1
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Whitfield GB, Brun YV. The type IVc pilus: just a Tad different. Curr Opin Microbiol 2024; 79:102468. [PMID: 38579360 DOI: 10.1016/j.mib.2024.102468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 04/07/2024]
Abstract
Bacteria utilize type IV pili (T4P) to interact with their environment, where they facilitate processes including motility, adherence, and DNA uptake. T4P require multisubunit, membrane-spanning nanomachines for assembly. The tight adherence (Tad) pili are an Archaea-derived T4P subgroup whose machinery exhibits significant mechanistic and architectural differences from bacterial type IVa and IVb pili. Most Tad biosynthetic genes are encoded in a single locus that is widespread in bacteria due to facile acquisition via horizontal gene transfer. These loci experience extensive structural rearrangements, including the acquisition of novel regulatory or biosynthetic genes, which fine-tune their function. This has permitted their integration into many different bacterial lifestyles, including the Caulobacter crescentus cell cycle, Myxococcus xanthus predation, and numerous plant and mammalian pathogens and symbionts.
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Affiliation(s)
- Gregory B Whitfield
- Département de Microbiologie, Infectiologie, et Immunologie, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, Québec H3C 3J7, Canada.
| | - Yves V Brun
- Département de Microbiologie, Infectiologie, et Immunologie, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, Québec H3C 3J7, Canada
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2
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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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3
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Kaimer C, Weltzer ML, Wall D. Two reasons to kill: predation and kin discrimination in myxobacteria. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001372. [PMID: 37494115 PMCID: PMC10433427 DOI: 10.1099/mic.0.001372] [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: 05/14/2023] [Accepted: 07/15/2023] [Indexed: 07/27/2023]
Abstract
Myxobacteria are social microbial predators that use cell-cell contacts to identify bacterial or fungal prey and to differentiate kin relatives to initiate cellular responses. For prey killing, they assemble Tad-like and type III-like secretion systems at contact sites. For kin discrimination (KD), they assemble outer membrane exchange complexes composed of the TraA and TraB receptors at contacts sites. A type VI secretion system and Rhs proteins also mediate KD. Following cellular recognition, these systems deliver appropriate effectors into target cells. For prey, this leads to cell death and lysis for nutrient consumption by myxobacteria. In KD, a panel of effectors are delivered, and if adjacent cells are clonal cells, resistance ensues because they express a cognate panel of immunity factors; while nonkin lack complete immunity and are intoxicated. This review compares and contrasts recent findings from these systems in myxobacteria.
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Affiliation(s)
- Christine Kaimer
- Department of Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Michael L. Weltzer
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
| | - Daniel Wall
- Department of Molecular Biology, University of Wyoming, Laramie, WY, USA
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4
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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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5
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Lai TF, Ford RM, Huwiler SG. Advances in cellular and molecular predatory biology of Bdellovibrio bacteriovorus six decades after discovery. Front Microbiol 2023; 14:1168709. [PMID: 37256055 PMCID: PMC10225642 DOI: 10.3389/fmicb.2023.1168709] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 04/14/2023] [Indexed: 06/01/2023] Open
Abstract
Since its discovery six decades ago, the predatory bacterium Bdellovibrio bacteriovorus has sparked recent interest as a potential remedy to the antibiotic resistance crisis. Here we give a comprehensive historical overview from discovery to progressive developments in microscopy and molecular mechanisms. Research on B. bacteriovorus has moved from curiosity to a new model organism, revealing over time more details on its physiology and fascinating predatory life cycle with the help of a variety of methods. Based on recent findings in cryo-electron tomography, we recapitulate on the intricate molecular details known in the predatory life cycle including how this predator searches for its prey bacterium, to how it attaches, grows, and divides all from within the prey cell. Finally, the newly developed B. bacteriovorus progeny leave the prey cell remnants in the exit phase. While we end with some unanswered questions remaining in the field, new imaging technologies and quantitative, systematic advances will likely help to unravel them in the next decades.
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Affiliation(s)
- Ting F. Lai
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Rhian M. Ford
- School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Simona G. Huwiler
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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6
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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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7
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Hyperactive nanobacteria with host-dependent traits pervade Omnitrophota. Nat Microbiol 2023; 8:727-744. [PMID: 36928026 PMCID: PMC10066038 DOI: 10.1038/s41564-022-01319-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 12/30/2022] [Indexed: 03/18/2023]
Abstract
Candidate bacterial phylum Omnitrophota has not been isolated and is poorly understood. We analysed 72 newly sequenced and 349 existing Omnitrophota genomes representing 6 classes and 276 species, along with Earth Microbiome Project data to evaluate habitat, metabolic traits and lifestyles. We applied fluorescence-activated cell sorting and differential size filtration, and showed that most Omnitrophota are ultra-small (~0.2 μm) cells that are found in water, sediments and soils. Omnitrophota genomes in 6 classes are reduced, but maintain major biosynthetic and energy conservation pathways, including acetogenesis (with or without the Wood-Ljungdahl pathway) and diverse respirations. At least 64% of Omnitrophota genomes encode gene clusters typical of bacterial symbionts, suggesting host-associated lifestyles. We repurposed quantitative stable-isotope probing data from soils dominated by andesite, basalt or granite weathering and identified 3 families with high isotope uptake consistent with obligate bacterial predators. We propose that most Omnitrophota inhabit various ecosystems as predators or parasites.
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8
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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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9
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Seef S, Herrou J, de Boissier P, My L, Brasseur G, Robert D, Jain R, Mercier R, Cascales E, Habermann BH, Mignot T. A Tad-like apparatus is required for contact-dependent prey killing in predatory social bacteria. eLife 2021; 10:72409. [PMID: 34505573 PMCID: PMC8460266 DOI: 10.7554/elife.72409] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/09/2021] [Indexed: 12/21/2022] Open
Abstract
Myxococcus xanthus, a soil bacterium, predates collectively using motility to invade prey colonies. Prey lysis is mostly thought to rely on secreted factors, cocktails of antibiotics and enzymes, and direct contact with Myxococcus cells. In this study, we show that on surfaces the coupling of A-motility and contact-dependent killing is the central predatory mechanism driving effective prey colony invasion and consumption. At the molecular level, contact-dependent killing involves a newly discovered type IV filament-like machinery (Kil) that both promotes motility arrest and prey cell plasmolysis. In this process, Kil proteins assemble at the predator-prey contact site, suggesting that they allow tight contact with prey cells for their intoxication. Kil-like systems form a new class of Tad-like machineries in predatory bacteria, suggesting a conserved function in predator-prey interactions. This study further reveals a novel cell-cell interaction function for bacterial pili-like assemblages.
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Affiliation(s)
- Sofiene Seef
- Aix-Marseille Université - CNRS UMR 7283, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Julien Herrou
- Aix-Marseille Université - CNRS UMR 7283, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Paul de Boissier
- Aix-Marseille Université - CNRS UMR 7288, Institut de Biologie du Développement de Marseille and Turing Center for Living Systems, Marseille, France
| | - Laetitia My
- Aix-Marseille Université - CNRS UMR 7283, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Gael Brasseur
- Aix-Marseille Université - CNRS UMR 7283, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Donovan Robert
- Aix-Marseille Université - CNRS UMR 7283, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Rikesh Jain
- Aix-Marseille Université - CNRS UMR 7283, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France.,Aix-Marseille Université - CNRS UMR 7288, Institut de Biologie du Développement de Marseille and Turing Center for Living Systems, Marseille, France
| | - Romain Mercier
- Aix-Marseille Université - CNRS UMR 7283, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
| | - Eric Cascales
- Aix-Marseille Université - CNRS UMR 7255, Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Bianca H Habermann
- Aix-Marseille Université - CNRS UMR 7288, Institut de Biologie du Développement de Marseille and Turing Center for Living Systems, Marseille, France
| | - Tâm Mignot
- Aix-Marseille Université - CNRS UMR 7283, Institut de Microbiologie de la Méditerranée and Turing Center for Living Systems, Marseille, France
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10
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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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11
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Blanco-Romero E, Garrido-Sanz D, Rivilla R, Redondo-Nieto M, Martín M. In Silico Characterization and Phylogenetic Distribution of Extracellular Matrix Components in the Model Rhizobacteria Pseudomonas fluorescens F113 and Other Pseudomonads. Microorganisms 2020; 8:E1740. [PMID: 33171989 PMCID: PMC7716237 DOI: 10.3390/microorganisms8111740] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/01/2020] [Accepted: 11/04/2020] [Indexed: 12/23/2022] Open
Abstract
Biofilms are complex structures that are crucial during host-bacteria interaction and colonization. Bacteria within biofilms are surrounded by an extracellular matrix (ECM) typically composed of proteins, polysaccharides, lipids, and DNA. Pseudomonads contain a variety of ECM components, some of which have been extensively characterized. However, neither the ECM composition of plant-associated pseudomonads nor their phylogenetic distribution within the genus has been so thoroughly studied. In this work, we use in silico methods to describe the ECM composition of Pseudomonas fluorescens F113, a plant growth-promoting rhizobacteria and model for rhizosphere colonization. These components include the polysaccharides alginate, poly-N-acetyl-glucosamine (PNAG) and levan; the adhesins LapA, MapA and PsmE; and the functional amyloids in Pseudomonas. Interestingly, we identified novel components: the Pseudomonas acidic polysaccharide (Pap), whose presence is limited within the genus; and a novel type of Flp/Tad pilus, partially different from the one described in P. aeruginosa. Furthermore, we explored the phylogenetic distribution of the most relevant ECM components in nearly 600 complete Pseudomonas genomes. Our analyses show that Pseudomonas populations contain a diverse set of gene/gene clusters potentially involved in the formation of their ECMs, showing certain commensal versus pathogen lifestyle specialization.
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Affiliation(s)
| | | | | | | | - Marta Martín
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin 2, 28049 Madrid, Spain; (E.B.-R.); (D.G.-S.); (R.R.); (M.R.-N.)
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12
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Sathyamoorthy R, Kushmaro Y, Rotem O, Matan O, Kadouri DE, Huppert A, Jurkevitch E. To hunt or to rest: prey depletion induces a novel starvation survival strategy in bacterial predators. ISME JOURNAL 2020; 15:109-123. [PMID: 32884113 DOI: 10.1038/s41396-020-00764-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/12/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
Abstract
The small size of bacterial cells necessitates rapid adaption to sudden environmental changes. In Bdellovibrio bacteriovorus, an obligate predator of bacteria common in oligotrophic environments, the non-replicative, highly motile attack phase (AP) cell must invade a prey to ensure replication. AP cells swim fast and respire at high rates, rapidly consuming their own contents. How the predator survives in the absence of prey is unknown. We show that starvation for prey significantly alters swimming patterns and causes exponential decay in prey-searching cells over hours, until population-wide swim-arrest. Swim-arrest is accompanied by changes in energy metabolism, enabling rapid swim-reactivation upon introduction of prey or nutrients, and a sweeping change in gene expression and gene regulation that largely differs from those of the paradigmatic stationary phase. Swim-arrest is costly as it imposes a fitness penalty in the form of delayed growth. We track the control of the swim arrest-reactivation process to cyclic-di-GMP (CdG) effectors, including two motility brakes. CRISPRi transcriptional inactivation, and in situ localization of the brakes to the cell pole, demonstrated their essential role for effective survival under prey-induced starvation. Thus, obligate predators evolved a unique CdG-controlled survival strategy, enabling them to sustain their uncommon lifestyle under fluctuating prey supply.
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Affiliation(s)
- Rajesh Sathyamoorthy
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
| | - Yuval Kushmaro
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
| | - Or Rotem
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel.,Seed-x., Magshimim, Israel
| | - Ofra Matan
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - Amit Huppert
- Bio-statistical Unit, The Gertner Institute for Epidemiology and Health Policy Research, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel.
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13
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Mu DS, Wang S, Liang QY, Du ZZ, Tian R, Ouyang Y, Wang XP, Zhou A, Gong Y, Chen GJ, Van Nostrand J, Yang Y, Zhou J, Du ZJ. Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments. MICROBIOME 2020; 8:126. [PMID: 32867860 PMCID: PMC7460792 DOI: 10.1186/s40168-020-00902-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/27/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Bradymonabacteria, representative of the novel order Bradymonadales in δ-Proteobacteria. Compared with those of other bacterial predators (e.g., Myxococcales and Bdellovibrionales), the predatory and living strategies of Bradymonadales are still largely unknown. RESULTS Based on individual coculture of Bradymonabacteria with 281 prey bacteria, Bradymonabacteria preyed on diverse bacteria but had a high preference for Bacteroidetes. Genomic analysis of 13 recently sequenced Bradymonabacteria indicated that these bacteria had conspicuous metabolic deficiencies, but they could synthesize many polymers, such as polyphosphate and polyhydroxyalkanoates. Dual transcriptome analysis of cocultures of Bradymonabacteria and prey suggested a potential contact-dependent predation mechanism. Comparative genomic analysis with 24 other bacterial predators indicated that Bradymonabacteria had different predatory and living strategies. Furthermore, we identified Bradymonadales from 1552 publicly available 16S rRNA amplicon sequencing samples, indicating that Bradymonadales was widely distributed and highly abundant in saline environments. Phylogenetic analysis showed that there may be six subgroups in this order; each subgroup occupied a different habitat. CONCLUSIONS Bradymonabacteria have unique living strategies that are transitional between the "obligate" and the so-called facultative predators. Thus, we propose a framework to categorize the current bacterial predators into 3 groups: (i) obligate predators (completely prey-dependent), (ii) facultative predators (facultatively prey-dependent), and (iii) opportunistic predators (prey-independent). Our findings provide an ecological and evolutionary framework for Bradymonadales and highlight their potential ecological roles in saline environments. Video abstract.
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Affiliation(s)
- Da-Shuai Mu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China
- Marine College, Shandong University, Weihai, 264209, China
| | - Shuo Wang
- Marine College, Shandong University, Weihai, 264209, China
| | - Qi-Yun Liang
- Marine College, Shandong University, Weihai, 264209, China
| | - Zhao-Zhong Du
- Marine College, Shandong University, Weihai, 264209, China
| | - Renmao Tian
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Yang Ouyang
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Xin-Peng Wang
- Marine College, Shandong University, Weihai, 264209, China
| | - Aifen Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Ya Gong
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China
- Marine College, Shandong University, Weihai, 264209, China
| | - Guan-Jun Chen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China
- Marine College, Shandong University, Weihai, 264209, China
| | - Joy Van Nostrand
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Jizhong Zhou
- Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, 73019, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Zong-Jun Du
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, No. 72, Jimo Binhai Road, Jimo, Qingdao, 266237, China.
- Marine College, Shandong University, Weihai, 264209, China.
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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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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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Andrade M, Wang N. The Tad Pilus Apparatus of ' Candidatus Liberibacter asiaticus' and Its Regulation by VisNR. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1175-1187. [PMID: 30925227 DOI: 10.1094/mpmi-02-19-0052-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Citrus huanglongbing (HLB) is one of the most destructive diseases affecting citrus plants. 'Candidatus Liberibacter asiaticus', an uncultivated α-proteobacteria, is the most widely spread causal agent of HLB and is transmitted by the Asian citrus psyllid Diaphorina citri. 'Ca. L. asiaticus' attachment to the psyllid midgut is believed to be critical to further infect other organs, including the salivary gland. In this study, the type IVc tight adherence (Tad) pilus locus encoded by 'Ca. L. asiaticus' was characterized. The Tad loci are conserved among members of Rhizobiaceae, including 'Ca. L. asiaticus' and Agrobacterium spp. Ectopic expression of the 'Ca. L. asiaticus' cpaF gene, an ATPase essential for the biogenesis and secretion of the Tad pilus, restored the adherence phenotype in cpaF mutant of A. tumefaciens, indicating CpaF of 'Ca. L. asiaticus' was functional and critical for bacterial adherence mediated by Tad pilus. Quantitative reverse transcription PCR (qRT-PCR) analysis revealed that 'Ca. L. asiaticus' Tad pilus-encoding genes and 'Ca. L. asiaticus' pilin gene flp3 were upregulated in psyllids compared with in planta. A bacterial one-hybrid assay showed that 'Ca. L. asiaticus' VisN and VisR, members of the LuxR transcriptional factor family, were bound to the flp3 promoter. VisNR regulate flp3. Negative regulation of the flp3 promoter by both VisN and VisR was demonstrated using a shuttle strategy, with analysis of the phenotypes and immunoblotting together with quantification of the expression of the flp3 promoter fused to the β-galactosidase reporter gene. Comparative expression analysis confirmed that 'Ca. L. asiaticus' visNR was less expressed in the psyllid than in the plant host. Further, motility and biofilm phenotypes of the visNR mutant of A. tumefaciens were fully complemented by expressing 'Ca. L. asiaticus' visNR together. The physical interaction between VisN and VisR was confirmed by pull-down and stability assays. The interaction of the flp3 promoter with VisR was verified by electrophoretic mobility shift assay. Taken together, the results revealed the contribution of the Tad pilus apparatus in the colonization of the insect vector by 'Ca. L. asiaticus' and shed light on the involvement of VisNR in regulation of the Tad locus.
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Affiliation(s)
- Maxuel Andrade
- Citrus Research and Education Center (CREC), Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850, U.S.A
| | - Nian Wang
- Citrus Research and Education Center (CREC), Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL 33850, U.S.A
- China-USA Citrus Huanglongbing Joint Laboratory (A joint laboratory of the University of Florida Institute of Food and Agricultural Sciences and Gannan Normal University), National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou 341000, China
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Abstract
Bdellovibrio bacteriovorus is a predatory bacterium that can kill a wide range of Gram-negative bacteria, including many human pathogens. Given the global rise of antibiotic resistance and dearth of new antibiotics discovered in the past 30 years, this predator has potential as an alternative to traditional antibiotics. For many years, B. bacteriovorus research was hampered by a lack of genetic tools, and the genetic mechanisms of predation have only recently begun to be established. Here, we comprehensively identify and characterize predator genes required for killing bacterial prey, as well as genes that interfere in this process, which may allow us to design better therapeutic predators. Based on our study, we and other researchers may ultimately be able to genetically engineer strains that have improved killing rates, target specific species of prey, or preferentially target prey in the planktonic or biofilm state. Bdellovibrio bacteriovorus is a bacterial predator capable of killing and replicating inside most Gram-negative bacteria, including antibiotic-resistant pathogens. Despite growing interest in this organism as a potential therapeutic, many of its genes remain uncharacterized. Here, we perform a high-throughput genetic screen with B. bacteriovorus using transposon sequencing (Tn-seq) to explore the genetic requirements of predation. Two hundred one genes were deemed essential for growth in the absence of prey, whereas over 100 genes were found to be specifically required for predative growth on the human pathogens Vibrio cholerae and Escherichia coli in both planktonic and biofilm states. To further this work, we created an ordered-knockout library in B. bacteriovorus and developed new high-throughput techniques to characterize the mutants by their stage of deficiency in the predator life cycle. Using microscopy and flow cytometry, we confirmed 10 mutants defective in prey attachment and eight mutants defective in prey rounding. The majority of these genes are hypothetical and previously uncharacterized. Finally, we propose new nomenclature to group B. bacteriovorus mutants into classes based on their stage of predation defect. These results contribute to our basic understanding of bacterial predation and may be useful for harnessing B. bacteriovorus to kill harmful pathogens in the clinical setting.
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Vibrio cholerae motility exerts drag force to impede attack by the bacterial predator Bdellovibrio bacteriovorus. Nat Commun 2018; 9:4757. [PMID: 30420597 PMCID: PMC6232129 DOI: 10.1038/s41467-018-07245-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 10/18/2018] [Indexed: 12/21/2022] Open
Abstract
The bacterial predator Bdellovibrio bacteriovorus is evolved to attack and kill other bacteria, including the human intestinal pathogen Vibrio cholerae. Although B. bacteriovorus exhibit a broad prey range, little is known about the genetic determinants of prey resistance and sensitivity. Here we perform a genetic screen on V. cholerae and identify five pathways contributing to predation susceptibility. We find that the essential virulence regulators ToxR/S increase susceptibility to predation, as mutants of these genes are more resistant to predation. We observe by flow cytometry that lipopolysaccharide is a critical defense, as mutants lacking O-antigen are rapidly attacked by predatory B. bacteriovorus. Using polymer solutions to alter media viscosity, we find that when B. bacteriovorus attacks motile V. cholerae, increased drag forces slow its ability to prey. These results provide insights into key prey resistance mechanisms, and may be useful in the application of B. bacteriovorus in treating infections. Prey bacteria have evolved different strategies to counteract predation but the genetic basis remains unclear. Here, Duncan et al. identify key genes involved in Vibrio cholerae sensitivity to Bdellovibrio bacteriovorus predation, providing new insights into prey resistance mechanisms.
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Bartling P, Vollmers J, Petersen J. The first world swimming championships of roseobacters—Phylogenomic insights into an exceptional motility phenotype. Syst Appl Microbiol 2018; 41:544-554. [DOI: 10.1016/j.syapm.2018.08.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/13/2018] [Accepted: 08/25/2018] [Indexed: 11/29/2022]
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Negus D, Moore C, Baker M, Raghunathan D, Tyson J, Sockett RE. Predator Versus Pathogen: How Does Predatory Bdellovibrio bacteriovorus Interface with the Challenges of Killing Gram-Negative Pathogens in a Host Setting? Annu Rev Microbiol 2018; 71:441-457. [PMID: 28886689 DOI: 10.1146/annurev-micro-090816-093618] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bdellovibrio bacteriovorus is a small deltaproteobacterial predator that has evolved to invade, reseal, kill, and digest other gram-negative bacteria in soils and water environments. It has a broad host range and kills many antibiotic-resistant, clinical pathogens in vitro, a potentially useful capability if it could be translated to a clinical setting. We review relevant mechanisms of B. bacteriovorus predation and the physiological properties that would influence its survival in a mammalian host. Bacterial pathogens increasingly display conventional antibiotic resistance by expressing and varying surface and soluble biomolecules. Predators coevolved alongside prey bacteria and so encode diverse predatory enzymes that are hard for pathogens to resist by simple mutation. Predators do not replicate outside pathogens and thus express few transport proteins and thus few surface epitopes for host immune recognition. We explain these features, relating them to the potential of predatory bacteria as cellular medicines.
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Affiliation(s)
- David Negus
- School of Life Science, University of Nottingham, University Park, Nottingham NG7 2UH, United Kingdom; , , , , ,
| | - Chris Moore
- School of Life Science, University of Nottingham, University Park, Nottingham NG7 2UH, United Kingdom; , , , , ,
| | - Michelle Baker
- School of Life Science, University of Nottingham, University Park, Nottingham NG7 2UH, United Kingdom; , , , , , .,School of Computer Science, University of Nottingham, University Park, Nottingham NG7 2UH, United Kingdom
| | - Dhaarini Raghunathan
- School of Life Science, University of Nottingham, University Park, Nottingham NG7 2UH, United Kingdom; , , , , ,
| | - Jess Tyson
- School of Life Science, University of Nottingham, University Park, Nottingham NG7 2UH, United Kingdom; , , , , ,
| | - R Elizabeth Sockett
- School of Life Science, University of Nottingham, University Park, Nottingham NG7 2UH, United Kingdom; , , , , ,
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