by 24 and 48 hours, with all but IL-13 returning to baseline by seven days. V4 16S rRNA gene sequencing of fecal DNA demonstrated minimal shifts in taxonomic representation over the week due to predatory bacteria. Changes in bacterial populations due to exposure to B. bacteriovorus are predicted to contribute to health, however, an overgrowth of Prevotella was observed due to exposure to M. aeruginosavorus. This study further addresses safety concerns associated with the potential use of predatory bacteria to treat infections.
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Chang YW, Kjær A, Ortega DR, Kovacikova G, Sutherland JA, Rettberg LA, Taylor RK, Jensen GJ. Architecture of the Vibrio cholerae toxin-coregulated pilus machine revealed by electron cryotomography. Nat Microbiol 2017; 2:16269. [PMID: 28165453 PMCID: PMC5302817 DOI: 10.1038/nmicrobiol.2016.269] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 12/14/2016] [Indexed: 01/22/2023]
Affiliation(s)
- Yi-Wei Chang
- California Institute of Technology, Pasadena, California 91125, USA
| | - Andreas Kjær
- University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Davi R Ortega
- California Institute of Technology, Pasadena, California 91125, USA
| | | | - John A Sutherland
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA
| | - Lee A Rettberg
- Howard Hughes Medical Institute, Pasadena, California 91125, USA
| | - Ronald K Taylor
- Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA
| | - Grant J Jensen
- California Institute of Technology, Pasadena, California 91125, USA.,Howard Hughes Medical Institute, Pasadena, California 91125, USA
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Shatzkes K, Singleton E, Tang C, Zuena M, Shukla S, Gupta S, Dharani S, Onyile O, Rinaggio J, Connell ND, Kadouri DE. Predatory Bacteria Attenuate Klebsiella pneumoniae Burden in Rat Lungs. mBio 2016; 7:e01847-16. [PMID: 27834203 PMCID: PMC5101354 DOI: 10.1128/mbio.01847-16] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 10/11/2016] [Indexed: 12/26/2022] Open
Abstract
Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus are predatory bacteria that naturally-and obligately-prey on other Gram-negative bacteria, and their use has been proposed as a potential new approach to control microbial infection. The ability of predatory bacteria to prey on Gram-negative human pathogens in vitro is well documented; however, the in vivo safety and efficacy of predatory bacteria have yet to be fully assessed. In this study, we examined whether predatory bacteria can reduce bacterial burden in the lungs in an in vivo mammalian system. Initial safety studies were performed by intranasal inoculation of rats with predatory bacteria. No adverse effects or lung pathology were observed in rats exposed to high concentrations of predatory bacteria at up to 10 days postinoculation. Enzyme-linked immunosorbent assay (ELISA) of the immune response revealed a slight increase in inflammatory cytokine levels at 1 h postinoculation that was not sustained by 48 h. Additionally, dissemination experiments showed that predators were efficiently cleared from the host by 10 days postinoculation. To measure the ability of predatory bacteria to reduce microbial burden in vivo, we introduced sublethal concentrations of Klebsiella pneumoniae into the lungs of rats via intranasal inoculation and followed with multiple doses of predatory bacteria over 24 h. Predatory bacteria were able to reduce K. pneumoniae bacterial burden, on average, by more than 3.0 log10 in the lungs of most rats as measured by CFU plating. The work presented here provides further support for the idea of developing predatory bacteria as a novel biocontrol agent. IMPORTANCE A widely held notion is that antibiotics are the greatest medical advance of the last 50 years. However, the rise of multidrug-resistant (MDR) bacterial infections has become a global health crisis over the last decade. As we enter the postantibiotic era, it is crucial that we begin to develop new strategies to combat bacterial infection. Here, we report one such new approach: the use of predatory bacteria (Bdellovibrio bacteriovorus and Micavibrio aeruginosavorus) that naturally-and obligately-prey on other Gram-negative bacteria. To our knowledge, this is the first study that demonstrated the ability of predatory bacteria to attenuate the bacterial burden of a key human pathogen in an in vivo mammalian system. As the prevalence of MDR infections continues to rise each year, our results may represent a shift in how we approach treating microbial infections in the future.
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Affiliation(s)
- Kenneth Shatzkes
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Eric Singleton
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Chi Tang
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Michael Zuena
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Sean Shukla
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Shilpi Gupta
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, New Jersey, USA
| | - Sonal Dharani
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, New Jersey, USA
| | - Onoyom Onyile
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Joseph Rinaggio
- Department of Diagnostic Sciences, Rutgers School of Dental Medicine, Newark, New Jersey, USA
| | - Nancy D Connell
- Division of Infectious Disease, Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, USA
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, New Jersey, USA
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Chang YW, Rettberg LA, Treuner-Lange A, Iwasa J, Søgaard-Andersen L, Jensen GJ. Architecture of the type IVa pilus machine. Science 2016; 351:aad2001. [PMID: 26965631 DOI: 10.1126/science.aad2001] [Citation(s) in RCA: 259] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 01/13/2016] [Indexed: 12/28/2022]
Abstract
Type IVa pili are filamentous cell surface structures observed in many bacteria. They pull cells forward by extending, adhering to surfaces, and then retracting. We used cryo-electron tomography of intact Myxococcus xanthus cells to visualize type IVa pili and the protein machine that assembles and retracts them (the type IVa pilus machine, or T4PM) in situ, in both the piliated and nonpiliated states, at a resolution of 3 to 4 nanometers. We found that T4PM comprises an outer membrane pore, four interconnected ring structures in the periplasm and cytoplasm, a cytoplasmic disc and dome, and a periplasmic stem. By systematically imaging mutants lacking defined T4PM proteins or with individual proteins fused to tags, we mapped the locations of all 10 T4PM core components and the minor pilins, thereby providing insights into pilus assembly, structure, and function.
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Affiliation(s)
- Yi-Wei Chang
- California Institute of Technology, Pasadena, CA 91125, USA. Howard Hughes Medical Institute, Pasadena, CA 91125, USA
| | - Lee A Rettberg
- Howard Hughes Medical Institute, Pasadena, CA 91125, USA
| | - Anke Treuner-Lange
- Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Janet Iwasa
- University of Utah, Salt Lake City, UT 84112, USA
| | | | - Grant J Jensen
- California Institute of Technology, Pasadena, CA 91125, USA. Howard Hughes Medical Institute, Pasadena, CA 91125, USA.
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46
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Microbial Surface Colonization and Biofilm Development in Marine Environments. Microbiol Mol Biol Rev 2015; 80:91-138. [PMID: 26700108 DOI: 10.1128/mmbr.00037-15] [Citation(s) in RCA: 462] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.
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47
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Lambert C, Cadby IT, Till R, Bui NK, Lerner TR, Hughes WS, Lee DJ, Alderwick LJ, Vollmer W, Sockett ER, Lovering AL. Ankyrin-mediated self-protection during cell invasion by the bacterial predator Bdellovibrio bacteriovorus. Nat Commun 2015; 6:8884. [PMID: 26626559 PMCID: PMC4686830 DOI: 10.1038/ncomms9884] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 10/12/2015] [Indexed: 11/30/2022] Open
Abstract
Predatory Bdellovibrio bacteriovorus are natural antimicrobial organisms, killing other bacteria by whole-cell invasion. Self-protection against prey-metabolizing enzymes is important for the evolution of predation. Initial prey entry involves the predator's peptidoglycan DD-endopeptidases, which decrosslink cell walls and prevent wasteful entry by a second predator. Here we identify and characterize a self-protection protein from B. bacteriovorus, Bd3460, which displays an ankyrin-based fold common to intracellular pathogens of eukaryotes. Co-crystal structures reveal Bd3460 complexation of dual targets, binding a conserved epitope of each of the Bd3459 and Bd0816 endopeptidases. Complexation inhibits endopeptidase activity and cell wall decrosslinking in vitro. Self-protection is vital - ΔBd3460 Bdellovibrio deleteriously decrosslink self-peptidoglycan upon invasion, adopt a round morphology, and lose predatory capacity and cellular integrity. Our analysis provides the first mechanistic examination of self-protection in Bdellovibrio, documents protection-multiplicity for products of two different genomic loci, and reveals an important evolutionary adaptation to an invasive predatory bacterial lifestyle.
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Affiliation(s)
- Carey Lambert
- Centre for Genetics and Genomics, School of Biology, Nottingham University, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Ian T. Cadby
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Rob Till
- Centre for Genetics and Genomics, School of Biology, Nottingham University, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Nhat Khai Bui
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Thomas R. Lerner
- Centre for Genetics and Genomics, School of Biology, Nottingham University, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - William S. Hughes
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - David J. Lee
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Luke J. Alderwick
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Waldemar Vollmer
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK
| | - Elizabeth R. Sockett
- Centre for Genetics and Genomics, School of Biology, Nottingham University, Medical School, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Andrew L. Lovering
- Institute for Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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Sangwan N, Lambert C, Sharma A, Gupta V, Khurana P, Khurana JP, Sockett RE, Gilbert JA, Lal R. Arsenic rich Himalayan hot spring metagenomics reveal genetically novel predator-prey genotypes. ENVIRONMENTAL MICROBIOLOGY REPORTS 2015; 7:812-23. [PMID: 25953741 DOI: 10.1111/1758-2229.12297] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 04/13/2015] [Indexed: 05/07/2023]
Abstract
Bdellovibrio bacteriovorus are small Deltaproteobacteria that invade, kill and assimilate their prey. Metagenomic assembly analysis of the microbial mats of an arsenic rich, hot spring was performed to describe the genotypes of the predator Bdellovibrio and the ecogenetically adapted taxa Enterobacter. The microbial mats were enriched with Bdellovibrio (1.3%) and several Gram-negative bacteria including Bordetella (16%), Enterobacter (6.8%), Burkholderia (4.8%), Acinetobacter (2.3%) and Yersinia (1%). A high-quality (47 contigs, 25X coverage; 3.5 Mbp) draft genome of Bdellovibrio (strain ArHS; Arsenic Hot Spring) was reassembled, which lacked the marker gene Bd0108 associated with the usual method of prey interaction and invasion for this genus, while maintaining genes coding for the hydrolytic enzymes necessary for prey assimilation. By filtering microbial mat samples (< 0.45 μm) to enrich for small predatory cell sizes, we observed Bdellovibrio-like cells attached side-on to E. coli through electron microscopy. Furthermore, a draft pan-genome of the dominant potential host taxon, Enterobacter cloacae ArHS (4.8 Mb), along with three of its viral genotypes (n = 3; 42 kb, 49 kb and 50 kb), was assembled. These data were further used to analyse the population level evolutionary dynamics (taxonomical and functional) of reconstructed genotypes.
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Affiliation(s)
- Naseer Sangwan
- Department of Zoology, University of Delhi, Delhi, 110007, India
- Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - Carey Lambert
- Institute of Genetics, School of Life Sciences, Nottingham University, Queen's Medical Centre, Nottingham, UK
| | - Anukriti Sharma
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Vipin Gupta
- Department of Zoology, University of Delhi, Delhi, 110007, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - R Elizabeth Sockett
- Institute of Genetics, School of Life Sciences, Nottingham University, Queen's Medical Centre, Nottingham, UK
| | - Jack A Gilbert
- Biosciences Division (BIO), Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
- Department of Ecology and Evolution, University of Chicago, 5640 South Ellis Avenue, Chicago, IL, 60637, USA
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Rup Lal
- Department of Zoology, University of Delhi, Delhi, 110007, India
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49
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Cell-cycle progress in obligate predatory bacteria is dependent upon sequential sensing of prey recognition and prey quality cues. Proc Natl Acad Sci U S A 2015; 112:E6028-37. [PMID: 26487679 DOI: 10.1073/pnas.1515749112] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Predators feed on prey to acquire the nutrients necessary to sustain their survival, growth, and replication. In Bdellovibrio bacteriovorus, an obligate predator of Gram-negative bacteria, cell growth and replication are tied to a shift from a motile, free-living phase of search and attack to a sessile, intracellular phase of growth and replication during which a single prey cell is consumed. Engagement and sustenance of growth are achieved through the sensing of two unidentified prey-derived cues. We developed a novel ex vivo cultivation system for B. bacteriovorus composed of prey ghost cells that are recognized and invaded by the predator. By manipulating their content, we demonstrated that an early cue is located in the prey envelope and a late cue is found within the prey soluble fraction. These spatially and temporally separated cues elicit discrete and combinatory regulatory effects on gene transcription. Together, they delimit a poorly characterized transitory phase between the attack phase and the growth phase, during which the bdelloplast (the invaded prey cell) is constructed. This transitory phase constitutes a checkpoint in which the late cue presumably acts as a determinant of the prey's nutritional value before the predator commits. These regulatory adaptations to a unique bacterial lifestyle have not been reported previously.
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50
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Prehna G, Ramirez BE, Lovering AL. The lifestyle switch protein Bd0108 of Bdellovibrio bacteriovorus is an intrinsically disordered protein. PLoS One 2014; 9:e115390. [PMID: 25514156 PMCID: PMC4267844 DOI: 10.1371/journal.pone.0115390] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 11/21/2014] [Indexed: 01/15/2023] Open
Abstract
Bdellovibrio bacteriovorus is a δ-proteobacterium that preys upon Salmonella spp., E. coli, and other Gram-negative bacteria. Bdellovibrio can grow axenically (host-independent, HI, rare and mutation-driven) or subsist via a predatory lifecycle (host-dependent, HD, the usual case). Upon contact with prey, B. bacteriovorus enters the host periplasm from where it slowly drains the host cytosol of nutrients for its own replication. At the core of this mechanism is a retractile pilus, whose architecture is regulated by the protein Bd0108 and its interaction with the neighboring gene product Bd0109. Deletion of bd0108 results in negligible pilus formation, whereas an internal deletion (the one that instigates host-independence) causes mis-regulation of pilus length. These mutations, along with a suite of naturally occurring bd0108 mutant strains, act to control the entry to HI growth. To further study the molecular mechanism of predatory regulation, we focused on the apparent lifecycle switch protein Bd0108. Here we characterize the solution structure and dynamics of Bd0108 using nuclear magnetic resonance (NMR) spectroscopy complemented with additional biophysical methods. We then explore the interaction between Bd0108 and Bd0109 in detail utilizing isothermal titration calorimetry (ITC) and NMR spectroscopy. Together our results demonstrate that Bd0108 is an intrinsically disordered protein (IDP) and that the interaction with Bd0109 is of low affinity. Furthermore, we observe that Bd0108 retains an IDP nature while binding Bd0109. From our data we conclude that Bdellovibrio bacteriovorus utilizes an intrinsically disordered protein to regulate its pilus and control predation signaling.
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Affiliation(s)
- Gerd Prehna
- Center for Structural Biology, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Benjamin E. Ramirez
- Center for Structural Biology, Research Resources Center, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Andrew L. Lovering
- Institute of Microbiology & Infection, School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- * E-mail:
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