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Lång E, Haugen K, Fleckenstein B, Homberset H, Frye SA, Ambur OH, Tønjum T. Identification of neisserial DNA binding components. MICROBIOLOGY-SGM 2009; 155:852-862. [PMID: 19246756 PMCID: PMC2885667 DOI: 10.1099/mic.0.022640-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Neisseria meningitidis, a causative agent of meningitis and septicaemia, expresses type IV pili, a feature correlating with the uptake of exogenous DNA from the environment by natural transformation. The outer membrane complex PilQ, through which pili are extruded and retracted, has previously been shown to bind DNA in its pore region. In order to further elucidate how DNA is transported across the membranes, we searched for DNA binding proteins within the meningococcal inner membrane. Inner membrane fractions from a panel of neisserial strains were subjected to a solid-phase overlay assay with DNA substrates, and MS was subsequently employed to identify proteins that bind DNA. A number of DNA binding components were detected, including the pilus biogenesis component PilG, the competence protein ComL, and the cell division ATP-binding protein FtsE, as well as two hypothetical proteins. The DNA binding activity of these components was not dependent on the presence of the neisserial DNA uptake sequence. Null mutants, corresponding to each of the proteins identified, were constructed to assess their phenotypes. Only mutants defective in pilus biogenesis were non-competent and non-piliated. The DNA binding activity of the pilus biogenesis components PilQ and PilG and the phenotypes of their respective null mutants suggest that these proteins are directly involved as players in natural transformation, and not only indirectly, through pilus biogenesis.
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Affiliation(s)
- Emma Lång
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Rikshospitalet, Oslo, Norway.,Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, N-0027 Oslo, Norway
| | - Kristine Haugen
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Rikshospitalet, Oslo, Norway
| | | | - Håvard Homberset
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, N-0027 Oslo, Norway
| | - Stephan A Frye
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Rikshospitalet, Oslo, Norway.,Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, N-0027 Oslo, Norway
| | - Ole Herman Ambur
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Rikshospitalet, Oslo, Norway.,Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, N-0027 Oslo, Norway
| | - Tone Tønjum
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, Rikshospitalet, Oslo, Norway.,Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, N-0027 Oslo, Norway
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Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, Bingen E, Bonacorsi S, Bouchier C, Bouvet O, Calteau A, Chiapello H, Clermont O, Cruveiller S, Danchin A, Diard M, Dossat C, Karoui ME, Frapy E, Garry L, Ghigo JM, Gilles AM, Johnson J, Le Bouguénec C, Lescat M, Mangenot S, Martinez-Jéhanne V, Matic I, Nassif X, Oztas S, Petit MA, Pichon C, Rouy Z, Ruf CS, Schneider D, Tourret J, Vacherie B, Vallenet D, Médigue C, Rocha EPC, Denamur E. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet 2009; 5:e1000344. [PMID: 19165319 PMCID: PMC2617782 DOI: 10.1371/journal.pgen.1000344] [Citation(s) in RCA: 778] [Impact Index Per Article: 51.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 12/16/2008] [Indexed: 01/01/2023] Open
Abstract
The Escherichia coli species represents one of the best-studied model organisms, but also encompasses a variety of commensal and pathogenic strains that diversify by high rates of genetic change. We uniformly (re-) annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Within the ∼18,000 families of orthologous genes, we found ∼2,000 common to all strains. Although recombination rates are much higher than mutation rates, we show, both theoretically and using phylogenetic inference, that this does not obscure the phylogenetic signal, which places the B2 phylogenetic group and one group D strain at the basal position. Based on this phylogeny, we inferred past evolutionary events of gain and loss of genes, identifying functional classes under opposite selection pressures. We found an important adaptive role for metabolism diversification within group B2 and Shigella strains, but identified few or no extraintestinal virulence-specific genes, which could render difficult the development of a vaccine against extraintestinal infections. Genome flux in E. coli is confined to a small number of conserved positions in the chromosome, which most often are not associated with integrases or tRNA genes. Core genes flanking some of these regions show higher rates of recombination, suggesting that a gene, once acquired by a strain, spreads within the species by homologous recombination at the flanking genes. Finally, the genome's long-scale structure of recombination indicates lower recombination rates, but not higher mutation rates, at the terminus of replication. The ensuing effect of background selection and biased gene conversion may thus explain why this region is A+T-rich and shows high sequence divergence but low sequence polymorphism. Overall, despite a very high gene flow, genes co-exist in an organised genome. Although abundant knowledge has been accumulated regarding the E. coli laboratory strain K-12, little is known about the evolutionary trajectories that have driven the high diversity observed among natural isolates of the species, which encompass both commensal and highly virulent intestinal and extraintestinal pathogenic strains. We have annotated or re-annotated the genomes of 20 commensal and pathogenic E. coli strains and one strain of E. fergusonii (the closest E. coli related species), including seven that we sequenced to completion. Although recombination rates are much higher than mutation rates, we were able to reconstruct a robust phylogeny based on the ∼2,000 genes common to all strains. Based on this phylogeny, we established the evolutionary scenario of gains and losses of thousands of specific genes, identifying functional classes under opposite selection pressures. This genome flux is confined to very few positions in the chromosome, which are the same for every genome. Notably, we identified few or no extraintestinal virulence-specific genes. We also defined a long-scale structure of recombination in the genome with lower recombination rates at the terminus of replication. These findings demonstrate that, despite a very high gene flow, genes can co-exist in an organised genome.
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Affiliation(s)
- Marie Touchon
- Atelier de BioInformatique, Université Pierre et Marie Curie - Paris 6 (UPMC), Paris, France
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS URA2171, Paris, France
| | - Claire Hoede
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | - Olivier Tenaillon
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | | | - Simon Baeriswyl
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France
| | - Philippe Bidet
- Université Paris 7 Denis Diderot, Hôpital Robert Debré (APHP), EA 3105, Paris, France
| | - Edouard Bingen
- Université Paris 7 Denis Diderot, Hôpital Robert Debré (APHP), EA 3105, Paris, France
| | - Stéphane Bonacorsi
- Université Paris 7 Denis Diderot, Hôpital Robert Debré (APHP), EA 3105, Paris, France
| | | | - Odile Bouvet
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | - Alexandra Calteau
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
| | - Hélène Chiapello
- UR1077 Mathématique, Informatique, et Génome, INRA, Jouy en Josas, France
| | - Olivier Clermont
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | - Stéphane Cruveiller
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
| | - Antoine Danchin
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, CNRS URA2171, Paris, France
| | - Médéric Diard
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France
| | | | - Meriem El Karoui
- UR888 Unité des Bactéries Lactiques et Pathogènes Opportunistes, INRA, Jouy en Josas, France
| | - Eric Frapy
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U570, Paris, France
| | - Louis Garry
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | - Jean Marc Ghigo
- Unité de Génétique des Biofilms, Institut Pasteur, CNRS URA2172, Paris, France
| | - Anne Marie Gilles
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, CNRS URA2171, Paris, France
| | - James Johnson
- Veterans Affairs Medical Center, Minneapolis, Minnesota, United States of America
- Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
| | | | - Mathilde Lescat
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | | | | | - Ivan Matic
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France
| | - Xavier Nassif
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U570, Paris, France
| | - Sophie Oztas
- Génoscope, Institut de Génomique, CEA, Evry, France
| | - Marie Agnès Petit
- UR888 Unité des Bactéries Lactiques et Pathogènes Opportunistes, INRA, Jouy en Josas, France
| | - Christophe Pichon
- Pathogénie Bactérienne des Muqueuses, Institut Pasteur, Paris, France
| | - Zoé Rouy
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
| | - Claude Saint Ruf
- Faculté de Médecine, Université Paris 5 René Descartes, INSERM U571, Paris, France
| | | | - Jérôme Tourret
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
| | | | - David Vallenet
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
| | - Claudine Médigue
- Laboratoire de Génomique Comparative, CNRS UMR8030, Institut de Génomique, CEA, Génoscope, Evry, France
- * E-mail: (CM); (EPCR); (ED)
| | - Eduardo P. C. Rocha
- Atelier de BioInformatique, Université Pierre et Marie Curie - Paris 6 (UPMC), Paris, France
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS URA2171, Paris, France
- * E-mail: (CM); (EPCR); (ED)
| | - Erick Denamur
- Faculté de Médecine, Université Paris 7 Denis Diderot, INSERM U722, Site Xavier Bichat, Paris, France
- * E-mail: (CM); (EPCR); (ED)
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