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Murphy J, Bottacini F, Mahony J, Kelleher P, Neve H, Zomer A, Nauta A, van Sinderen D. Comparative genomics and functional analysis of the 936 group of lactococcal Siphoviridae phages. Sci Rep 2016; 6:21345. [PMID: 26892066 PMCID: PMC4759559 DOI: 10.1038/srep21345] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 01/21/2016] [Indexed: 01/14/2023] Open
Abstract
Genome sequencing and comparative analysis of bacteriophage collections has greatly enhanced our understanding regarding their prevalence, phage-host interactions as well as the overall biodiversity of their genomes. This knowledge is very relevant to phages infecting Lactococcus lactis, since they constitute a significant risk factor for dairy fermentations. Of the eighty four lactococcal phage genomes currently available, fifty five belong to the so-called 936 group, the most prevalent of the ten currently recognized lactococcal phage groups. Here, we report the genetic characteristics of a new collection of 936 group phages. By combining these genomes to those sequenced previously we determined the core and variable elements of the 936 genome. Genomic variation occurs across the 936 phage genome, such as genetic elements that (i) lead to a +1 translational frameshift resulting in the formation of additional structures on the phage tail, (ii) specify a double neck passage structure, and (iii) encode packaging module-associated methylases. Hierarchical clustering of the gene complement of the 936 group phages and nucleotide alignments allowed grouping of the ninety 936 group phages into distinct clusters, which in general appear to correspond with their geographical origin.
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Affiliation(s)
- James Murphy
- School of Microbiology, University College Cork, Cork, Ireland
| | | | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
| | - Philip Kelleher
- School of Microbiology, University College Cork, Cork, Ireland
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Aldert Zomer
- School of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
| | - Arjen Nauta
- FrieslandCampina, Amersfoort, The Netherlands
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland
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Ainsworth S, Stockdale S, Bottacini F, Mahony J, van Sinderen D. The Lactococcus lactis plasmidome: much learnt, yet still lots to discover. FEMS Microbiol Rev 2014; 38:1066-88. [PMID: 24861818 DOI: 10.1111/1574-6976.12074] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 04/17/2014] [Accepted: 05/07/2014] [Indexed: 01/20/2023] Open
Abstract
Lactococcus lactis is used extensively worldwide for the production of a variety of fermented dairy products. The ability of L. lactis to successfully grow and acidify milk has long been known to be reliant on a number of plasmid-encoded traits. The recent availability of low-cost, high-quality genome sequencing, and the quest for novel, technologically desirable characteristics, such as novel flavour development and increased stress tolerance, has led to a steady increase in the number of available lactococcal plasmid sequences. We will review both well-known and very recent discoveries regarding plasmid-encoded traits of biotechnological significance. The acquired lactococcal plasmid sequence information has in recent years progressed our understanding of the origin of lactococcal dairy starter cultures. Salient points on the acquisition and evolution of lactococcal plasmids will be discussed in this review, as well as prospects of finding novel plasmid-encoded functions.
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Affiliation(s)
- Stuart Ainsworth
- Department of Microbiology, University College Cork, Cork, Ireland
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Effect of the abortive infection mechanism and type III toxin/antitoxin system AbiQ on the lytic cycle of Lactococcus lactis phages. J Bacteriol 2013; 195:3947-56. [PMID: 23813728 DOI: 10.1128/jb.00296-13] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
To survive in phage-containing environments, bacteria have evolved an array of antiphage systems. Similarly, phages have overcome these hurdles through various means. Here, we investigated how phages are able to circumvent the Lactococcus lactis AbiQ system, a type III toxin-antitoxin with antiviral activities. Lactococcal phage escape mutants were obtained in the laboratory, and their genomes were sequenced. Three unrelated genes of unknown function were mutated in derivatives of three distinct lactococcal siphophages: orf38 of phage P008, m1 of phage bIL170, and e19 of phage c2. One-step growth curve experiments revealed that the phage mutations had a fitness cost while transcriptional analyses showed that AbiQ modified the early-expressed phage mRNA profiles. The L. lactis AbiQ system was also transferred into Escherichia coli MG1655 and tested against several coliphages. While AbiQ was efficient against phages T4 (Myoviridae) and T5 (Siphoviridae), escape mutants of only phage 2 (Myoviridae) could be isolated. Genome sequencing revealed a mutation in gene orf210, a putative DNA polymerase. Taking these observations together, different phage genes or gene products are targeted or involved in the AbiQ phenotype. Moreover, this antiviral system is active against various phage families infecting Gram-positive and Gram-negative bacteria. A model for the mode of action of AbiQ is proposed.
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Coevolution of bacteria and their viruses. Folia Microbiol (Praha) 2012; 58:177-86. [PMID: 22993102 DOI: 10.1007/s12223-012-0195-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Accepted: 09/06/2012] [Indexed: 01/21/2023]
Abstract
Coevolution between bacteria and bacteriophages can be characterized as an infinitive constant evolutionary battle (phage-host arm race), which starts during phage adsorption and penetration into host cell, continues during phage replication inside the cells, and remains preserved also during prophage lysogeny. Bacteriophage may exist inside the bacterial cells in four forms with different evolutionary strategies: as a replicating virus during the lytic cycle, in an unstable carrier state termed pseudolysogeny, as a prophage with complete genome during the lysogeny, or as a defective cryptic prophage. Some defensive mechanisms of bacteria and virus countermeasures are characterized, and some evolutionary questions concerning phage-host relationship are discussed.
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Lactococcal abortive infection protein AbiV interacts directly with the phage protein SaV and prevents translation of phage proteins. Appl Environ Microbiol 2010; 76:7085-92. [PMID: 20851990 DOI: 10.1128/aem.00093-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
AbiV is an abortive infection protein that inhibits the lytic cycle of several virulent phages infecting Lactococcus lactis, while a mutation in the phage gene sav confers insensitivity to AbiV. In this study, we have further characterized the effects of the bacterial AbiV and its interaction with the phage p2 protein SaV. First, we showed that during phage infection of lactococcal AbiV(+) cells, AbiV rapidly inhibited protein synthesis. Among early phage transcripts, sav gene transcription was slightly inhibited while the SaV protein could not be detected. Analyses of other phage p2 mRNAs and proteins suggested that AbiV blocks the activation of late gene transcription, probably by a general inhibition of translation. Using size exclusion chromatography coupled with on-line static light scattering and refractometry, as well as fluorescence quenching experiments, we also demonstrated that both AbiV and SaV formed homodimers and that they strongly and specifically interact with each other to form a stable protein complex.
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Abstract
Phages are now acknowledged as the most abundant microorganisms on the planet and are also possibly the most diversified. This diversity is mostly driven by their dynamic adaptation when facing selective pressure such as phage resistance mechanisms, which are widespread in bacterial hosts. When infecting bacterial cells, phages face a range of antiviral mechanisms, and they have evolved multiple tactics to avoid, circumvent or subvert these mechanisms in order to thrive in most environments. In this Review, we highlight the most important antiviral mechanisms of bacteria as well as the counter-attacks used by phages to evade these systems.
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Affiliation(s)
- Simon J Labrie
- Department of Civil & Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Domingues S, McGovern S, Plochocka D, Santos MA, Ehrlich SD, Polard P, Chopin MC. The lactococcal abortive infection protein AbiP is membrane-anchored and binds nucleic acids. Virology 2008; 373:14-24. [DOI: 10.1016/j.virol.2007.11.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 10/19/2007] [Accepted: 11/06/2007] [Indexed: 10/22/2022]
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Labrie SJ, Moineau S. Abortive infection mechanisms and prophage sequences significantly influence the genetic makeup of emerging lytic lactococcal phages. J Bacteriol 2006; 189:1482-7. [PMID: 17041060 PMCID: PMC1797345 DOI: 10.1128/jb.01111-06] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we demonstrated the remarkable genome plasticity of lytic lactococcal phages that allows them to rapidly adapt to the dynamic dairy environment. The lytic double-stranded DNA phage ul36 was used to sequentially infect a wild-type strain of Lactococcus lactis and two isogenic derivatives with genes encoding two phage resistance mechanisms, AbiK and AbiT. Four phage mutants resistant to one or both Abi mechanisms were isolated. Comparative analysis of their complete genomes, as well as morphological observations, revealed that phage ul36 extensively evolved by large-scale homologous and nonhomologous recombination events with the inducible prophage present in the host strain. One phage mutant exchanged as much as 79% of its genome compared to the core genome of ul36. Thus, natural phage defense mechanisms and prophage elements found in bacterial chromosomes contribute significantly to the evolution of the lytic phage population.
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Affiliation(s)
- Simon J Labrie
- Département de Biochimie et de Microbiologie, Groupe de Recherche en Ecologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec, Canada
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Chopin MC, Chopin A, Bidnenko E. Phage abortive infection in lactococci: variations on a theme. Curr Opin Microbiol 2005; 8:473-9. [PMID: 15979388 DOI: 10.1016/j.mib.2005.06.006] [Citation(s) in RCA: 240] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2005] [Accepted: 06/14/2005] [Indexed: 10/25/2022]
Abstract
Abortive infection (Abi) systems, also called phage exclusion, block phage multiplication and cause premature bacterial cell death upon phage infection. This decreases the number of progeny particles and limits their spread to other cells allowing the bacterial population to survive. Twenty Abi systems have been isolated in Lactococcus lactis, a bacterium used in cheese-making fermentation processes, where phage attacks are of economical importance. Recent insights in their expression and mode of action indicate that, behind diverse phenotypic and molecular effects, lactococcal Abis share common traits with the well-studied Escherichia coli systems Lit and Prr. Abis are widespread in bacteria, and recent analysis indicates that Abis might have additional roles other than conferring phage resistance.
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Rakonjac J, O'Toole PW, Lubbers M. Isolation of lactococcal prolate phage-phage recombinants by an enrichment strategy reveals two novel host range determinants. J Bacteriol 2005; 187:3110-21. [PMID: 15838038 PMCID: PMC1082804 DOI: 10.1128/jb.187.9.3110-3121.2005] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Virulent lactococcal prolate (or c2-like) phages are the second most common phage group that causes fermentation failure in the dairy industry. We have mapped two host range determinants in two lactococcal prolate phages, c2 and 923, for the host strains MG1363 and 112. Each phage replicates on only one of the two host strains: c2 on MG1363 and 923 on 112. Phage-phage recombinants that replicated on both strains were isolated by a new method that does not require direct selection but rather employs an enrichment protocol. After initial mixed infection of strain 112, two rotations, the first of which was carried out on strain MG1363 and the second on 112, permitted continuous amplification of double-plating recombinants while rendering one of the parent phages unamplified in each of the two rotations. Mapping of the recombination endpoints showed that the presence of the N-terminal two-thirds of the tail protein L10 of phage c2 and a 1,562-bp cosR-terminal fragment of phage 923 genome overcame blocks of infection in strains MG1363 and 112, respectively. Both infection inhibition mechanisms act at the stage of DNA entry; in strain MG1363, the infection block acts early, before phage DNA enters the cytoplasm, and in strain 112, it acts late, after most of the DNA has entered the cell but before it undergoes cos-end ligation. These are the first reported host range determinants in bacteriophage of lactic acid bacteria required for overcoming inhibition of infection at the stage of DNA entry and cos-end ligation.
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Affiliation(s)
- Jasna Rakonjac
- Institute of Molecular BioSciences, Massey University, Private Bag 11-222, Palmerston North, New Zealand.
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