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Itaya M, Kataoka M. Integrated conjugal plasmid pLS20 in the Bacillus subtilis genome produced 850-kbp circular subgenomes transmissible to another B. subtilis. Genes Cells 2024; 29:584-588. [PMID: 38660704 DOI: 10.1111/gtc.13120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/14/2024] [Accepted: 04/14/2024] [Indexed: 04/26/2024]
Abstract
Bacillus subtilis was engineered to produce circular subgenomes that are directly transmittable to another B. subtilis. The conjugational plasmid pLS20 integrated into the B. subtilis genome supported not only subgenome replication but also transmission to another B. subtilis species. The subgenome system developed in this study completes a streamlined platform from the synthesis to the transmission of giant DNA by B. subtilis.
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Affiliation(s)
- Mitsuhiro Itaya
- Department of Biomedical Engineering Graduate School of Science and Technology, Shinshu University, Nagano, Japan
| | - Masakazu Kataoka
- Department of Biomedical Engineering Graduate School of Science and Technology, Shinshu University, Nagano, Japan
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2
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Vincent J, Tenore A, Mattei MR, Frunzo L. Modelling Plasmid-Mediated Horizontal Gene Transfer in Biofilms. Bull Math Biol 2024; 86:63. [PMID: 38664322 DOI: 10.1007/s11538-024-01289-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/27/2024] [Indexed: 05/23/2024]
Abstract
In this study, we present a mathematical model for plasmid spread in a growing biofilm, formulated as a nonlocal system of partial differential equations in a 1-D free boundary domain. Plasmids are mobile genetic elements able to transfer to different phylotypes, posing a global health problem when they carry antibiotic resistance factors. We model gene transfer regulation influenced by nearby potential receptors to account for recipient-sensing. We also introduce a promotion function to account for trace metal effects on conjugation, based on literature data. The model qualitatively matches experimental results, showing that contaminants like toxic metals and antibiotics promote plasmid persistence by favoring plasmid carriers and stimulating conjugation. Even at higher contaminant concentrations inhibiting conjugation, plasmid spread persists by strongly inhibiting plasmid-free cells. The model also replicates higher plasmid density in biofilm's most active regions.
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Affiliation(s)
- Julien Vincent
- Department of Mathematics and Applications "Renato Caccioppoli", University of Naples Federico II, Via Cintia 26, 80126, Monte S. Angelo, Naples, Italy
- Microbial Ecology Laboratory, University of Galway, University Road, Galway, H91 TK33, Ireland
| | - Alberto Tenore
- Department of Mathematics and Applications "Renato Caccioppoli", University of Naples Federico II, Via Cintia 26, 80126, Monte S. Angelo, Naples, Italy
| | - Maria Rosaria Mattei
- Department of Mathematics and Applications "Renato Caccioppoli", University of Naples Federico II, Via Cintia 26, 80126, Monte S. Angelo, Naples, Italy.
| | - Luigi Frunzo
- Department of Mathematics and Applications "Renato Caccioppoli", University of Naples Federico II, Via Cintia 26, 80126, Monte S. Angelo, Naples, Italy
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3
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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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4
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Bareia T, Pollak S, Guler P, Puyesky S, Eldar A. Major distinctions between the two oligopeptide permease systems of Bacillus subtilis with respect to signaling, development and evolutionary divergence. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001382. [PMID: 37755230 PMCID: PMC10569065 DOI: 10.1099/mic.0.001382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 08/02/2023] [Indexed: 09/28/2023]
Abstract
Oligopeptide-permeases (Opps) are used by bacteria to import short peptides. In addition to their metabolic benefit, imported short peptides are used in many Gram-positive bacteria as signalling molecules of the RRNPP super-family of quorum-sensing systems, making Opps an integral part of cell–cell communication. In some Gram-positive bacteria there exist multiple Opps and the relative importance of those to RRNPP quorum sensing are not fully clear. Specifically, in Bacillus subtilis , the Gram-positive model species, there exist two homologous oligopeptide permeases named Opp and App. Previous work showed that the App system is mutated in lab strain 168 and its recovery partially complements an Opp mutation for several developmental processes. Yet, the nature of the impact of App on signalling and development in wild-type strains, where both permeases are active was not studied. Here we re-examine the impact of the two permease systems. We find that App has a minor contribution to biofilm formation, surfactin production and phage infection compared to the effect of Opp. This reduced effect is also reflected in its lower ability to import the signals of four different Rap-Phr RRNPP systems. Further analysis of the App system revealed that, unlike Opp, some App genes have undergone horizontal transfer, resulting in two distinct divergent alleles of this system in B. subtilis strains. We found that both alleles were substantially better adapted than the Opp system to import an exogenous RRNPP signal of the Bacillus cereus group PlcR-PapR system. In summary, we find that the App system has only a minor role in signalling but may still be crucial for the import of other peptides.
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Affiliation(s)
- Tasneem Bareia
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978, Israel
- Present address: Department of Plant & Environmental Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Shaul Pollak
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978, Israel
- Present address: Division of Microbial Ecology, Centre for Microbiology and Environmental Science, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Polina Guler
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Shani Puyesky
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Avigdor Eldar
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, 69978, Israel
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5
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Miguel-Arribas A, Martín-María A, Alaerds ECW, Val-Calvo J, Yuste L, Rojo F, Abia D, Wu L, Meijer WJJ. Extraordinary long-stem confers resistance of intrinsic terminators to processive antitermination. Nucleic Acids Res 2023; 51:6073-6086. [PMID: 37125647 PMCID: PMC10325885 DOI: 10.1093/nar/gkad333] [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: 10/06/2022] [Revised: 03/14/2023] [Accepted: 04/20/2023] [Indexed: 05/02/2023] Open
Abstract
Many prokaryotic operons encode a processive antitermination (P-AT) system. Transcription complexes associated with an antitermination factor can bypass multiple transcription termination signals regardless of their sequences. However, to avoid compromising transcriptional regulation of downstream regions, the terminator at the end of the operon needs to be resistant to antitermination. So far, no studies on the mechanism of resistance to antitermination have been reported. The recently discovered conAn P-AT system is composed of two components that are encoded at the start of many conjugation operons on plasmids of Gram-positive bacteria. Here we report the identification of a conAn-resistant terminator, named TerR, in the conjugation operon of the Bacillus subtilis plasmid pLS20, re-defining the end of the conjugation operon. We investigated the various characteristics of TerR and show that its extraordinary long stem is the determining feature for resistance to antitermination. This is the first P-AT resistance mechanism to be reported.
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Affiliation(s)
- Andrés Miguel-Arribas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Ana Martín-María
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Eef C W Alaerds
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Jorge Val-Calvo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Luis Yuste
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, C. Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - Fernando Rojo
- Departamento de Biotecnología Microbiana, Centro Nacional de Biotecnología, CSIC, C. Darwin 3, Cantoblanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular “Severo Ochoa”, (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK
| | - Wilfried J J Meijer
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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6
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Morawska LP, Kuipers OP. Cell-to-cell non-conjugative plasmid transfer between Bacillus subtilis and lactic acid bacteria. Microb Biotechnol 2023; 16:784-798. [PMID: 36547214 PMCID: PMC10034627 DOI: 10.1111/1751-7915.14195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 11/15/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Bacillus subtilis is a soil-dwelling bacterium that can interact with a plethora of other microorganisms in its natural habitat. Due to the versatile interactions and its ability to form nanotubes, i.e., recently described membrane structures that trade cytoplasmic content between neighbouring cells, we investigated the potential of HGT from B. subtilis to industrially-relevant members of lactic acid bacteria (LAB). To explore the interspecies HGT events, we developed a co-culturing protocol and provided proof of transfer of a small high copy non-conjugative plasmid from B. subtilis to LABs. Interestingly, the plasmid transfer did not involve conjugation nor activation of the competent state by B. subtilis. Moreover, our study shows for the first time non-conjugative cell-to-cell intraspecies plasmid transfer for non-competent Lactococcus lactis sp. cremoris strains. Our study indicates that cell-to-cell transformation is a ubiquitous form of HGT and can be potentially utilized as an alternative tool for natural (non-GMO) strain improvement.
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Affiliation(s)
- Luiza P Morawska
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Oscar P Kuipers
- Molecular Genetics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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7
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Bernardo N, Crespo I, Cuppari A, Meijer WJJ, Boer DR. A tetramerization domain in prokaryotic and eukaryotic transcription regulators homologous to p53. Acta Crystallogr D Struct Biol 2023; 79:259-267. [PMID: 36876435 PMCID: PMC9986798 DOI: 10.1107/s2059798323001298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
Transcriptional regulation usually requires the action of several proteins that either repress or activate a promotor of an open reading frame. These proteins can counteract each other, thus allowing tight regulation of the transcription of the corresponding genes, where tight repression is often linked to DNA looping or cross-linking. Here, the tetramerization domain of the bacterial gene repressor Rco from Bacillus subtilis plasmid pLS20 (RcopLS20) has been identified and its structure is shown to share high similarity to the tetramerization domain of the well known p53 family of human tumor suppressors, despite lacking clear sequence homology. In RcopLS20, this tetramerization domain is responsible for inducing DNA looping, a process that involves multiple tetramers. In accordance, it is shown that RcopLS20 can form octamers. This domain was named TetDloop and its occurrence was identified in other Bacillus species. The TetDloop fold was also found in the structure of a transcriptional repressor from Salmonella phage SPC32H. It is proposed that the TetDloop fold has evolved through divergent evolution and that the TetDloop originates from a common ancestor predating the occurrence of multicellular life.
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Affiliation(s)
- Nerea Bernardo
- Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2–26, 08290 Cerdanyola del Vallès, Catalunya, Spain
| | - Isidro Crespo
- Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2–26, 08290 Cerdanyola del Vallès, Catalunya, Spain
| | - Anna Cuppari
- Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2–26, 08290 Cerdanyola del Vallès, Catalunya, Spain
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC–UAM), Universidad Autónoma de Madrid, Calle Nicolás Cabrera 1, Canto Blanco, 28049 Madrid, Spain
| | - D. Roeland Boer
- Experiments Division, ALBA Synchrotron Light Source, Carrer de la Llum 2–26, 08290 Cerdanyola del Vallès, Catalunya, Spain
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8
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Erkelens AM, Qin L, van Erp B, Miguel-Arribas A, Abia D, Keek HGJ, Markus D, Cajili MKM, Schwab S, Meijer WJJ, Dame R. The B. subtilis Rok protein is an atypical H-NS-like protein irresponsive to physico-chemical cues. Nucleic Acids Res 2022; 50:12166-12185. [PMID: 36408910 PMCID: PMC9757077 DOI: 10.1093/nar/gkac1064] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 10/20/2022] [Accepted: 10/26/2022] [Indexed: 11/22/2022] Open
Abstract
Nucleoid-associated proteins (NAPs) play a central role in chromosome organization and environment-responsive transcription regulation. The Bacillus subtilis-encoded NAP Rok binds preferentially AT-rich regions of the genome, which often contain genes of foreign origin that are silenced by Rok binding. Additionally, Rok plays a role in chromosome architecture by binding in genomic clusters and promoting chromosomal loop formation. Based on this, Rok was proposed to be a functional homolog of E. coli H-NS. However, it is largely unclear how Rok binds DNA, how it represses transcription and whether Rok mediates environment-responsive gene regulation. Here, we investigated Rok's DNA binding properties and the effects of physico-chemical conditions thereon. We demonstrate that Rok is a DNA bridging protein similar to prototypical H-NS-like proteins. However, unlike these proteins, the DNA bridging ability of Rok is not affected by changes in physico-chemical conditions. The DNA binding properties of the Rok interaction partner sRok are affected by salt concentration. This suggests that in a minority of Bacillus strains Rok activity can be modulated by sRok, and thus respond indirectly to environmental stimuli. Despite several functional similarities, the absence of a direct response to physico-chemical changes establishes Rok as disparate member of the H-NS family.
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Affiliation(s)
| | | | - Bert van Erp
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands,Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Helena G J Keek
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Dorijn Markus
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands
| | - Marc K M Cajili
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands,Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Samuel Schwab
- Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333CC Leiden, The Netherlands,Centre for Microbial Cell Biology, Leiden University, Leiden, The Netherlands,Centre for Interdisciplinary Genome Research, Leiden University, Leiden, The Netherlands
| | - Wilfried J J Meijer
- Correspondence may also be addressed to Wilfried J.J. Meijer. Tel: +34 91 196 4539;
| | - Remus T Dame
- To whom correspondence should be addressed. Tel: +31 71 527 5605;
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9
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Amatsu R, Mori K, Ishikawa S, Meijer WJJ, Yoshida KI. A New Tool for the Flexible Genetic Manipulation of Geobacillus kaustophilus. Bio Protoc 2022; 12:e4502. [PMID: 36213108 PMCID: PMC9501723 DOI: 10.21769/bioprotoc.4502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/08/2022] [Accepted: 07/25/2022] [Indexed: 12/29/2022] Open
Abstract
Geobacillus kaustophilus , a thermophilic Gram-positive bacterium, is an attractive host for the development of high-temperature bioprocesses. However, its reluctance against genetic manipulation by standard methodologies hampers its exploitation. Here, we describe a simple methodology in which an artificial DNA segment on the chromosome of Bacillus subtilis can be transferred via pLS20-mediated conjugation resulting in subsequent integration in the genome of G. kaustophilus. Therefore, we have developed a transformation strategy to design an artificial DNA segment on the chromosome of B. subtilis and introduce it into G. kaustophilus . The artificial DNA segment can be freely designed by taking advantage of the plasticity of the B. subtilis genome and combined with the simplicity of pLS20 conjugation transfer. This transformation strategy would adapt to various Gram-positive bacteria other than G. kaustophilus . Graphical abstract.
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Affiliation(s)
- Ryotaro Amatsu
- Department of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Kotaro Mori
- Department of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Shu Ishikawa
- Department of Science, Technology and Innovation, Kobe University, Kobe, Japan
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular ‘Severo Ochoa’, CSIC-UAM Universidad Autónoma Madrid, Canto Blanco, 28049, Madrid, Spain
| | - Ken-Ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, Kobe, Japan
,
*For correspondence:
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Itaya M, Sato M, Watanabe S, Kataoka M. Effective plasmid delivery to a plasmid-free Bacillus natto strain by a conjugational transfer system. J Biochem 2022; 172:313-319. [PMID: 36047835 DOI: 10.1093/jb/mvac069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/22/2022] [Indexed: 11/12/2022] Open
Abstract
In this study, a Bacillus natto strain named NEST141 was constructed. The strain carries no plasmids and is an authentic proline auxotroph-a feature that confers effective selection conditions for plasmids transferred from a donor, such as B. subtilis 168, via a pLS20-based conjugational transfer system. We have provided a standard effective protocol for the delivery of plasmids larger than 50 kilobase pairs. These results indicate that the B. natto NEST141 strain can become a standard model, like B. subtilis 168, for extensive genetic engineering with diverse applications.
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Affiliation(s)
- Mitsuhiro Itaya
- Department of Biomedical Engineering Graduate School of Science and Technology, Shinshu University, Wakasato 4-17-1, Nagano-shi, Nagano 380-8553, Japan.,Institute for Advanced Biosciences, Keio University, Nipponkoku, Tsuruoka, Yamagata 997-0017, Japan
| | - Mitsuru Sato
- Institute for Advanced Biosciences, Keio University, Nipponkoku, Tsuruoka, Yamagata 997-0017, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Masakazu Kataoka
- Department of Biomedical Engineering Graduate School of Science and Technology, Shinshu University, Wakasato 4-17-1, Nagano-shi, Nagano 380-8553, Japan
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11
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Gurinovich AS, Titok MA. Molecular Genetic and Functional Analysis of the Conjugation System of the pBS72 Plasmid from Bacillus subtilis Environmental Isolates. Microbiology (Reading) 2022. [DOI: 10.1134/s002626172230018x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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12
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Dimitriu T. Evolution of horizontal transmission in antimicrobial resistance plasmids. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35849537 DOI: 10.1099/mic.0.001214] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Mobile genetic elements (MGEs) are one of the main vectors for the spread of antimicrobial resistance (AMR) across bacteria, due to their ability to move horizontally between bacterial lineages. Horizontal transmission of AMR can increase AMR prevalence at multiple scales, from increasing the prevalence of infections by resistant bacteria to pathogen epidemics and worldwide spread of AMR across species. Among MGEs, conjugative plasmids are the main contributors to the spread of AMR. This review discusses the selective pressures acting on MGEs and their hosts to promote or limit the horizontal transmission of MGEs, the mechanisms by which transmission rates can evolve, and their implications for limiting the spread of AMR, with a focus on AMR plasmids.
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13
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A New Variant of the aadE-sat4-aphA-3 Gene Cluster Found in a Conjugative Plasmid from a MDR Campylobacter jejuni Isolate. Antibiotics (Basel) 2022; 11:antibiotics11040466. [PMID: 35453217 PMCID: PMC9032879 DOI: 10.3390/antibiotics11040466] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/22/2022] [Accepted: 03/28/2022] [Indexed: 11/17/2022] Open
Abstract
Campylobacter jejuni is a foodborne pathogen causing bacterial gastroenteritis, with the highest incidence reported in Europe. The prevalence of antibiotic resistance in C. jejuni, as well as in many other bacterial pathogens, has increased over the last few years. In this report, we describe the presence of a plasmid in a multi-drug-resistant C. jejuni strain isolated from a gastroenteritis patient. Mating experiments demonstrated the transference of this genetic element (pCjH01) among C. jejuni by plasmid conjugation. The pCjH01 plasmid was sequenced and assembled, revealing high similarity (97% identity) with pTet, a described tetracycline resistance encoding plasmid. pCjH01 (47.7 kb) is a mosaic plasmid composed of a pTet backbone that has acquired two discrete DNA regions. Remarkably, one of the acquired sequences carried an undescribed variant of the aadE-sat4-aphA-3 gene cluster, providing resistance to at least kanamycin and gentamycin. Aside from the antibiotic resistance genes, the cluster also carries genes coding for putative regulators, such as a sigma factor of the RNA polymerase and an antisigma factor. Homology searches suggest that Campylobacter exchanges genetic material with distant G-positive bacterial genera.
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14
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Mori K, Fukui K, Amatsu R, Ishikawa S, Verrone V, Wipat A, Meijer WJJ, Yoshida KI. A novel method for transforming Geobacillus kaustophilus with a chromosomal segment of Bacillus subtilis transferred via pLS20-dependent conjugation. Microb Cell Fact 2022; 21:34. [PMID: 35260160 PMCID: PMC8903633 DOI: 10.1186/s12934-022-01759-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 02/19/2022] [Indexed: 12/05/2022] Open
Abstract
Background Geobacillus kaustophilus is a thermophilic Gram-positive bacterium. Methods for its transformation are still under development. Earlier studies have demonstrated that pLS20catΔoriT mobilized the resident mobile plasmids from Bacillus subtilis to G. kaustophilus and transferred long segments of chromosome from one cell to another between B. subtilis. Results In this study, we applied mobilization of the B. subtilis chromosome mediated by pLS20catΔoriT to transform G. kaustophilus. We constructed a gene cassette to be integrated into G. kaustophilus and designed it within the B. subtilis chromosome. The pLS20catΔoriT-mediated conjugation successfully transferred the gene cassette from the B. subtilis chromosome into the G. kaustophilus allowing for the desired genetic transformation. Conclusions This transformation approach described here will provide a new tool to facilitate the flexible genetic manipulation of G. kaustophilus. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01759-8.
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Affiliation(s)
- Kotaro Mori
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 5801, Japan
| | - Kaho Fukui
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 5801, Japan
| | - Ryotaro Amatsu
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 5801, Japan
| | - Shu Ishikawa
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 5801, Japan
| | - Valeria Verrone
- School of Computing, Newcastle University, 1 Science Square, Science Central, Newcastle upon Tyne, NE4 5TG, UK
| | - Anil Wipat
- School of Computing, Newcastle University, 1 Science Square, Science Central, Newcastle upon Tyne, NE4 5TG, UK
| | - Wilfried J J Meijer
- Centro de Biología Molecular 'Severo Ochoa', CSIC-UAM Universidad Autónoma Madrid, Canto Blanco, 28049, Madrid, Spain
| | - Ken-Ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 5801, Japan.
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15
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Miguel-Arribas A, Wu LJ, Michaelis C, Yoshida KI, Grohmann E, Meijer WJJ. Conjugation Operons in Gram-Positive Bacteria with and without Antitermination Systems. Microorganisms 2022; 10:microorganisms10030587. [PMID: 35336162 PMCID: PMC8955417 DOI: 10.3390/microorganisms10030587] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 02/01/2023] Open
Abstract
Genes involved in the same cellular process are often clustered together in an operon whose expression is controlled by an upstream promoter. Generally, the activity of the promoter is strictly controlled. However, spurious transcription undermines this strict regulation, particularly affecting large operons. The negative effects of spurious transcription can be mitigated by the presence of multiple terminators inside the operon, in combination with an antitermination system. Antitermination systems modify the transcription elongation complexes and enable them to bypass terminators. Bacterial conjugation is the process by which a conjugative DNA element is transferred from a donor to a recipient cell. Conjugation involves many genes that are mostly organized in one or a few large operons. It has recently been shown that many conjugation operons present on plasmids replicating in Gram-positive bacteria possess a bipartite antitermination system that allows not only many terminators inside the conjugation operon to be bypassed, but also the differential expression of a subset of genes. Here, we show that some conjugation operons on plasmids belonging to the Inc18 family of Gram-positive broad host-range plasmids do not possess an antitermination system, suggesting that the absence of an antitermination system may have advantages. The possible (dis)advantages of conjugation operons possessing (or not) an antitermination system are discussed.
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Affiliation(s)
- Andrés Miguel-Arribas
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Instituto de Biología Molecular Eladio Viñuela (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain;
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Medical Faculty, Biosciences Institute, Newcastle University, Richardson Road, Newcastle upon Tyne NE2 4AX, UK;
| | - Claudia Michaelis
- School of Life Sciences and Technology, Berlin University of Applied Sciences, Seestrasse 64, 13347 Berlin, Germany;
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan;
| | - Elisabeth Grohmann
- School of Life Sciences and Technology, Berlin University of Applied Sciences, Seestrasse 64, 13347 Berlin, Germany;
- Correspondence: (E.G.); (W.J.J.M.); Tel.: +49-30-4504-3942 (E.G.); +34-91-196-4539 (W.J.J.M.)
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Instituto de Biología Molecular Eladio Viñuela (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain;
- Correspondence: (E.G.); (W.J.J.M.); Tel.: +49-30-4504-3942 (E.G.); +34-91-196-4539 (W.J.J.M.)
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16
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Itaya M. <i>Bacillus subtilis</i> 168 as a unique platform enabling synthesis and dissemination of genomes. J GEN APPL MICROBIOL 2022; 68:45-53. [DOI: 10.2323/jgam.2021.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Mitsuhiro Itaya
- Graduate School of Science and Technology, Shinshu University
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17
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Val-Calvo J, Miguel-Arribas A, Abia D, Wu LJ, Meijer WJJ. pLS20 is the archetype of a new family of conjugative plasmids harboured by Bacillus species. NAR Genom Bioinform 2021; 3:lqab096. [PMID: 34729475 PMCID: PMC8557374 DOI: 10.1093/nargab/lqab096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 09/03/2021] [Accepted: 10/04/2021] [Indexed: 12/12/2022] Open
Abstract
Conjugation plays important roles in genome plasticity, adaptation and evolution but is also the major horizontal gene-transfer route responsible for spreading toxin, virulence and antibiotic resistance genes. A better understanding of the conjugation process is required for developing drugs and strategies to impede the conjugation-mediated spread of these genes. So far, only a limited number of conjugative elements have been studied. For most of them, it is not known whether they represent a group of conjugative elements, nor about their distribution patterns. Here we show that pLS20 from the Gram-positive bacterium Bacillus subtilis is the prototype conjugative plasmid of a family of at least 35 members that can be divided into four clades, and which are harboured by different Bacillus species found in different global locations and environmental niches. Analyses of their phylogenetic relationship and their conjugation operons have expanded our understanding of a family of conjugative plasmids of Gram-positive origin.
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Affiliation(s)
- Jorge Val-Calvo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049, Madrid, Spain
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049, Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049, Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4AX, UK
| | - Wilfried J J Meijer
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049, Madrid, Spain
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18
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Mori K, Verrone V, Amatsu R, Fukui K, Meijer WJJ, Ishikawa S, Wipat A, Yoshida KI. Assessment of Bacillus subtilis Plasmid pLS20 Conjugation in the Absence of Quorum Sensing Repression. Microorganisms 2021; 9:microorganisms9091931. [PMID: 34576826 PMCID: PMC8470214 DOI: 10.3390/microorganisms9091931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 12/21/2022] Open
Abstract
Bacillus subtilis conjugative plasmid pLS20 uses a quorum-sensing mechanism to control expression levels of its conjugation genes, involving the repressor RcopLS20, the anti-repressor RappLS20, and the signaling peptide Phr*pLS20. In previous studies, artificial overexpression of rappLS20 in the donor cells was shown to enhance conjugation efficiency. However, we found that the overexpression of rappLS20 led to various phenotypic traits, including cell aggregation and death, which might have affected the correct determination of the conjugation efficiency when determined by colony formation assay. In the current study, conjugation efficiencies were determined under different conditions using a two-color fluorescence-activated flow cytometry method and measuring a single-round of pLS20-mediated transfer of a mobilizable plasmid. Under standard conditions, the conjugation efficiency obtained by fluorescence-activated flow cytometry was 23-fold higher than that obtained by colony formation. Furthermore, the efficiency difference increased to 45-fold when rappLS20 was overexpressed.
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Affiliation(s)
- Kotaro Mori
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
| | - Valeria Verrone
- School of Computing, Newcastle University, 1 Science Square, Science Central, Newcastle upon Tyne NE4 5TG, UK; (V.V.); (A.W.)
| | - Ryotaro Amatsu
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
| | - Kaho Fukui
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain;
| | - Shu Ishikawa
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
| | - Anil Wipat
- School of Computing, Newcastle University, 1 Science Square, Science Central, Newcastle upon Tyne NE4 5TG, UK; (V.V.); (A.W.)
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (K.M.); (R.A.); (K.F.); (S.I.)
- Correspondence: ; Tel.: +81-78-803-5891
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19
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Miguel-Arribas A, Val-Calvo J, Gago-Córdoba C, Izquierdo JM, Abia D, Wu LJ, Errington J, Meijer WJJ. A novel bipartite antitermination system widespread in conjugative elements of Gram-positive bacteria. Nucleic Acids Res 2021; 49:5553-5567. [PMID: 33999173 PMCID: PMC8191782 DOI: 10.1093/nar/gkab360] [Citation(s) in RCA: 3] [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: 02/22/2021] [Revised: 04/09/2021] [Accepted: 04/23/2021] [Indexed: 11/18/2022] Open
Abstract
Transcriptional regulation allows adaptive and coordinated gene expression, and is essential for life. Processive antitermination systems alter the transcription elongation complex to allow the RNA polymerase to read through multiple terminators in an operon. Here, we describe the discovery of a novel bipartite antitermination system that is widespread among conjugative elements from Gram-positive bacteria, which we named conAn. This system is composed of a large RNA element that exerts antitermination, and a protein that functions as a processivity factor. Besides allowing coordinated expression of very long operons, we show that these systems allow differential expression of genes within an operon, and probably contribute to strict regulation of the conjugation genes by minimizing the effects of spurious transcription. Mechanistic features of the conAn system are likely to decisively influence its host range, with important implications for the spread of antibiotic resistance and virulence genes.
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Affiliation(s)
- Andrés Miguel-Arribas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Jorge Val-Calvo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - César Gago-Córdoba
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - José M Izquierdo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular "Severo Ochoa", (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK
| | - Jeff Errington
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE2 4AX, UK
| | - Wilfried J J Meijer
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma de Madrid, Canto Blanco, 28049 Madrid, Spain
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20
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A native conjugative plasmid confers potential selective advantages to plant growth-promoting Bacillus velezensis strain GH1-13. Commun Biol 2021; 4:582. [PMID: 33990691 PMCID: PMC8121941 DOI: 10.1038/s42003-021-02107-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/13/2021] [Indexed: 02/04/2023] Open
Abstract
The conjugative plasmid (pBV71) possibly confers a selective advantage to Bacillus velezensis strain GH1-13, although a selective marker gene is yet to be identified. Here we show that few non-mucoid wild-type GH1-13 cells are spontaneously converted to mucoid variants with or without the loss of pBV71. Mucoid phenotypes, which contain or lack the plasmid, become sensitive to bacitracin, gramicidin, selenite, and tellurite. Using the differences in antibiotic resistance and phenotype, we isolated a reverse complement (COM) and a transconjugant of strain FZB42 with the native pBV71. Transformed COM and FZB42p cells were similar to the wild-type strain GH1-13 with high antibiotic resistance and slow growth rates on lactose compared to those of mucoid phenotypes. RT-PCR analysis revealed that the expression of plasmid-encoded orphan aspartate phosphatase (pRapD) was coordinated with a new quorum-sensing (QS) cassette of RapF2-PhrF2 present in the chromosome of strain GH1-13, but not in strain FZB42. Multi-omics analysis on wild-type and plasmid-cured cells of strain GH1-13 suggested that the conjugative plasmid expression has a crucial role in induction of early envelope stress response that promotes cell morphogenesis, biofilm formation, catabolite repression, and biosynthesis of extracellular-matrix components and antibiotics for protection of host cell during exponential phase.
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21
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Abstract
Bacteriophages are the most diverse and abundant biological entities on the Earth and require host bacteria to replicate. Because of this obligate relationship, in addition to the challenging conditions of surrounding environments, phages must integrate information about extrinsic and intrinsic factors when infecting their host. This integration helps to determine whether the infection becomes lytic or lysogenic, which likely influences phage spreading and long-term survival. Although a variety of environmental and physiological clues are known to modulate lysis-lysogeny decisions, the social interplay among phages and host populations has been overlooked until recently. A growing body of evidence indicates that cell-cell communication in bacteria and, more recently, peptide-based communication among phage-phage populations, affect phage-host interactions by controlling phage lysis-lysogeny decisions and phage counter-defensive strategies in bacteria. Here, we explore and discuss the role of signal molecules as well as quorum sensing and quenching factors that mediate phage-host interactions. Our aim is to provide an overview of population-dependent mechanisms that influence phage replication, and how social communication may affect the dynamics and evolution of microbial communities, including their implications in phage therapy.
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22
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van Gestel J, Bareia T, Tenennbaum B, Dal Co A, Guler P, Aframian N, Puyesky S, Grinberg I, D’Souza GG, Erez Z, Ackermann M, Eldar A. Short-range quorum sensing controls horizontal gene transfer at micron scale in bacterial communities. Nat Commun 2021; 12:2324. [PMID: 33875666 PMCID: PMC8055654 DOI: 10.1038/s41467-021-22649-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 03/17/2021] [Indexed: 02/02/2023] Open
Abstract
In bacterial communities, cells often communicate by the release and detection of small diffusible molecules, a process termed quorum-sensing. Signal molecules are thought to broadly diffuse in space; however, they often regulate traits such as conjugative transfer that strictly depend on the local community composition. This raises the question how nearby cells within the community can be detected. Here, we compare the range of communication of different quorum-sensing systems. While some systems support long-range communication, we show that others support a form of highly localized communication. In these systems, signal molecules propagate no more than a few microns away from signaling cells, due to the irreversible uptake of the signal molecules from the environment. This enables cells to accurately detect micron scale changes in the community composition. Several mobile genetic elements, including conjugative elements and phages, employ short-range communication to assess the fraction of susceptible host cells in their vicinity and adaptively trigger horizontal gene transfer in response. Our results underscore the complex spatial biology of bacteria, which can communicate and interact at widely different spatial scales.
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Affiliation(s)
- Jordi van Gestel
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland ,grid.418656.80000 0001 1551 0562Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland ,grid.7400.30000 0004 1937 0650Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland ,grid.419765.80000 0001 2223 3006Swiss Institute of Bioinformatics, Lausanne, Switzerland ,grid.266102.10000 0001 2297 6811Present Address: Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA USA
| | - Tasneem Bareia
- grid.12136.370000 0004 1937 0546The Shmunis School of Biomedicine and Cancer Research, Tel-Aviv University, Tel-Aviv, Israel
| | - Bar Tenennbaum
- grid.12136.370000 0004 1937 0546The Shmunis School of Biomedicine and Cancer Research, Tel-Aviv University, Tel-Aviv, Israel
| | - Alma Dal Co
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland ,grid.418656.80000 0001 1551 0562Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland ,grid.38142.3c000000041936754XSchool of Engineering and Applied Sciences, Harvard University, Cambridge, MA USA
| | - Polina Guler
- grid.12136.370000 0004 1937 0546The Shmunis School of Biomedicine and Cancer Research, Tel-Aviv University, Tel-Aviv, Israel
| | - Nitzan Aframian
- grid.12136.370000 0004 1937 0546The Shmunis School of Biomedicine and Cancer Research, Tel-Aviv University, Tel-Aviv, Israel
| | - Shani Puyesky
- grid.12136.370000 0004 1937 0546The Shmunis School of Biomedicine and Cancer Research, Tel-Aviv University, Tel-Aviv, Israel
| | - Ilana Grinberg
- grid.12136.370000 0004 1937 0546The Shmunis School of Biomedicine and Cancer Research, Tel-Aviv University, Tel-Aviv, Israel
| | - Glen G. D’Souza
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland ,grid.418656.80000 0001 1551 0562Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Zohar Erez
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Martin Ackermann
- grid.5801.c0000 0001 2156 2780Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland ,grid.418656.80000 0001 1551 0562Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Avigdor Eldar
- grid.12136.370000 0004 1937 0546The Shmunis School of Biomedicine and Cancer Research, Tel-Aviv University, Tel-Aviv, Israel
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23
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Meijer WJJ, Boer DR, Ares S, Alfonso C, Rojo F, Luque-Ortega JR, Wu LJ. Multiple Layered Control of the Conjugation Process of the Bacillus subtilis Plasmid pLS20. Front Mol Biosci 2021; 8:648468. [PMID: 33816561 PMCID: PMC8014075 DOI: 10.3389/fmolb.2021.648468] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 02/08/2021] [Indexed: 11/24/2022] Open
Abstract
Bacterial conjugation is the main horizontal gene transfer route responsible for the spread of antibiotic resistance, virulence and toxin genes. During conjugation, DNA is transferred from a donor to a recipient cell via a sophisticated channel connecting the two cells. Conjugation not only affects many different aspects of the plasmid and the host, ranging from the properties of the membrane and the cell surface of the donor, to other developmental processes such as competence, it probably also poses a burden on the donor cell due to the expression of the large number of genes involved in the conjugation process. Therefore, expression of the conjugation genes must be strictly controlled. Over the past decade, the regulation of the conjugation genes present on the conjugative Bacillus subtilis plasmid pLS20 has been studied using a variety of methods including genetic, biochemical, biophysical and structural approaches. This review focuses on the interplay between RcopLS20, RappLS20 and Phr*pLS20, the proteins that control the activity of the main conjugation promoter Pc located upstream of the conjugation operon. Proper expression of the conjugation genes requires the following two fundamental elements. First, conjugation is repressed by default and an intercellular quorum-signaling system is used to sense conditions favorable for conjugation. Second, different layers of regulation act together to repress the Pc promoter in a strict manner but allowing rapid activation. During conjugation, ssDNA is exported from the cell by a membrane-embedded DNA translocation machine. Another membrane-embedded DNA translocation machine imports ssDNA in competent cells. Evidences are reviewed indicating that conjugation and competence are probably mutually exclusive processes. Some of the questions that remain unanswered are discussed.
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Affiliation(s)
- Wilfried J J Meijer
- Laboratory 402, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | | | - Saúl Ares
- Laboratory 35, C. Grupo Interdisciplinar de Sistemas Complejos and Departamento de Biología de Sistemas, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Carlos Alfonso
- Laboratory B08, Systems Biochemistry of Bacterial Division Lab, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Fernando Rojo
- Laboratory 216, Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Juan R Luque-Ortega
- Laboratory S07, Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, United Kingdom
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24
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Gago-Córdoba C, Val-Calvo J, Abia D, Díaz-Talavera A, Miguel-Arribas A, Aguilar Suárez R, van Dijl JM, Wu LJ, Meijer WJJ. A Conserved Class II Type Thioester Domain-Containing Adhesin Is Required for Efficient Conjugation in Bacillus subtilis. mBio 2021; 12:e00104-21. [PMID: 33727345 PMCID: PMC8092201 DOI: 10.1128/mbio.00104-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/05/2021] [Indexed: 12/16/2022] Open
Abstract
Conjugation, the process by which a DNA element is transferred from a donor to a recipient cell, is the main horizontal gene transfer route responsible for the spread of antibiotic resistance and virulence genes. Contact between a donor and a recipient cell is a prerequisite for conjugation, because conjugative DNA is transferred into the recipient via a channel connecting the two cells. Conjugative elements encode proteins dedicated to facilitating the recognition and attachment to recipient cells, also known as mating pair formation. A subgroup of the conjugative elements is able to mediate efficient conjugation during planktonic growth, and mechanisms facilitating mating pair formation will be particularly important in these cases. Conjugative elements of Gram-negative bacteria encode conjugative pili, also known as sex pili, some of which are retractile. Far less is known about mechanisms that promote mating pair formation in Gram-positive bacteria. The conjugative plasmid pLS20 of the Gram-positive bacterium Bacillus subtilis allows efficient conjugation in liquid medium. Here, we report the identification of an adhesin gene in the pLS20 conjugation operon. The N-terminal region of the adhesin contains a class II type thioester domain (TED) that is essential for efficient conjugation, particularly in liquid medium. We show that TED-containing adhesins are widely conserved in Gram-positive bacteria, including pathogens where they often play crucial roles in pathogenesis. Our study is the first to demonstrate the involvement of a class II type TED-containing adhesin in conjugation.IMPORTANCE Bacterial resistance to antibiotics has become a serious health care problem. The spread of antibiotic resistance genes between bacteria of the same or different species is often mediated by a process named conjugation, where a donor cell transfers DNA to a recipient cell through a connecting channel. The first step in conjugation is recognition and attachment of the donor to a recipient cell. Little is known about this first step, particularly in Gram-positive bacteria. Here, we show that the conjugative plasmid pLS20 of Bacillus subtilis encodes an adhesin protein that is essential for effective conjugation. This adhesin protein has a structural organization similar to adhesins produced by other Gram-positive bacteria, including major pathogens, where the adhesins serve in attachment to host tissues during colonization and infection. Our findings may thus also open novel avenues to design drugs that inhibit the spread of antibiotic resistance by blocking the first recipient-attachment step in conjugation.
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Affiliation(s)
- César Gago-Córdoba
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | - Jorge Val-Calvo
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | - David Abia
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | - Alberto Díaz-Talavera
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
| | - Rocío Aguilar Suárez
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jan Maarten van Dijl
- University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Wilfried J J Meijer
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Universidad Autónoma, Madrid, Spain
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25
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Jones JM, Grinberg I, Eldar A, Grossman AD. A mobile genetic element increases bacterial host fitness by manipulating development. eLife 2021; 10:65924. [PMID: 33655883 PMCID: PMC8032392 DOI: 10.7554/elife.65924] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/01/2021] [Indexed: 01/30/2023] Open
Abstract
Horizontal gene transfer is a major force in bacterial evolution. Mobile genetic elements are responsible for much of horizontal gene transfer and also carry beneficial cargo genes. Uncovering strategies used by mobile genetic elements to benefit host cells is crucial for understanding their stability and spread in populations. We describe a benefit that ICEBs1, an integrative and conjugative element of Bacillus subtilis, provides to its host cells. Activation of ICEBs1 conferred a frequency-dependent selective advantage to host cells during two different developmental processes: biofilm formation and sporulation. These benefits were due to inhibition of biofilm-associated gene expression and delayed sporulation by ICEBs1-containing cells, enabling them to exploit their neighbors and grow more prior to development. A single ICEBs1 gene, devI (formerly ydcO), was both necessary and sufficient for inhibition of development. Manipulation of host developmental programs allows ICEBs1 to increase host fitness, thereby increasing propagation of the element. Many bacteria can ‘have sex’ – that is, they can share their genetic information and trade off segments of DNA. While these mobile genetic elements can be parasites that use the resources of their host to make more of themselves, some carry useful genes which, for example, help bacteria to fight off antibiotics. Integrative and conjugative elements (or ICEs) are a type of mobile segments that normally stay inside the genetic information of their bacterial host but can sometimes replicate and be pumped out to another cell. ICEBs1 for instance, is an element found in the common soil bacterium Bacillus subtilis. Scientists know that ICEBs1 can rapidly spread in biofilms – the slimly, crowded communities where bacteria live tightly connected – but it is still unclear whether it helps or hinders its hosts. Using genetic manipulations and tracking the survival of different groups of cells, Jones et al. show that carrying ICEBs1 confers an advantage under many conditions. When B. subtilis forms biofilms, the presence of the devI gene in ICEBs1 helps the cells to delay the production of the costly mucus that keeps bacteria together, allowing the organisms to ‘cheat’ for a little while and benefit from the tight-knit community without contributing to it. As nutrients become scarce in biofilms, the gene also allows the bacteria to grow for longer before they start to form spores – the dormant bacterial form that can weather difficult conditions. Mobile elements can carry genes that make bacteria resistant to antibiotics, harmful to humans, or able to use new food sources; they could even be used to artificially introduce genes of interest in these cells. The work by Jones et al. helps to understand the way these elements influence the fate of their host, providing insight into how they could be harnessed for the benefit of human health.
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Affiliation(s)
- Joshua M Jones
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Ilana Grinberg
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Avigdor Eldar
- The Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Alan D Grossman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
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26
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Shu CC, Chen WC, Chang YD, Chen JN, Liu FY, Huang YS, You CX, Wu EH. Exposure to One Antibiotic Leads to Acquisition of Resistance to Another Antibiotic via Quorum Sensing Mechanisms. Front Microbiol 2021; 11:580466. [PMID: 33552007 PMCID: PMC7855173 DOI: 10.3389/fmicb.2020.580466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 12/11/2020] [Indexed: 11/13/2022] Open
Abstract
The vancomycin-resistant Enterococci (VRE) have progressively become a severe medical problem. Although clinics have started to reduce vancomycin prescription, vancomycin resistance has not been contained. We found that the transfer of vancomycin resistance in Enterococcus faecalis increased more than 30-fold upon treatment by streptomycin. Notably, treatment with an antibiotic caused the bacteria to become resistant to another. The response was even stronger in the well-studied plasmid pCF10 and the number of transconjugants increased about 100,000-fold. We tested four different antibiotics, and all of them induced conjugal response. Through a mathematical model based on gene regulation, we found a plausible explanation. Via quorum sensing, the change of the cell density triggers the conjugation. Moreover, we searched for generality and found a similar strategy in Bacillus subtilis. The outcome of the present study suggests that even common antibiotics must not be overused.
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Affiliation(s)
- Che-Chi Shu
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan
| | - Wan-Ci Chen
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan
| | - Yao-Duo Chang
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan
| | - Jyy-Ning Chen
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan
| | - Feng-You Liu
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan
| | - Yu-Shan Huang
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan
| | - Chao-Xuan You
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan
| | - En Hsuan Wu
- Department of Chemical Engineering and Biotechnology, National Taipei University of Technology, Taipei, Taiwan
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27
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Pessione E. The Less Expensive Choice: Bacterial Strategies to Achieve Successful and Sustainable Reciprocal Interactions. Front Microbiol 2021; 11:571417. [PMID: 33584557 PMCID: PMC7873842 DOI: 10.3389/fmicb.2020.571417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/11/2020] [Indexed: 12/22/2022] Open
Abstract
Bacteria, the first organisms that appeared on Earth, continue to play a central role in ensuring life on the planet, both as biogeochemical agents and as higher organisms' symbionts. In the last decades, they have been employed both as bioremediation agents for cleaning polluted sites and as bioconversion effectors for obtaining a variety of products from wastes (including eco-friendly plastics and green energies). However, some recent reports suggest that bacterial biodiversity can be negatively affected by the present environmental crisis (global warming, soil desertification, and ocean acidification). This review analyzes the behaviors positively selected by evolution that render bacteria good models of sustainable practices (urgent in these times of climate change and scarcity of resources). Actually, bacteria display a tendency to optimize rather than maximize, to economize energy and building blocks (by using the same molecule for performing multiple functions), and to recycle and share metabolites, and these are winning strategies when dealing with sustainability. Furthermore, their ability to establish successful reciprocal relationships by means of anticipation, collective actions, and cooperation can also constitute an example highlighting how evolutionary selection favors behaviors that can be strategic to contain the present environmental crisis.
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Affiliation(s)
- Enrica Pessione
- Department of Life Sciences and Systems Biology, Università degli Studi di Torino, Torino, Italy
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28
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Affiliation(s)
- Olivia P. Duddy
- Department of Molecular Biology, Princeton University, Princeton, United States of America
| | - Bonnie L. Bassler
- Department of Molecular Biology, Princeton University, Princeton, United States of America
- Howard Hughes Medical Institute, Chevy Chase, United States of America
- * E-mail:
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29
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Dragoš A, Priyadarshini B, Hasan Z, Strube ML, Kempen PJ, Maróti G, Kaspar C, Bose B, Burton BM, Bischofs IB, Kovács ÁT. Pervasive prophage recombination occurs during evolution of spore-forming Bacilli. ISME JOURNAL 2020; 15:1344-1358. [PMID: 33343000 DOI: 10.1038/s41396-020-00854-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 11/12/2020] [Accepted: 11/20/2020] [Indexed: 02/06/2023]
Abstract
Phages are the main source of within-species bacterial diversity and drivers of horizontal gene transfer, but we know little about the mechanisms that drive genetic diversity of these mobile genetic elements (MGEs). Recently, we showed that a sporulation selection regime promotes evolutionary changes within SPβ prophage of Bacillus subtilis, leading to direct antagonistic interactions within the population. Herein, we reveal that under a sporulation selection regime, SPβ recombines with low copy number phi3Ts phage DNA present within the B. subtilis population. Recombination results in a new prophage occupying a different integration site, as well as the spontaneous release of virulent phage hybrids. Analysis of Bacillus sp. strains suggests that SPβ and phi3T belong to a distinct cluster of unusually large phages inserted into sporulation-related genes that are equipped with a spore-related genetic arsenal. Comparison of Bacillus sp. genomes indicates that similar diversification of SPβ-like phages takes place in nature. Our work is a stepping stone toward empirical studies on phage evolution, and understanding the eco-evolutionary relationships between bacteria and their phages. By capturing the first steps of new phage evolution, we reveal striking relationship between survival strategy of bacteria and evolution of their phages.
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Affiliation(s)
- Anna Dragoš
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
| | - B Priyadarshini
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Zahraa Hasan
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Mikael Lenz Strube
- Bacterial Ecophysiology and Biotechnology Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Paul J Kempen
- Department of Health Technology, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Gergely Maróti
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, H-6701, Hungary
| | - Charlotte Kaspar
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | | | - Briana M Burton
- Department of Bacteriology, University of Wisconsin, Madison, WI, 53706, USA
| | - Ilka B Bischofs
- BioQuant Center of the University of Heidelberg, 69120, Heidelberg, Germany.,Max-Planck-Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kongens Lyngby, Denmark.
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30
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Crespo I, Bernardo N, Miguel-Arribas A, Singh PK, Luque-Ortega JR, Alfonso C, Malfois M, Meijer WJJ, Boer DR. Inactivation of the dimeric RappLS20 anti-repressor of the conjugation operon is mediated by peptide-induced tetramerization. Nucleic Acids Res 2020; 48:8113-8127. [PMID: 32658272 PMCID: PMC7430634 DOI: 10.1093/nar/gkaa540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/08/2020] [Accepted: 06/15/2020] [Indexed: 12/21/2022] Open
Abstract
Quorum sensing allows bacterial cells to communicate through the release of soluble signaling molecules into the surrounding medium. It plays a pivotal role in controlling bacterial conjugation in Gram-positive cells, a process that has tremendous impact on health. Intracellular regulatory proteins of the RRNPP family are common targets of these signaling molecules. The RRNPP family of gene regulators bind signaling molecules at their C-terminal domain (CTD), but have highly divergent functionalities at their N-terminal effector domains (NTD). This divergence is also reflected in the functional states of the proteins, and is highly interesting from an evolutionary perspective. RappLS20 is an RRNPP encoded on the Bacillus subtilis plasmid pLS20. It relieves the gene repression effectuated by RcopLS20 in the absence of the mature pLS20 signaling peptide Phr*pLS20. We report here an in-depth structural study of apo and Phr*pLS20-bound states of RappLS20 at various levels of atomic detail. We show that apo-RappLS20 is dimeric and that Phr*pLS20-bound Rap forms NTD-mediated tetramers. In addition, we show that RappLS20 binds RcopLS20 directly in the absence of Phr*pLS20 and that addition of Phr*pLS20 releases RcopLS20 from RappLS20. This allows RcopLS20 to bind the promotor region of crucial conjugation genes blocking their expression.
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Affiliation(s)
- Isidro Crespo
- ALBA Synchrotron Light Source, C. de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Nerea Bernardo
- ALBA Synchrotron Light Source, C. de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Praveen K Singh
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Juan R Luque-Ortega
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C. Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Carlos Alfonso
- Systems Biochemistry of Bacterial Division Lab, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C. Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Marc Malfois
- ALBA Synchrotron Light Source, C. de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
| | - Wilfried J J Meijer
- Centro de Biología Molecular 'Severo Ochoa' (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Dirk Roeland Boer
- ALBA Synchrotron Light Source, C. de la Llum 2-26, Cerdanyola del Vallès, 08290 Barcelona, Spain
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31
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Singh PK, Serrano E, Ramachandran G, Miguel-Arribas A, Gago-Cordoba C, Val-Calvo J, López-Pérez A, Alfonso C, Wu LJ, Luque-Ortega JR, Meijer WJJ. Reversible regulation of conjugation of Bacillus subtilis plasmid pLS20 by the quorum sensing peptide responsive anti-repressor RappLS20. Nucleic Acids Res 2020; 48:10785-10801. [PMID: 33045732 PMCID: PMC7641744 DOI: 10.1093/nar/gkaa797] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/02/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022] Open
Abstract
Quorum sensing plays crucial roles in bacterial communication including in the process of conjugation, which has large economical and health-related impacts by spreading antibiotic resistance. The conjugative Bacillus subtilis plasmid pLS20 uses quorum sensing to determine when to activate the conjugation genes. The main conjugation promoter, Pc, is by default repressed by a regulator RcopLS20 involving DNA looping. A plasmid-encoded signalling peptide, Phr*pLS20, inactivates the anti-repressor of RcopLS20, named RappLS20, which belongs to the large group of RRNPP family of regulatory proteins. Here we show that DNA looping occurs through interactions between two RcopLS20 tetramers, each bound to an operator site. We determined the relative promoter strengths for all the promoters involved in synthesizing the regulatory proteins of the conjugation genes, and constructed an in vivo system uncoupling these regulatory genes to show that RappLS20 is sufficient for activating conjugation in vivo. We also show that RappLS20 actively detaches RcopLS20 from DNA by preferentially acting on the RcopLS20 molecules involved in DNA looping, resulting in sequestration but not inactivation of RcopLS20. Finally, results presented here in combination with our previous results show that activation of conjugation inhibits competence and competence development inhibits conjugation, indicating that both processes are mutually exclusive.
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Affiliation(s)
- Praveen K Singh
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Ester Serrano
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Gayetri Ramachandran
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - César Gago-Cordoba
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Jorge Val-Calvo
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Arancha López-Pérez
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), C. Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Juan R Luque-Ortega
- Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas (CSIC), C. Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Wilfried J J Meijer
- Centro de Biología Molecular “Severo Ochoa’’ (CSIC-UAM), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
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32
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Rap-Phr Systems from Plasmids pAW63 and pHT8-1 Act Together To Regulate Sporulation in the Bacillus thuringiensis Serovar kurstaki HD73 Strain. Appl Environ Microbiol 2020; 86:AEM.01238-20. [PMID: 32680861 DOI: 10.1128/aem.01238-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 07/13/2020] [Indexed: 02/07/2023] Open
Abstract
Bacillus thuringiensis is a Gram-positive spore-forming bacterium pathogenic to various insect species. This property is due to the Cry toxins encoded by plasmid genes and mostly produced during sporulation. B. thuringiensis contains a remarkable number of extrachromosomal DNA molecules and a great number of plasmid rap-phr genes. Rap-Phr quorum-sensing systems regulate different bacterial processes, notably the commitment to sporulation in Bacillus species. Rap proteins are quorum sensors acting as phosphatases on Spo0F, an intermediate of the sporulation phosphorelay, and are inhibited by Phr peptides that function as signaling molecules. In this study, we characterize the Rap63-Phr63 system encoded by the pAW63 plasmid from the B. thuringiensis serovar kurstaki HD73 strain. Rap63 has moderate activity on sporulation and is inhibited by the Phr63 peptide. The rap63-phr63 genes are cotranscribed, and the phr63 gene is also transcribed from a σH-specific promoter. We show that Rap63-Phr63 regulates sporulation together with the Rap8-Phr8 system harbored by plasmid pHT8_1 of the HD73 strain. Interestingly, the deletion of both phr63 and phr8 genes in the same strain has a greater negative effect on sporulation than the sum of the loss of each phr gene. Despite the similarities in the Phr8 and Phr63 sequences, there is no cross talk between the two systems. Our results suggest a synergism of these two Rap-Phr systems in the regulation of the sporulation of B. thuringiensis at the end of the infectious cycle in insects, thus pointing out the roles of the plasmids in the fitness of the bacterium.IMPORTANCE The life cycle of Bacillus thuringiensis in insect larvae is regulated by quorum-sensing systems of the RNPP family. After the toxemia caused by Cry insecticidal toxins, the sequential activation of these systems allows the bacterium to trigger first a state of virulence (regulated by PlcR-PapR) and then a necrotrophic lifestyle (regulated by NprR-NprX); ultimately, sporulation is controlled by the Rap-Phr systems. Our study describes a new rap-phr operon carried by a B. thuringiensis plasmid and shows that the Rap protein has a moderate effect on sporulation. However, this system, in combination with another plasmidic rap-phr operon, provides effective control of sporulation when the bacteria develop in the cadavers of infected insect larvae. Overall, this study highlights the important adaptive role of the plasmid Rap-Phr systems in the developmental fate of B. thuringiensis and its survival within its ecological niche.
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33
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Stokar-Avihail A, Tal N, Erez Z, Lopatina A, Sorek R. Widespread Utilization of Peptide Communication in Phages Infecting Soil and Pathogenic Bacteria. Cell Host Microbe 2019; 25:746-755.e5. [PMID: 31071296 DOI: 10.1016/j.chom.2019.03.017] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/04/2019] [Accepted: 03/25/2019] [Indexed: 11/27/2022]
Abstract
Temperate phages can adopt either a lytic or lysogenic lifestyle within their host bacteria. It was recently shown that Bacillus-subtilis-infecting phages of the SPbeta group utilize a peptide-based communication system called arbitrium to coordinate the lysogeny decision. The occurrence of peptide-based communication systems among phages more broadly remains to be explored. Here, we uncover a wide array of peptide-based communication systems utilized by phages for lysogeny decisions. These arbitrium-like systems show diverse peptide codes and can be detected in numerous genetically distant phage types and conjugative elements. The pathogens Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis are commonly infected by arbitrium-carrying mobile elements, which often carry toxins essential for pathogenicity. Experiments with phages containing these arbitrium-like systems demonstrate their involvement in lysogeny decisions. Finally, our results suggest that the peptide-based decision is executed by an antisense RNA that controls the regulator of the lysogenic state.
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Affiliation(s)
| | - Nitzan Tal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Zohar Erez
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Anna Lopatina
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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34
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Itaya M, Sato M, Watanabe S, Yoshikawa H, Tomita M, Sato R. Stable mutants of restriction-deficient/modification-proficient Bacillus subtilis 168: hub strains for giant DNA engineering. J Biochem 2019; 166:231-236. [PMID: 31004491 DOI: 10.1093/jb/mvz031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/14/2019] [Indexed: 11/14/2022] Open
Abstract
Bacillus subtilis 168 has been explored as a platform for the synthesis and transmission of large DNA. Two inherent DNA incorporation systems, natural transformation and pLS20-based conjugation transfer, enable rapid handling of target DNA. Both systems are affected by the Bsu restriction-modification system that recognizes and cleaves unmethylated XhoI sites, limiting the choice of target DNA. We constructed B. subtilis 168 with stable mutation for restriction-deficient and modification-proficient (r-m+). It was demonstrated that the r-m+ strains can incorporate and transfer synthesized DNA with multiple XhoI sites. These should be of value as hub strains to integrate and disseminate giant DNA between B. subtilis 168 derivatives.
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Affiliation(s)
- Mitsuhiro Itaya
- Institute for Advanced Biosciences, Keio University, Nipponkoku, Daihoji, Tsuruoka-shi, Yamagata, Japan
| | - Mitsuru Sato
- Institute for Advanced Biosciences, Keio University, Nipponkoku, Daihoji, Tsuruoka-shi, Yamagata, Japan
| | - Satoru Watanabe
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, Japan
| | - Hirofumi Yoshikawa
- Department of Bioscience, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Nipponkoku, Daihoji, Tsuruoka-shi, Yamagata, Japan
| | - Rintaro Sato
- Institute for Advanced Biosciences, Keio University, Nipponkoku, Daihoji, Tsuruoka-shi, Yamagata, Japan
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35
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Gago-Córdoba C, Val-Calvo J, Miguel-Arribas A, Serrano E, Singh PK, Abia D, Wu LJ, Meijer WJJ. Surface Exclusion Revisited: Function Related to Differential Expression of the Surface Exclusion System of Bacillus subtilis Plasmid pLS20. Front Microbiol 2019; 10:1502. [PMID: 31354647 PMCID: PMC6635565 DOI: 10.3389/fmicb.2019.01502] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Accepted: 06/14/2019] [Indexed: 11/17/2022] Open
Abstract
During conjugation a genetic element is transferred from a bacterial donor to a recipient cell via a connecting channel. It is the major route responsible for the spread of antibiotic resistance. Conjugative elements can contain exclusion system(s) that inhibit its transfer to a cell already harboring the element. Our limited knowledge on exclusion systems is mainly based on plasmids of Gram-negative bacteria. Here we studied the conjugative plasmid pLS20 of the Gram-positive Bacillus subtilis. We demonstrate that pLS20 contains an exclusion system and identified the single gene responsible for exclusion, named sespLS20 , which is embedded in the conjugation operon. SespLS20 is the founding member of a novel family of surface exclusion proteins encoded by conjugative elements of Gram-positive origin. We show that the extent of surface exclusion correlates with the level of sespLS20 expression, and that sespLS20 is expressed at basal low-levels in all donor cells but becomes highly expressed in conjugating cells. Accordingly, the transfer of pLS20 from a conjugation-primed donor cell to an un-primed or conjugation-primed donor is inhibited moderately and very efficiently, respectively. The consequences of this differential regulation, which appears to be a conserved feature of surface exclusion systems of Gram-positive and Gram-negative origin, are discussed.
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Affiliation(s)
- César Gago-Córdoba
- Laboratory 402, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Department of Virology and Microbiology, Autonomous University of Madrid, Madrid, Spain
| | - Jorge Val-Calvo
- Laboratory 402, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Department of Virology and Microbiology, Autonomous University of Madrid, Madrid, Spain
| | - Andrés Miguel-Arribas
- Laboratory 402, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Department of Virology and Microbiology, Autonomous University of Madrid, Madrid, Spain
| | - Ester Serrano
- Laboratory 402, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Department of Virology and Microbiology, Autonomous University of Madrid, Madrid, Spain
| | - Praveen K. Singh
- Laboratory 402, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Department of Virology and Microbiology, Autonomous University of Madrid, Madrid, Spain
| | - David Abia
- Laboratory 402, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Department of Virology and Microbiology, Autonomous University of Madrid, Madrid, Spain
| | - Ling Juan Wu
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Wilfried J. J. Meijer
- Laboratory 402, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Department of Virology and Microbiology, Autonomous University of Madrid, Madrid, Spain
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36
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Val-Calvo J, Luque-Ortega JR, Crespo I, Miguel-Arribas A, Abia D, Sánchez-Hevia DL, Serrano E, Gago-Córdoba C, Ares S, Alfonso C, Rojo F, Wu LJ, Boer DR, Meijer WJJ. Novel regulatory mechanism of establishment genes of conjugative plasmids. Nucleic Acids Res 2019; 46:11910-11926. [PMID: 30380104 PMCID: PMC6294495 DOI: 10.1093/nar/gky996] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/10/2018] [Indexed: 11/12/2022] Open
Abstract
The principal route for dissemination of antibiotic resistance genes is conjugation by which a conjugative DNA element is transferred from a donor to a recipient cell. Conjugative elements contain genes that are important for their establishment in the new host, for instance by counteracting the host defense mechanisms acting against incoming foreign DNA. Little is known about these establishment genes and how they are regulated. Here, we deciphered the regulation mechanism of possible establishment genes of plasmid p576 from the Gram-positive bacterium Bacillus pumilus. Unlike the ssDNA promoters described for some conjugative plasmids, the four promoters of these p576 genes are repressed by a repressor protein, which we named Reg576. Reg576 also regulates its own expression. After transfer of the DNA, these genes are de-repressed for a period of time until sufficient Reg576 is synthesized to repress the promoters again. Complementary in vivo and in vitro analyses showed that different operator configurations in the promoter regions of these genes lead to different responses to Reg576. Each operator is bound with extreme cooperativity by two Reg576-dimers. The X-ray structure revealed that Reg576 has a Ribbon-Helix-Helix core and provided important insights into the high cooperativity of DNA recognition.
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Affiliation(s)
- Jorge Val-Calvo
- Department of Virology and Microbiology, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Juan R Luque-Ortega
- Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Isidro Crespo
- ALBA Synchrotron Light Source, Carrer de la Llum 2-26, Cerdanyola del Vallès, Barcelona 08290, Spain
| | - Andrés Miguel-Arribas
- Department of Virology and Microbiology, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - David Abia
- Bioinformatics Facility, Centro de Biología Molecular "Severo Ochoa"
| | | | - Ester Serrano
- Department of Virology and Microbiology, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - César Gago-Córdoba
- Department of Virology and Microbiology, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Saúl Ares
- Centro Nacional de Biotecnología (CSIC), Darwin 3, 28049 Madrid, Spain.,Grupo Interdisciplinar de Sistemas Complejos (GISC) and Departamento de Matemáticas, Universidad Carlos III de Madrid, 28911 Leganes, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Fernando Rojo
- Centro Nacional de Biotecnología (CSIC), Darwin 3, 28049 Madrid, Spain
| | - Ling J Wu
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Richardson Road, Newcastle Upon Tyne, NE4AX, UK
| | - D Roeland Boer
- ALBA Synchrotron Light Source, Carrer de la Llum 2-26, Cerdanyola del Vallès, Barcelona 08290, Spain
| | - Wilfried J J Meijer
- Department of Virology and Microbiology, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), C. Nicolás Cabrera 1, Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
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37
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Kohler V, Keller W, Grohmann E. Regulation of Gram-Positive Conjugation. Front Microbiol 2019; 10:1134. [PMID: 31191478 PMCID: PMC6540685 DOI: 10.3389/fmicb.2019.01134] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/03/2019] [Indexed: 12/20/2022] Open
Abstract
Type IV Secretion Systems (T4SSs) are membrane-spanning multiprotein complexes dedicated to protein secretion or conjugative DNA transport (conjugation systems) in bacteria. The prototype and best-characterized T4SS is that of the Gram-negative soil bacterium Agrobacterium tumefaciens. For Gram-positive bacteria, only conjugative T4SSs have been characterized in some biochemical, structural, and mechanistic details. These conjugation systems are predominantly encoded by self-transmissible plasmids but are also increasingly detected on integrative and conjugative elements (ICEs) and transposons. Here, we report regulatory details of conjugation systems from Enterococcus model plasmids pIP501 and pCF10, Bacillus plasmid pLS1, Clostridium plasmid pCW3, and staphylococcal plasmid pSK41. In addition, regulation of conjugative processes of ICEs (ICEBs1, ICESt1, ICESt3) by master regulators belonging to diverse repressor families will be discussed. A special focus of this review lies on the comparison of regulatory mechanisms executed by proteins belonging to the RRNPP family. These regulators share a common fold and govern several essential bacterial processes, including conjugative transfer.
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Affiliation(s)
- Verena Kohler
- Institute of Molecular Biosciences, BioTechMed Graz, University of Graz, Graz, Austria
| | - Walter Keller
- Institute of Molecular Biosciences, BioTechMed Graz, University of Graz, Graz, Austria
| | - Elisabeth Grohmann
- Life Sciences and Technology, Beuth University of Applied Sciences Berlin, Berlin, Germany
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38
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Cardoso PDF, Perchat S, Vilas-Boas LA, Lereclus D, Vilas-Bôas GT. Diversity of the Rap-Phr quorum-sensing systems in the Bacillus cereus group. Curr Genet 2019; 65:1367-1381. [PMID: 31104082 DOI: 10.1007/s00294-019-00993-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 05/10/2019] [Accepted: 05/13/2019] [Indexed: 12/20/2022]
Abstract
Bacteria of the Bacillus cereus group colonize several ecological niches and infect different hosts. Bacillus cereus, a ubiquitous species causing food poisoning, Bacillus thuringiensis, an entomopathogen, and Bacillus anthracis, which is highly pathogenic to mammals, are the most important species of this group. These species are closely related genetically, and their specific toxins are encoded by plasmids. The infectious cycle of B. thuringiensis in its insect host is regulated by quorum-sensing systems from the RNPP family. Among them, the Rap-Phr systems, which are well-described in Bacillus subtilis, regulate essential processes, such as sporulation. Given the importance of these systems, we performed a global in silico analysis to investigate their prevalence, distribution, diversity and their role in sporulation in B. cereus group species. The rap-phr genes were identified in all selected strains with 30% located on plasmids, predominantly in B. thuringiensis. Despite a high variability in their sequences, there is a remarkable association between closely related strains and their Rap-Phr profile. Based on the key residues involved in RapH phosphatase activity, we predicted that 32% of the Rap proteins could regulate sporulation by preventing the phosphorylation of Spo0F. These Rap are preferentially located on plasmids and mostly related to B. thuringiensis. The predictions were partially validated by in vivo sporulation experiments suggesting that the residues linked to the phosphatase function are necessary but not sufficient to predict this activity. The wide distribution and diversity of Rap-Phr systems could strictly control the commitment to sporulation and then improve the adaptation capacities of the bacteria to environmental changes.
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Affiliation(s)
- Priscilla de F Cardoso
- Depto. Biologia Geral, Universidade Estadual de Londrina, Londrina, Brazil.,Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Stéphane Perchat
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | | | - Didier Lereclus
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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39
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Itaya M, Nagasaku M, Shimada T, Ohtani N, Shiwa Y, Yoshikawa H, Kaneko S, Tomita M, Sato M. Stable and efficient delivery of DNA to Bacillus subtilis (natto) using pLS20 conjugational transfer plasmids. FEMS Microbiol Lett 2019; 366:5307882. [PMID: 30726909 DOI: 10.1093/femsle/fnz032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 02/05/2019] [Indexed: 11/13/2022] Open
Abstract
Bacillus subtilis (natto) is generally regarded as a safe bacterium and used as a host for the production of several materials. However, genetic engineering of B. subtilis (natto) is not well established because of poor DNA delivery methods and the lack of a standard strain for the aim. Here, we developed a genetic delivery tool in B. subtilis (natto) using the pLS20 conjugational plasmid (65 kbp). Transmission of pLS20 from B. subtilis 168 to wild-type B. subtilis (natto) did not occur via established mating protocols. We isolated B. subtilis (natto) mutants showing dramatically increased recipient activity. Whole-genome sequence analyses revealed three common alterations: mutations in the restriction endonuclease gene and in the methyl-accepting chemotaxis protein gene, and a 43-kbp deletion at the genome replication termination locus. A representative strain named NEST116 was generated as the first B. subtilis (natto) strain suitable for exploring pLS20-based genetic engineering.
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Affiliation(s)
- Mitsuhiro Itaya
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
| | - Mayumi Nagasaku
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
| | - Tomoe Shimada
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
| | - Naoto Ohtani
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
| | - Yuh Shiwa
- NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Hirofumi Yoshikawa
- NODAI Genome Research Center, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Shinya Kaneko
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
| | - Mitsuru Sato
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Tsuruoka-shi, Yamagata 997-0017, Japan
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40
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Kalamara M, Spacapan M, Mandic‐Mulec I, Stanley‐Wall NR. Social behaviours by Bacillus subtilis: quorum sensing, kin discrimination and beyond. Mol Microbiol 2018; 110:863-878. [PMID: 30218468 PMCID: PMC6334282 DOI: 10.1111/mmi.14127] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/04/2018] [Accepted: 09/09/2018] [Indexed: 12/14/2022]
Abstract
Here, we review the multiple mechanisms that the Gram‐positive bacterium Bacillus subtilis uses to allow it to communicate between cells and establish community structures. The modes of action that are used are highly varied and include routes that sense pheromone levels during quorum sensing and control gene regulation, the intimate coupling of cells via nanotubes to share cytoplasmic contents, and long‐range electrical signalling to couple metabolic processes both within and between biofilms. We explore the ability of B. subtilis to detect ‘kin’ (and ‘cheater cells’) by looking at the mechanisms used to potentially ensure beneficial sharing (or limit exploitation) of extracellular ‘public goods’. Finally, reflecting on the array of methods that a single bacterium has at its disposal to ensure maximal benefit for its progeny, we highlight that a large future challenge will be integrating how these systems interact in mixed‐species communities.
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Affiliation(s)
- Margarita Kalamara
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD15EHUK
| | - Mihael Spacapan
- Department of Food Science and Technology, Biotechnical FacultyUniversity of LjubljanaLjubljana1000Slovenia
| | - Ines Mandic‐Mulec
- Department of Food Science and Technology, Biotechnical FacultyUniversity of LjubljanaLjubljana1000Slovenia
| | - Nicola R. Stanley‐Wall
- Division of Molecular Microbiology, School of Life SciencesUniversity of DundeeDundeeDD15EHUK
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41
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Miyano M, Tanaka K, Ishikawa S, Mori K, Miguel-Arribas A, Meijer WJJ, Yoshida KI. A novel method for transforming the thermophilic bacterium Geobacillus kaustophilus. Microb Cell Fact 2018; 17:127. [PMID: 30119674 PMCID: PMC6098629 DOI: 10.1186/s12934-018-0969-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 07/28/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bacterial strains of the genus Geobacillus grow at high temperatures of 50-75 °C and could thus be useful for biotechnological applications. However, genetic manipulation of these species is difficult because the current techniques for transforming Geobacillus species are not efficient. In this study, we developed an easy and efficient method for transforming Geobacillus kaustophilus using the conjugative plasmid pLS20cat. RESULTS We constructed a transformation system comprising (i) a mobilizable Bacillus subtilis-G. kaustophilus shuttle plasmid named pGK1 that carries the elements for selection and replication in Geobacillus, and (ii) a pLS20cat-harboring B. subtilis donor strain expressing the dam methylase gene of Escherichia coli and the conjugation-stimulating rapLS20 gene of pLS20cat. This system can be used to efficiently introduce pGK1 into G. kaustophilus by mobilization in a pLS20cat-dependent way. Whereas the thermostable kanamycin marker and Geobacillus replication origin of pGK1 as well as expression of dam methylase in the donor were indispensable for mobilization, ectopic expression of rapLS20 increased its efficiency. In addition, the conditions of the recipient influenced mobilization efficiency: the highest mobilization efficiencies were obtained using recipient cells that were in the exponential growth phase. Furthermore, elimination of the origin of transfer from pLS20cat enhanced the mobilization. CONCLUSIONS We describe a novel method of plasmid mobilization into G. kaustophilus recipient from B. subtilis donor depending on the helper function of pLS20cat, which enables simple, rapid, and easy transformation of the thermophilic Gram-positive bacterium.
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Grants
- 17K19237 Ministry of Education, Culture, Sports, Science and Technology
- 18H02128 Ministry of Education, Culture, Sports, Science and Technology
- Bio2013-41489-P Ministerio de Economía, Industria y Competitividad, Gobierno de España
- BIO2016-77883-C2-1-P Ministerio de Economía, Industria y Competitividad, Gobierno de España
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Affiliation(s)
- Megumi Miyano
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Kosei Tanaka
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Shu Ishikawa
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Kotaro Mori
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Instituto de Biología Molecular ‘Eladio Viñuela’ (CSIC), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Instituto de Biología Molecular ‘Eladio Viñuela’ (CSIC), Universidad Autónoma, Canto Blanco, 28049 Madrid, Spain
| | - Ken-ichi Yoshida
- Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
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Rapid conjugative mobilization of a 100 kb segment of Bacillus subtilis chromosomal DNA is mediated by a helper plasmid with no ability for self-transfer. Microb Cell Fact 2018; 17:13. [PMID: 29374463 PMCID: PMC5787278 DOI: 10.1186/s12934-017-0855-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 12/20/2017] [Indexed: 11/14/2022] Open
Abstract
Background The conjugative plasmid, pLS20, isolated from Bacillus subtilis natto, has an outstanding capacity for rapid self-transfer. In addition, it can function as a helper plasmid, mediating the mobilization of an independently replicating co-resident plasmid. Results In this study, the oriT sequence of pLS20cat (oriTLS20) was eliminated to obtain the plasmid, pLS20catΔoriT. This resulted in the complete loss of the conjugative transfer of the plasmid but still allowed it to mobilize a co-resident mobilizable plasmid. Moreover, pLS20catΔoriT was able to mobilize longer DNA segments, up to 113 kb of chromosomal DNA containing oriTLS20, after mixing the liquid cultures of the donor and recipient for only 15 min. Conclusions The chromosomal DNA mobilization mediated by pLS20catΔoriT will allow us to develop a novel genetic tool for the rapid, easy, and repetitive mobilization of longer DNA segments into a recipient chromosome.
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43
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Itaya M, Hasegawa M, Tomita M, Sato M. The first high frequency of recombination-like conjugal transfer from an integrated origin of transfer sequence in Bacillus subtilis 168. Biosci Biotechnol Biochem 2018; 82:356-362. [PMID: 29316866 DOI: 10.1080/09168451.2017.1422970] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Bacillus subtilis 168 was developed as a genome vector to manipulate large DNA fragments. The system is based on the inherent natural transformation (TF) activity. However, DNA size transferred by TF is limited up to approximately 100 kb. A conjugal transfer system capable of transferring DNA fragments considerably larger than those transferred by TF was developed. A well-defined oriT110 sequence and a cognate relaxase gene from the pUB110 plasmid were inserted into the xkdE gene of the B. subtilis genome. Transfer of antibiotic resistance markers distant from the oriT110 locus to the recipient B. subtilis occurred only in the presence of pLS20, a helper plasmid that provides a type IV secretion system. Marker transmission was consistent with the orientation of oriT110 and required a recA-proficient recipient. The first conjugal transfer system of genomic DNA should provide a valuable alternative genetic tool for editing the B. subtilis genome.
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Affiliation(s)
- Mitsuhiro Itaya
- a Institute for Advanced Biosciences , Keio University , Tsuruoka-shi, Japan
| | - Miki Hasegawa
- a Institute for Advanced Biosciences , Keio University , Tsuruoka-shi, Japan
| | - Masaru Tomita
- a Institute for Advanced Biosciences , Keio University , Tsuruoka-shi, Japan
| | - Mitsuru Sato
- a Institute for Advanced Biosciences , Keio University , Tsuruoka-shi, Japan
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44
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Miguel-Arribas A, Hao JA, Luque-Ortega JR, Ramachandran G, Val-Calvo J, Gago-Córdoba C, González-Álvarez D, Abia D, Alfonso C, Wu LJ, Meijer WJJ. The Bacillus subtilis Conjugative Plasmid pLS20 Encodes Two Ribbon-Helix-Helix Type Auxiliary Relaxosome Proteins That Are Essential for Conjugation. Front Microbiol 2017; 8:2138. [PMID: 29163424 PMCID: PMC5675868 DOI: 10.3389/fmicb.2017.02138] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 10/19/2017] [Indexed: 12/15/2022] Open
Abstract
Bacterial conjugation is the process by which a conjugative element (CE) is transferred horizontally from a donor to a recipient cell via a connecting pore. One of the first steps in the conjugation process is the formation of a nucleoprotein complex at the origin of transfer (oriT), where one of the components of the nucleoprotein complex, the relaxase, introduces a site- and strand specific nick to initiate the transfer of a single DNA strand into the recipient cell. In most cases, the nucleoprotein complex involves, besides the relaxase, one or more additional proteins, named auxiliary proteins, which are encoded by the CE and/or the host. The conjugative plasmid pLS20 replicates in the Gram-positive Firmicute bacterium Bacillus subtilis. We have recently identified the relaxase gene and the oriT of pLS20, which are separated by a region of almost 1 kb. Here we show that this region contains two auxiliary genes that we name aux1LS20 and aux2LS20 , and which we show are essential for conjugation. Both Aux1LS20 and Aux2LS20 are predicted to contain a Ribbon-Helix-Helix DNA binding motif near their N-terminus. Analyses of the purified proteins show that Aux1LS20 and Aux2LS20 form tetramers and hexamers in solution, respectively, and that they both bind preferentially to oriTLS20 , although with different characteristics and specificities. In silico analyses revealed that genes encoding homologs of Aux1LS20 and/or Aux2LS20 are located upstream of almost 400 relaxase genes of the RelLS20 family (MOBL) of relaxases. Thus, Aux1LS20 and Aux2LS20 of pLS20 constitute the founding member of the first two families of auxiliary proteins described for CEs of Gram-positive origin.
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Affiliation(s)
- Andrés Miguel-Arribas
- Department of Virology and Microbiology, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Autonomous University of Madrid, Madrid, Spain
| | - Jian-An Hao
- Department of Virology and Microbiology, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Autonomous University of Madrid, Madrid, Spain
- The Institute of Seawater Desalination and Multipurpose Utilization (SOA), Tianjin, China
| | | | - Gayetri Ramachandran
- Department of Virology and Microbiology, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Autonomous University of Madrid, Madrid, Spain
| | - Jorge Val-Calvo
- Department of Virology and Microbiology, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Autonomous University of Madrid, Madrid, Spain
| | - César Gago-Córdoba
- Department of Virology and Microbiology, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Autonomous University of Madrid, Madrid, Spain
| | - Daniel González-Álvarez
- Department of Virology and Microbiology, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Autonomous University of Madrid, Madrid, Spain
| | - David Abia
- Department of Virology and Microbiology, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Autonomous University of Madrid, Madrid, Spain
| | - Carlos Alfonso
- Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Ling J. Wu
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Wilfried J. J. Meijer
- Department of Virology and Microbiology, Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Instituto de Biología Molecular “Eladio Viñuela” (CSIC), Autonomous University of Madrid, Madrid, Spain
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Fazion F, Perchat S, Buisson C, Vilas-Bôas G, Lereclus D. A plasmid-borne Rap-Phr system regulates sporulation ofBacillus thuringiensisin insect larvae. Environ Microbiol 2017; 20:145-155. [DOI: 10.1111/1462-2920.13946] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/28/2017] [Accepted: 09/23/2017] [Indexed: 10/18/2022]
Affiliation(s)
- Fernanda Fazion
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay; 78350 Jouy-en-Josas France
- Universidade Estadual de Londrina, Bio/CCB; Londrina Brazil
| | - Stéphane Perchat
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay; 78350 Jouy-en-Josas France
| | - Christophe Buisson
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay; 78350 Jouy-en-Josas France
| | | | - Didier Lereclus
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay; 78350 Jouy-en-Josas France
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46
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Hall JPJ, Brockhurst MA, Dytham C, Harrison E. The evolution of plasmid stability: Are infectious transmission and compensatory evolution competing evolutionary trajectories? Plasmid 2017; 91:90-95. [PMID: 28461121 DOI: 10.1016/j.plasmid.2017.04.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 04/27/2017] [Accepted: 04/27/2017] [Indexed: 11/16/2022]
Abstract
Conjugative plasmids are widespread and play an important role in bacterial evolution by accelerating adaptation through horizontal gene transfer. However, explaining the long-term stability of plasmids remains challenging because segregational loss and the costs of plasmid carriage should drive the loss of plasmids though purifying selection. Theoretical and experimental studies suggest two key evolutionary routes to plasmid stability: First, the evolution of high conjugation rates would allow plasmids to survive through horizontal transmission as infectious agents, and second, compensatory evolution to ameliorate the cost of plasmid carriage can weaken purifying selection against plasmids. How these two evolutionary strategies for plasmid stability interact is unclear. Here, we summarise the literature on the evolution of plasmid stability and then use individual based modelling to investigate the evolutionary interplay between the evolution of plasmid conjugation rate and cost amelioration. We find that, individually, both strategies promote plasmid stability, and that they act together to increase the likelihood of plasmid survival. However, due to the inherent costs of increasing conjugation rate, particularly where conjugation is unlikely to be successful, our model predicts that amelioration is the more likely long-term solution to evolving stable bacteria-plasmid associations. Our model therefore suggests that bacteria-plasmid relationships should evolve towards lower plasmid costs that may forestall the evolution of highly conjugative, 'infectious' plasmids.
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Affiliation(s)
- James P J Hall
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Calvin Dytham
- Department of Biology, University of York, York YO10 5DD, UK
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
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Ramachandran G, Miguel-Arribas A, Abia D, Singh PK, Crespo I, Gago-Córdoba C, Hao JA, Luque-Ortega JR, Alfonso C, Wu LJ, Boer DR, Meijer WJJ. Discovery of a new family of relaxases in Firmicutes bacteria. PLoS Genet 2017; 13:e1006586. [PMID: 28207825 PMCID: PMC5313138 DOI: 10.1371/journal.pgen.1006586] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 01/16/2017] [Indexed: 11/19/2022] Open
Abstract
Antibiotic resistance is a serious global problem. Antibiotic resistance genes (ARG), which are widespread in environmental bacteria, can be transferred to pathogenic bacteria via horizontal gene transfer (HGT). Gut microbiomes are especially apt for the emergence and dissemination of ARG. Conjugation is the HGT route that is predominantly responsible for the spread of ARG. Little is known about conjugative elements of Gram-positive bacteria, including those of the phylum Firmicutes, which are abundantly present in gut microbiomes. A critical step in the conjugation process is the relaxase-mediated site- and strand-specific nick in the oriT region of the conjugative element. This generates a single-stranded DNA molecule that is transferred from the donor to the recipient cell via a connecting channel. Here we identified and characterized the relaxosome components oriT and the relaxase of the conjugative plasmid pLS20 of the Firmicute Bacillus subtilis. We show that the relaxase gene, named relLS20, is essential for conjugation, that it can function in trans and provide evidence that Tyr26 constitutes the active site residue. In vivo and in vitro analyses revealed that the oriT is located far upstream of the relaxase gene and that the nick site within oriT is located on the template strand of the conjugation genes. Surprisingly, the RelLS20 shows very limited similarity to known relaxases. However, more than 800 genes to which no function had been attributed so far are predicted to encode proteins showing significant similarity to RelLS20. Interestingly, these putative relaxases are encoded almost exclusively in Firmicutes bacteria. Thus, RelLS20 constitutes the prototype of a new family of relaxases. The identification of this novel relaxase family will have an important impact in different aspects of future research in the field of HGT in Gram-positive bacteria in general, and specifically in the phylum of Firmicutes, and in gut microbiome research.
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Affiliation(s)
- Gayetri Ramachandran
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Andrés Miguel-Arribas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - David Abia
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Praveen K. Singh
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Isidro Crespo
- XALOC beamline, ALBA synchrotron Light Source, Cerdanyola del Vallès, Barcelona, Spain
| | - César Gago-Córdoba
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | - Jian An Hao
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
| | | | - Carlos Alfonso
- Centro de Investigaciones Biológicas (CSIC), Madrid, Spain
| | - Ling J. Wu
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - D. Roeland Boer
- XALOC beamline, ALBA synchrotron Light Source, Cerdanyola del Vallès, Barcelona, Spain
| | - Wilfried J. J. Meijer
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Instituto de Biología Molecular "Eladio Viñuela" (CSIC), Universidad Autónoma, Canto Blanco, Madrid, Spain
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48
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Grohmann E, Keller W, Muth G. Mechanisms of Conjugative Transfer and Type IV Secretion-Mediated Effector Transport in Gram-Positive Bacteria. Curr Top Microbiol Immunol 2017. [PMID: 29536357 DOI: 10.1007/978-3-319-75241-9_5] [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] [Indexed: 12/25/2022]
Abstract
Conjugative DNA transfer is the most important means to transfer antibiotic resistance genes and virulence determinants encoded by plasmids, integrative conjugative elements (ICE), and pathogenicity islands among bacteria. In gram-positive bacteria, there exist two types of conjugative systems, (i) type IV secretion system (T4SS)-dependent ones, like those encoded by the Enterococcus, Streptococcus, Staphylococcus, Bacillus, and Clostridia mobile genetic elements and (ii) T4SS-independent ones, as those found on Streptomyces plasmids. Interestingly, very recently, on the Streptococcus suis genome, the first gram-positive T4SS not only involved in conjugative DNA transfer but also in effector translocation to the host was detected. Although no T4SS core complex structure from gram-positive bacteria is available, several structures from T4SS protein key factors from Enterococcus and Clostridia plasmids have been solved. In this chapter, we summarize the current knowledge on the molecular mechanisms and structure-function relationships of the diverse conjugation machineries and emerging research needs focused on combatting infections and spread of multiple resistant gram-positive pathogens.
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Affiliation(s)
- Elisabeth Grohmann
- Beuth University of Applied Sciences Berlin, Life Sciences and Technology, 13347, Berlin, Germany.
| | - Walter Keller
- Institute of Molecular Biosciences, BioTechMed, University of Graz, 8010, Graz, Austria
| | - Günther Muth
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, University Tübingen, 72076, Tübingen, Germany
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49
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Transient Duplication-Dependent Divergence and Horizontal Transfer Underlie the Evolutionary Dynamics of Bacterial Cell-Cell Signaling. PLoS Biol 2016; 14:e2000330. [PMID: 28033323 PMCID: PMC5199041 DOI: 10.1371/journal.pbio.2000330] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 12/02/2016] [Indexed: 01/01/2023] Open
Abstract
Evolutionary expansion of signaling pathway families often underlies the evolution of regulatory complexity. Expansion requires the acquisition of a novel homologous pathway and the diversification of pathway specificity. Acquisition can occur either vertically, by duplication, or through horizontal transfer, while divergence of specificity is thought to occur through a promiscuous protein intermediate. The way by which these mechanisms shape the evolution of rapidly diverging signaling families is unclear. Here, we examine this question using the highly diversified Rap-Phr cell-cell signaling system, which has undergone massive expansion in the genus Bacillus. To this end, genomic sequence analysis of >300 Bacilli genomes was combined with experimental analysis of the interaction of Rap receptors with Phr autoinducers and downstream targets. Rap-Phr expansion is shown to have occurred independently in multiple Bacillus lineages, with >80 different putative rap-phr alleles evolving in the Bacillius subtilis group alone. The specificity of many rap-phr alleles and the rapid gain and loss of Rap targets are experimentally demonstrated. Strikingly, both horizontal and vertical processes were shown to participate in this expansion, each with a distinct role. Horizontal gene transfer governs the acquisition of already diverged rap-phr alleles, while intralocus duplication and divergence of the phr gene create the promiscuous intermediate required for the divergence of Rap-Phr specificity. Our results suggest a novel role for transient gene duplication and divergence during evolutionary shifts in specificity.
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50
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Lopatkin AJ, Sysoeva TA, You L. Dissecting the effects of antibiotics on horizontal gene transfer: Analysis suggests a critical role of selection dynamics. Bioessays 2016; 38:1283-1292. [PMID: 27699821 DOI: 10.1002/bies.201600133] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Horizontal gene transfer (HGT) is a major mechanism responsible for the spread of antibiotic resistance. Conversely, it is often assumed that antibiotics promote HGT. Careful dissection of the literature, however, suggests a lack of conclusive evidence supporting this notion in general. This is largely due to the lack of well-defined quantitative experiments to address this question in an unambiguous manner. In this review, we discuss the extent to which HGT is responsible for the spread of antibiotic resistance and examine what is known about the effect of antibiotics on the HGT dynamics. We focus on conjugation, which is the dominant mode of HGT responsible for spreading antibiotic resistance on the global scale. Our analysis reveals a need to design experiments to quantify HGT in such a way to facilitate rigorous data interpretation. Such measurements are critical for developing novel strategies to combat resistance spread through HGT.
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Affiliation(s)
| | - Tatyana A Sysoeva
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Lingchong You
- Department of Biomedical Engineering, Duke University, Durham, NC, USA.,Center for Genomic and Computational Biology, Duke University, Durham, NC, USA.,Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC, USA
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