1
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Ahator SD, Sagar S, Zhu M, Wang J, Zhang LH. Nutrient Availability and Phage Exposure Alter the Quorum-Sensing and CRISPR-Cas-Controlled Population Dynamics of Pseudomonas aeruginosa. mSystems 2022; 7:e0009222. [PMID: 35699339 PMCID: PMC9426516 DOI: 10.1128/msystems.00092-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/10/2022] [Indexed: 11/20/2022] Open
Abstract
Quorum sensing (QS) coordinates bacterial communication and cooperation essential for virulence and dominance in polymicrobial settings. QS also regulates the CRISPR-Cas system for targeted defense against parasitic genomes from phages and horizontal gene transfer. Although the QS and CRISPR-Cas systems are vital for bacterial survival, they undergo frequent selection in response to biotic and abiotic factors. Using the opportunistic Pseudomonas aeruginosa with well-established QS and CRISPR-Cas systems, we show how the social interactions between the acyl-homoserine lactone (AHL)-QS signal-blind mutants (ΔlasRrhlR) and the CRISPR-Cas mutants are affected by phage exposure and nutrient availability. We demonstrate that media conditions and phage exposure alter the resistance and relative fitness of ΔlasRrhlR and CRISPR-Cas mutants while tipping the fitness advantage in favor of the QS signal-blind mutants under nutrient-limiting conditions. We also show that the AHL signal-blind mutants are less selected by phages under QS-inducing conditions than the CRISPR-Cas mutants, whereas the mixed population of the CRISPR-Cas and AHL signal-blind mutants reduce phage infectivity, which can improve survival during phage exposure. Our data reveal that phage exposure and nutrient availability reshape the population dynamics between the ΔlasRrhlR QS mutants and CRISPR-Cas mutants, with key indications for cooperation and conflict between the strains. IMPORTANCE The increase in antimicrobial resistance has created the need for alternative interventions such as phage therapy. However, as previously observed with antimicrobial resistance, phage therapy will not be effective if bacteria evolve resistance and persist in the presence of the phages. The QS is commonly known as an arsenal for bacteria communication, virulence, and regulation of the phage defense mechanism, the CRISPR-Cas system. The QS and CRISPR-Cas systems are widespread in bacteria. However, they are known to evolve rapidly under the influence of biotic and abiotic factors in the bacterial environment, resulting in alteration in bacterial genotypes, which enhance phage resistance and fitness. We believe that adequate knowledge of the influence of environmental factors on the bacterial community lifestyle and phage defense mechanisms driven by the QS and CRISPR-Cas system is necessary for developing effective phage therapy.
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Affiliation(s)
- Stephen Dela Ahator
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Centre for New Antibacterial Strategies (CANS) & Research Group for Host-Microbe Interactions, Faculty of Health Sciences, The Arctic University of Norway, Tromsø, Norway
| | - Sadhanna Sagar
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Minya Zhu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Jianhe Wang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, China
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2
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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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3
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Bartlett LJ, Visher E, Haro Y, Roberts KE, Boots M. The target of selection matters: An established resistance-development-time negative genetic trade-off is not found when selecting on development time. J Evol Biol 2020; 33:1109-1119. [PMID: 32390292 DOI: 10.1111/jeb.13639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 04/22/2020] [Accepted: 05/02/2020] [Indexed: 11/30/2022]
Abstract
Trade-offs are fundamental to evolutionary outcomes and play a central role in eco-evolutionary theory. They are often examined by experimentally selecting on one life-history trait and looking for negative correlations in other traits. For example, populations of the moth Plodia interpunctella selected to resist viral infection show a life-history cost with longer development times. However, we rarely examine whether the detection of such negative genetic correlations depends on the trait on which we select. Here, we examine a well-characterized negative genotypic trade-off between development time and resistance to viral infection in the moth Plodia interpunctella and test whether selection on a phenotype known to be a cost of resistance (longer development time) leads to the predicted correlated increase in resistance. If there is tight pleiotropic relationship between genes that determine development time and resistance underpinning this trade-off, we might expect increased resistance when we select on longer development time. However, we show that selecting for longer development time in this system selects for reduced resistance when compared to selection for shorter development time. This shows how phenotypes typically characterized by a trade-off can deviate from that trade-off relationship, and suggests little genetic linkage between the genes governing viral resistance and those that determine response to selection on the key life-history trait. Our results are important for both selection strategies in applied biological systems and for evolutionary modelling of host-parasite interactions.
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Affiliation(s)
- Lewis J Bartlett
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, UK
- Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Elisa Visher
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | | | - Katherine E Roberts
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, UK
| | - Mike Boots
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, UK
- Department of Integrative Biology, University of California, Berkeley, CA, USA
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4
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Jiang M, Yang L, Chen Z, Lai S, Zheng J, Peng B. Exogenous maltose enhances Zebrafish immunity to levofloxacin-resistant Vibrio alginolyticus. Microb Biotechnol 2020; 13:1213-1227. [PMID: 32364684 PMCID: PMC7264874 DOI: 10.1111/1751-7915.13582] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 04/09/2020] [Accepted: 04/10/2020] [Indexed: 12/18/2022] Open
Abstract
Understanding the interplay between bacterial fitness, antibiotic resistance, host immunity and host metabolism could guide treatment and improve immunity against antibiotic-resistant pathogens. The acquisition of levofloxacin (Lev) resistance affects the fitness of Vibrio alginolyticus in vitro and in vivo. Lev-resistant (Lev-R) V. alginolyticus exhibits slow growth, reduced pathogenicity and greater resistance to killing by the host, Danio rerio (zebrafish), than Lev-sensitive (Lev-S) V. alginolyticus, suggesting that Lev-R V. alginolyticus triggers a weaker innate immune response in D. rerio than Lev-S V. alginolyticus. Differences were detected in the metabolome of D. rerio infected with Lev-S or Lev-R V. alginolyticus. Maltose, a crucial metabolite, is significantly downregulated in D. rerio infected with Lev-R V. alginolyticus, and exogenous maltose enhances the immune response of D. rerio to Lev-R V. alginolyticus, leading to better clearance of the infection. Furthermore, we demonstrate that exogenous maltose stimulates the host production of lysozyme and its binding to Lev-R V. alginolyticus, which depends on bacterial membrane potential. We suggest that exogenous exposure to crucial metabolites could be an effective strategy for treating and/or managing infections with antibiotic-resistant bacteria.
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Affiliation(s)
- Ming Jiang
- The Third Affiliated HospitalState Key Laboratory of BiocontrolGuangdong Key Laboratory of Pharmaceutical Functional GenesSchool of Life SciencesSun Yat-sen UniversityGuangzhou510275China
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdao266071China
| | - Lifen Yang
- The Third Affiliated HospitalState Key Laboratory of BiocontrolGuangdong Key Laboratory of Pharmaceutical Functional GenesSchool of Life SciencesSun Yat-sen UniversityGuangzhou510275China
| | - Zhuang‐gui Chen
- The Third Affiliated HospitalState Key Laboratory of BiocontrolGuangdong Key Laboratory of Pharmaceutical Functional GenesSchool of Life SciencesSun Yat-sen UniversityGuangzhou510275China
| | - Shi‐shi Lai
- The Third Affiliated HospitalState Key Laboratory of BiocontrolGuangdong Key Laboratory of Pharmaceutical Functional GenesSchool of Life SciencesSun Yat-sen UniversityGuangzhou510275China
| | - Jun Zheng
- Faculty of Health SciencesUniversity of MacauMacau SARChina
| | - Bo Peng
- The Third Affiliated HospitalState Key Laboratory of BiocontrolGuangdong Key Laboratory of Pharmaceutical Functional GenesSchool of Life SciencesSun Yat-sen UniversityGuangzhou510275China
- Laboratory for Marine Biology and BiotechnologyQingdao National Laboratory for Marine Science and TechnologyQingdao266071China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)Zhuhai519000China
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5
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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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6
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Safari F, Sharifi M, Farajnia S, Akbari B, Karimi Baba Ahmadi M, Negahdaripour M, Ghasemi Y. The interaction of phages and bacteria: the co-evolutionary arms race. Crit Rev Biotechnol 2019; 40:119-137. [PMID: 31793351 DOI: 10.1080/07388551.2019.1674774] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Since the dawn of life, bacteria and phages are locked in a constant battle and both are perpetually changing their tactics to overcome each other. Bacteria use various strategies to overcome the invading phages, including adsorption inhibition, restriction-modification (R/E) systems, CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) systems, abortive infection (Abi), etc. To counteract, phages employ intelligent tactics for the nullification of bacterial defense systems, such as accessing host receptors, evading R/E systems, and anti-CRISPR proteins. Intense knowledge about the details of these defense pathways is the basis for their broad utilities in various fields of research from microbiology to biotechnology. Hence, in this review, we discuss some strategies used by bacteria to inhibit phage infections as well as phage tactics to circumvent bacterial defense systems. In addition, the application of these strategies will be described as a lesson learned from bacteria and phage combats. The ecological factors that affect the evolution of bacterial immune systems is the other issue represented in this review.
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Affiliation(s)
- Fatemeh Safari
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehrdad Sharifi
- Department of Emergency Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Safar Farajnia
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahman Akbari
- Department of Medical Biotechnology, School of Medical Sciences, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | | | - Manica Negahdaripour
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.,Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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7
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Shehreen S, Chyou TY, Fineran PC, Brown CM. Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180384. [PMID: 30905286 PMCID: PMC6452267 DOI: 10.1098/rstb.2018.0384] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas systems are widespread in bacterial and archaeal genomes, and in their canonical role in phage defence they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. Newly discovered features within these evolutionary dynamics are anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR genes in genomes that harbour CRISPR-Cas systems and horizontally acquired antibiotic resistance genes. To assess that question, we analysed correlations between the CRISPR-Cas, anti-CRISPR and antibiotic resistance gene content of 104 947 reference genomes, including 5677 different species. In most species, the presence of CRISPR-Cas systems did not correlate with the presence of antibiotic resistance genes. However, in some clinically important species, we observed either a positive or negative correlation of CRISPR-Cas with antibiotic resistance genes. Anti-CRISPR genes were common enough in four species to be analysed. In Pseudomonas aeruginosa, the presence of anti-CRISPRs was associated with antibiotic resistance genes. This analysis indicates that the role of CRISPR-Cas and anti-CRISPRs in the spread of antibiotic resistance is likely to be very different in particular pathogenic species and clinical environments. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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Affiliation(s)
- Saadlee Shehreen
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Te-yuan Chyou
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Peter C. Fineran
- Department of Microbiology and Immunology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, New Zealand
| | - Chris M. Brown
- Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9054, New Zealand
- Genetics Otago, University of Otago, New Zealand
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8
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Chevallereau A, Meaden S, van Houte S, Westra ER, Rollie C. The effect of bacterial mutation rate on the evolution of CRISPR-Cas adaptive immunity. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180094. [PMID: 30905293 PMCID: PMC6452272 DOI: 10.1098/rstb.2018.0094] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2018] [Indexed: 01/07/2023] Open
Abstract
CRISPR-Cas immune systems are present in around half of bacterial genomes. Given the specificity and adaptability of this immune mechanism, it is perhaps surprising that they are not more widespread. Recent insights into the requirement for specific host factors for the function of some CRISPR-Cas subtypes, as well as the negative epistasis between CRISPR-Cas and other host genes, have shed light on potential reasons for the partial distribution of this immune strategy in bacteria. In this study, we examined how mutations in the bacterial mismatch repair system, which are frequently observed in natural and clinical isolates and cause elevated host mutation rates, influence the evolution of CRISPR-Cas-mediated immunity. We found that hosts with a high mutation rate very rarely evolved CRISPR-based immunity to phage compared to wild-type hosts. We explored the reason for this effect and found that the higher frequency at which surface mutants pre-exist in the mutator host background causes them to rapidly become the dominant phenotype under phage infection. These findings suggest that natural variation in bacterial mutation rates may, therefore, influence the distribution of CRISPR-Cas adaptive immune systems. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
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Affiliation(s)
| | | | | | - Edze R. Westra
- ESI and CEC, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9EZ, UK
| | - Clare Rollie
- ESI and CEC, Biosciences, University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9EZ, UK
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9
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Gulbudak H, Weitz JS. Heterogeneous viral strategies promote coexistence in virus-microbe systems. J Theor Biol 2019; 462:65-84. [DOI: 10.1016/j.jtbi.2018.10.056] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 09/15/2018] [Accepted: 10/29/2018] [Indexed: 01/21/2023]
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10
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Tavalire HF, Beechler BR, Buss PE, Gorsich EE, Hoal EG, le Roex N, Spaan JM, Spaan RS, van Helden PD, Ezenwa VO, Jolles AE. Context-dependent costs and benefits of tuberculosis resistance traits in a wild mammalian host. Ecol Evol 2018; 8:12712-12726. [PMID: 30619576 PMCID: PMC6308860 DOI: 10.1002/ece3.4699] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 10/02/2018] [Accepted: 10/12/2018] [Indexed: 12/24/2022] Open
Abstract
Disease acts as a powerful driver of evolution in natural host populations, yet individuals in a population often vary in their susceptibility to infection. Energetic trade-offs between immune and reproductive investment lead to the evolution of distinct life history strategies, driven by the relative fitness costs and benefits of resisting infection. However, examples quantifying the cost of resistance outside of the laboratory are rare. Here, we observe two distinct forms of resistance to bovine tuberculosis (bTB), an important zoonotic pathogen, in a free-ranging African buffalo (Syncerus caffer) population. We characterize these phenotypes as "infection resistance," in which hosts delay or prevent infection, and "proliferation resistance," in which the host limits the spread of lesions caused by the pathogen after infection has occurred. We found weak evidence that infection resistance to bTB may be heritable in this buffalo population (h 2 = 0.10) and comes at the cost of reduced body condition and marginally reduced survival once infected, but also associates with an overall higher reproductive rate. Infection-resistant animals thus appear to follow a "fast" pace-of-life syndrome, in that they reproduce more quickly but die upon infection. In contrast, proliferation resistance had no apparent costs and was associated with measures of positive host health-such as having a higher body condition and reproductive rate. This study quantifies striking phenotypic variation in pathogen resistance and provides evidence for a link between life history variation and a disease resistance trait in a wild mammalian host population.
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Affiliation(s)
- Hannah F. Tavalire
- Department of Integrative BiologyOregon State UniversityCorvallisOregon
- The Institute of Ecology and EvolutionUniversity of OregonEugeneOregon
- Present address:
Prevention Science InstituteUniversity of OregonEugeneOregon
- Present address:
Institute of Ecology and EvolutionUniversity of OregonEugeneOregon
| | | | | | - Erin E. Gorsich
- College of Veterinary MedicineOregon State UniversityCorvallisOregon
- Present address:
Erin E. Gorsich, Zeeman Institute: Systems Biology and Infectious Disease Epidemiology Research (SBIDER)University of WarwickCoventryUK
- Present address:
School of Life SciencesUniversity of WarwickCoventryUK
| | - Eileen G. Hoal
- South African Medical Research Council, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Health SciencesStellenbosch UniversityTygerbergSouth Africa
| | - Nikki le Roex
- South African Medical Research Council, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Health SciencesStellenbosch UniversityTygerbergSouth Africa
| | - Johannie M. Spaan
- Department of Integrative BiologyOregon State UniversityCorvallisOregon
| | - Robert S. Spaan
- Department of Fisheries and WildlifeOregon State UniversityCorvallisOregon
| | - Paul D. van Helden
- South African Medical Research Council, DST/NRF Centre of Excellence for Biomedical TB Research, Division of Molecular Biology and Human Genetics, Faculty of Health SciencesStellenbosch UniversityTygerbergSouth Africa
| | - Vanessa O. Ezenwa
- Odum School of Ecology and Department of Infectious Diseases, College of Veterinary MedicineUniversity of GeorgiaAthensGeorgia
| | - Anna E. Jolles
- Department of Integrative BiologyOregon State UniversityCorvallisOregon
- College of Veterinary MedicineOregon State UniversityCorvallisOregon
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11
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Bartlett LJ, Wilfert L, Boots M. A genotypic trade-off between constitutive resistance to viral infection and host growth rate. Evolution 2018; 72:2749-2757. [PMID: 30298913 PMCID: PMC6492093 DOI: 10.1111/evo.13623] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/05/2018] [Indexed: 02/07/2023]
Abstract
Genotypic trade‐offs are fundamental to the understanding of the evolution of life‐history traits. In particular, the evolution of optimal host defense and the maintenance of variation in defense against infectious disease is thought to be underpinned by such evolutionary trade‐offs. However, empirical demonstrations of these trade‐offs that satisfy the strict assumptions made by theoretical models are rare. Additionally, none of these trade‐offs have yet been shown to be robustly replicable using a variety of different experimental approaches to rule out confounding issues with particular experimental designs. Here, we use inbred isolines as a novel experimental approach to test whether a trade‐off between viral resistance and growth rate in Plodia interpunctella, previously demonstrated by multiple selection experiments, is robust and meets the strict criteria required to underpin theoretical work in this field. Critically, we demonstrate that this trade‐off is both genetic and constitutive. This finding helps support the large body of theory that relies on these assumptions, and makes this trade‐off for resistance unique in being replicated through multiple experimental approaches and definitively shown to be genetic and constitutive.
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Affiliation(s)
- Lewis J Bartlett
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Lena Wilfert
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, United Kingdom
| | - Michael Boots
- Department of Integrative Biology, University of California, Berkeley, California, 94720
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12
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Gupta V, Vasanthakrishnan RB, Siva-Jothy J, Monteith KM, Brown SP, Vale PF. The route of infection determines Wolbachia antibacterial protection in Drosophila. Proc Biol Sci 2017; 284:20170809. [PMID: 28592678 PMCID: PMC5474083 DOI: 10.1098/rspb.2017.0809] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 05/12/2017] [Indexed: 12/03/2022] Open
Abstract
Bacterial symbionts are widespread among metazoans and provide a range of beneficial functions. Wolbachia-mediated protection against viral infection has been extensively demonstrated in Drosophila. In mosquitoes that are artificially transinfected with Drosophila melanogaster Wolbachia (wMel), protection from both viral and bacterial infections has been demonstrated. However, no evidence for Wolbachia-mediated antibacterial protection has been demonstrated in Drosophila to date. Here, we show that the route of infection is key for Wolbachia-mediated antibacterial protection. Drosophila melanogaster carrying Wolbachia showed reduced mortality during enteric-but not systemic-infection with the opportunist pathogen Pseudomonas aeruginosaWolbachia-mediated protection was more pronounced in male flies and is associated with increased early expression of the antimicrobial peptide Attacin A, and also increased expression of a reactive oxygen species detoxification gene (Gst D8). These results highlight that the route of infection is important for symbiont-mediated protection from infection, that Wolbachia can protect hosts by eliciting a combination of resistance and disease tolerance mechanisms, and that these effects are sexually dimorphic. We discuss the importance of using ecologically relevant routes of infection to gain a better understanding of symbiont-mediated protection.
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Affiliation(s)
- Vanika Gupta
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | | | - Jonathon Siva-Jothy
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Katy M Monteith
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sam P Brown
- School of Biology, Georgia Institute of Technology, Atlanta, GA 30332-0230, USA
| | - Pedro F Vale
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
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13
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Gupta V, Stewart CO, Rund SSC, Monteith K, Vale PF. Costs and benefits of sublethal Drosophila C virus infection. J Evol Biol 2017; 30:1325-1335. [PMID: 28425174 DOI: 10.1111/jeb.13096] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 04/10/2017] [Accepted: 04/12/2017] [Indexed: 01/24/2023]
Abstract
Viruses are major evolutionary drivers of insect immune systems. Much of our knowledge of insect immune responses derives from experimental infections using the fruit fly Drosophila melanogaster. Most experiments, however, employ lethal pathogen doses through septic injury, frequently overwhelming host physiology. While this approach has revealed several immune mechanisms, it is less informative about the fitness costs hosts may experience during infection in the wild. Using both systemic and oral infection routes, we find that even apparently benign, sublethal infections with the horizontally transmitted Drosophila C virus (DCV) can cause significant physiological and behavioural morbidity that is relevant for host fitness. We describe DCV-induced effects on fly reproductive output, digestive health and locomotor activity, and we find that viral morbidity varies according to the concentration of pathogen inoculum, host genetic background and sex. Notably, sublethal DCV infection resulted in a significant increase in fly reproduction, but this effect depended on host genotype. We discuss the relevance of sublethal morbidity for Drosophila ecology and evolution, and more broadly, we remark on the implications of deleterious and beneficial infections for the evolution of insect immunity.
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Affiliation(s)
- V Gupta
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - C O Stewart
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - S S C Rund
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, Scotland
| | - K Monteith
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland
| | - P F Vale
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland.,Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, Scotland
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14
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Schroeder M, Brooks BD, Brooks AE. The Complex Relationship between Virulence and Antibiotic Resistance. Genes (Basel) 2017; 8:E39. [PMID: 28106797 PMCID: PMC5295033 DOI: 10.3390/genes8010039] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/21/2016] [Accepted: 01/07/2017] [Indexed: 12/17/2022] Open
Abstract
Antibiotic resistance, prompted by the overuse of antimicrobial agents, may arise from a variety of mechanisms, particularly horizontal gene transfer of virulence and antibiotic resistance genes, which is often facilitated by biofilm formation. The importance of phenotypic changes seen in a biofilm, which lead to genotypic alterations, cannot be overstated. Irrespective of if the biofilm is single microbe or polymicrobial, bacteria, protected within a biofilm from the external environment, communicate through signal transduction pathways (e.g., quorum sensing or two-component systems), leading to global changes in gene expression, enhancing virulence, and expediting the acquisition of antibiotic resistance. Thus, one must examine a genetic change in virulence and resistance not only in the context of the biofilm but also as inextricably linked pathologies. Observationally, it is clear that increased virulence and the advent of antibiotic resistance often arise almost simultaneously; however, their genetic connection has been relatively ignored. Although the complexities of genetic regulation in a multispecies community may obscure a causative relationship, uncovering key genetic interactions between virulence and resistance in biofilm bacteria is essential to identifying new druggable targets, ultimately providing a drug discovery and development pathway to improve treatment options for chronic and recurring infection.
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Affiliation(s)
- Meredith Schroeder
- Department of Microbiological Sciences; North Dakota State University, Fargo, ND 58105, USA.
| | - Benjamin D Brooks
- Department of Electrical and Computer Engineering; North Dakota State University, Fargo, ND 58105, USA.
| | - Amanda E Brooks
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58105, USA.
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15
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The effect of competition and horizontal trait inheritance on invasion, fixation, and polymorphism. J Theor Biol 2016; 411:48-58. [DOI: 10.1016/j.jtbi.2016.10.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 09/19/2016] [Accepted: 10/06/2016] [Indexed: 11/19/2022]
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16
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Westra ER, Dowling AJ, Broniewski JM, van Houte S. Evolution and Ecology of CRISPR. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2016. [DOI: 10.1146/annurev-ecolsys-121415-032428] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Edze R. Westra
- Environment and Sustainability Institute and Centre for Ecology and Conservation, Biosciences, University of Exeter, Tremough Campus, Penryn TR10 9FE, United Kingdom;
| | - Andrea J. Dowling
- Environment and Sustainability Institute and Centre for Ecology and Conservation, Biosciences, University of Exeter, Tremough Campus, Penryn TR10 9FE, United Kingdom;
| | - Jenny M. Broniewski
- Environment and Sustainability Institute and Centre for Ecology and Conservation, Biosciences, University of Exeter, Tremough Campus, Penryn TR10 9FE, United Kingdom;
| | - Stineke van Houte
- Environment and Sustainability Institute and Centre for Ecology and Conservation, Biosciences, University of Exeter, Tremough Campus, Penryn TR10 9FE, United Kingdom;
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17
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van Houte S, Buckling A, Westra ER. Evolutionary Ecology of Prokaryotic Immune Mechanisms. Microbiol Mol Biol Rev 2016; 80:745-63. [PMID: 27412881 PMCID: PMC4981670 DOI: 10.1128/mmbr.00011-16] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteria have a range of distinct immune strategies that provide protection against bacteriophage (phage) infections. While much has been learned about the mechanism of action of these defense strategies, it is less clear why such diversity in defense strategies has evolved. In this review, we discuss the short- and long-term costs and benefits of the different resistance strategies and, hence, the ecological conditions that are likely to favor the different strategies alone and in combination. Finally, we discuss some of the broader consequences, beyond resistance to phage and other genetic elements, resulting from the operation of different immune strategies.
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Affiliation(s)
- Stineke van Houte
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Angus Buckling
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Edze R Westra
- ESI and CEC, Department of Biosciences, University of Exeter, Exeter, United Kingdom
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18
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Lough G, Kyriazakis I, Bergmann S, Lengeling A, Doeschl-Wilson AB. Health trajectories reveal the dynamic contributions of host genetic resistance and tolerance to infection outcome. Proc Biol Sci 2016; 282:rspb.2015.2151. [PMID: 26582028 PMCID: PMC4685823 DOI: 10.1098/rspb.2015.2151] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Resistance and tolerance are two alternative strategies hosts can adopt to survive infections. Both strategies may be genetically controlled. To date, the relative contribution of resistance and tolerance to infection outcome is poorly understood. Here, we use a bioluminescent Listeria monocytogenes (Lm) infection challenge model to study the genetic determination and dynamic contributions of host resistance and tolerance to listeriosis in four genetically diverse mouse strains. Using conventional statistical analyses, we detect significant genetic variation in both resistance and tolerance, but cannot capture the time-dependent relative importance of either host strategy. We overcome these limitations through the development of novel statistical tools to analyse individual infection trajectories portraying simultaneous changes in infection severity and health. Based on these tools, early expression of resistance followed by expression of tolerance emerge as important hallmarks for surviving Lm infections. Our trajectory analysis further reveals that survivors and non-survivors follow distinct infection paths (which are also genetically determined) and provides new survival thresholds as objective endpoints in infection experiments. Future studies may use trajectories as novel traits for mapping and identifying genes that control infection dynamics and outcome. A Matlab script for user-friendly trajectory analysis is provided.
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Affiliation(s)
- Graham Lough
- Genetics and Genomics Division, The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
| | - Ilias Kyriazakis
- School of Agriculture, Food and Rural Development, Newcastle University, Newcastle upon Tyne, UK
| | - Silke Bergmann
- Department of Infection Genetics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Andreas Lengeling
- Infection and Immunity Division, The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
| | - Andrea B Doeschl-Wilson
- Genetics and Genomics Division, The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, UK
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19
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Vale PF, Lafforgue G, Gatchitch F, Gardan R, Moineau S, Gandon S. Costs of CRISPR-Cas-mediated resistance in Streptococcus thermophilus. Proc Biol Sci 2016. [PMID: 26224708 DOI: 10.1098/rspb.2015.1270] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas is a form of adaptive sequence-specific immunity in microbes. This system offers unique opportunities for the study of coevolution between bacteria and their viral pathogens, bacteriophages. A full understanding of the coevolutionary dynamics of CRISPR-Cas requires knowing the magnitude of the cost of resisting infection. Here, using the gram-positive bacterium Streptococcus thermophilus and its associated virulent phage 2972, a well-established model system harbouring at least two type II functional CRISPR-Cas systems, we obtained different fitness measures based on growth assays in isolation or in pairwise competition. We measured the fitness cost associated with different components of this adaptive immune system: the cost of Cas protein expression, the constitutive cost of increasing immune memory through additional spacers, and the conditional costs of immunity during phage exposure. We found that Cas protein expression is particularly costly, as Cas-deficient mutants achieved higher competitive abilities than the wild-type strain with functional Cas proteins. Increasing immune memory by acquiring up to four phage-derived spacers was not associated with fitness costs. In addition, the activation of the CRISPR-Cas system during phage exposure induces significant but small fitness costs. Together these results suggest that the costs of the CRISPR-Cas system arise mainly due to the maintenance of the defence system. We discuss the implications of these results for the evolution of CRISPR-Cas-mediated immunity.
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Affiliation(s)
- Pedro F Vale
- Centre for Immunity, Infection, and Evolution, Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT, UK
| | - Guillaume Lafforgue
- CEFE UMR 5175, CNRS-Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, 1919, route de Mende 34293 Montpellier Cedex 5, France
| | - Francois Gatchitch
- CEFE UMR 5175, CNRS-Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, 1919, route de Mende 34293 Montpellier Cedex 5, France
| | | | - Sylvain Moineau
- GREB and Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Québec, Canada G1V 0A6 Département de biochimie, de microbiologie et de bio-informatique and PROTEO, Faculté des sciences et de génie, Université Laval, Québec, Canada G1V 0A6
| | - Sylvain Gandon
- CEFE UMR 5175, CNRS-Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, 1919, route de Mende 34293 Montpellier Cedex 5, France
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20
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Kumar MS, Plotkin JB, Hannenhalli S. Regulated CRISPR Modules Exploit a Dual Defense Strategy of Restriction and Abortive Infection in a Model of Prokaryote-Phage Coevolution. PLoS Comput Biol 2015; 11:e1004603. [PMID: 26544847 PMCID: PMC4636164 DOI: 10.1371/journal.pcbi.1004603] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Accepted: 10/14/2015] [Indexed: 11/23/2022] Open
Abstract
CRISPRs offer adaptive immunity in prokaryotes by acquiring genomic fragments from infecting phage and subsequently exploiting them for phage restriction via an RNAi-like mechanism. Here, we develop and analyze a dynamical model of CRISPR-mediated prokaryote-phage coevolution that incorporates classical CRISPR kinetics along with the recently discovered infection-induced activation and autoimmunity side effects. Our analyses reveal two striking characteristics of the CRISPR defense strategy: that both restriction and abortive infections operate during coevolution with phages, driving phages to much lower densities than possible with restriction alone, and that CRISPR maintenance is determined by a key dimensionless combination of parameters, which upper bounds the activation level of CRISPRs in uninfected populations. We contrast these qualitative observations with experimental data on CRISPR kinetics, which offer insight into the spacer deletion mechanism and the observed low CRISPR prevalence in clinical isolates. More generally, we exploit numerical simulations to delineate four regimes of CRISPR dynamics in terms of its host, kinetic, and regulatory parameters. To counteract viral infections, bacteria and archaea have evolved a variety of defense systems. These can broadly be classified into either restriction or suicide mechanisms. The former enforces nicks in the invading DNA making it unusable for production of further infectious particles; the latter, by contrast, induces cell death whereby an infected cell activates specific host suicidal pathways that are otherwise strongly repressed, thus inhibiting further infection. Examples of the former class include restriction-modification (R-M) and the recently discovered CRISPR systems, while the latter class includes a variety of toxin/anti-toxin systems. CRISPRs, in contrast to R-Ms, adapt to target viral genomes by updating the database of target sites they recognize. The adverse side effect of such a mechanism, however, is that CRISPRs can target the host genome itself resulting in undesirable cell death (autoimmunity). The recent discovery of infection-induced activation of CRISPR systems suggests that these negative side effects may be limited to periods of infection. This led us to hypothesize that such regulatory control—similar to abortive infection mechanisms—can be advantageous by limiting viral spread through suicide of infected cells. To test this hypothesis, we mathematically model CRISPR induced prokaryote-phage coevolutionary dynamics in the presence of infection-regulated CRISPR activity. Our results indicate that, except in limited growth rates, regulated CRISPRs exploit both autoimmunity and target restriction and can therefore be considered a hybrid class that leverages both restriction and suicide mechanisms to limit phage infection.
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Affiliation(s)
- M. Senthil Kumar
- Graduate Program in Bioinformatics, University of Maryland, College Park, Maryland, United States of America
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- * E-mail: (MSK); (JBP); (SH)
| | - Joshua B. Plotkin
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail: (MSK); (JBP); (SH)
| | - Sridhar Hannenhalli
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
- * E-mail: (MSK); (JBP); (SH)
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21
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Vale PF, Jardine MD. Sex-specific behavioural symptoms of viral gut infection and Wolbachia in Drosophila melanogaster. JOURNAL OF INSECT PHYSIOLOGY 2015; 82:28-32. [PMID: 26301521 DOI: 10.1016/j.jinsphys.2015.08.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/15/2015] [Accepted: 08/18/2015] [Indexed: 05/11/2023]
Abstract
All organisms are infected with a range of symbionts spanning the spectrum of beneficial mutualists to detrimental parasites. The fruit fly Drosophila melanogaster is a good example, as both endosymbiotic Wolbachia, and pathogenic Drosophila C Virus (DCV) commonly infect it. While the pathophysiology and immune responses against both symbionts are the focus of intense study, the behavioural effects of these infections have received less attention. Here we report sex-specific behavioural responses to these infections in D. melanogaster. DCV infection caused increased sleep in female flies, but had no detectable effect in male flies. The presence of Wolbachia did not reduce this behavioural response to viral infection. We also found evidence for a sex-specific cost of Wolbachia, as male flies infected with the endosymbiont became more lethargic when awake. We discuss these behavioural symptoms as potentially adaptive sickness behaviours.
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Affiliation(s)
- Pedro F Vale
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom; Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom.
| | - Michael D Jardine
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
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22
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Blosser TR, Loeff L, Westra ER, Vlot M, Künne T, Sobota M, Dekker C, Brouns SJJ, Joo C. Two distinct DNA binding modes guide dual roles of a CRISPR-Cas protein complex. Mol Cell 2015; 58:60-70. [PMID: 25752578 DOI: 10.1016/j.molcel.2015.01.028] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 12/29/2014] [Accepted: 01/20/2015] [Indexed: 12/21/2022]
Abstract
Small RNA-guided protein complexes play an essential role in CRISPR-mediated immunity in prokaryotes. While these complexes initiate interference by flagging cognate invader DNA for destruction, recent evidence has implicated their involvement in new CRISPR memory formation, called priming, against mutated invader sequences. The mechanism by which the target recognition complex mediates these disparate responses-interference and priming-remains poorly understood. Using single-molecule FRET, we visualize how bona fide and mutated targets are differentially probed by E. coli Cascade. We observe that the recognition of bona fide targets is an ordered process that is tightly controlled for high fidelity. Mutated targets are recognized with low fidelity, which is featured by short-lived and PAM- and seed-independent binding by any segment of the crRNA. These dual roles of Cascade in immunity with distinct fidelities underpin CRISPR-Cas robustness, allowing for efficient degradation of bona fide targets and priming of mutated DNA targets.
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Affiliation(s)
- Timothy R Blosser
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, 2628 CJ, Delft, The Netherlands
| | - Luuk Loeff
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, 2628 CJ, Delft, The Netherlands
| | - Edze R Westra
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB, Wageningen, The Netherlands
| | - Marnix Vlot
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB, Wageningen, The Netherlands
| | - Tim Künne
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB, Wageningen, The Netherlands
| | - Małgorzata Sobota
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB, Wageningen, The Netherlands
| | - Cees Dekker
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, 2628 CJ, Delft, The Netherlands
| | - Stan J J Brouns
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, 6703 HB, Wageningen, The Netherlands
| | - Chirlmin Joo
- Kavli Institute of NanoScience and Department of BioNanoScience, Delft University of Technology, 2628 CJ, Delft, The Netherlands
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23
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Childs LM, England WE, Young MJ, Weitz JS, Whitaker RJ. CRISPR-induced distributed immunity in microbial populations. PLoS One 2014; 9:e101710. [PMID: 25000306 PMCID: PMC4084950 DOI: 10.1371/journal.pone.0101710] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 06/11/2014] [Indexed: 01/08/2023] Open
Abstract
In bacteria and archaea, viruses are the primary infectious agents, acting as virulent, often deadly pathogens. A form of adaptive immune defense known as CRISPR-Cas enables microbial cells to acquire immunity to viral pathogens by recognizing specific sequences encoded in viral genomes. The unique biology of this system results in evolutionary dynamics of host and viral diversity that cannot be fully explained by the traditional models used to describe microbe-virus coevolutionary dynamics. Here, we show how the CRISPR-mediated adaptive immune response of hosts to invading viruses facilitates the emergence of an evolutionary mode we call distributed immunity - the coexistence of multiple, equally-fit immune alleles among individuals in a microbial population. We use an eco-evolutionary modeling framework to quantify distributed immunity and demonstrate how it emerges and fluctuates in multi-strain communities of hosts and viruses as a consequence of CRISPR-induced coevolution under conditions of low viral mutation and high relative numbers of viral protospacers. We demonstrate that distributed immunity promotes sustained diversity and stability in host communities and decreased viral population density that can lead to viral extinction. We analyze sequence diversity of experimentally coevolving populations of Streptococcus thermophilus and their viruses where CRISPR-Cas is active, and find the rapid emergence of distributed immunity in the host population, demonstrating the importance of this emergent phenomenon in evolving microbial communities.
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Affiliation(s)
- Lauren M. Childs
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Whitney E. England
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Mark J. Young
- Thermal Biology Institute and Department of Plant Sciences and Plant Pathology, Montana State University, Montana, United States of America
| | - Joshua S. Weitz
- School of Biology and School of Physics, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail: (JSW); (RJW)
| | - Rachel J. Whitaker
- Department of Microbiology and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- * E-mail: (JSW); (RJW)
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24
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Berezovskaya FS, Wolf YI, Koonin EV, Karev GP. Pseudo-chaotic oscillations in CRISPR-virus coevolution predicted by bifurcation analysis. Biol Direct 2014; 9:13. [PMID: 24986220 PMCID: PMC4096434 DOI: 10.1186/1745-6150-9-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 06/26/2014] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The CRISPR-Cas systems of adaptive antivirus immunity are present in most archaea and many bacteria, and provide resistance to specific viruses or plasmids by inserting fragments of foreign DNA into the host genome and then utilizing transcripts of these spacers to inactivate the cognate foreign genome. The recent development of powerful genome engineering tools on the basis of CRISPR-Cas has sharply increased the interest in the diversity and evolution of these systems. Comparative genomic data indicate that during evolution of prokaryotes CRISPR-Cas loci are lost and acquired via horizontal gene transfer at high rates. Mathematical modeling and initial experimental studies of CRISPR-carrying microbes and viruses reveal complex coevolutionary dynamics. RESULTS We performed a bifurcation analysis of models of coevolution of viruses and microbial host that possess CRISPR-Cas hereditary adaptive immunity systems. The analyzed Malthusian and logistic models display complex, and in particular, quasi-chaotic oscillation regimes that have not been previously observed experimentally or in agent-based models of the CRISPR-mediated immunity. The key factors for the appearance of the quasi-chaotic oscillations are the non-linear dependence of the host immunity on the virus load and the partitioning of the hosts into the immune and susceptible populations, so that the system consists of three components. CONCLUSIONS Bifurcation analysis of CRISPR-host coevolution model predicts complex regimes including quasi-chaotic oscillations. The quasi-chaotic regimes of virus-host coevolution are likely to be biologically relevant given the evolutionary instability of the CRISPR-Cas loci revealed by comparative genomics. The results of this analysis might have implications beyond the CRISPR-Cas systems, i.e. could describe the behavior of any adaptive immunity system with a heritable component, be it genetic or epigenetic. These predictions are experimentally testable. REVIEWERS' REPORTS This manuscript was reviewed by Sandor Pongor, Sergei Maslov and Marek Kimmel. For the complete reports, go to the Reviewers' Reports section.
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Affiliation(s)
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Georgy P Karev
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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