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Grafakou A, Mosterd C, Beck MH, Kelleher P, McDonnell B, de Waal PP, van Rijswijck IMH, van Peij NNME, Cambillau C, Mahony J, van Sinderen D. Discovery of antiphage systems in the lactococcal plasmidome. Nucleic Acids Res 2024; 52:9760-9776. [PMID: 39119896 PMCID: PMC11381338 DOI: 10.1093/nar/gkae671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
Until the late 2000s, lactococci substantially contributed to the discovery of various plasmid-borne phage defence systems, rendering these bacteria an excellent antiphage discovery resource. Recently, there has been a resurgence of interest in identifying novel antiphage systems in lactic acid bacteria owing to recent reports of so-called 'defence islands' in diverse bacterial genera. Here, 321 plasmid sequences from 53 lactococcal strains were scrutinized for the presence of antiphage systems. Systematic evaluation of 198 candidates facilitated the discovery of seven not previously described antiphage systems, as well as five systems, of which homologues had been described in other bacteria. All described systems confer resistance against the most prevalent lactococcal phages, and act post phage DNA injection, while all except one behave like abortive infection systems. Structure and domain predictions provided insights into their mechanism of action and allow grouping of several genetically distinct systems. Although rare within our plasmid collection, homologues of the seven novel systems appear to be widespread among bacteria. This study highlights plasmids as a rich repository of as yet undiscovered antiphage systems.
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Affiliation(s)
- Andriana Grafakou
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Cas Mosterd
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Matthias H Beck
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Philip Kelleher
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Brian McDonnell
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Paul P de Waal
- dsm-firmenich, Taste, Texture & Health, Center for Food Innovation, Delft 2613 AX, The Netherlands
| | - Irma M H van Rijswijck
- dsm-firmenich, Taste, Texture & Health, Center for Food Innovation, Delft 2613 AX, The Netherlands
| | - Noël N M E van Peij
- dsm-firmenich, Taste, Texture & Health, Center for Food Innovation, Delft 2613 AX, The Netherlands
| | - Christian Cambillau
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IMM), Aix-Marseille Université - CNRS, UMR 7255 Marseille, France
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Cork T12 YT20, Ireland
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Ortiz Charneco G, McDonnell B, Kelleher P, Buivydas A, Dashko S, de Waal PP, van Rijswijck I, van Peij NNME, Mahony J, Van Sinderen D. Plasmid-mediated horizontal gene mobilisation: Insights from two lactococcal conjugative plasmids. Microb Biotechnol 2024; 17:e14421. [PMID: 38752994 PMCID: PMC11097999 DOI: 10.1111/1751-7915.14421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/18/2024] [Accepted: 01/21/2024] [Indexed: 05/18/2024] Open
Abstract
The distinct conjugation machineries encoded by plasmids pNP40 and pUC11B represent the most prevalent plasmid transfer systems among lactococcal strains. In the current study, we identified genetic determinants that underpin pNP40- and pUC11B-mediated, high-frequency mobilisation of other, non-conjugative plasmids. The mobilisation frequencies of the smaller, non-conjugative plasmids and the minimal sequences required for their mobilisation were determined, owing to the determination of the oriT sequences of both pNP40 and pUC11B, which allowed the identification of similar sequences in some of the non-conjugative plasmids that were shown to promote their mobilisation. Furthermore, the auxiliary gene mobC, two distinct functional homologues of which are present in several plasmids harboured by the pNP40- and pUC11B-carrying host strains, was observed to confer a high-frequency mobilisation phenotype. These findings provide mechanistic insights into how lactococcal conjugative plasmids achieve conjugation and promote mobilisation of non-conjugative plasmids. Ultimately, these insights would be harnessed to optimise conjugation and mobilisation strategies for the rapid and predictable development of robust and technologically improved strains.
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Affiliation(s)
| | - Brian McDonnell
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Philip Kelleher
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Andrius Buivydas
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Sofia Dashko
- dsm‐firmenich, Taste, Texture & Health, Center for Food InnovationDelftThe Netherlands
| | - Paul P. de Waal
- dsm‐firmenich, Taste, Texture & Health, Center for Food InnovationDelftThe Netherlands
| | - Irma van Rijswijck
- dsm‐firmenich, Taste, Texture & Health, Center for Food InnovationDelftThe Netherlands
| | | | - Jennifer Mahony
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
| | - Douwe Van Sinderen
- School of Microbiology & APC Microbiome IrelandUniversity College CorkCorkIreland
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Ortiz Charneco G, Kelleher P, Buivydas A, de Waal PP, van Rijswijck IM, van Peij NN, Cambillau C, Mahony J, Van Sinderen D. Discovering genetic determinants for cell-to-cell adhesion in two prevalent conjugative lactococcal plasmids. CURRENT RESEARCH IN MICROBIAL SCIENCES 2024; 6:100239. [PMID: 38706493 PMCID: PMC11067333 DOI: 10.1016/j.crmicr.2024.100239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024] Open
Abstract
Plasmids pNP40 and pUC11B encode two prevalent yet divergent conjugation systems, which have been characterized in detail recently. Here, we report the elucidation of the putative adhesins of the pNP40 and pUC11B conjugation systems, encoded by traAd and trsAd, respectively. Despite their significant sequence divergence, TraAd and TrsAd represent the most conserved component between the pNP40- and the pUC11B-encoded conjugation systems and share similar peptidoglycan-hydrolase domains. Protein structure prediction using AlphaFold2 highlighted the structural similarities between their predicted domains, as well as the potential homo-dimeric state of both proteins. Expression of the putative surface adhesins resulted in a cell clumping phenotype not only among cells expressing these surface adhesins but also between adhesin-expressing and non-producing cells. Furthermore, mutant derivatives of plasmids pNP40 or pUC11B carrying a mutation in traAd or trsAd, respectively, were shown to act as efficient donors provided the corresponding recipient expresses either traAd or trsAd, thus demonstrating in trans reciprocal complementarity of these proteins in conjugation systems.
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Affiliation(s)
- Guillermo Ortiz Charneco
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Philip Kelleher
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Andrius Buivydas
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Paul P. de Waal
- dsm-firmenich; Taste, Texture & Health, Center for Food Innovation, Alexander Fleminglaan 1, 2613 AX Delft, the Netherlands
| | - Irma M.H. van Rijswijck
- dsm-firmenich; Taste, Texture & Health, Center for Food Innovation, Alexander Fleminglaan 1, 2613 AX Delft, the Netherlands
| | - Noël N.M.E. van Peij
- dsm-firmenich; Taste, Texture & Health, Center for Food Innovation, Alexander Fleminglaan 1, 2613 AX Delft, the Netherlands
| | - Christian Cambillau
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM), Institut de Microbiologie, Bioénergies et Biotechnologie (IMM), Aix-Marseille Université – CNRS, UMR 7255, Marseille, France
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
| | - Douwe Van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork, Ireland
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Michaelis C, Berger TMI, Kuhlmann K, Ghulam R, Petrowitsch L, Besora Vecino M, Gesslbauer B, Pavkov-Keller T, Keller W, Grohmann E. Effect of TraN key residues involved in DNA binding on pIP501 transfer rates in Enterococcus faecalis. Front Mol Biosci 2024; 11:1268647. [PMID: 38380428 PMCID: PMC10877727 DOI: 10.3389/fmolb.2024.1268647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/04/2024] [Indexed: 02/22/2024] Open
Abstract
Conjugation is a major mechanism that facilitates the exchange of antibiotic resistance genes among bacteria. The broad-host-range Inc18 plasmid pIP501 harbors 15 genes that encode for a type IV secretion system (T4SS). It is a membrane-spanning multiprotein complex formed between conjugating donor and recipient cells. The penultimate gene of the pIP501 operon encodes for the cytosolic monomeric protein TraN. This acts as a transcriptional regulator by binding upstream of the operon promotor, partially overlapping with the origin of transfer. Additionally, TraN regulates traN and traO expression by binding upstream of the PtraNO promoter. This study investigates the impact of nine TraN amino acids involved in binding to pIP501 DNA through site-directed mutagenesis by exchanging one to three residues by alanine. For three traN variants, complementation of the pIP501∆traN knockout resulted in an increase of the transfer rate by more than 1.5 orders of magnitude compared to complementation of the mutant with native traN. Microscale thermophoresis (MST) was used to assess the binding affinities of three TraN double-substituted variants and one triple-substituted variant to its cognate pIP501 double-stranded DNA. The MST data strongly correlated with the transfer rates obtained by biparental mating assays in Enterococcus faecalis. The TraN variants TraN_R23A-N24A-Q28A, TraN_H82A-R86A, and TraN_G100A-K101A not only exhibited significantly lower DNA binding affinities but also, upon complementation of the pIP501∆traN knockout, resulted in the highest pIP501 transfer rates. This confirms the important role of the TraN residues R23, N24, Q28, H82, R86, G100, and K101 in downregulating pIP501 transfer. Although TraN is not part of the mating pair formation complex, TraE, TraF, TraH, TraJ, TraK, and TraM were coeluted with TraN in a pull-down. Moreover, TraN homologs are present not only in Inc18 plasmids but also in RepA_N and Rep_3 family plasmids, which are frequently found in enterococci, streptococci, and staphylococci. This points to a widespread role of this repressor in conjugative plasmid transfer among Firmicutes.
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Affiliation(s)
- Claudia Michaelis
- Faculty of Life Sciences and Technology, Department of Microbiology, Berliner Hochschule für Technik, Berlin, Germany
| | | | - Kirill Kuhlmann
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Rangina Ghulam
- Faculty of Life Sciences and Technology, Department of Microbiology, Berliner Hochschule für Technik, Berlin, Germany
| | - Lukas Petrowitsch
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | - Bernd Gesslbauer
- Institute of Pharmaceutical Sciences, Division of Pharmaceutical Chemistry, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
- Field of Excellence BioHealth—University of Graz, Graz, Austria
| | - Tea Pavkov-Keller
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
- Field of Excellence BioHealth—University of Graz, Graz, Austria
| | - Walter Keller
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed Graz, Graz, Austria
- Field of Excellence BioHealth—University of Graz, Graz, Austria
| | - Elisabeth Grohmann
- Faculty of Life Sciences and Technology, Department of Microbiology, Berliner Hochschule für Technik, Berlin, Germany
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