1
|
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.
Collapse
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.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Brussowvirus SW13 requires a cell surface-associated polysaccharide to recognise its Streptococcus thermophilus host. Appl Environ Microbiol 2021; 88:e0172321. [PMID: 34669424 PMCID: PMC8752142 DOI: 10.1128/aem.01723-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Four bacteriophage-insensitive mutants (BIMs) of the dairy starter bacterium Streptococcus thermophilus UCCSt50 were isolated following challenge with Brussowvirus SW13. The BIMs displayed an altered sedimentation phenotype. Whole-genome sequencing and comparative genomic analysis of the BIMs uncovered mutations within a family 2 glycosyltransferase-encoding gene (orf06955UCCSt50) located within the variable region of the cell wall-associated rhamnose-glucose polymer (Rgp) biosynthesis locus (designated the rgp gene cluster here). Complementation of a representative BIM, S. thermophilus B1, with native orf06955UCCSt50 restored phage sensitivity comparable to that of the parent strain. Detailed bioinformatic analysis of the gene product of orf06955UCCSt50 identified it as a functional homolog of the Lactococcus lactispolysaccharide pellicle (PSP) initiator WpsA. Biochemical analysis of cell wall fractions of strains UCCSt50 and B1 determined that mutations within orf06955UCCSt50 result in the loss of the side chain decoration from the Rgp backbone structure. Furthermore, it was demonstrated that the intact Rgp structure incorporating the side chain structure is essential for phage binding through fluorescence labeling studies. Overall, this study confirms that the rgp gene cluster of S. thermophilus encodes the biosynthetic machinery for a cell surface-associated polysaccharide that is essential for binding and subsequent infection by Brussowviruses, thus enhancing our understanding of S. thermophilus phage-host dynamics. IMPORTANCEStreptococcus thermophilus is an important starter culture bacterium in global dairy fermentation processes, where it is used for the production of various cheeses and yogurt. Bacteriophage predation of the species can result in substandard product quality and, in rare cases, complete fermentation collapse. To mitigate these risks, it is necessary to understand the phage-host interaction process, which commences with the recognition of, and adsorption to, specific host-encoded cell surface receptors by bacteriophage(s). As new groups of S. thermophilus phages are being discovered, the importance of underpinning the genomic elements that specify the surface receptor(s) is apparent. Our research identifies a single gene that is critical for the biosynthesis of a saccharidic moiety required for phage adsorption to its S. thermophilus host. The acquired knowledge provides novel insights into phage-host interactions for this economically important starter species.
Collapse
|
4
|
Philippe C, Moineau S. The endless battle between phages and CRISPR-Cas systems in Streptococcus thermophilus. Biochem Cell Biol 2021; 99:397-402. [PMID: 33534660 DOI: 10.1139/bcb-2020-0593] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
This review describes the contribution of basic research on phage-bacteria interactions to the understanding of CRISPR-Cas systems and their various applications. It focuses on the natural function of CRISPR-Cas systems as adaptive defense mechanisms against mobile genetic elements such as bacteriophage genomes and plasmids. Some of the advances in the characterization of the type II-A CRISPR-Cas system of Streptococcus thermophilus and Streptococcus pyogenes led to the development of the CRISPR-Cas9 genome-editing technology. We mostly discuss the 3 stages of the CRISPR-Cas system in S. thermophilus, namely the adaptation stage, which is unique to this resistance mechanism; the CRISPR RNA biogenesis; and the DNA-cutting activity in the interference stage to protect bacteria against phages. Finally, we look into applications of CRISPR-Cas in microbiology, including overcoming limitations in genome editing.
Collapse
Affiliation(s)
- Cécile Philippe
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec, QC G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, 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, Université Laval, Québec, QC G1V 0A6, Canada
| |
Collapse
|
5
|
Santini G, Bonazza F, Pucciarelli S, Polidori P, Ricciutelli M, Klimanova Y, Silvi S, Polzonetti V, Vincenzetti S. Proteomic characterization of kefir milk by two-dimensional electrophoresis followed by mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4635. [PMID: 32767505 DOI: 10.1002/jms.4635] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/16/2020] [Accepted: 07/26/2020] [Indexed: 06/11/2023]
Abstract
Kefir is a type of fermented milk obtained thanks to the introduction of "kefir grains" in mammalian milk. Kefir grains consist of lactic and acetic acid bacteria and yeasts in alternative proportions that are held together by a matrix of complex sugars known as "kefiran." Thanks to the fermentative process, the kefir milk is rich in nutraceutical substances such as amino acids, vitamins, and mineral salts. The most valuable compounds of kefir fermentation are mainly lactic acid, exopolysaccharides, and bioactive peptides, the resulting products of proteolytic release from milk proteins (caseins and whey proteins). Among the nutraceutical properties of kefir are antimicrobial and antitumor activity, immunomodulating effect, and cholesterol-lowering effect. Therefore, in light of these intriguing properties of kefir milk, in this work, a proteomic analysis, by two-dimensional electrophoresis followed by mass spectrometry, has been performed. As a result, milk-derived polypeptides were identified in commercial kefir milk from organic farming. In particular, polypeptides deriving from κ-, αs1 -, and αs2 -caseins that may have potentially beneficial effects on human health have been detected.
Collapse
Affiliation(s)
- Giuseppe Santini
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Francesca Bonazza
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Stefania Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Paolo Polidori
- School of Pharmacy, University of Camerino, Camerino, Italy
| | | | - Yulia Klimanova
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Stefania Silvi
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Valeria Polzonetti
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Silvia Vincenzetti
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| |
Collapse
|
6
|
Novel Genus of Phages Infecting Streptococcus thermophilus: Genomic and Morphological Characterization. Appl Environ Microbiol 2020; 86:AEM.00227-20. [PMID: 32303549 DOI: 10.1128/aem.00227-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 04/13/2020] [Indexed: 12/26/2022] Open
Abstract
Streptococcus thermophilus is a lactic acid bacterium commonly used for the manufacture of yogurt and specialty cheeses. Virulent phages represent a major risk for milk fermentation processes worldwide, as they can inactivate the added starter bacterial cells, leading to low-quality fermented dairy products. To date, four genetically distinct groups of phages infecting S. thermophilus have been described. Here, we describe a fifth group. Phages P738 and D4446 are virulent siphophages that infect a few industrial strains of S. thermophilus The genomes of phages P738 and D4446 were sequenced and found to contain 34,037 and 33,656 bp as well as 48 and 46 open reading frames, respectively. Comparative genomic analyses revealed that the two phages are closely related to each other but display very limited similarities to other S. thermophilus phages. In fact, these two novel S. thermophilus phages share similarities with streptococcal phages of nondairy origin, suggesting that they emerged recently in the dairy environment.IMPORTANCE Despite decades of research and adapted antiphage strategies such as CRISPR-Cas systems, virulent phages are still a persistent risk for the milk fermentation industry worldwide, as they can cause manufacturing failures and alter product quality. Phages P738 and D4446 are novel virulent phages that infect the food-grade Gram-positive bacterial species Streptococcus thermophilus These two related viruses represent a fifth group of S. thermophilus phages, as they are significantly distinct from other known S. thermophilus phages. Both phages share similarities with phages infecting nondairy streptococci, suggesting their recent emergence and probable coexistence in dairy environments. These findings highlight the necessity of phage surveillance programs as the phage population evolves in response to the application of antiphage strategies.
Collapse
|
7
|
Chabas H, Nicot A, Meaden S, Westra ER, Tremblay DM, Pradier L, Lion S, Moineau S, Gandon S. Variability in the durability of CRISPR-Cas immunity. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180097. [PMID: 30905283 DOI: 10.1098/rstb.2018.0097] [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] [Indexed: 12/30/2022] Open
Abstract
The durability of host resistance is challenged by the ability of pathogens to escape the defence of their hosts. Understanding the variability in the durability of host resistance is of paramount importance for designing more effective control strategies against infectious diseases. Here, we study the durability of various clustered regularly interspaced short palindromic repeats-Cas (CRISPR-Cas) alleles of the bacteria Streptococcus thermophilus against lytic phages. We found substantial variability in durability among different resistant bacteria. Since the escape of the phage is driven by a mutation in the phage sequence targeted by CRISPR-Cas, we explored the fitness costs associated with these escape mutations. We found that, on average, escape mutations decrease the fitness of the phage. Yet, the magnitude of this fitness cost does not predict the durability of CRISPR-Cas immunity. We contend that this variability in the durability of resistance may be because of variations in phage mutation rate or in the proportion of lethal mutations across the phage genome. These results have important implications on the coevolutionary dynamics between bacteria and phages and for the optimal deployment of resistance strategies against pathogens and pests. Understanding the durability of CRISPR-Cas immunity may also help develop more effective gene-drive strategies based on CRISPR-Cas9 technology. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
Collapse
Affiliation(s)
- Hélène Chabas
- 1 CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE , 1919, Route de Mende, 34293 Montpellier Cedex 5, Paris , France
| | - Antoine Nicot
- 1 CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE , 1919, Route de Mende, 34293 Montpellier Cedex 5, Paris , France
| | - Sean Meaden
- 2 Environment and Sustainability Institute, University of Exeter , Penryn Campus, Penryn, Cornwall TR10 9FE , UK
| | - Edze R Westra
- 2 Environment and Sustainability Institute, University of Exeter , Penryn Campus, Penryn, Cornwall TR10 9FE , UK
| | - Denise M Tremblay
- 3 Département de Biochimie, Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval , 1045 Avenue de la Médecine, Québec City, Quebec , Canada G1V 0A6.,4 Félix d'Hérelle Reference Center for Bacterial Viruses and Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval , Québec City, Qubec , Canada G1V 0A6
| | - Léa Pradier
- 1 CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE , 1919, Route de Mende, 34293 Montpellier Cedex 5, Paris , France
| | - Sébastien Lion
- 1 CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE , 1919, Route de Mende, 34293 Montpellier Cedex 5, Paris , France
| | - Sylvain Moineau
- 3 Département de Biochimie, Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval , 1045 Avenue de la Médecine, Québec City, Quebec , Canada G1V 0A6.,4 Félix d'Hérelle Reference Center for Bacterial Viruses and Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval , Québec City, Qubec , Canada G1V 0A6
| | - Sylvain Gandon
- 1 CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE , 1919, Route de Mende, 34293 Montpellier Cedex 5, Paris , France
| |
Collapse
|
8
|
Labrie SJ, Mosterd C, Loignon S, Dupuis MÈ, Desjardins P, Rousseau GM, Tremblay DM, Romero DA, Horvath P, Fremaux C, Moineau S. A mutation in the methionine aminopeptidase gene provides phage resistance in Streptococcus thermophilus. Sci Rep 2019; 9:13816. [PMID: 31554834 PMCID: PMC6761271 DOI: 10.1038/s41598-019-49975-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/31/2019] [Indexed: 12/26/2022] Open
Abstract
Streptococcus thermophilus is a lactic acid bacterium widely used by the dairy industry for the manufacture of yogurt and specialty cheeses. It is also a Gram-positive bacterial model to study phage-host interactions. CRISPR-Cas systems are one of the most prevalent phage resistance mechanisms in S. thermophilus. Little information is available about other host factors involved in phage replication in this food-grade streptococcal species. We used the model strain S. thermophilus SMQ-301 and its virulent phage DT1, harboring the anti-CRISPR protein AcrIIA6, to show that a host gene coding for a methionine aminopeptidase (metAP) is necessary for phage DT1 to complete its lytic cycle. A single mutation in metAP provides S. thermophilus SMQ-301 with strong resistance against phage DT1. The mutation impedes a late step of the lytic cycle since phage adsorption, DNA replication, and protein expression were not affected. When the mutated strain was complemented with the wild-type version of the gene, the phage sensitivity phenotype was restored. When this mutation was introduced into other S. thermophilus strains it provided resistance against cos-type (Sfi21dt1virus genus) phages but replication of pac-type (Sfi11virus genus) phages was not affected. The mutation in the gene coding for the MetAP induces amino acid change in a catalytic domain conserved across many bacterial species. Introducing the same mutation in Streptococcus mutans also provided a phage resistance phenotype, suggesting the wide-ranging importance of the host methionine aminopeptidase in phage replication.
Collapse
Affiliation(s)
- Simon J Labrie
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,SyntBioLab Inc., 4820-250, rue de la Pascaline, Lévis, G6W 0L9, Canada
| | - Cas Mosterd
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Stéphanie Loignon
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Marie-Ève Dupuis
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Philippe Desjardins
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Geneviève M Rousseau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Denise M Tremblay
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada
| | - Dennis A Romero
- DuPont Nutrition and Biosciences, 3329 Agriculture Dr, Madison, WI, 53716, USA
| | - Philippe Horvath
- DuPont Nutrition and Biosciences, BP10, Dangé-Saint-Romain, 86220, France
| | - Christophe Fremaux
- DuPont Nutrition and Biosciences, BP10, Dangé-Saint-Romain, 86220, France
| | - Sylvain Moineau
- Département de biochimie, de microbiologie, et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, G1V 0A6, Canada. .,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada. .,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.
| |
Collapse
|
9
|
Szymczak P, Rau MH, Monteiro JM, Pinho MG, Filipe SR, Vogensen FK, Zeidan AA, Janzen T. A comparative genomics approach for identifying host-range determinants in Streptococcus thermophilus bacteriophages. Sci Rep 2019; 9:7991. [PMID: 31142793 PMCID: PMC6541646 DOI: 10.1038/s41598-019-44481-z] [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] [Received: 10/03/2018] [Accepted: 05/07/2019] [Indexed: 12/17/2022] Open
Abstract
Comparative genomics has proven useful in exploring the biodiversity of phages and understanding phage-host interactions. This knowledge is particularly useful for phages infecting Streptococcus thermophilus, as they constitute a constant threat during dairy fermentations. Here, we explore the genetic diversity of S. thermophilus phages to identify genetic determinants with a signature for host specificity, which could be linked to the bacterial receptor genotype. A comparative genomic analysis was performed on 142 S. thermophilus phage genomes, 55 of which were sequenced in this study. Effectively, 94 phages were assigned to the group cos (DT1), 36 to the group pac (O1205), six to the group 5093, and six to the group 987. The core genome-based phylogeny of phages from the two dominating groups and their receptor binding protein (RBP) phylogeny corresponded to the phage host-range. A role of RBP in host recognition was confirmed by constructing a fluorescent derivative of the RBP of phage CHPC951, followed by studying the binding of the protein to the host strain. Furthermore, the RBP phylogeny of the cos group was found to correlate with the host genotype of the exocellular polysaccharide-encoding operon. These findings provide novel insights towards developing strategies to combat phage infections in dairies.
Collapse
Affiliation(s)
- Paula Szymczak
- Bacterial Physiology, R&D, Chr. Hansen A/S, 2970, Hørsholm, Denmark
- Department of Food Science, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Martin Holm Rau
- Bacterial Physiology, R&D, Chr. Hansen A/S, 2970, Hørsholm, Denmark
| | - João M Monteiro
- Laboratory of Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Mariana G Pinho
- Laboratory of Bacterial Cell Biology, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Sérgio Raposo Filipe
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, 2829-516, Caparica, Portugal
- Laboratory of Bacterial Cell Surfaces and Pathogenesis, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157, Oeiras, Portugal
| | - Finn Kvist Vogensen
- Department of Food Science, University of Copenhagen, 1958, Frederiksberg, Denmark
| | - Ahmad A Zeidan
- Bacterial Physiology, R&D, Chr. Hansen A/S, 2970, Hørsholm, Denmark
| | - Thomas Janzen
- Bacterial Physiology, R&D, Chr. Hansen A/S, 2970, Hørsholm, Denmark.
| |
Collapse
|
10
|
Common J, Morley D, Westra ER, van Houte S. CRISPR-Cas immunity leads to a coevolutionary arms race between Streptococcus thermophilus and lytic phage. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180098. [PMID: 30905285 PMCID: PMC6452269 DOI: 10.1098/rstb.2018.0098] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [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: 01/22/2023] Open
Abstract
CRISPR-Cas is an adaptive prokaryotic immune system that prevents phage infection. By incorporating phage-derived 'spacer' sequences into CRISPR loci on the host genome, future infections from the same phage genotype can be recognized and the phage genome cleaved. However, the phage can escape CRISPR degradation by mutating the sequence targeted by the spacer, allowing them to re-infect previously CRISPR-immune hosts, and theoretically leading to coevolution. Previous studies have shown that phage can persist over long periods in populations of Streptococcus thermophilus that can acquire CRISPR-Cas immunity, but it has remained less clear whether this coexistence was owing to coevolution, and if so, what type of coevolutionary dynamics were involved. In this study, we performed highly replicated serial transfer experiments over 30 days with S. thermophilus and a lytic phage. Using a combination of phenotypic and genotypic data, we show that CRISPR-mediated resistance and phage infectivity coevolved over time following an arms race dynamic, and that asymmetry between phage infectivity and host resistance within this system eventually causes phage extinction. This work provides further insight into the way CRISPR-Cas systems shape the population and coevolutionary dynamics of bacteria-phage interactions. This article is part of a discussion meeting issue 'The ecology and evolution of prokaryotic CRISPR-Cas adaptive immune systems'.
Collapse
Affiliation(s)
| | | | | | - Stineke van Houte
- ESI and CEC, Biosciences, University of Exeter, Cornwall Campus, Penryn TR10 9EZ, UK
| |
Collapse
|
11
|
Szymczak P, Vogensen FK, Janzen T. Novel isolates of Streptococcus thermophilus bacteriophages from group 5093 identified with an improved multiplex PCR typing method. Int Dairy J 2019. [DOI: 10.1016/j.idairyj.2018.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
12
|
da Silva Duarte V, Giaretta S, Campanaro S, Treu L, Armani A, Tarrah A, Oliveira de Paula S, Giacomini A, Corich V. A Cryptic Non-Inducible Prophage Confers Phage-Immunity on the Streptococcus thermophilus M17PTZA496. Viruses 2018; 11:v11010007. [PMID: 30583530 PMCID: PMC6356513 DOI: 10.3390/v11010007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/14/2018] [Accepted: 12/19/2018] [Indexed: 12/26/2022] Open
Abstract
Streptococcus thermophilus is considered one of the most important species for the dairy industry. Due to their diffusion in dairy environments, bacteriophages can represent a threat to this widely used bacterial species. Despite the presence of a CRISPR-Cas system in the S. thermophilus genome, some lysogenic strains harbor cryptic prophages that can increase the phage-host resistance defense. This characteristic was identified in the dairy strain S. thermophilus M17PTZA496, which contains two integrated prophages 51.8 and 28.3 Kb long, respectively. In the present study, defense mechanisms, such as a lipoprotein-encoding gene and Siphovirus Gp157, the last associated to the presence of a noncoding viral DNA element, were identified in the prophage M17PTZA496 genome. The ability to overexpress genes involved in these defense mechanisms under specific stressful conditions, such as phage attack, has been demonstrated. Despite the addition of increasing amounts of Mitomycin C, M17PTZA496 was found to be non-inducible. However, the transcriptional activity of the phage terminase large subunit was detected in the presence of the antagonist phage vB_SthS-VA460 and of Mitomycin C. The discovery of an additional immune mechanism, associated with bacteriophage-insensitive strains, is of utmost importance, for technological applications and industrial processes. To our knowledge, this is the first study reporting the capability of a prophage integrated into the S. thermophilus genome expressing different phage defense mechanisms. Bacteriophages are widespread entities that constantly threaten starter cultures in the dairy industry. In cheese and yogurt manufacturing, the lysis of Streptococcus thermophilus cultures by viral attacks can lead to huge economic losses. Nowadays S. thermophilus is considered a well-stablished model organism for the study of natural adaptive immunity (CRISPR-Cas) against phage and plasmids, however, the identification of novel bacteriophage-resistance mechanisms, in this species, is strongly desirable. Here, we demonstrated that the presence of a non-inducible prophage confers phage-immunity to an S. thermophilus strain, by the presence of ltp and a viral noncoding region. S. thermophilus M17PTZA496 arises as an unconventional model to study phage resistance and potentially represents an alternative starter strain for dairy productions.
Collapse
Affiliation(s)
- Vinícius da Silva Duarte
- Department of Microbiology, Universidade Federal de Viçosa, Av. Peter Henry Rolfs, s/n, Campus Universitário, Viçosa-MG 36570-900, Brazil.
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| | - Sabrina Giaretta
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| | | | - Laura Treu
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
- Department of Biology, University of Padova, 35121 Padova, Italy.
| | - Andrea Armani
- Venetian Institute of Molecular Medicine, 35129 Padova, Italy.
| | - Armin Tarrah
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| | | | - Alessio Giacomini
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| | - Viviana Corich
- Department of Agronomy Food Natural Resources Animals and Environment, University of Padova, 35020 Legnaro, Italy.
| |
Collapse
|
13
|
Biodiversity of Streptococcus thermophilus Phages in Global Dairy Fermentations. Viruses 2018; 10:v10100577. [PMID: 30360457 PMCID: PMC6213268 DOI: 10.3390/v10100577] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 12/26/2022] Open
Abstract
Streptococcus thermophilus strains are among the most widely employed starter cultures in dairy fermentations, second only to those of Lactococcus lactis. The extensive application of this species provides considerable opportunity for the proliferation of its infecting (bacterio)phages. Until recently, dairy streptococcal phages were classified into two groups (cos and pac groups), while more recently, two additional groups have been identified (5093 and 987 groups). This highlights the requirement for consistent monitoring of phage populations in the industry. Here, we report a survey of 35 samples of whey derived from 27 dairy fermentation facilities in ten countries against a panel of S. thermophilus strains. This culminated in the identification of 172 plaque isolates, which were characterized by multiplex PCR, restriction fragment length polymorphism analysis, and host range profiling. Based on this characterisation, 39 distinct isolates representing all four phage groups were selected for genome sequencing. Genetic diversity was observed among the cos isolates and correlations between receptor binding protein phylogeny and host range were also clear within this phage group. The 987 phages isolated within this study shared high levels of sequence similarity, yet displayed reduced levels of similarity to those identified in previous studies, indicating that they are subject to ongoing genetic diversification.
Collapse
|
14
|
Manning KA, Quiles-Puchalt N, Penadés JR, Dokland T. A novel ejection protein from bacteriophage 80α that promotes lytic growth. Virology 2018; 525:237-247. [PMID: 30308422 DOI: 10.1016/j.virol.2018.09.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/28/2018] [Accepted: 09/28/2018] [Indexed: 12/30/2022]
Abstract
Many staphylococcal bacteriophages encode a minor capsid protein between the genes for the portal and scaffolding proteins. In Staphylococcus aureus bacteriophage 80α, this protein, called gp44, is essential for the production of viable phage, but dispensable for the phage-mediated mobilization of S. aureus pathogenicity islands. We show here that gp44 is not required for capsid assembly, DNA packaging or ejection of the DNA, nor for generalized transduction of plasmids. An 80α Δ44 mutant could be complemented in trans by gp44 expressed from a plasmid, indicating that gp44 plays a post-injection role in the host. Our results show that gp44 is an ejection (pilot) protein that is involved in deciding the fate of the phage DNA after injection. Our data are consistent with a model in which gp44 acts as a regulatory protein that promotes progression to the lytic cycle.
Collapse
Affiliation(s)
- Keith A Manning
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Nuria Quiles-Puchalt
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Terje Dokland
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| |
Collapse
|
15
|
Abstract
CRISPR-Cas (Clustered regularly interspaced short palindromic repeats-CRISPR associated proteins) loci, which provide a specific immunity against exogenous elements, are hypervariable among distinct prokaryotes. Based on previous researches, this review focuses on concluding systematical genome editing protocols in Streptococcus thermophilus. Firstly, its protocols and optimized conditions in gene editing are introduced. What’s more, classification and diversity analyses of S. thermophilus CRISPR-Cas benefit the further understanding of evolution relationship among Streptococcus. Ability of its foreign segment integration and spacer source analyses also indicate a new direction of phage resistance. Above all, all of these point out its potential to be regarded as another model system other than type II CRISPR-Cas in Streptococcus pyogenes.
Collapse
Affiliation(s)
- Mengyuan Hao
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Yanhua Cui
- Department of Food Science and Engineering, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Xiaojun Qu
- Institute of Microbiology, Heilongjiang Academy of Sciences, Harbin, China
| |
Collapse
|
16
|
McDonnell B, Mahony J, Hanemaaijer L, Neve H, Noben JP, Lugli GA, Ventura M, Kouwen TR, van Sinderen D. Global Survey and Genome Exploration of Bacteriophages Infecting the Lactic Acid Bacterium Streptococcus thermophilus. Front Microbiol 2017; 8:1754. [PMID: 28955321 PMCID: PMC5601072 DOI: 10.3389/fmicb.2017.01754] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/29/2017] [Indexed: 01/31/2023] Open
Abstract
Despite the persistent and costly problem caused by (bacterio)phage predation of Streptococcus thermophilus in dairy plants, DNA sequence information relating to these phages remains limited. Genome sequencing is necessary to better understand the diversity and proliferative strategies of virulent phages. In this report, whole genome sequences of 40 distinct bacteriophages infecting S. thermophilus were analyzed for general characteristics, genomic structure and novel features. The bacteriophage genomes display a high degree of conservation within defined groupings, particularly across the structural modules. Supporting this observation, four novel members of a recently discovered third group of S. thermophilus phages (termed the 5093 group) were found to be conserved relative to both phage 5093 and to each other. Replication modules of S. thermophilus phages generally fall within two main groups, while such phage genomes typically encode one putative transcriptional regulator. Such features are indicative of widespread functional synteny across genetically distinct phage groups. Phage genomes also display nucleotide divergence between groups, and between individual phages of the same group (within replication modules and at the 3′ end of the lysis module)—through various insertions and/or deletions. A previously described multiplex PCR phage detection system was updated to reflect current knowledge on S. thermophilus phages. Furthermore, the structural protein complement as well as the antireceptor (responsible for the initial attachment of the phage to the host cell) of a representative of the 5093 group was defined. Our data more than triples the currently available genomic information on S. thermophilus phages, being of significant value to the dairy industry, where genetic knowledge of lytic phages is crucial for phage detection and monitoring purposes. In particular, the updated PCR detection methodology for S. thermophilus phages is highly useful in monitoring particular phage group(s) present in a given whey sample. Studies of this nature therefore not only provide information on the prevalence and associated threat of known S. thermophilus phages, but may also uncover newly emerging and genomically distinct phages infecting this dairy starter bacterium.
Collapse
Affiliation(s)
- Brian McDonnell
- School of Microbiology, College of Science, Engineering and Food Science, University College CorkCork, Ireland
| | - Jennifer Mahony
- School of Microbiology, College of Science, Engineering and Food Science, University College CorkCork, Ireland.,APC Microbiome Institute, University College CorkCork, Ireland
| | | | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-InstitutKiel, Germany
| | - Jean-Paul Noben
- Biomedical Research Institute, Hasselt UniversityDiepenbeek, Belgium
| | - Gabriele A Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of ParmaParma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of ParmaParma, Italy
| | | | - Douwe van Sinderen
- School of Microbiology, College of Science, Engineering and Food Science, University College CorkCork, Ireland.,APC Microbiome Institute, University College CorkCork, Ireland
| |
Collapse
|
17
|
Phage-host interactions in Streptococcus thermophilus: Genome analysis of phages isolated in Uruguay and ectopic spacer acquisition in CRISPR array. Sci Rep 2017; 7:43438. [PMID: 28262818 PMCID: PMC5338259 DOI: 10.1038/srep43438] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 01/23/2017] [Indexed: 12/26/2022] Open
Abstract
Three cos-type virulent Streptococcus thermophilus phages were isolated from failed mozzarella production in Uruguay. Genome analyses showed that these phages are similar to those isolated elsewhere around the world. The CRISPR1 and CRISPR3 arrays of the three S. thermophilus host strains from Uruguay were also characterized and similarities were noted with previously described model strains SMQ-301, LMD-9 and DGCC7710. Spontaneous bacteriophage-insensitive S. thermophilus mutants (BIMs) were obtained after challenging the phage-sensitive wild-type strain Uy02 with the phage 128 and their CRISPR content was analyzed. Analysis of 23 BIMs indicated that all of them had acquired at least one new spacer in their CRISPR1 array. While 14 BIMs had acquired spacer at the 5′-end of the array, 9 other BIMs acquired a spacer within the array. Comparison of the leader sequence in strains Uy02 and DGCC7710 showed a nucleotide deletion at position -1 in Uy02, which may be responsible for the observed ectopic spacer acquisition. Analysis of the spacer sequences upstream the newly acquired ectopic spacer indicated presence of a conserved adenine residue at position -2. This study indicates that natural strains of S. thermophilus can also acquire spacers within a CRISPR array.
Collapse
|
18
|
YMC-2011, a Temperate Phage of Streptococcus salivarius 57.I. Appl Environ Microbiol 2017; 83:AEM.03186-16. [PMID: 28062463 DOI: 10.1128/aem.03186-16] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/04/2017] [Indexed: 11/20/2022] Open
Abstract
Streptococcus salivarius is an abundant isolate of the oral cavity. The genome of S. salivarius 57.I consists of a 2-Mb chromosome and a 40,758-bp circular molecule, designated YMC-2011. Annotation of YMC-2011 revealed 55 open reading frames, most of them associated with phage production, although plaque formation is not observed in S. salivarius 57.I after lytic induction using mitomycin C. Results from Southern hybridization and quantitative real-time PCR confirmed that YMC-2011 exists extrachromosomally, with an estimated copy number of 3 to 4. Phage particles were isolated from the supernatant of mitomycin C-treated S. salivarius 57.I cultures, and transmission electron microscopic examination indicated that YMC-2011 belongs to the Siphoviridae family. Phylogenetic analysis suggests that phage YMC-2011 and the cos-type phages of Streptococcus thermophilus originated from a common ancestor. An extended -10 element (p L ) and a σ70-like promoter (p R ) were mapped 5' to Ssal_phage00013 (encoding a CI-like repressor) and Ssal_phage00014 (encoding a hypothetical protein), respectively, using 5' rapid amplification of cDNA ends, indicating that YMC-2011 transcribes at least two mRNAs in opposite orientations. Studies using promoter-chloramphenicol acetyltransferase reporter gene fusions revealed that p R , but not p L , was sensitive to mitomycin C induction, suggesting that the switch from lysogenic growth to lytic growth was controlled mainly by the activity of these two promoters. In conclusion, a lysogenic state is maintained in S. salivarius 57.I, presumably by the repression of genes encoding proteins for lytic growth.IMPORTANCE The movement of mobile genetic elements such as bacteriophages and the establishment of lysogens may have profound effects on the balance of microbial ecology where lysogenic bacteria reside. The discovery of phage YMC-2011 from Streptococcus salivarius 57.I suggests that YMC-2011 and Streptococcus thermophilus-infecting phages share an ancestor. Although S. salivarius and S. thermophilus are close phylogenetically, S. salivarius is a natural inhabitant of the human mouth, whereas S. thermophilus is commonly found in the mammary mucosa of bovine species. Thus, the identification of YMC-2011 suggests that horizontal gene transfer via phage infection could take place between species from different ecological niches.
Collapse
|
19
|
Identification and Analysis of a Novel Group of Bacteriophages Infecting the Lactic Acid Bacterium Streptococcus thermophilus. Appl Environ Microbiol 2016; 82:5153-65. [PMID: 27316953 DOI: 10.1128/aem.00835-16] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/09/2016] [Indexed: 01/18/2023] Open
Abstract
UNLABELLED We present the complete genome sequences of four members of a novel group of phages infecting Streptococcus thermophilus, designated here as the 987 group. Members of this phage group appear to have resulted from genetic exchange events, as evidenced by their "hybrid" genomic architecture, exhibiting DNA sequence relatedness to the morphogenesis modules of certain P335 group Lactococcus lactis phages and to the replication modules of S. thermophilus phages. All four identified members of the 987 phage group were shown to elicit adsorption affinity to both their cognate S. thermophilus hosts and a particular L. lactis starter strain. The receptor binding protein of one of these phages (as a representative of this novel group) was defined using an adsorption inhibition assay. The emergence of a novel phage group infecting S. thermophilus highlights the continuous need for phage monitoring and development of new phage control measures. IMPORTANCE Phage predation of S. thermophilus is an important issue for the dairy industry, where viral contamination can lead to fermentation inefficiency or complete fermentation failure. Genome information and phage-host interaction studies of S. thermophilus phages, particularly those emerging in the marketplace, are an important part of limiting the detrimental impact of these viruses in the dairy environment.
Collapse
|
20
|
Abstract
UNLABELLED The adaptive immune system of prokaryotes, called CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated genes), results in specific cleavage of invading nucleic acid sequences recognized by the cell's "memory" of past encounters. Here, we exploited the properties of native CRISPR-Cas systems to program the natural "memorization" process, efficiently generating immunity not only to a bacteriophage or plasmid but to any specifically chosen DNA sequence. IMPORTANCE CRISPR-Cas systems have entered the public consciousness as genome editing tools due to their readily programmable nature. In industrial settings, natural CRISPR-Cas immunity is already exploited to generate strains resistant to potentially disruptive viruses. However, the natural process by which bacteria acquire new target specificities (adaptation) is difficult to study and manipulate. The target against which immunity is conferred is selected stochastically. By biasing the immunization process, we offer a means to generate customized immunity, as well as provide a new tool to study adaptation.
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Mahony J, McDonnell B, Casey E, van Sinderen D. Phage-Host Interactions of Cheese-Making Lactic Acid Bacteria. Annu Rev Food Sci Technol 2016; 7:267-85. [PMID: 26735798 DOI: 10.1146/annurev-food-041715-033322] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cheese production is a global biotechnological practice that is reliant on robust and technologically appropriate starter and adjunct starter cultures to acidify the milk and impart particular flavor and textural properties to specific cheeses. To this end, lactic acid bacteria, including Lactococcus lactis, Streptococcus thermophilus, and Lactobacillus and Leuconostoc spp., are routinely employed. However, these bacteria are susceptible to infection by (bacterio)phages. Over the past decade in particular, significant advances have been achieved in defining the receptor molecules presented by lactococcal host bacteria and in the structural analysis of corresponding phage-encoded receptor-binding proteins. These lactococcal model systems are expanding toward understanding phage-host interactions of other LAB species. Ultimately, such scientific efforts will uncover the mechanistic (dis)similarities among these phages and define how these phages recognize and infect their hosts. This review presents the current status of the LAB-phage interactome, highlighting the most recent and significant developments in this active research field.
Collapse
Affiliation(s)
| | | | | | - Douwe van Sinderen
- School of Microbiology;,APC Microbiome Institute, University College Cork, Western Road, Cork, Ireland;
| |
Collapse
|
23
|
Acar-Soykut E, Tunail N. Classification of S
treptococcus thermophilus
Phages Originating from Turkey. J Food Saf 2015. [DOI: 10.1111/jfs.12226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Esra Acar-Soykut
- Food Research Center; Hacettepe University; Beytepe Ankara 06800 Turkey
| | - Nezihe Tunail
- Food Engineering Department; Ankara University; Ankara Turkey
| |
Collapse
|
24
|
|
25
|
Iannelli F, Santagati M, Santoro F, Oggioni MR, Stefani S, Pozzi G. Nucleotide sequence of conjugative prophage Φ1207.3 (formerly Tn1207.3) carrying the mef(A)/msr(D) genes for efflux resistance to macrolides in Streptococcus pyogenes. Front Microbiol 2014; 5:687. [PMID: 25538698 PMCID: PMC4260502 DOI: 10.3389/fmicb.2014.00687] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 11/21/2014] [Indexed: 12/02/2022] Open
Abstract
Genetic element Φ1207.3 (formerly Tn1207.3) is a prophage of Streptococcus pyogenes which carries the macrolide efflux resistance genes mef(A)/msr(D) and is capable of conjugal transfer among streptococci. Complete nucleotide sequence showed that Φ1207.3 is 52,491 bp in length and contained 58 open reading frames (ORFs). A manual homology-based annotation with functional prediction of the hypothetical gene product was possible only for 34 out of 58 ORFs. Φ1207.3 codes for two different C-methylation systems, several phage structural genes, a lysis cassette (composed by a holin and a peptidoglycan hydrolase), and three site-specific resolvases of the serine recombinase family.
Collapse
Affiliation(s)
- Francesco Iannelli
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena Siena, Italy
| | - Maria Santagati
- Section of Microbiology, Department of Biomedical and Biotechnological Sciences, University of Catania Catania, Italy
| | - Francesco Santoro
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena Siena, Italy
| | - Marco R Oggioni
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena Siena, Italy
| | - Stefania Stefani
- Section of Microbiology, Department of Biomedical and Biotechnological Sciences, University of Catania Catania, Italy
| | - Gianni Pozzi
- Laboratory of Molecular Microbiology and Biotechnology, Department of Medical Biotechnologies, University of Siena Siena, Italy
| |
Collapse
|
26
|
Abstract
The genus Lelliottia was recently created from the group of environmental gammaproteobacteria previously included in the genus Enterobacter. Here, we report the complete genome sequence of phD2B, the first (according to our current knowledge) known phage that infects bacterium from the taxon.
Collapse
|
27
|
Adriaenssens EM, Edwards R, Nash JHE, Mahadevan P, Seto D, Ackermann HW, Lavigne R, Kropinski AM. Integration of genomic and proteomic analyses in the classification of the Siphoviridae family. Virology 2014; 477:144-154. [PMID: 25466308 DOI: 10.1016/j.virol.2014.10.016] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/08/2014] [Accepted: 10/17/2014] [Indexed: 11/26/2022]
Abstract
Using a variety of genomic (BLASTN, ClustalW) and proteomic (Phage Proteomic Tree, CoreGenes) tools we have tackled the taxonomic status of members of the largest bacteriophage family, the Siphoviridae. In all over 400 phages were examined and we were able to propose 39 new genera, comprising 216 phage species, and add 62 species to two previously defined genera (Phic3unalikevirus; L5likevirus) grouping, in total, 390 fully sequenced phage isolates. Many of the remainders are orphans which the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) chooses not to ascribe genus status at the time being.
Collapse
Affiliation(s)
- Evelien M Adriaenssens
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of Pretoria, Lynnwood Road, Pretoria 0028, South Africa
| | - Rob Edwards
- Geology, Mathematics, and Computer Science, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA
| | - John H E Nash
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 110 Stone Road West, Guelph, ON, Canada N1G 3W4
| | | | - Donald Seto
- Bioinformatics and Computational Biology Program, School of Systems Biology, George Mason University, 10900 University Blvd, Manassas, VA 20110, USA
| | - Hans-Wolfgang Ackermann
- Département de Microbiologie-infectiologie et immunologie, Faculté de médecine, Université Laval, Québec, QC, Canada G1K 7P4
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, KasteelparkArenberg 21 - b2462, Heverlee 3001, Belgium.
| | - Andrew M Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 110 Stone Road West, Guelph, ON, Canada N1G 3W4; Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON, Canada N1G 2A1.
| |
Collapse
|
28
|
Martel B, Moineau S. CRISPR-Cas: an efficient tool for genome engineering of virulent bacteriophages. Nucleic Acids Res 2014; 42:9504-13. [PMID: 25063295 PMCID: PMC4132740 DOI: 10.1093/nar/gku628] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Bacteriophages are now widely recognized as major players in a wide variety of ecosystems. Novel genes are often identified in newly isolated phages as well as in environmental metavirome studies. Most of these novel viral genes have unknown functions but appear to be coding for small, non-structural proteins. To understand their biological role, very efficient genetic tools are required to modify them, especially in the genome of virulent phages. We first show that specific point mutations and large deletions can be engineered in the genome of the virulent phage 2972 using the Streptococcus thermophilus CRISPR-Cas Type II-A system as a selective pressure to increase recombination efficiencies. Of significance, all the plaques tested contained recombinant phages with the desired mutation. Furthermore, we show that the CRISPR-Cas engineering system can be used to efficiently introduce a functional methyltransferase gene into a virulent phage genome. Finally, synthetic CRISPR bacteriophage insensitive mutants were constructed by cloning a spacer-repeat unit in a low-copy vector illustrating the possibility to target multiple regions of the phage genome. Taken together, this data shows that the CRISPR-Cas system is an efficient and adaptable tool for editing the otherwise intractable genomes of virulent phages and to better understand phage-host interactions.
Collapse
Affiliation(s)
- Bruno Martel
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec city, Quebec, G1V 0A6, Canada Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Quebec City, Quebec, G1V 0A6, Canada
| | - Sylvain Moineau
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Quebec city, Quebec, G1V 0A6, Canada Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Quebec City, Quebec, G1V 0A6, Canada
| |
Collapse
|
29
|
Hynes AP, Villion M, Moineau S. Adaptation in bacterial CRISPR-Cas immunity can be driven by defective phages. Nat Commun 2014; 5:4399. [DOI: 10.1038/ncomms5399] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 06/13/2014] [Indexed: 12/21/2022] Open
|
30
|
Ishlimova D, Urshev Z, Stoyancheva G, Petrova P, Minkova S, Doumanova L. Genetic Diversity of Bacteriophages Highly Specific forStreptococcus ThermophilusStrain Lbb.A. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.2009.10817666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
31
|
Ali Y, Koberg S, Heßner S, Sun X, Rabe B, Back A, Neve H, Heller KJ. Temperate Streptococcus thermophilus phages expressing superinfection exclusion proteins of the Ltp type. Front Microbiol 2014; 5:98. [PMID: 24659988 PMCID: PMC3952083 DOI: 10.3389/fmicb.2014.00098] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 02/23/2014] [Indexed: 11/17/2022] Open
Abstract
Lipoprotein Ltp encoded by temperate Streptococcus thermophilus phage TP-J34 is the prototype of the wide-spread family of host cell surface-exposed lipoproteins involved in superinfection exclusion (sie). When screening for other S. thermophilus phages expressing this type of lipoprotein, three temperate phages—TP-EW, TP-DSM20617, and TP-778—were isolated. In this communication we present the total nucleotide sequences of TP-J34 and TP-778L. For TP-EW, a phage almost identical to TP-J34, besides the ltp gene only the two regions of deviation from TP-J34 DNA were analyzed: the gene encoding the tail protein causing an assembly defect in TP-J34 and the gene encoding the lysin, which in TP-EW contains an intron. For TP-DSM20617 only the sequence of the lysogeny module containing the ltp gene was determined. The region showed high homology to the same region of TP-778. For TP-778 we could show that absence of the attR region resulted in aberrant excision of phage DNA. The amino acid sequence of mature LtpTP-EW was shown to be identical to that of mature LtpTP-J34, whereas the amino acid sequence of mature LtpTP-778 was shown to differ from mature LtpTP-J34 in eight amino acid positions. LtpTP-DSM20617 was shown to differ from LtpTP-778 in just one amino acid position. In contrast to LtpTP-J34, LtpTP-778 did not affect infection of lactococcal phage P008 instead increased activity against phage P001 was noticed.
Collapse
Affiliation(s)
- Yahya Ali
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food) Kiel, Germany ; Medical Biology Department, Faculty of Medicine, Jazan University Jazan, Kingdom of Saudi Arabia ; Department of Biotechnology, Agricultural Research Center, Animal Health Research Institute Cairo, Egypt
| | - Sabrina Koberg
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food) Kiel, Germany
| | - Stefanie Heßner
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food) Kiel, Germany
| | - Xingmin Sun
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food) Kiel, Germany
| | - Björn Rabe
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food) Kiel, Germany
| | - Angela Back
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food) Kiel, Germany
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food) Kiel, Germany
| | - Knut J Heller
- Department of Microbiology and Biotechnology, Max Rubner-Institut (Federal Research Institute of Nutrition and Food) Kiel, Germany
| |
Collapse
|
32
|
Ma C, Pan N, Chen Z, Liu Z, Gong G, Ma A. Geographical diversity of Streptococcus thermophilus phages in Chinese yoghurt plants. Int Dairy J 2014. [DOI: 10.1016/j.idairyj.2013.10.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
33
|
Campagna C, Villion M, Labrie SJ, Duchaine C, Moineau S. Inactivation of dairy bacteriophages by commercial sanitizers and disinfectants. Int J Food Microbiol 2014; 171:41-7. [DOI: 10.1016/j.ijfoodmicro.2013.11.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 11/01/2013] [Accepted: 11/11/2013] [Indexed: 01/14/2023]
|
34
|
Mahony J, van Sinderen D. Current taxonomy of phages infecting lactic acid bacteria. Front Microbiol 2014; 5:7. [PMID: 24478767 PMCID: PMC3900856 DOI: 10.3389/fmicb.2014.00007] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 01/07/2014] [Indexed: 01/29/2023] Open
Abstract
Phages infecting lactic acid bacteria have been the focus of significant research attention over the past three decades. Through the isolation and characterization of hundreds of phage isolates, it has been possible to classify phages of the dairy starter and adjunct bacteria Lactococus lactis, Streptococcus thermophilus, Leuconostoc spp., and Lactobacillus spp. Among these, phages of L. lactis have been most thoroughly scrutinized and serve as an excellent model system to address issues that arise when attempting taxonomic classification of phages infecting other LAB species. Here, we present an overview of the current taxonomy of phages infecting LAB genera of industrial significance, the methods employed in these taxonomic efforts and how these may be employed for the taxonomy of phages of currently underrepresented and emerging phage species.
Collapse
Affiliation(s)
- Jennifer Mahony
- Department of Microbiology, University College Cork Cork, Ireland
| | - Douwe van Sinderen
- Department of Microbiology, University College Cork Cork, Ireland ; Alimentary Pharmabiotic Centre, Biosciences Institute, University College Cork Cork, Ireland
| |
Collapse
|
35
|
Dupuis MÈ, Villion M, Magadán AH, Moineau S. CRISPR-Cas and restriction–modification systems are compatible and increase phage resistance. Nat Commun 2013; 4:2087. [DOI: 10.1038/ncomms3087] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 05/30/2013] [Indexed: 12/24/2022] Open
|
36
|
Levin BR, Moineau S, Bushman M, Barrangou R. The population and evolutionary dynamics of phage and bacteria with CRISPR-mediated immunity. PLoS Genet 2013; 9:e1003312. [PMID: 23516369 PMCID: PMC3597502 DOI: 10.1371/journal.pgen.1003312] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 12/21/2012] [Indexed: 12/14/2022] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), together with associated genes (cas), form the CRISPR–cas adaptive immune system, which can provide resistance to viruses and plasmids in bacteria and archaea. Here, we use mathematical models, population dynamic experiments, and DNA sequence analyses to investigate the host–phage interactions in a model CRISPR–cas system, Streptococcus thermophilus DGCC7710 and its virulent phage 2972. At the molecular level, the bacteriophage-immune mutant bacteria (BIMs) and CRISPR–escape mutant phage (CEMs) obtained in this study are consistent with those anticipated from an iterative model of this adaptive immune system: resistance by the addition of novel spacers and phage evasion of resistance by mutation in matching sequences or flanking motifs. While CRISPR BIMs were readily isolated and CEMs generated at high rates (frequencies in excess of 10−6), our population studies indicate that there is more to the dynamics of phage–host interactions and the establishment of a BIM–CEM arms race than predicted from existing assumptions about phage infection and CRISPR–cas immunity. Among the unanticipated observations are: (i) the invasion of phage into populations of BIMs resistant by the acquisition of one (but not two) spacers, (ii) the survival of sensitive bacteria despite the presence of high densities of phage, and (iii) the maintenance of phage-limited communities due to the failure of even two-spacer BIMs to become established in populations with wild-type bacteria and phage. We attribute (i) to incomplete resistance of single-spacer BIMs. Based on the results of additional modeling and experiments, we postulate that (ii) and (iii) can be attributed to the phage infection-associated production of enzymes or other compounds that induce phenotypic phage resistance in sensitive bacteria and kill resistant BIMs. We present evidence in support of these hypotheses and discuss the implications of these results for the ecology and (co)evolution of bacteria and phage. The evidence that the CRISPR regions of the genomes of archaea and bacteria play a role in the ecology and (co)evolution of these microbes and their viruses is overwhelming: (i) the spacers (variable sequences of 26–72 bp of DNA between the repeats of this region) of these prokaryotes are homologous to the DNA of viruses in their communities; (ii) experimentally, the acquisition and incorporation of spacers of viral DNA can protect these organisms from subsequent infection by these viruses; (iii) experimentally, viruses evade this immunity by mutation in homologous protospacers or protospacer-adjacent motifs (PAMs). Not so clear are the nature and magnitude of the role CRISPR plays in this ecology and evolution. Here, we use mathematical models, experiments with Streptococcus thermophilus and the phage 2972, and DNA sequence analyses to explore the contribution of CRISPR–cas immunity to the ecology and (co)evolution of bacteria and their viruses. The results of this study suggest that the contribution of CRISPR to the ecology of bacteria and phage is more modest and limited, and the conditions for a CRISPR–mediated coevolutionary arms race between these organisms more restrictive, than anticipated from models based on the canonical view of phage infection and CRISPR–cas immunity.
Collapse
Affiliation(s)
- Bruce R Levin
- Department of Biology, Emory University, Atlanta, Georgia, United States of America.
| | | | | | | |
Collapse
|
37
|
Strong bias in the bacterial CRISPR elements that confer immunity to phage. Nat Commun 2013; 4:1430. [DOI: 10.1038/ncomms2440] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 12/19/2012] [Indexed: 12/22/2022] Open
|
38
|
Hosseinidoust Z, Tufenkji N, van de Ven TGM. Formation of biofilms under phage predation: considerations concerning a biofilm increase. BIOFOULING 2013; 29:457-468. [PMID: 23597188 DOI: 10.1080/08927014.2013.779370] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Bacteriophages are emerging as strong candidates for combating bacterial biofilms. However, reports indicating that host populations can, in some cases, respond to phage predation by an increase in biofilm formation are of concern. This study investigates whether phage predation can enhance the formation of biofilm and if so, if this phenomenon is governed by the emergence of phage-resistance or by non-evolutionary mechanisms (eg spatial refuge). Single-species biofilms of three bacterial pathogens (Pseudomonas aeruginosa, Salmonella enterica serotype Typhimurium, and Staphylococcus aureus) were pretreated and post-treated with species-specific phages. Some of the phage treatments resulted in an increase in the levels of biofilm of their host. It is proposed that the phenotypic change brought about by acquiring phage resistance is the main reason for the increase in the level of biofilm of P. aeruginosa. For biofilms of S. aureus and S. enterica Typhimurium, although resistance was detected, increased formation of biofilm appeared to be a result of non-evolutionary mechanisms.
Collapse
|
39
|
Sun CL, Barrangou R, Thomas BC, Horvath P, Fremaux C, Banfield JF. Phage mutations in response to CRISPR diversification in a bacterial population. Environ Microbiol 2012; 15:463-70. [DOI: 10.1111/j.1462-2920.2012.02879.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 06/21/2012] [Accepted: 08/15/2012] [Indexed: 12/26/2022]
|
40
|
Involvement of the major capsid protein and two early-expressed phage genes in the activity of the lactococcal abortive infection mechanism AbiT. Appl Environ Microbiol 2012; 78:6890-9. [PMID: 22820334 DOI: 10.1128/aem.01755-12] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The dairy industry uses the mesophilic, Gram-positive, lactic acid bacterium (LAB) Lactococcus lactis to produce an array of fermented milk products. Milk fermentation processes are susceptible to contamination by virulent phages, but a plethora of phage control strategies are available. One of the most efficient is to use LAB strains carrying phage resistance systems such as abortive infection (Abi) mechanisms. Yet, the mode of action of most Abi systems remains poorly documented. Here, we shed further light on the antiviral activity of the lactococcal AbiT system. Twenty-eight AbiT-resistant phage mutants derived from the wild-type AbiT-sensitive lactococcal phages p2, bIL170, and P008 were isolated and characterized. Comparative genomic analyses identified three different genes that were mutated in these virulent AbiT-insensitive phage derivatives: e14 (bIL170 [e14(bIL170)]), orf41 (P008 [orf41(P008)]), and orf6 (p2 [orf6(p2)] and P008 [orf6(P008)]). The genes e14(bIL170) and orf41(P008) are part of the early-expressed genomic region, but bioinformatic analyses did not identify their putative function. orf6 is found in the phage morphogenesis module. Antibodies were raised against purified recombinant ORF6, and immunoelectron microscopy revealed that it is the major capsid protein (MCP). Coexpression in L. lactis of ORF6(p2) and ORF5(p2), a protease, led to the formation of procapsids. To our knowledge, AbiT is the first Abi system involving distinct phage genes.
Collapse
|
41
|
Magadán AH, Dupuis MÈ, Villion M, Moineau S. Cleavage of phage DNA by the Streptococcus thermophilus CRISPR3-Cas system. PLoS One 2012; 7:e40913. [PMID: 22911717 PMCID: PMC3401199 DOI: 10.1371/journal.pone.0040913] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Accepted: 06/15/2012] [Indexed: 12/26/2022] Open
Abstract
Streptococcus thermophilus, similar to other Bacteria and Archaea, has developed defense mechanisms to protect cells against invasion by foreign nucleic acids, such as virus infections and plasmid transformations. One defense system recently described in these organisms is the CRISPR-Cas system (Clustered Regularly Interspaced Short Palindromic Repeats loci coupled to CRISPR-associated genes). Two S. thermophilus CRISPR-Cas systems, CRISPR1-Cas and CRISPR3-Cas, have been shown to actively block phage infection. The CRISPR1-Cas system interferes by cleaving foreign dsDNA entering the cell in a length-specific and orientation-dependant manner. Here, we show that the S. thermophilus CRISPR3-Cas system acts by cleaving phage dsDNA genomes at the same specific position inside the targeted protospacer as observed with the CRISPR1-Cas system. Only one cleavage site was observed in all tested strains. Moreover, we observed that the CRISPR1-Cas and CRISPR3-Cas systems are compatible and, when both systems are present within the same cell, provide increased resistance against phage infection by both cleaving the invading dsDNA. We also determined that overall phage resistance efficiency is correlated to the total number of newly acquired spacers in both CRISPR loci.
Collapse
Affiliation(s)
- Alfonso H. Magadán
- Département de Biochimie, de Microbiologie et Bio-Informatiques, Faculté des Sciences et de Génie, Groupe de Recherche en Ecologie Buccale, Université Laval, Québec, Canada
| | - Marie-Ève Dupuis
- Département de Biochimie, de Microbiologie et Bio-Informatiques, Faculté des Sciences et de Génie, Groupe de Recherche en Ecologie Buccale, Université Laval, Québec, Canada
| | - Manuela Villion
- Département de Biochimie, de Microbiologie et Bio-Informatiques, Faculté des Sciences et de Génie, Groupe de Recherche en Ecologie Buccale, Université Laval, Québec, Canada
| | - Sylvain Moineau
- Département de Biochimie, de Microbiologie et Bio-Informatiques, Faculté des Sciences et de Génie, Groupe de Recherche en Ecologie Buccale, Université Laval, Québec, Canada
- Félix d’Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec, Canada
- * E-mail:
| |
Collapse
|
42
|
Young JC, Dill BD, Pan C, Hettich RL, Banfield JF, Shah M, Fremaux C, Horvath P, Barrangou R, VerBerkmoes NC. Phage-induced expression of CRISPR-associated proteins is revealed by shotgun proteomics in Streptococcus thermophilus. PLoS One 2012; 7:e38077. [PMID: 22666452 PMCID: PMC3364186 DOI: 10.1371/journal.pone.0038077] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 04/30/2012] [Indexed: 12/26/2022] Open
Abstract
The CRISPR/Cas system, comprised of clustered regularly interspaced short palindromic repeats along with their associated (Cas) proteins, protects bacteria and archaea from viral predation and invading nucleic acids. While the mechanism of action for this acquired immunity is currently under investigation, the response of Cas protein expression to phage infection has yet to be elucidated. In this study, we employed shotgun proteomics to measure the global proteome expression in a model system for studying the CRISPR/Cas response in S. thermophilus DGCC7710 infected with phage 2972. Host and viral proteins were simultaneously measured following inoculation at two different multiplicities of infection and across various time points using two-dimensional liquid chromatography tandem mass spectrometry. Thirty-seven out of forty predicted viral proteins were detected, including all proteins of the structural virome and viral effector proteins. In total, 1,013 of 2,079 predicted S. thermophilus proteins were detected, facilitating the monitoring of host protein synthesis changes in response to virus infection. Importantly, Cas proteins from all four CRISPR loci in the S. thermophilus DGCC7710 genome were detected, including loci previously thought to be inactive. Many Cas proteins were found to be constitutively expressed, but several demonstrated increased abundance following infection, including the signature Cas9 proteins from the CRISPR1 and CRISPR3 loci, which are key players in the interference phase of the CRISPR/Cas response. Altogether, these results provide novel insights into the proteomic response of S. thermophilus, specifically CRISPR-associated proteins, upon phage 2972 infection.
Collapse
Affiliation(s)
- Jacque C. Young
- Graduate School for Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, United States of America
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Brian D. Dill
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Chongle Pan
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Robert L. Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Jillian F. Banfield
- Department of Earth and Planetary Sciences, University of California, Berkeley, California, United States of America
| | - Manesh Shah
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | | | | | - Rodolphe Barrangou
- DuPont Nutrition and Health, Madison, Wisconsin, United States of America
| | - Nathan C. VerBerkmoes
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail:
| |
Collapse
|
43
|
Abstract
M102AD is the new designation for a Streptococcus mutans phage described in 1993 as phage M102. This change was necessitated by the genome analysis of another S. mutans phage named M102, which revealed differences from the genome sequence reported here. Additional host range analyses confirmed that S. mutans phage M102AD infects only a few serotype c strains. Phage M102AD adsorbed very slowly to its host, and it cannot adsorb to serotype e and f strains of S. mutans. M102AD adsorption was blocked by c-specific antiserum. Phage M102AD also adsorbed equally well to heat-treated and trypsin-treated cells, suggesting carbohydrate receptors. Saliva and polysaccharide production did not inhibit plaque formation. The genome of this siphophage consisted of a linear, double-stranded, 30,664-bp DNA molecule, with a GC content of 39.6%. Analysis of the genome extremities indicated the presence of a 3'-overhang cos site that was 11 nucleotides long. Bioinformatic analyses identified 40 open reading frames, all in the same orientation. No lysogeny-related genes were found, indicating that phage M102AD is strictly virulent. No obvious virulence factor gene candidates were found. Twelve proteins were identified in the virion structure by mass spectrometry. Comparative genomic analysis revealed a close relationship between S. mutans phages M102AD and M102 as well as with Streptococcus thermophilus phages. This study also highlights the importance of conducting research with biological materials obtained from recognized microbial collections.
Collapse
|
44
|
Mills S, Griffin C, O’Sullivan O, Coffey A, McAuliffe O, Meijer W, Serrano L, Ross R. A new phage on the ‘Mozzarella’ block: Bacteriophage 5093 shares a low level of homology with other Streptococcus thermophilus phages. Int Dairy J 2011. [DOI: 10.1016/j.idairyj.2011.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
45
|
Lee YD, Chang HI, Park JH. Complete genomic sequence of virulent Cronobacter sakazakii phage ESSI-2 isolated from swine feces. Arch Virol 2011; 156:721-4. [PMID: 21311921 DOI: 10.1007/s00705-011-0934-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2010] [Accepted: 01/22/2011] [Indexed: 11/28/2022]
Abstract
A newly identified virulent Cronobacter sakazakii phage, ESSI-2, was isolated from fecal samples from swine. The morphological characteristics evident under a transmission electron microscope indicated that phage ESSI-2 belonged to the family Myoviridae. The genome of phage ESSI-2 comprised a double-stranded DNA of 28,765 bp with a G+C content of 55.17%. Bioinformatic analysis of the phage genome identified 36 putative open reading frames (ORFs). The genome of phage ESSI-2 was not significantly similar to that of a previously reported bacteriophage of the members of Enterobacteriaceae. A lysogeny module was found within the genome of this virulent phage.
Collapse
Affiliation(s)
- Young-Duck Lee
- School of Life Science and Biotechnology, Korea University, Anam-Dong, Sungbuk-Gu, Seoul, South Korea
| | | | | |
Collapse
|
46
|
The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA. Nature 2011; 468:67-71. [PMID: 21048762 DOI: 10.1038/nature09523] [Citation(s) in RCA: 1512] [Impact Index Per Article: 116.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Accepted: 09/20/2010] [Indexed: 01/06/2023]
Abstract
Bacteria and Archaea have developed several defence strategies against foreign nucleic acids such as viral genomes and plasmids. Among them, clustered regularly interspaced short palindromic repeats (CRISPR) loci together with cas (CRISPR-associated) genes form the CRISPR/Cas immune system, which involves partially palindromic repeats separated by short stretches of DNA called spacers, acquired from extrachromosomal elements. It was recently demonstrated that these variable loci can incorporate spacers from infecting bacteriophages and then provide immunity against subsequent bacteriophage infections in a sequence-specific manner. Here we show that the Streptococcus thermophilus CRISPR1/Cas system can also naturally acquire spacers from a self-replicating plasmid containing an antibiotic-resistance gene, leading to plasmid loss. Acquired spacers that match antibiotic-resistance genes provide a novel means to naturally select bacteria that cannot uptake and disseminate such genes. We also provide in vivo evidence that the CRISPR1/Cas system specifically cleaves plasmid and bacteriophage double-stranded DNA within the proto-spacer, at specific sites. Our data show that the CRISPR/Cas immune system is remarkably adapted to cleave invading DNA rapidly and has the potential for exploitation to generate safer microbial strains.
Collapse
|
47
|
|
48
|
Zinno P, Janzen T, Bennedsen M, Ercolini D, Mauriello G. Characterization of Streptococcus thermophilus lytic bacteriophages from mozzarella cheese plants. Int J Food Microbiol 2009; 138:137-44. [PMID: 20060612 DOI: 10.1016/j.ijfoodmicro.2009.12.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2009] [Revised: 12/02/2009] [Accepted: 12/05/2009] [Indexed: 11/17/2022]
Abstract
Phage infection still represents the main cause of fermentation failure during the mozzarella cheese manufacturing, where Streptococcus thermophilus is widely employed as starter culture. Thereby, the success of commercial lactic starter cultures is closely related to the use of strains with low susceptibility to phage attack. The characterization of lytic S. thermophilus bacteriophages is an important step for the selection and use of starter cultures. The aim of this study was to characterize 26 bacteriophages isolated from mozzarella cheese plants in terms of their host range, DNA restriction profile, DNA packaging mechanism, and the variable region VR2 of the antireceptor gene. The DNA restriction analysis was carried out by using the restriction enzymes EcoRV, PstI, and HindIII. The bacteriophages were distinguished into two main groups of S. thermophilus phages (cos- and pac-type) using a multiplex PCR method based on the amplification of conserved regions in the genes coding for the major structural proteins. All the phages belonged to the cos-type group except one, phage 1042, which gave a PCR fragment distinctive of pac-type group. Furthermore, DNA sequencing of the variable region VR2 of the antireceptor gene allowed to classify the phages and examine the correlation between typing profile and host range. Finally, bacterial strains used in this study were investigated for the presence of temperate phages by induction with mitomycin C and only S. thermophilus CHCC2070 was shown to be lysogenic.
Collapse
Affiliation(s)
- P Zinno
- Dipartimento di Scienza degli Alimenti, Università degli Studi di Napoli Federico II, Portici, Italy
| | | | | | | | | |
Collapse
|
49
|
Guglielmotti DM, Deveau H, Binetti AG, Reinheimer JA, Moineau S, Quiberoni A. Genome analysis of two virulent Streptococcus thermophilus phages isolated in Argentina. Int J Food Microbiol 2009; 136:101-9. [DOI: 10.1016/j.ijfoodmicro.2009.09.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 08/31/2009] [Accepted: 09/06/2009] [Indexed: 11/30/2022]
|
50
|
Streptococcus thermophilus phage monitoring in a cheese factory: Phage characteristics and starter sensitivity. Int Dairy J 2009. [DOI: 10.1016/j.idairyj.2009.02.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|