1
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Castledine M, Buckling A. Critically evaluating the relative importance of phage in shaping microbial community composition. Trends Microbiol 2024; 32:957-969. [PMID: 38604881 DOI: 10.1016/j.tim.2024.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/13/2024]
Abstract
The ubiquity of bacteriophages (phages) and the major evolutionary and ecological impacts they can have on their microbial hosts has resulted in phages often cited as key drivers shaping microbial community composition (the relative abundances of species). However, the evidence for the importance of phages is mixed. Here, we critically review the theory and data exploring the role of phages in communities, identifying the conditions when phages are likely to be important drivers of community composition. At ecological scales, we conclude that phages are often followers rather than drivers of microbial population and community dynamics. While phages can affect strain diversity within species, there is yet to be strong evidence suggesting that fluctuations in species' strains affects community composition.
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Affiliation(s)
- Meaghan Castledine
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK.
| | - Angus Buckling
- Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
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2
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Liaghat A, Yang J, Whitaker R, Pascual M. Punctuated virus-driven succession generates dynamical alternations in CRISPR-mediated microbe-virus coevolution. J R Soc Interface 2024; 21:20240195. [PMID: 39165171 PMCID: PMC11336687 DOI: 10.1098/rsif.2024.0195] [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: 03/22/2024] [Revised: 05/30/2024] [Accepted: 07/08/2024] [Indexed: 08/22/2024] Open
Abstract
The coevolutionary dynamics of lytic viruses and microbes with CRISPR-Cas immunity exhibit alternations between sustained host control of viral proliferation and major viral epidemics in previous computational models. These alternating dynamics have yet to be observed in other host-pathogen systems. Here, we address the breakdown of control and transition to large outbreaks with a stochastic eco-evolutionary model. We establish the role of host density-dependent competition in punctuated virus-driven succession and associated diversity trends that concentrate escape pathways during control phases. Using infection and escape networks, we derive the viral emergence probability whose fluctuations of increasing size and frequency characterize the approach to large outbreaks. We explore alternation probabilities as a function of non-dimensional parameters related to the probability of viral escape and host competition. Our results demonstrate how emergent feedbacks between host competition and viral diversification render the host immune structure fragile, potentiating a dynamical transition to large epidemics.
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Affiliation(s)
- Armun Liaghat
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Department of Biology, New York University, New York, NY, USA
| | - Jiayue Yang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Rachel Whitaker
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Mercedes Pascual
- Department of Biology, New York University, New York, NY, USA
- Department of Environmental Studies, New York University, New York, NY, USA
- Santa Fe Institute, Santa Fe, NM, USA
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3
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Lievens EJP, Kühn S, Horas EL, Le Pennec G, Peter S, Petrosky AD, Künzel S, Feulner PGD, Becks L. High parasite diversity maintained after an alga-virus coevolutionary arms race. J Evol Biol 2024; 37:795-806. [PMID: 38699979 DOI: 10.1093/jeb/voae053] [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: 10/01/2023] [Revised: 02/27/2024] [Accepted: 05/02/2024] [Indexed: 05/05/2024]
Abstract
Arms race dynamics are a common outcome of host-parasite coevolution. While they can theoretically be maintained indefinitely, realistic arms races are expected to be finite. Once an arms race has ended, for example due to the evolution of a generalist-resistant host, the system may transition into coevolutionary dynamics that favour long-term diversity. In microbial experiments, host-parasite arms races often transition into a stable coexistence of generalist-resistant hosts, (semi-)susceptible hosts, and parasites. While long-term host diversity is implicit in these cases, parasite diversity is usually overlooked. In this study, we examined parasite diversity after the end of an experimental arms race between a unicellular alga (Chlorella variabilis) and its lytic virus (PBCV-1). First, we isolated virus genotypes from multiple time points from two replicate microcosms. A time-shift experiment confirmed that the virus isolates had escalating host ranges, i.e., that arms races had occurred. We then examined the phenotypic and genetic diversity of virus isolates from the post-arms race phase. Post-arms race virus isolates had diverse host ranges, survival probabilities, and growth rates; they also clustered into distinct genetic groups. Importantly, host range diversity was maintained throughout the post-arms race phase, and the frequency of host range phenotypes fluctuated over time. We hypothesize that this dynamic polymorphism was maintained by a combination of fluctuating selection and demographic stochasticity. Together with previous work in prokaryotic systems, our results link experimental observations of arms races to natural observations of long-term host and parasite diversity.
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Affiliation(s)
- Eva J P Lievens
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Samuel Kühn
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Elena L Horas
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Guénolé Le Pennec
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Sarah Peter
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Azade D Petrosky
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Department of Biology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Lutz Becks
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
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4
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Özcan A, Yıbar A, Kiraz D, Ilıkkan ÖK. Comprehensive analysis of the CRISPR-Cas systems in Streptococcus thermophilus strains isolated from traditional yogurts. Antonie Van Leeuwenhoek 2024; 117:63. [PMID: 38561518 DOI: 10.1007/s10482-024-01960-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/20/2024] [Indexed: 04/04/2024]
Abstract
Phage resistance is crucial for lactic acid bacteria in the dairy industry. However, identifying all phages affecting these bacteria is challenging. CRISPR-Cas systems offer a resistance mechanism developed by bacteria and archaea against phages and plasmids. In this study, 11 S. thermophilus strains from traditional yogurts underwent analysis using next-generation sequencing (NGS) and bioinformatics tools. Initial characterization involved molecular ribotyping. Bioinformatics analysis of the NGS raw data revealed that all 11 strains possessed at least one CRISPR type. A total of 21 CRISPR loci were identified, belonging to CRISPR types II-A, II-C, and III-A, including 13 Type II-A, 1 Type III-C, and 7 Type III-A CRISPR types. By analyzing spacer sequences in S. thermophilus bacterial genomes and matching them with phage/plasmid genomes, notable strains emerged. SY9 showed prominence with 132 phage matches and 30 plasmid matches, followed by SY12 with 35 phage matches and 25 plasmid matches, and SY18 with 49 phage matches and 13 plasmid matches. These findings indicate the potential of S. thermophilus strains in phage/plasmid resistance for selecting starter cultures, ultimately improving the quality and quantity of dairy products. Nevertheless, further research is required to validate these results and explore the practical applications of this approach.
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Affiliation(s)
- Ali Özcan
- Animal Originated Foodstuffs Department, Central Research Institute of Food and Feed Control, Bursa, Turkey.
- Food Hygiene and Technology Department, Faculty of Veterinary Medicine, Uludağ University, Bursa, Turkey.
| | - Artun Yıbar
- Food Hygiene and Technology Department, Faculty of Veterinary Medicine, Uludağ University, Bursa, Turkey
| | - Deniz Kiraz
- Animal Originated Foodstuffs Department, Central Research Institute of Food and Feed Control, Bursa, Turkey
| | - Özge Kahraman Ilıkkan
- Kahramankazan Vocational School, Food Quality Control and Analysis Program, Başkent University, Ankara, Turkey
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5
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Gandon S, Guillemet M, Gatchitch F, Nicot A, Renaud AC, Tremblay DM, Moineau S. Building pyramids against the evolutionary emergence of pathogens. Proc Biol Sci 2024; 291:20231529. [PMID: 38471546 DOI: 10.1098/rspb.2023.1529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 01/29/2024] [Indexed: 03/14/2024] Open
Abstract
Mutations allowing pathogens to escape host immunity promote the spread of infectious diseases in heterogeneous host populations and can lead to major epidemics. Understanding the conditions that slow down this evolution is key for the development of durable control strategies against pathogens. Here, we use theory and experiments to compare the efficacy of three strategies for the deployment of resistance: (i) a mixing strategy where the host population contains two single-resistant genotypes, (ii) a pyramiding strategy where the host carries a double-resistant genotype, (iii) a combining strategy where the host population is a mix of a single-resistant genotype and a double-resistant genotype. First, we use evolutionary epidemiology theory to clarify the interplay between demographic stochasticity and evolutionary dynamics to show that the pyramiding strategy always yields lower probability of evolutionary emergence. Second, we test experimentally these predictions with the introduction of bacteriophages into bacterial populations where we manipulated the diversity and the depth of immunity using a Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated (CRISPR-Cas) system. These biological assays confirm that pyramiding multiple defences into the same host genotype and avoiding combination with single-defence genotypes is a robust way to reduce pathogen evolutionary emergence. The experimental validation of these theoretical recommendations has practical implications in various areas, including for the optimal deployment of resistance varieties in agriculture and for the design of durable vaccination strategies.
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Affiliation(s)
- Sylvain Gandon
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | | | - Antoine Nicot
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Ariane C Renaud
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec city, Canada G1V0A6
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Canada G1V 0A6
| | - Denise M Tremblay
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Canada G1V 0A6
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec city, Canada G1V0A6
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Canada G1V 0A6
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6
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Siedentop B, Rüegg D, Bonhoeffer S, Chabas H. My host's enemy is my enemy: plasmids carrying CRISPR-Cas as a defence against phages. Proc Biol Sci 2024; 291:20232449. [PMID: 38262608 PMCID: PMC10805597 DOI: 10.1098/rspb.2023.2449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024] Open
Abstract
Bacteria are infected by mobile genetic elements like plasmids and virulent phages, and those infections significantly impact bacterial ecology and evolution. Recent discoveries reveal that some plasmids carry anti-phage immune systems like CRISPR-Cas, suggesting that plasmids may participate in the coevolutionary arms race between virulent phages and bacteria. Intuitively, this seems reasonable as virulent phages kill the plasmid's obligate host. However, the efficiency of CRISPR-Cas systems carried by plasmids can be expected to be lower than those carried by the chromosome due to continuous segregation loss, creating susceptible cells for phage amplification. To evaluate the anti-phage protection efficiency of CRISPR-Cas on plasmids, we develop a stochastic model describing the dynamics of a virulent phage infection against which a conjugative plasmid defends using CRISPR-Cas. We show that CRISPR-Cas on plasmids provides robust protection, except in limited parameter sets. In these cases, high segregation loss favours phage outbreaks by generating a population of defenceless cells on which the phage can evolve and escape CRISPR-Cas immunity. We show that the phage's ability to exploit segregation loss depends strongly on the evolvability of both CRISPR-Cas and the phage itself.
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Affiliation(s)
- Berit Siedentop
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
| | - Dario Rüegg
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
| | | | - Hélène Chabas
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
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7
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Watson BNJ, Capria L, Alseth EO, Pons BJ, Biswas A, Lenzi L, Buckling A, van Houte S, Westra ER, Meaden S. CRISPR-Cas in Pseudomonas aeruginosa provides transient population-level immunity against high phage exposures. THE ISME JOURNAL 2024; 18:wrad039. [PMID: 38366022 PMCID: PMC10873826 DOI: 10.1093/ismejo/wrad039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/12/2023] [Accepted: 01/02/2024] [Indexed: 02/18/2024]
Abstract
The prokaryotic adaptive immune system, CRISPR-Cas (clustered regularly interspaced short palindromic repeats; CRISPR-associated), requires the acquisition of spacer sequences that target invading mobile genetic elements such as phages. Previous work has identified ecological variables that drive the evolution of CRISPR-based immunity of the model organism Pseudomonas aeruginosa PA14 against its phage DMS3vir, resulting in rapid phage extinction. However, it is unclear if and how stable such acquired immunity is within bacterial populations, and how this depends on the environment. Here, we examine the dynamics of CRISPR spacer acquisition and loss over a 30-day evolution experiment and identify conditions that tip the balance between long-term maintenance of immunity versus invasion of alternative resistance strategies that support phage persistence. Specifically, we find that both the initial phage dose and reinfection frequencies determine whether or not acquired CRISPR immunity is maintained in the long term, and whether or not phage can coexist with the bacteria. At the population genetics level, emergence and loss of CRISPR immunity are associated with high levels of spacer diversity that subsequently decline due to invasion of bacteria carrying pilus-associated mutations. Together, these results provide high resolution of the dynamics of CRISPR immunity acquisition and loss and demonstrate that the cumulative phage burden determines the effectiveness of CRISPR over ecologically relevant timeframes.
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Affiliation(s)
- Bridget N J Watson
- Biosciences, University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom
| | - Loris Capria
- Biosciences, University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom
| | - Ellinor O Alseth
- Biosciences, University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Benoit J Pons
- Biosciences, University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom
| | - Ambarish Biswas
- Department of Microbiology and Immunology, University of Otago, Dunedin, 9059, Otago, New Zealand
| | - Luca Lenzi
- Institute of Integrative Biology, University of Liverpool, Liverpool, Merseyside, L69 7BE, United Kingdom
| | - Angus Buckling
- Biosciences, University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom
| | - Stineke van Houte
- Biosciences, University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom
| | - Edze R Westra
- Biosciences, University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom
| | - Sean Meaden
- Biosciences, University of Exeter, Penryn, Cornwall, TR10 9FE, United Kingdom
- Department of Biology, University of York, Wentworth Way, York, North Yorkshire YO10 3DB, United Kingdom
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8
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Van Cauwenberghe J, Simms EL. How might bacteriophages shape biological invasions? mBio 2023; 14:e0188623. [PMID: 37812005 PMCID: PMC10653932 DOI: 10.1128/mbio.01886-23] [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] [Indexed: 10/10/2023] Open
Abstract
Invasions by eukaryotes dependent on environmentally acquired bacterial mutualists are often limited by the ability of bacterial partners to survive and establish free-living populations. Focusing on the model legume-rhizobium mutualism, we apply invasion biology hypotheses to explain how bacteriophages can impact the competitiveness of introduced bacterial mutualists. Predicting how phage-bacteria interactions affect invading eukaryotic hosts requires knowing the eco-evolutionary constraints of introduced and native microbial communities, as well as their differences in abundance and diversity. By synthesizing research from invasion biology, as well as bacterial, viral, and community ecology, we create a conceptual framework for understanding and predicting how phages can affect biological invasions through their effects on bacterial mutualists.
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Affiliation(s)
- Jannick Van Cauwenberghe
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Ellen L. Simms
- Department of Integrative Biology, University of California, Berkeley, California, USA
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9
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Carscadden KA, Batstone RT, Hauser FE. Origins and evolution of biological novelty. Biol Rev Camb Philos Soc 2023; 98:1472-1491. [PMID: 37056155 DOI: 10.1111/brv.12963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/30/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.
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Affiliation(s)
- Kelly A Carscadden
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, 1900 Pleasant St, Boulder, CO, 80309, USA
| | - Rebecca T Batstone
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Frances E Hauser
- Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, Ontario, M1C 1A4, Canada
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10
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Watson BNJ, Pursey E, Gandon S, Westra ER. Transient eco-evolutionary dynamics early in a phage epidemic have strong and lasting impact on the long-term evolution of bacterial defences. PLoS Biol 2023; 21:e3002122. [PMID: 37713428 PMCID: PMC10530023 DOI: 10.1371/journal.pbio.3002122] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 09/27/2023] [Accepted: 08/07/2023] [Indexed: 09/17/2023] Open
Abstract
Organisms have evolved a range of constitutive (always active) and inducible (elicited by parasites) defence mechanisms, but we have limited understanding of what drives the evolution of these orthogonal defence strategies. Bacteria and their phages offer a tractable system to study this: Bacteria can acquire constitutive resistance by mutation of the phage receptor (surface mutation, sm) or induced resistance through their CRISPR-Cas adaptive immune system. Using a combination of theory and experiments, we demonstrate that the mechanism that establishes first has a strong advantage because it weakens selection for the alternative resistance mechanism. As a consequence, ecological factors that alter the relative frequencies at which the different resistances are acquired have a strong and lasting impact: High growth conditions promote the evolution of sm resistance by increasing the influx of receptor mutation events during the early stages of the epidemic, whereas a high infection risk during this stage of the epidemic promotes the evolution of CRISPR immunity, since it fuels the (infection-dependent) acquisition of CRISPR immunity. This work highlights the strong and lasting impact of the transient evolutionary dynamics during the early stages of an epidemic on the long-term evolution of constitutive and induced defences, which may be leveraged to manipulate phage resistance evolution in clinical and applied settings.
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Affiliation(s)
| | - Elizabeth Pursey
- ESI, Biosciences, University of Exeter, Cornwall Campus, Penryn, United Kingdom
| | - Sylvain Gandon
- Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), UMR 5175, CNRS-Université de Montpellier-Université Paul-Valéry Montpellier-EPHE, Montpellier, France
| | - Edze Rients Westra
- ESI, Biosciences, University of Exeter, Cornwall Campus, Penryn, United Kingdom
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11
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Rasmussen TS, Koefoed AK, Deng L, Muhammed MK, Rousseau GM, Kot W, Sprotte S, Neve H, Franz CMAP, Hansen AK, Vogensen FK, Moineau S, Nielsen DS. CRISPR-Cas provides limited phage immunity to a prevalent gut bacterium in gnotobiotic mice. THE ISME JOURNAL 2023; 17:432-442. [PMID: 36631688 PMCID: PMC9938214 DOI: 10.1038/s41396-023-01358-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 12/22/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023]
Abstract
Many bacteria and archaea harbor the adaptive CRISPR-Cas system, which stores small nucleotide fragments from previous invasions of nucleic acids via viruses or plasmids. This molecular archive blocks further invaders carrying identical or similar nucleotide sequences. However, few of these systems have been confirmed experimentally to be active in gut bacteria. Here, we demonstrate experimentally that the type I-C CRISPR-Cas system of the prevalent gut bacterium Eggerthella lenta can specifically target and cleave foreign DNA in vitro by using a plasmid transformation assay. We also show that the CRISPR-Cas system acquires new immunities (spacers) from the genome of a virulent E. lenta phage using traditional phage assays in vitro but also in vivo using gnotobiotic (GB) mice. Both high phage titer and an increased number of spacer acquisition events were observed when E. lenta was exposed to a low multiplicity of infection in vitro, and three phage genes were found to contain protospacer hotspots. Fewer new spacer acquisitions were detected in vivo than in vitro. Longitudinal analysis of phage-bacteria interactions showed sustained coexistence in the gut of GB mice, with phage abundance being approximately one log higher than the bacteria. Our findings show that while the type I-C CRISPR-Cas system is active in vitro and in vivo, a highly virulent phage in vitro was still able to co-exist with its bacterial host in vivo. Taken altogether, our results suggest that the CRISPR-Cas defense system of E. lenta provides only partial immunity in the gut.
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Affiliation(s)
- Torben Sølbeck Rasmussen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark.
| | - Anna Kirstine Koefoed
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Ling Deng
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Musemma K Muhammed
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Geneviève M Rousseau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de 1enie, Université Laval, Québec, QC, G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Witold Kot
- Section of Microbial Ecology and Biotechnology, Department of Plant and Environmental Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark
| | - Sabrina Sprotte
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103, Kiel, Germany
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103, Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103, Kiel, Germany
| | - Axel Kornerup Hansen
- Section of Experimental Animal Models, Department of Veterinary and Animal Sciences, University of Copenhagen, 1871, Frederiksberg, Denmark
| | - Finn Kvist Vogensen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de 1enie, Université Laval, Québec, QC, G1V 0A6, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC, G1V 0A6, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Dennis Sandris Nielsen
- Section of Microbiology and Fermentation, Department of Food Science, Faculty of Science, University of Copenhagen, 1958, Frederiksberg, Denmark.
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12
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Ecology and evolution of phages encoding anti-CRISPR proteins. J Mol Biol 2023; 435:167974. [PMID: 36690071 DOI: 10.1016/j.jmb.2023.167974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/21/2023]
Abstract
CRISPR-Cas are prokaryotic defence systems that provide protection against invasion by mobile genetic elements (MGE), including bacteriophages. MGE can overcome CRISPR-Cas defences by encoding anti-CRISPR (Acr) proteins. These proteins are produced in the early stages of the infection and inhibit the CRISPR-Cas machinery to allow phage replication. While research on Acr has mainly focused on their discovery, structure and mode of action, and their applications in biotechnology, the impact of Acr on the ecology of MGE as well as on the coevolution with their bacterial hosts only begins to be unravelled. In this review, we summarise our current understanding on the distribution of anti-CRISPR genes in MGE, the ecology of phages encoding Acr, and their coevolution with bacterial defence mechanisms. We highlight the need to use more diverse and complex experimental models to better understand the impact of anti-CRISPR in MGE-host interactions.
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13
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Shaer Tamar E, Kishony R. Multistep diversification in spatiotemporal bacterial-phage coevolution. Nat Commun 2022; 13:7971. [PMID: 36577749 PMCID: PMC9797572 DOI: 10.1038/s41467-022-35351-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 11/29/2022] [Indexed: 12/29/2022] Open
Abstract
The evolutionary arms race between phages and bacteria, where bacteria evolve resistance to phages and phages retaliate with resistance-countering mutations, is a major driving force of molecular innovation and genetic diversification. Yet attempting to reproduce such ongoing retaliation dynamics in the lab has been challenging; laboratory coevolution experiments of phage and bacteria are typically performed in well-mixed environments and often lead to rapid stagnation with little genetic variability. Here, co-culturing motile E. coli with the lytic bacteriophage T7 on swimming plates, we observe complex spatiotemporal dynamics with multiple genetically diversifying adaptive cycles. Systematically quantifying over 10,000 resistance-infectivity phenotypes between evolved bacteria and phage isolates, we observe diversification into multiple coexisting ecotypes showing a complex interaction network with both host-range expansion and host-switch tradeoffs. Whole-genome sequencing of these evolved phage and bacterial isolates revealed a rich set of adaptive mutations in multiple genetic pathways including in genes not previously linked with phage-bacteria interactions. Synthetically reconstructing these new mutations, we discover phage-general and phage-specific resistance phenotypes as well as a strong synergy with the more classically known phage-resistance mutations. These results highlight the importance of spatial structure and migration for driving phage-bacteria coevolution, providing a concrete system for revealing new molecular mechanisms across diverse phage-bacterial systems.
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Affiliation(s)
- Einat Shaer Tamar
- grid.6451.60000000121102151Faculty of Biology, Technion–Israel Institute of Technology, Haifa, Israel
| | - Roy Kishony
- grid.6451.60000000121102151Faculty of Biology, Technion–Israel Institute of Technology, Haifa, Israel ,grid.6451.60000000121102151Faculty of Computer Science, Technion–Israel Institute of Technology, Haifa, Israel ,grid.6451.60000000121102151Faculty of Biomedical Engineering, Technion–Israel Institute of Technology, Haifa, Israel
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14
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Guillemet M, Chabas H, Nicot A, Gatchich F, Ortega-Abboud E, Buus C, Hindhede L, Rousseau GM, Bataillon T, Moineau S, Gandon S. Competition and coevolution drive the evolution and the diversification of CRISPR immunity. Nat Ecol Evol 2022; 6:1480-1488. [PMID: 35970864 DOI: 10.1038/s41559-022-01841-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 06/28/2022] [Indexed: 01/21/2023]
Abstract
The diversity of resistance challenges the ability of pathogens to spread and to exploit host populations. Yet, how this host diversity evolves over time remains unclear because it depends on the interplay between intraspecific competition among host genotypes and coevolution with pathogens. Here we study experimentally the effect of coevolving phage populations on the diversification of bacterial CRISPR immunity across space and time. We demonstrate that the negative-frequency-dependent selection generated by coevolution is a powerful force that maintains host resistance diversity and selects for new resistance mutations in the host. We also find that host evolution is driven by asymmetries in competitive abilities among different host genotypes. Even if the fittest host genotypes are targeted preferentially by the evolving phages, they often escape extinctions through the acquisition of new CRISPR immunity. Together, these fluctuating selective pressures maintain diversity, but not by preserving the pre-existing host composition. Instead, we repeatedly observe the introduction of new resistance genotypes stemming from the fittest hosts in each population. These results highlight the importance of competition on the transient dynamics of host-pathogen coevolution.
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Affiliation(s)
| | - Hélène Chabas
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
- Institute of Integrative Biology, Department for Environmental System Science, ETH Zurich, Zurich, Switzerland
| | - Antoine Nicot
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
| | | | | | - Cornelia Buus
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Lotte Hindhede
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Geneviève M Rousseau
- Département de biochimie, microbiologie, et bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Canada
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Sylvain Moineau
- Département de biochimie, microbiologie, et bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, Canada
| | - Sylvain Gandon
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France.
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15
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Somerville V, Schowing T, Chabas H, Schmidt RS, von Ah U, Bruggmann R, Engel P. Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities. MICROBIOME 2022; 10:137. [PMID: 36028909 PMCID: PMC9419375 DOI: 10.1186/s40168-022-01328-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 07/17/2022] [Indexed: 05/14/2023]
Abstract
BACKGROUND Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments. RESULTS We corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles. CONCLUSIONS Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry. Video Abstract.
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Affiliation(s)
- Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
- Agroscope, Bern, Switzerland.
| | - Thibault Schowing
- Agroscope, Bern, Switzerland
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Hélène Chabas
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
| | | | | | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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16
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Chabas H, Müller V, Bonhoeffer S, Regoes RR. Epidemiological and evolutionary consequences of different types of CRISPR-Cas systems. PLoS Comput Biol 2022; 18:e1010329. [PMID: 35881633 PMCID: PMC9355216 DOI: 10.1371/journal.pcbi.1010329] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/05/2022] [Accepted: 06/27/2022] [Indexed: 11/19/2022] Open
Abstract
Bacteria have adaptive immunity against viruses (phages) in the form of CRISPR-Cas immune systems. Currently, 6 types of CRISPR-Cas systems are known and the molecular study of three of these has revealed important molecular differences. It is unknown if and how these molecular differences change the outcome of phage infection and the evolutionary pressure the CRISPR-Cas systems faces. To determine the importance of these molecular differences, we model a phage outbreak entering a population defending exclusively with a type I/II or a type III CRISPR-Cas system. We show that for type III CRISPR-Cas systems, rapid phage extinction is driven by the probability to acquire at least one resistance spacer. However, for type I/II CRISPR-Cas systems, rapid phage extinction is characterized by an a threshold-like behaviour: any acquisition probability below this threshold leads to phage survival whereas any acquisition probability above it, results in phage extinction. We also show that in the absence of autoimmunity, high acquisition rates evolve. However, when CRISPR-Cas systems are prone to autoimmunity, intermediate levels of acquisition are optimal during a phage outbreak. As we predict an optimal probability of spacer acquisition 2 factors of magnitude above the one that has been measured, we discuss the origin of such a discrepancy. Finally, we show that in a biologically relevant parameter range, a type III CRISPR-Cas system can outcompete a type I/II CRISPR-Cas system with a slightly higher probability of acquisition. CRISPR-Cas systems are adaptive immune systems that use a complex 3-step molecular mechanism to defend prokaryotes against phages. Viral infections of populations defending themselves with CRISPR-Cas can result in rapid phage extinction or in medium-term phage maintenance. To investigate what controls the fate of the phage population, we use mathematical modeling of type I/II and type III CRISPR-Cas systems, and show that two parameters control the epidemiological short-term outcome: the type of CRISPR-Cas systems and CRISPR-Cas probability of resistance acquisition. Furthermore, the latter impacts host fitness. From this, we derive that 1) for both types, CRISPR-Cas acquisition probability is a key predictor of the efficiency and of the cost of a CRISPR-Cas system, 2) during an outbreak, there is an optimal probability of resistance acquisition balancing the cost of autoimmunity and immune efficiency and 3) type I/II CRISPR-Cas systems are likely to evolve higher acquisition probability than type III.
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Affiliation(s)
- Hélène Chabas
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
- * E-mail:
| | - Viktor Müller
- Institute of Biology, Eötvös Loránd University, Budapest, Hungary
| | | | - Roland R. Regoes
- Institute for Integrative Biology, ETH Zürich, Zürich, Switzerland
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17
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Parlindungan E, McDonnell B, Lugli GA, Ventura M, van Sinderen D, Mahony J. Dairy streptococcal cell wall and exopolysaccharide genome diversity. Microb Genom 2022; 8. [PMID: 35442186 PMCID: PMC9453073 DOI: 10.1099/mgen.0.000803] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The large-scale and high-intensity application of
Streptococcus thermophilus
species in milk fermentation processes is associated with a persistent threat of (bacterio)phage infection. Phage infection of starter cultures may cause inconsistent, slow or even failed fermentations with consequent diminished product quality and/or output. The phage life cycle commences with the recognition of, and binding to, a specific host-encoded and surface-exposed receptor, which in the case of
S. thermophilus
can be the rhamnose-glucose polysaccharide (RGP; specified by the rgp gene cluster) or exopolysaccharide (EPS; specified by the eps gene cluster). The genomic diversity of 23
S
.
thermophilus
strains isolated from unpasteurized dairy products was evaluated, including a detailed analysis of the rgp and eps loci. In the present study, five novel eps genotypes were identified while variations of currently recognized rgp gene cluster types were also observed. Furthermore, the diversity of rgp genotypes amongst retrieved isolates positively correlated with phage diversity based on phageome analysis of eight representative dairy products. Our findings therefore substantially expand our knowledge on S. thermophilus’ strain and phage diversity in (artisanal) dairy products and highlight the merit of phageome analysis of artisanal and traditional fermented foods as a sensitive marker of dominant microbiota involved in the fermentation.
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Affiliation(s)
- Elvina Parlindungan
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland
| | - Brian McDonnell
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland
| | - Gabriele A Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland
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18
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Somerville V, Berthoud H, Schmidt RS, Bachmann HP, Meng YH, Fuchsmann P, von Ah U, Engel P. Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures. THE ISME JOURNAL 2022; 16:388-399. [PMID: 34363005 PMCID: PMC8776748 DOI: 10.1038/s41396-021-01071-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 02/07/2023]
Abstract
Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.
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Affiliation(s)
- Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
- Agroscope, Bern, Switzerland.
| | | | | | | | | | | | | | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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19
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Somerville V, Berthoud H, Schmidt RS, Bachmann HP, Meng YH, Fuchsmann P, von Ah U, Engel P. Functional strain redundancy and persistent phage infection in Swiss hard cheese starter cultures. THE ISME JOURNAL 2022; 16:388-399. [PMID: 34363005 DOI: 10.1101/2021.01.14.426499v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 05/27/2023]
Abstract
Undefined starter cultures are poorly characterized bacterial communities from environmental origin used in cheese making. They are phenotypically stable and have evolved through domestication by repeated propagation in closed and highly controlled environments over centuries. This makes them interesting for understanding eco-evolutionary dynamics governing microbial communities. While cheese starter cultures are known to be dominated by a few bacterial species, little is known about the composition, functional relevance, and temporal dynamics of strain-level diversity. Here, we applied shotgun metagenomics to an important Swiss cheese starter culture and analyzed historical and experimental samples reflecting 82 years of starter culture propagation. We found that the bacterial community is highly stable and dominated by only a few coexisting strains of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. lactis. Genome sequencing, metabolomics analysis, and co-culturing experiments of 43 isolates show that these strains are functionally redundant, but differ tremendously in their phage resistance potential. Moreover, we identified two highly abundant Streptococcus phages that seem to stably coexist in the community without any negative impact on bacterial growth or strain persistence, and despite the presence of a large and diverse repertoire of matching CRISPR spacers. Our findings show that functionally equivalent strains can coexist in domesticated microbial communities and highlight an important role of bacteria-phage interactions that are different from kill-the-winner dynamics.
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Affiliation(s)
- Vincent Somerville
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
- Agroscope, Bern, Switzerland.
| | | | | | | | | | | | | | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland.
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20
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Dewald-Wang EA, Parr N, Tiley K, Lee A, Koskella B. Multiyear Time-Shift Study of Bacteria and Phage Dynamics in the Phyllosphere. Am Nat 2022; 199:126-140. [DOI: 10.1086/717181] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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21
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Wang Y, Mao T, Li Y, Xiao W, Liang X, Duan G, Yang H. Characterization of 67 Confirmed Clustered Regularly Interspaced Short Palindromic Repeats Loci in 52 Strains of Staphylococci. Front Microbiol 2021; 12:736565. [PMID: 34751223 PMCID: PMC8571024 DOI: 10.3389/fmicb.2021.736565] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/27/2021] [Indexed: 12/26/2022] Open
Abstract
Staphylococcus aureus (S. aureus), which is one of the most important species of Staphylococci, poses a great threat to public health. Clustered regularly interspaced short palindromic repeats (CRISPR) and their CRISPR-associated proteins (Cas) are an adaptive immune platform to combat foreign mobile genetic elements (MGEs) such as plasmids and phages. The aim of this study is to describe the distribution and structure of CRISPR-Cas system in S. aureus, and to explore the relationship between CRISPR and horizontal gene transfer (HGT). Here, we analyzed 67 confirmed CRISPR loci and 15 companion Cas proteins in 52 strains of Staphylococci with bioinformatics methods. Comparing with the orphan CRISPR loci in Staphylococci, the strains harboring complete CRISPR-Cas systems contained multiple CRISPR loci, direct repeat sequences (DR) forming stable RNA secondary structures with lower minimum free energy (MFE), and variable spacers with detectable protospacers. In S. aureus, unlike the orphan CRISPRs away from Staphylococcal cassette chromosome mec (SCCmec), the complete CRISPR-Cas systems were in J1 region of SCCmec. In addition, we found a conserved motif 5'-TTCTCGT-3' that may protect their downstream sequences from DNA interference. In general, orphan CRISPR locus in S. aureus differed greatly from the structural characteristics of the CRISPR-Cas system. Collectively, our results provided new insight into the diversity and characterization of the CRISPR-Cas system in S. aureus.
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Affiliation(s)
- Ying Wang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Tingting Mao
- The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yinxia Li
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Wenwei Xiao
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Xuan Liang
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Guangcai Duan
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | - Haiyan Yang
- College of Public Health, Zhengzhou University, Zhengzhou, China
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22
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Dimitriu T, Szczelkun MD, Westra ER. Evolutionary Ecology and Interplay of Prokaryotic Innate and Adaptive Immune Systems. Curr Biol 2021; 30:R1189-R1202. [PMID: 33022264 DOI: 10.1016/j.cub.2020.08.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Like many organisms, bacteria and archaea have both innate and adaptive immune systems to defend against infection by viruses and other parasites. Innate immunity most commonly relies on the endonuclease-mediated cleavage of any incoming DNA that lacks a specific epigenetic modification, through a system known as restriction-modification. CRISPR-Cas-mediated adaptive immunity relies on the insertion of short DNA sequences from parasite genomes into CRISPR arrays on the host genome to provide sequence-specific protection. The discovery of each of these systems has revolutionised our ability to carry out genetic manipulations, and, as a consequence, the enzymes involved have been characterised in exquisite detail. In comparison, much less is known about the importance of these two arms of the defence for the ecology and evolution of prokaryotes and their parasites. Here, we review our current ecological and evolutionary understanding of these systems in isolation, and discuss the need to study how innate and adaptive immune responses are integrated when they coexist in the same cell.
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Affiliation(s)
- Tatiana Dimitriu
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK.
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.
| | - Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn TR10 9FE, UK.
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23
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Wheatley RM, MacLean RC. CRISPR-Cas systems restrict horizontal gene transfer in Pseudomonas aeruginosa. THE ISME JOURNAL 2021; 15:1420-1433. [PMID: 33349652 PMCID: PMC8105352 DOI: 10.1038/s41396-020-00860-3] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 11/06/2020] [Accepted: 11/26/2020] [Indexed: 11/29/2022]
Abstract
CRISPR-Cas systems provide bacteria and archaea with an adaptive immune system that targets foreign DNA. However, the xenogenic nature of immunity provided by CRISPR-Cas raises the possibility that these systems may constrain horizontal gene transfer. Here we test this hypothesis in the opportunistic pathogen Pseudomonas aeruginosa, which has emerged as an important model system for understanding CRISPR-Cas function. Across the diversity of P. aeruginosa, active CRISPR-Cas systems are associated with smaller genomes and higher GC content, suggesting that CRISPR-Cas inhibits the acquisition of foreign DNA. Although phage is the major target of CRISPR-Cas spacers, more than 80% of isolates with an active CRISPR-Cas system have spacers that target integrative conjugative elements (ICE) or the conserved conjugative transfer machinery used by plasmids and ICE. Consistent with these results, genomes containing active CRISPR-Cas systems harbour a lower abundance of both prophage and ICE. Crucially, spacers in genomes with active CRISPR-Cas systems map to ICE and phage that are integrated into the chromosomes of closely related genomes lacking CRISPR-Cas immunity. We propose that CRISPR-Cas acts as an important constraint to horizontal gene transfer, and the evolutionary mechanisms that ensure its maintenance or drive its loss are key to the ability of this pathogen to adapt to new niches and stressors.
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Affiliation(s)
| | - R Craig MacLean
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
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24
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Abstract
CRISPR-Cas systems provide bacteria and archaea with adaptive, heritable immunity against their viruses (bacteriophages and phages) and other parasitic genetic elements. CRISPR-Cas systems are highly diverse, and we are only beginning to understand their relative importance in phage defense. In this review, we will discuss when and why CRISPR-Cas immunity against phages evolves, and how this, in turn, selects for the evolution of immune evasion by phages. Finally, we will discuss our current understanding of if, and when, we observe coevolution between CRISPR-Cas systems and phages, and how this may be influenced by the mechanism of CRISPR-Cas immunity.
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25
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Guerrero LD, Pérez MV, Orellana E, Piuri M, Quiroga C, Erijman L. Long-run bacteria-phage coexistence dynamics under natural habitat conditions in an environmental biotechnology system. THE ISME JOURNAL 2021; 15:636-648. [PMID: 33067586 PMCID: PMC8027832 DOI: 10.1038/s41396-020-00802-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 09/21/2020] [Accepted: 10/01/2020] [Indexed: 01/30/2023]
Abstract
Bacterial viruses are widespread and abundant across natural and engineered habitats. They influence ecosystem functioning through interactions with their hosts. Laboratory studies of phage-host pairs have advanced our understanding of phenotypic and genetic diversification in bacteria and phages. However, the dynamics of phage-host interactions have been seldom recorded in complex natural environments. We conducted an observational metagenomic study of the dynamics of interaction between Gordonia and their phages using a three-year data series of samples collected from a full-scale wastewater treatment plant. The aim was to obtain a comprehensive picture of the coevolution dynamics in naturally evolving populations at relatively high time resolution. Coevolution was followed by monitoring changes over time in the CRISPR loci of Gordonia metagenome-assembled genome, and reciprocal changes in the viral genome. Genome-wide analysis indicated low strain variability of Gordonia, and almost clonal conservation of the trailer end of the CRISPR loci. Incorporation of newer spacers gave rise to multiple coexisting bacterial populations. The host population carrying a shorter CRISPR locus that contain only ancestral spacers, which has not acquired newer spacers against the coexisting phages, accounted for more than half of the total host abundance in the majority of samples. Phages genome co-evolved by introducing directional changes, with no preference for mutations within the protospacer and PAM regions. Metagenomic reconstruction of time-resolved variants of host and viral genomes revealed how the complexity at the population level has important consequences for bacteria-phage coexistence.
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Affiliation(s)
- Leandro D. Guerrero
- grid.423606.50000 0001 1945 2152Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr Héctor N. Torres” (INGEBI-CONICET), Vuelta de Obligado 2490, C1428ADN Buenos Aires, Argentina
| | - María V. Pérez
- grid.423606.50000 0001 1945 2152Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr Héctor N. Torres” (INGEBI-CONICET), Vuelta de Obligado 2490, C1428ADN Buenos Aires, Argentina ,Agua y Saneamientos Argentinos S.A., Tucumán 752, C1049APP Buenos Aires, Argentina
| | - Esteban Orellana
- grid.423606.50000 0001 1945 2152Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr Héctor N. Torres” (INGEBI-CONICET), Vuelta de Obligado 2490, C1428ADN Buenos Aires, Argentina
| | - Mariana Piuri
- Departamento de Química Biológica, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, CONICET, Intendente Güiraldes 2160, C1428EGA Buenos Aires, Argentina
| | - Cecilia Quiroga
- Instituto de Investigaciones en Microbiología y Parasitología Médica (IMPaM), Facultad de Medicina, Universidad de Buenos Aires, CONICET, Paraguay 2155, C1121ABG Buenos Aires, Argentina
| | - Leonardo Erijman
- grid.423606.50000 0001 1945 2152Instituto de Investigaciones en Ingeniería Genética y Biología Molecular “Dr Héctor N. Torres” (INGEBI-CONICET), Vuelta de Obligado 2490, C1428ADN Buenos Aires, Argentina ,grid.7345.50000 0001 0056 1981Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires, Intendente Güiraldes 2160s, C1428EGA Buenos Aires, Argentina
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26
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Tian F, Li J, Nazir A, Tong Y. Bacteriophage - A Promising Alternative Measure for Bacterial Biofilm Control. Infect Drug Resist 2021; 14:205-217. [PMID: 33505163 PMCID: PMC7829120 DOI: 10.2147/idr.s290093] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/23/2020] [Indexed: 01/09/2023] Open
Abstract
Bacterial biofilms can enhance bacteria's viability by providing resistance against antibiotics and conventional disinfectants. The existence of biofilm is a serious threat to human health, causing incalculable loss. Therefore, new strategies to deal with bacterial biofilms are needed. Bacteriophages are unique due to their activity on bacteria and do not pose a threat to humans. Consequently, they are considered safe alternatives to drugs for the treatment of bacterial diseases. They can effectively obliterate bacterial biofilms and have great potential in medical treatment, the food industry, and pollution control. There are intricate mechanisms of interaction between phages and biofilms. Biofilms may prevent the invasion of phages, and phages can kill bacteria for biofilm control purposes or influence the formation of biofilms. At present, there are various measures for the prevention and control of biofilms through phages, including the combined use of drugs and the application of phage cocktails. This article mainly reviews the function and formation process of bacterial biofilms, summarizes the different mechanisms between phages and biofilms, briefly explains the phage usage for the control of bacterial biofilms, and promotes phage application maintenance human health and the protection of the natural environment.
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Affiliation(s)
- Fengjuan Tian
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Jing Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Amina Nazir
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
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27
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Westra ER, Levin BR. It is unclear how important CRISPR-Cas systems are for protecting natural populations of bacteria against infections by mobile genetic elements. Proc Natl Acad Sci U S A 2020; 117:27777-27785. [PMID: 33122438 PMCID: PMC7668106 DOI: 10.1073/pnas.1915966117] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Articles on CRISPR commonly open with some variant of the phrase "these short palindromic repeats and their associated endonucleases (Cas) are an adaptive immune system that exists to protect bacteria and archaea from viruses and infections with other mobile genetic elements." There is an abundance of genomic data consistent with the hypothesis that CRISPR plays this role in natural populations of bacteria and archaea, and experimental demonstrations with a few species of bacteria and their phage and plasmids show that CRISPR-Cas systems can play this role in vitro. Not at all clear are the ubiquity, magnitude, and nature of the contribution of CRISPR-Cas systems to the ecology and evolution of natural populations of microbes and the strength of selection mediated by different types of phage and plasmids to the evolution and maintenance of CRISPR-Cas systems. In this perspective, with the aid of heuristic mathematical-computer simulation models, we explore the a priori conditions under which exposure to lytic and temperate phage and conjugative plasmids will select for and maintain CRISPR-Cas systems in populations of bacteria and archaea. We review the existing literature addressing these ecological and evolutionary questions and highlight the experimental and other evidence needed to fully understand the conditions responsible for the evolution and maintenance of CRISPR-Cas systems and the contribution of these systems to the ecology and evolution of bacteria, archaea, and the mobile genetic elements that infect them.
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Affiliation(s)
- Edze R Westra
- Environment and Sustainability Institute, Biosciences, University of Exeter, Penryn, TR10 9FE Cornwall, United Kingdom;
| | - Bruce R Levin
- Department of Biology, Emory University, Atlanta, GA 30307
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28
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Molina F, Simancas A, Tabla R, Gómez A, Roa I, Rebollo JE. Diversity and Local Coadaptation of Escherichia coli and Coliphages From Small Ruminants. Front Microbiol 2020; 11:564522. [PMID: 33178150 PMCID: PMC7596221 DOI: 10.3389/fmicb.2020.564522] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/17/2020] [Indexed: 01/21/2023] Open
Abstract
Bacteriophages are highly specific predators that drive bacterial diversity through coevolution while striking tradeoffs among preserving host populations for long-term exploitation and increasing their virulence, structural stability, or host range. Escherichia coli and other coliform bacteria present in the microbiota of milk and during early ripening of raw milk cheeses have been linked to the production of gas, manifested by the appearance of eyes, and the development of off-flavors; thus, they might cause early blowing and cheese spoilage. Here, we report the characterization of coliphages isolated from manure from small ruminant farms and E. coli strains isolated from goat and sheep raw milk cheese. Additionally, the virulence and host range of locally isolated and laboratory collection phages were determined by comparing the susceptibility of E. coli strains from different sources. In agreement with the high genetic diversity found within the species E. coli, clustering analysis of whole-cell protein revealed a total of 13 distinct profiles but none of the raw milk cheese isolates showed inhibition of growth by reference or water-isolated coliphages. Conversely, 10 newly isolated phages had a broad host range (i.e., able to lyse ≥50% of bacterial hosts tested), thus exhibiting utility for biocontrol and only one cheese-isolated E. coli strain was resistant to all the phages. Whereas there was a high positive correlation between bacterial susceptibility range and lysis intensity, the phages virulence decreased as range increased until reaching a plateau. These results suggest local gene-for-gene coevolution between hosts and phages with selective tradeoffs for both resistance and competitive ability of the bacteria and host-range extension and virulence of the phage populations. Hence, different phage cocktail formulations might be required when devising long-term and short-term biocontrol strategies.
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Affiliation(s)
- Felipe Molina
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Alfredo Simancas
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
| | - Rafael Tabla
- Dairy Department, Technological Institute of Food and Agriculture - Scientific and Technological Research Centre of Extremadura, Junta de Extremadura, Badajoz, Spain
| | - Antonia Gómez
- Dairy Department, Technological Institute of Food and Agriculture - Scientific and Technological Research Centre of Extremadura, Junta de Extremadura, Badajoz, Spain
| | - Isidro Roa
- Dairy Department, Technological Institute of Food and Agriculture - Scientific and Technological Research Centre of Extremadura, Junta de Extremadura, Badajoz, Spain
| | - José Emilio Rebollo
- Department of Biochemistry, Molecular Biology and Genetics, University of Extremadura, Badajoz, Spain
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29
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Common J, Walker-Sünderhauf D, van Houte S, Westra ER. Diversity in CRISPR-based immunity protects susceptible genotypes by restricting phage spread and evolution. J Evol Biol 2020; 33:1097-1108. [PMID: 32383796 DOI: 10.1111/jeb.13638] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/13/2020] [Accepted: 04/27/2020] [Indexed: 12/26/2022]
Abstract
Diversity in host resistance often associates with reduced pathogen spread. This may result from ecological and evolutionary processes, likely with feedback between them. Theory and experiments on bacteria-phage interactions have shown that genetic diversity of the bacterial adaptive immune system can limit phage evolution to overcome resistance. Using the CRISPR-Cas bacterial immune system and lytic phage, we engineered a host-pathogen system where each bacterial host genotype could be infected by only one phage genotype. With this model system, we explored how CRISPR diversity impacts the spread of phage when they can overcome a resistance allele, how immune diversity affects the evolution of the phage to increase its host range and if there was feedback between these processes. We show that increasing CRISPR diversity benefits susceptible bacteria via a dilution effect, which limits the spread of the phage. We suggest that this ecological effect impacts the evolution of novel phage genotypes, which then feeds back into phage population dynamics.
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Affiliation(s)
- Jack Common
- ESI and CEC, Biosciences, University of Exeter, Penryn, UK
| | - David Walker-Sünderhauf
- European Centre for Environment and Human Health, ESI, University of Exeter Medical School, Penryn, UK
| | | | - Edze R Westra
- ESI and CEC, Biosciences, University of Exeter, Penryn, UK
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30
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DeWerff SJ, Bautista MA, Pauly M, Zhang C, Whitaker RJ. Killer Archaea: Virus-Mediated Antagonism to CRISPR-Immune Populations Results in Emergent Virus-Host Mutualism. mBio 2020; 11:e00404-20. [PMID: 32345641 PMCID: PMC7188992 DOI: 10.1128/mbio.00404-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/02/2020] [Indexed: 02/05/2023] Open
Abstract
Theory, simulation, and experimental evolution demonstrate that diversified CRISPR-Cas immunity to lytic viruses can lead to stochastic virus extinction due to a limited number of susceptible hosts available to each potential new protospacer escape mutation. Under such conditions, theory predicts that to evade extinction, viruses evolve toward decreased virulence and promote vertical transmission and persistence in infected hosts. To better understand the evolution of host-virus interactions in microbial populations with active CRISPR-Cas immunity, we studied the interaction between CRISPR-immune Sulfolobus islandicus cells and immune-deficient strains that are infected by the chronic virus SSV9. We demonstrate that Sulfolobus islandicus cells infected with SSV9, and with other related SSVs, kill uninfected, immune strains through an antagonistic mechanism that is a protein and is independent of infectious virus. Cells that are infected with SSV9 are protected from killing and persist in the population. We hypothesize that this infection acts as a form of mutualism between the host and the virus by removing competitors in the population and ensuring continued vertical transmission of the virus within populations with diversified CRISPR-Cas immunity.IMPORTANCE Multiple studies, especially those focusing on the role of lytic viruses in key model systems, have shown the importance of viruses in shaping microbial populations. However, it has become increasingly clear that viruses with a long host-virus interaction, such as those with a chronic lifestyle, can be important drivers of evolution and have large impacts on host ecology. In this work, we describe one such interaction with the acidic crenarchaeon Sulfolobus islandicus and its chronic virus Sulfolobus spindle-shaped virus 9. Our work expands the view in which this symbiosis between host and virus evolved, describing a killing phenotype which we hypothesize has evolved in part due to the high prevalence and diversity of CRISPR-Cas immunity seen in natural populations. We explore the implications of this phenotype in population dynamics and host ecology, as well as the implications of mutualism between this virus-host pair.
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Affiliation(s)
- Samantha J DeWerff
- Department of Microbiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Maria A Bautista
- Department of Microbiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Matthew Pauly
- Department of Microbiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Changyi Zhang
- Department of Microbiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
- Infection Genomics for One Health Theme, Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, Illinois, USA
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31
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Weissman JL, Stoltzfus A, Westra ER, Johnson PLF. Avoidance of Self during CRISPR Immunization. Trends Microbiol 2020; 28:543-553. [PMID: 32544441 DOI: 10.1016/j.tim.2020.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 02/05/2020] [Accepted: 02/25/2020] [Indexed: 02/07/2023]
Abstract
The battle between microbes and their viruses is ancient and ongoing. Clustered regularly interspaced short palindromic repeat (CRISPR) immunity, the first and, to date, only form of adaptive immunity found in prokaryotes, represents a flexible mechanism to recall past infections while also adapting to a changing pathogenic environment. Critical to the role of CRISPR as an adaptive immune mechanism is its capacity for self versus non-self recognition when acquiring novel immune memories. Yet, CRISPR systems vary widely in both how and to what degree they can distinguish foreign from self-derived genetic material. We document known and hypothesized mechanisms that bias the acquisition of immune memory towards non-self targets. We demonstrate that diversity is the rule, with many widespread but no universal mechanisms for self versus non-self recognition.
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Affiliation(s)
- Jake L Weissman
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Arlin Stoltzfus
- Office of Data and Informatics, Material Measurement Laboratory, NIST, Gaithersburg, MD 20899, USA; Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, MD 20850, USA
| | - Edze R Westra
- Environment and Sustainability Institute, Centre for Ecology and Conservation, University of Exeter, Biosciences, Penryn, Cornwall, UK
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32
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Pyenson NC, Marraffini LA. Co-evolution within structured bacterial communities results in multiple expansion of CRISPR loci and enhanced immunity. eLife 2020; 9:e53078. [PMID: 32223887 PMCID: PMC7105378 DOI: 10.7554/elife.53078] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 02/12/2020] [Indexed: 12/26/2022] Open
Abstract
Type II CRISPR-Cas systems provide immunity against phages and plasmids that infect bacteria through the insertion of a short sequence from the invader's genome, known as the 'spacer', into the CRISPR locus. Spacers are transcribed into guide RNAs that direct the Cas9 nuclease to its target on the invader. In liquid cultures, most bacteria acquire a single spacer. Multiple spacer integration is a rare event which significance for immunity is poorly understood. Here, we found that when phage infections occur on solid media, a high proportion of the surviving colonies display complex morphologies that contain cells with multiple spacers. This is the result of the viral-host co-evolution, in which the immunity provided by the initial acquired spacer is easily overcome by escaper phages. Our results reveal the versatility of CRISPR-Cas immunity, which can respond with both single or multiple spacer acquisition schemes to solve challenges presented by different environments.
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Affiliation(s)
- Nora C Pyenson
- Laboratory of Bacteriology, The Rockefeller UniversityNew YorkUnited States
| | - Luciano A Marraffini
- Laboratory of Bacteriology, The Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical Institute, The Rockefeller UniversityNew YorkUnited States
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33
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Westra ER, van Houte S, Gandon S, Whitaker R. The ecology and evolution of microbial CRISPR-Cas adaptive immune systems. Philos Trans R Soc Lond B Biol Sci 2020; 374:20190101. [PMID: 30905294 DOI: 10.1098/rstb.2019.0101] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Edze R Westra
- 1 ESI and CEC, Biosciences, University of Exeter , Cornwall Campus, Penryn TR10 9EZ , UK
| | - Stineke van Houte
- 1 ESI and CEC, Biosciences, University of Exeter , Cornwall Campus, Penryn TR10 9EZ , UK
| | - Sylvain Gandon
- 2 CEFE UMR 5175, CNRS Université de Montpellier Université Paul-Valéry Montpellier EPHE , 34293 Montpellier Cedex 5 , France
| | - Rachel Whitaker
- 3 Department of Microbiology, University of Illinois , Urbana-Champaign, 601 S. Goodwin Avenue, Urbana, IL 61801 , USA
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34
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Valero‐Rello A. Diversity, specificity and molecular evolution of the lytic arsenal of
Pseudomonas
phages:
in silico
perspective. Environ Microbiol 2019; 21:4136-4150. [DOI: 10.1111/1462-2920.14767] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 01/21/2023]
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