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Misson P, Bruder E, Cornuault JK, De Paepe M, Nicolas P, Demarre G, Lakisic G, Petit MA, Espeli O, Lecointe F. Phage production is blocked in the adherent-invasive Escherichia coli LF82 upon macrophage infection. PLoS Pathog 2023; 19:e1011127. [PMID: 36730457 PMCID: PMC9928086 DOI: 10.1371/journal.ppat.1011127] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 02/14/2023] [Accepted: 01/17/2023] [Indexed: 02/04/2023] Open
Abstract
Adherent-invasive Escherichia coli (AIEC) strains are frequently recovered from stools of patients with dysbiotic microbiota. They have remarkable properties of adherence to the intestinal epithelium, and survive better than other E. coli in macrophages. The best studied of these AIEC is probably strain LF82, which was isolated from a Crohn's disease patient. This strain contains five complete prophages, which have not been studied until now. We undertook their analysis, both in vitro and inside macrophages, and show that all of them form virions. The Gally prophage is by far the most active, generating spontaneously over 108 viral particles per mL of culture supernatants in vitro, more than 100-fold higher than the other phages. Gally is also over-induced after a genotoxic stress generated by ciprofloxacin and trimethoprim. However, upon macrophage infection, a genotoxic environment, this over-induction is not observed. Analysis of the transcriptome and key steps of its lytic cycle in macrophages suggests that the excision of the Gally prophage continues to be repressed in macrophages. We conclude that strain LF82 has evolved an efficient way to block the lytic cycle of its most active prophage upon macrophage infection, which may participate to its good survival in macrophages.
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Affiliation(s)
- Pauline Misson
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Emma Bruder
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
| | - Jeffrey K. Cornuault
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Marianne De Paepe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Pierre Nicolas
- Université Paris-Saclay, INRAE, MaIAGE, Jouy-en-Josas, France
| | - Gaëlle Demarre
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
| | - Goran Lakisic
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Olivier Espeli
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
| | - François Lecointe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- * E-mail:
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Prudent V, Demarre G, Vazeille E, Wery M, Quenech'Du N, Ravet A, Dauverd-Girault J, van Dijk E, Bringer MA, Descrimes M, Barnich N, Rimsky S, Morillon A, Espéli O. The Crohn's disease-related bacterial strain LF82 assembles biofilm-like communities to protect itself from phagolysosomal attack. Commun Biol 2021; 4:627. [PMID: 34035436 PMCID: PMC8149705 DOI: 10.1038/s42003-021-02161-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 04/28/2021] [Indexed: 11/09/2022] Open
Abstract
Patients with Crohn's disease exhibit abnormal colonization of the intestine by adherent invasive E. coli (AIEC). They adhere to epithelial cells, colonize them and survive inside macrophages. It appeared recently that AIEC LF82 adaptation to phagolysosomal stress involves a long lag phase in which many LF82 cells become antibiotic tolerant. Later during infection, they proliferate in vacuoles and form colonies harboring dozens of LF82 bacteria. In the present work, we investigated the mechanism sustaining this phase of growth. We found that intracellular LF82 produced an extrabacterial matrix that acts as a biofilm and controls the formation of LF82 intracellular bacterial communities (IBCs) for several days post infection. We revealed the crucial role played by the pathogenicity island encoding the yersiniabactin iron capture system to form IBCs and for optimal LF82 survival. These results illustrate that AIECs use original strategies to establish their replicative niche within macrophages.
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Affiliation(s)
- Victoria Prudent
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Gaëlle Demarre
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Emilie Vazeille
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte. UMR Inserm/ Université de Clermont -Auvergne U1071, USC INRA 2018, Clermont, Ferrand, France
| | - Maxime Wery
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne University, CNRS UMR 3244, Paris, France
| | - Nicole Quenech'Du
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Antinéa Ravet
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Julie Dauverd-Girault
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Erwin van Dijk
- Next-Generation Sequencing Service - I2BC, I2BC-CNRS, Gif-sur-Yvette, France
| | - Marie-Agnès Bringer
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte. UMR Inserm/ Université de Clermont -Auvergne U1071, USC INRA 2018, Clermont, Ferrand, France
- Centre des Sciences du Goût et de l'Alimentation, AgroSup Dijon, CNRS, INRA, Université Bourgogne Franche-Comté, Dijon, France
| | - Marc Descrimes
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne University, CNRS UMR 3244, Paris, France
| | - Nicolas Barnich
- Microbes, Intestin, Inflammation et Susceptibilité de l'Hôte. UMR Inserm/ Université de Clermont -Auvergne U1071, USC INRA 2018, Clermont, Ferrand, France
| | - Sylvie Rimsky
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France
| | - Antonin Morillon
- ncRNA, Epigenetic and Genome Fluidity, Institut Curie, Sorbonne University, CNRS UMR 3244, Paris, France
| | - Olivier Espéli
- CIRB - Collège de France, CNRS-UMR7241, INSERM U1050, PSL Research University, Paris, France.
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Abstract
The study of the bacterial cell cycle at the single cell level can not only give insights on the fitness of the bacterial population but also reveal heterogeneous behavior. Typically, the DNA replication, the cell division, and the nucleoid conformation are appropriate representatives of the bacterial cell cycle. Because bacteria rapidly adapt their growth rate to environmental changes, the measure of cell cycle parameters gives valuable insights for the study of bacterial stress response or host-pathogen interactions. Here we describe methods to first introduce fluorescent fusion proteins and fluorescent tag within the chromosome of pathogenic bacteria to study these cell cycle steps; then to follow them within macrophages using a confocal spinning disk microscope.
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Affiliation(s)
- Gaëlle Demarre
- CIRB, Collège de France, UMR CNRS 7241 INSERM U1050, 11 Place Marcelin Berthelot, 75005, Paris, France.
| | - Victoria Prudent
- CIRB, Collège de France, UMR CNRS 7241 INSERM U1050, 11 Place Marcelin Berthelot, 75005, Paris, France
| | - Olivier Espéli
- CIRB, Collège de France, UMR CNRS 7241 INSERM U1050, 11 Place Marcelin Berthelot, 75005, Paris, France.
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Demarre G, Galli E, Muresan L, Paly E, David A, Possoz C, Barre FX. Differential management of the replication terminus regions of the two Vibrio cholerae chromosomes during cell division. PLoS Genet 2014; 10:e1004557. [PMID: 25255436 PMCID: PMC4177673 DOI: 10.1371/journal.pgen.1004557] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 06/25/2014] [Indexed: 12/04/2022] Open
Abstract
The replication terminus region (Ter) of the unique chromosome of most bacteria locates at mid-cell at the time of cell division. In several species, this localization participates in the necessary coordination between chromosome segregation and cell division, notably for the selection of the division site, the licensing of the division machinery assembly and the correct alignment of chromosome dimer resolution sites. The genome of Vibrio cholerae, the agent of the deadly human disease cholera, is divided into two chromosomes, chrI and chrII. Previous fluorescent microscopy observations suggested that although the Ter regions of chrI and chrII replicate at the same time, chrII sister termini separated before cell division whereas chrI sister termini were maintained together at mid-cell, which raised questions on the management of the two chromosomes during cell division. Here, we simultaneously visualized the location of the dimer resolution locus of each of the two chromosomes. Our results confirm the late and early separation of chrI and chrII Ter sisters, respectively. They further suggest that the MatP/matS macrodomain organization system specifically delays chrI Ter sister separation. However, TerI loci remain in the vicinity of the cell centre in the absence of MatP and a genetic assay specifically designed to monitor the relative frequency of sister chromatid contacts during constriction suggest that they keep colliding together until the very end of cell division. In contrast, we found that even though it is not able to impede the separation of chrII Ter sisters before septation, the MatP/matS macrodomain organization system restricts their movement within the cell and permits their frequent interaction during septum constriction. The genome of Vibrio cholerae is divided into two circular chromosomes, chrI and chrII. ChrII is derived from a horizontally acquired mega-plasmid, which raised questions on the necessary coordination of the processes that ensure its segregation with the cell division cycle. Here, we show that the MatP/matS macrodomain organization system impedes the separation of sister copies of the terminus region of chrI before the initiation of septum constriction. In its absence, however, chrI sister termini remain sufficiently close to mid-cell to be processed by the FtsK cell division translocase. In contrast, we show that MatP cannot impede the separation of chrII sister termini before constriction. However, it restricts their movements within the cell, which allows for their processing by FtsK at the time of cell division. These results suggest that multiple redundant factors, including MatP in the enterobacteriaceae and the Vibrios, ensure that sister copies of the terminus region of bacterial chromosomes remain sufficiently close to mid-cell to be processed by FtsK.
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Affiliation(s)
- Gaëlle Demarre
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Elisa Galli
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Leila Muresan
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Evelyne Paly
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Ariane David
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Christophe Possoz
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - François-Xavier Barre
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
- * E-mail:
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David A, Demarre G, Muresan L, Paly E, Barre FX, Possoz C. The two Cis-acting sites, parS1 and oriC1, contribute to the longitudinal organisation of Vibrio cholerae chromosome I. PLoS Genet 2014; 10:e1004448. [PMID: 25010199 PMCID: PMC4091711 DOI: 10.1371/journal.pgen.1004448] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 05/07/2014] [Indexed: 11/19/2022] Open
Abstract
The segregation of bacterial chromosomes follows a precise choreography of spatial organisation. It is initiated by the bipolar migration of the sister copies of the replication origin (ori). Most bacterial chromosomes contain a partition system (Par) with parS sites in close proximity to ori that contribute to the active mobilisation of the ori region towards the old pole. This is thought to result in a longitudinal chromosomal arrangement within the cell. In this study, we followed the duplication frequency and the cellular position of 19 Vibrio cholerae genome loci as a function of cell length. The genome of V. cholerae is divided between two chromosomes, chromosome I and II, which both contain a Par system. The ori region of chromosome I (oriI) is tethered to the old pole, whereas the ori region of chromosome II is found at midcell. Nevertheless, we found that both chromosomes adopted a longitudinal organisation. Chromosome I extended over the entire cell while chromosome II extended over the younger cell half. We further demonstrate that displacing parS sites away from the oriI region rotates the bulk of chromosome I. The only exception was the region where replication terminates, which still localised to the septum. However, the longitudinal arrangement of chromosome I persisted in Par mutants and, as was reported earlier, the ori region still localised towards the old pole. Finally, we show that the Par-independent longitudinal organisation and oriI polarity were perturbed by the introduction of a second origin. Taken together, these results suggest that the Par system is the major contributor to the longitudinal organisation of chromosome I but that the replication program also influences the arrangement of bacterial chromosomes.
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Affiliation(s)
- Ariane David
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Gaëlle Demarre
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Leila Muresan
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - Evelyne Paly
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
| | - François-Xavier Barre
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
- * E-mail: (FXB); (CP)
| | - Christophe Possoz
- CNRS, Centre de Génétique Moléculaire, Gif-sur-Yvette, France
- Université Paris-Sud, Orsay, France
- * E-mail: (FXB); (CP)
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Abstract
Interest for proteins of the FtsK family initially arose from their implication in many primordial processes in which DNA needs to be transported from one cell compartment to another in eubacteria. In the first section of this chapter, we address a list of the cellular functions of the different members of the FtsK family that have been so far studied. Soon after their discovery, interest for the FstK proteins spread because of their unique biochemical properties: most DNA transport systems rely on the assembly of complex multicomponent machines. In contrast, six FtsK proteins are sufficient to assemble into a fast and powerful DNA pump; the pump transports closed circular double stranded DNA molecules without any covalent-bond breakage nor topological alteration; transport is oriented despite the intrinsic symmetrical nature of the double stranded DNA helix and can occur across cell membranes. The different activities required for the oriented transport of DNA across cell compartments are achieved by three separate modules within the FtsK proteins: a DNA translocation module, an orientation module and an anchoring module. In the second part of this chapter, we review the structural and biochemical properties of these different modules.
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Affiliation(s)
- Gaëlle Demarre
- Centre de Génétique Moléculaire, CNRS, Gif sur Yvette, Cedex, France,
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Jha JK, Demarre G, Venkova-Canova T, Chattoraj DK. Replication regulation of Vibrio cholerae chromosome II involves initiator binding to the origin both as monomer and as dimer. Nucleic Acids Res 2012; 40:6026-38. [PMID: 22447451 PMCID: PMC3401445 DOI: 10.1093/nar/gks260] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The origin region of Vibrio cholerae chromosome II (chrII) resembles plasmid origins that have repeated initiator-binding sites (iterons). Iterons are essential for initiation as well as preventing over-initiation of plasmid replication. In chrII, iterons are also essential for initiation but over-initiation is prevented by sites called 39-mers. Both iterons and 39-mers are binding sites of the chrII specific initiator, RctB. Here, we have isolated RctB mutants that permit over-initiation in the presence of 39-mers. Characterization of two of the mutants showed that both are defective in 39-mer binding, which helps to explain their over-initiation phenotype. In vitro, RctB bound to 39-mers as monomers, and to iterons as both monomers and dimers. Monomer binding to iterons increased in both the mutants, suggesting that monomers are likely to be the initiators. We suggest that dimers might be competitive inhibitors of monomer binding to iterons and thus help control replication negatively. ChrII replication was found to be dependent on chaperones DnaJ and DnaK in vivo. The chaperones preferentially improved dimer binding in vitro, further suggesting the importance of dimer binding in the control of chrII replication.
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Affiliation(s)
- Jyoti K Jha
- Laboratory of Biochemistry and Molecular Biology, NCI, 37 Convent Drive, NIH, Bethesda, MD 20892-4260, USA
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Demarre G, Chattoraj DK. DNA adenine methylation is required to replicate both Vibrio cholerae chromosomes once per cell cycle. PLoS Genet 2010; 6:e1000939. [PMID: 20463886 PMCID: PMC2865523 DOI: 10.1371/journal.pgen.1000939] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 04/06/2010] [Indexed: 11/19/2022] Open
Abstract
DNA adenine methylation is widely used to control many DNA transactions, including replication. In Escherichia coli, methylation serves to silence newly synthesized (hemimethylated) sister origins. SeqA, a protein that binds to hemimethylated DNA, mediates the silencing, and this is necessary to restrict replication to once per cell cycle. The methylation, however, is not essential for replication initiation per se but appeared so when the origins (oriI and oriII) of the two Vibrio cholerae chromosomes were used to drive plasmid replication in E. coli. Here we show that, as in the case of E. coli, methylation is not essential for oriI when it drives chromosomal replication and is needed for once-per-cell-cycle replication in a SeqA-dependent fashion. We found that oriII also needs SeqA for once-per-cell-cycle replication and, additionally, full methylation for efficient initiator binding. The requirement for initiator binding might suffice to make methylation an essential function in V. cholerae. The structure of oriII suggests that it originated from a plasmid, but unlike plasmids, oriII makes use of methylation for once-per-cell-cycle replication, the norm for chromosomal but not plasmid replication. Bacteria usually have one chromosome but can have extrachromosomal replicons, called plasmids. Although normally dispensable, plasmids can confer adaptive advantage to cells in stressful environments. Bacteria can also have multiple chromosomes, each carrying essential genes, as in eukaryotes. In all organisms, chromosomes duplicate once before the cells divide so that the daughter cells can receive equal genetic dowry, but this is not usually the case with bacterial plasmids. Vibrio cholerae, the causative agent for the disease cholera, has a typical bacterial chromosome like the chromosome of the well-studied bacterium Escherichia coli and has a second chromosome with many signatures indicating its origin from a plasmid. Here we show that, in spite of the distinct nature of the two chromosomes, they both duplicate once per cell cycle, and they both require DNA adenine methylation for this purpose. Our study suggests that once-per-cell-cycle replication is a necessary feature of a chromosome in multichromosome bacteria, and provides a paradigm of how methylation could endow extrachromosomal replicons with the capacity to duplicate like chromosomes.
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Affiliation(s)
- Gaëlle Demarre
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Dhruba K. Chattoraj
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail:
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Demarre G, Frumerie C, Gopaul DN, Mazel D. Identification of key structural determinants of the IntI1 integron integrase that influence attC x attI1 recombination efficiency. Nucleic Acids Res 2007; 35:6475-89. [PMID: 17884913 PMCID: PMC2095811 DOI: 10.1093/nar/gkm709] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
The integron platform codes for an integrase (IntI) from the tyrosine family of recombinases that mediates recombination between a proximal double-strand recombination site, attI and a single-strand target recombination site, attC. The attI site is only recognized by its cognate integrase, while the various tested attCs sites are recombined by several different IntI integrases. We have developed a genetic system to enrich and select mutants of IntI1 that provide a higher yield of recombination in order to identify key protein structural elements important for attC × attI1 recombination. We isolated mutants with higher activity on wild type and mutant attC sites. Interestingly, three out of four characterized IntI1 mutants selected on different substrates are mutants of the conserved aspartic acid in position 161. The IntI1 model we made based on the VchIntIA 3D structure suggests that substitution at this position, which plays a central role in multimer assembly, can increase or decrease the stability of the complex and accordingly influence the rate of attI × attC recombination versus attC × attC. These results suggest that there is a balance between the specificity of the protein and the protein/protein interactions in the recombination synapse.
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Affiliation(s)
- Gaëlle Demarre
- Unité Plasticité du Génome Bactérien, CNRS URA 2171 and Laboratoire de Biochimie et Biophysique des Macromolécules, CNRS URA 2185, Institut Pasteur, 25 rue du Dr Roux, 75724, Paris 75724, France
| | - Clara Frumerie
- Unité Plasticité du Génome Bactérien, CNRS URA 2171 and Laboratoire de Biochimie et Biophysique des Macromolécules, CNRS URA 2185, Institut Pasteur, 25 rue du Dr Roux, 75724, Paris 75724, France
| | - Deshmukh N. Gopaul
- Unité Plasticité du Génome Bactérien, CNRS URA 2171 and Laboratoire de Biochimie et Biophysique des Macromolécules, CNRS URA 2185, Institut Pasteur, 25 rue du Dr Roux, 75724, Paris 75724, France
| | - Didier Mazel
- Unité Plasticité du Génome Bactérien, CNRS URA 2171 and Laboratoire de Biochimie et Biophysique des Macromolécules, CNRS URA 2185, Institut Pasteur, 25 rue du Dr Roux, 75724, Paris 75724, France
- *To whom correspondence should be addressed. +33 1 40 61 32 84+33 1 45 68 88 34
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MacDonald D, Demarre G, Bouvier M, Mazel D, Gopaul DN. Structural basis for broad DNA-specificity in integron recombination. Nature 2006; 440:1157-62. [PMID: 16641988 DOI: 10.1038/nature04643] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2005] [Accepted: 02/10/2006] [Indexed: 11/08/2022]
Abstract
Lateral DNA transfer--the movement of genetic traits between bacteria--has a profound impact on genomic evolution and speciation. The efficiency with which bacteria incorporate genetic information reflects their capacity to adapt to changing environmental conditions. Integron integrases are proteins that mediate site-specific DNA recombination between a proximal primary site (attI) and a secondary target site (attC) found within mobile gene cassettes encoding resistance or virulence factors. The lack of sequence conservation among attC sites has led to the hypothesis that a sequence-independent structural recognition determinant must exist within attC. Here we report the crystal structure of an integron integrase bound to an attC substrate. The structure shows that DNA target site recognition and high-order synaptic assembly are not dependent on canonical DNA but on the position of two flipped-out bases that interact in cis and in trans with the integrase. These extrahelical bases, one of which is required for recombination in vivo, originate from folding of the bottom strand of attC owing to its imperfect internal dyad symmetry. The mechanism reported here supports a new paradigm for how sequence-degenerate single-stranded genetic material is recognized and exchanged between bacteria.
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Affiliation(s)
- Douglas MacDonald
- Laboratoire de Biochimie et Biophysique des Macromolécules, Département de Biologie Structurale et Chimie, CNRS URA 2171, Institut Pasteur, 75724 Paris Cedex 15, France
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Bouvier M, Demarre G, Mazel D. Integron cassette insertion: a recombination process involving a folded single strand substrate. EMBO J 2005; 24:4356-67. [PMID: 16341091 PMCID: PMC1356339 DOI: 10.1038/sj.emboj.7600898] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Accepted: 11/11/2005] [Indexed: 11/08/2022] Open
Abstract
Integrons play a major role in the dissemination of antibiotic resistance genes among Gram-negative pathogens. Integron gene cassettes form circular intermediates carrying a recombination site, attC, and insert into an integron platform at a second site, attI, in a reaction catalyzed by an integron-specific integrase IntI. The IntI1 integron integrase preferentially binds to the 'bottom strand' of single-stranded attC. We have addressed the insertion mechanism in vivo using a recombination assay exploiting plasmid conjugation to exclusively deliver either the top or bottom strand of different integrase recombination substrates. Recombination of a single-stranded attC site with an attI site was 1000-fold higher for one strand than for the other. Conversely, following conjugative transfer of either attI strand, recombination with attC is highly unfavorable. These results and those obtained using mutations within a putative attC stem-and-loop strongly support a novel integron cassette insertion model in which the single bottom attC strand adopts a folded structure generating a double strand recombination site. Thus, recombination would insert a single strand cassette, which must be subsequently processed.
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Affiliation(s)
- Marie Bouvier
- Unité Postulante Plasticité du Génome Bactérien, CNRS URA 2171, Institut Pasteur, Paris, France
| | - Gaëlle Demarre
- Unité Postulante Plasticité du Génome Bactérien, CNRS URA 2171, Institut Pasteur, Paris, France
| | - Didier Mazel
- Unité Postulante Plasticité du Génome Bactérien, CNRS URA 2171, Institut Pasteur, Paris, France
- Unité Postulante Plasticité du Génome Bactérien, CNRS URA 2171, Institut Pasteur, 25 rue du Dr Roux, 75724, Paris, France. Tel.: +33 1 4061 3284; Fax: +33 1 4568 8834; E-mail:
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Demarre G, Guérout AM, Matsumoto-Mashimo C, Rowe-Magnus DA, Marlière P, Mazel D. A new family of mobilizable suicide plasmids based on broad host range R388 plasmid (IncW) and RP4 plasmid (IncPalpha) conjugative machineries and their cognate Escherichia coli host strains. Res Microbiol 2005; 156:245-55. [PMID: 15748991 DOI: 10.1016/j.resmic.2004.09.007] [Citation(s) in RCA: 240] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2004] [Accepted: 09/22/2004] [Indexed: 11/19/2022]
Abstract
We describe the construction of the pSW family of conditionally replicating plasmids which are based on the IncX oriV origin (oriV(R6Kgamma)) of replication that is dependent on the pir-encoded protein. We constructed several Escherichia coli derivatives expressing pir from different chromosomal loci, and the pir gene could be transduced by phage P1 to any E. coli strain. These chromosomal constructions generate dapA and thyA knockouts, which lead to diaminopimelate or thymidine auxotrophies, respectively, and they serve to provide absolute counterselection even in rich media. These strains can be easily counterselected if used in plasmid transfer experiments into markerless recipients, and they have been demonstrated to work efficiently in E. coli xVibrio or E. coli xBartonella matings. We constructed different pSW plasmids carrying either the oriT(RP4) or the oriT(R388), and we demonstrated that these derivatives can be efficiently transferred using RP4 and R388 conjugation machineries, respectively. We also constructed two plasmids expressing the R388 conjugation machinery, but lacking the oriT(R388). We demonstrated that these plasmids enabled efficient and exclusive transfer of a pSW-oriT(R388) derivative from E. coli to V. cholerae, and we offer an alternative to the popular RP4-based delivery system.
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Affiliation(s)
- Gaëlle Demarre
- Unité Postulante Plasticité du Génome Bactérien, CNRS URA 2171, Institut Pasteur, 25, rue du Dr. Roux, 75724 Paris, France
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