Call of the wild: antibiotic resistance genes in natural environments, Nature Reviews Microbiology, vol.22, issue.4, pp.251-259, 2010. ,
DOI : 10.1038/nrmicro2312
Biological Diversity of Prokaryotic Type IV Secretion Systems, Microbiology and Molecular Biology Reviews, vol.73, issue.4, pp.775-808, 2009. ,
DOI : 10.1128/MMBR.00023-09
Bacterial plasmids and gene flux, Cell, vol.70, issue.2, pp.189-199, 1992. ,
DOI : 10.1016/0092-8674(92)90095-T
Membrane sphingolipids as essential molecular signals for Bacteroides survival in the intestine, Proceedings of the National Academy of Sciences, vol.108, issue.Supplement_1, pp.4666-4671, 2011. ,
DOI : 10.1073/pnas.1001501107
Efficient Gene Transfer in Bacterial Cell Chains, mBio, vol.2, issue.2, pp.27-38, 2011. ,
DOI : 10.1128/mBio.00027-11
The Agrobacterium tumefaciens virB4 gene product is an essential virulence protein requiring an intact nucleoside triphosphate-binding domain., Journal of Bacteriology, vol.175, issue.6, pp.1723-1734, 1993. ,
DOI : 10.1128/jb.175.6.1723-1734.1993
Genetic complementation analysis of the Agrobacterium tumefaciens virB operon: virB2 through virB11 are essential virulence genes., Journal of Bacteriology, vol.176, issue.12, pp.3646-3660, 1994. ,
DOI : 10.1128/jb.176.12.3646-3660.1994
FtsK, a literate chromosome segregation machine, Molecular Microbiology, vol.180, issue.6, pp.1434-1441, 2007. ,
DOI : 10.1111/j.1365-2958.2007.05755.x
URL : https://hal.archives-ouvertes.fr/hal-00154604
Conjugative transposons: the tip of the iceberg, Molecular Microbiology, vol.67, issue.3, pp.601-610, 2002. ,
DOI : 10.1046/j.1365-2958.2002.03191.x
Membrane-associated nanomotors for macromolecular transport, Current Opinion in Biotechnology, vol.23, issue.4, pp.537-581, 2012. ,
DOI : 10.1016/j.copbio.2011.11.031
The Pseudomonas aeruginosa Pathogenicity Island PAPI-1 Is Transferred via a Novel Type IV Pilus, Journal of Bacteriology, vol.192, issue.13, pp.3249-3258, 2010. ,
DOI : 10.1128/JB.00041-10
The Ins and Outs of DNA Transfer in Bacteria, Science, vol.310, issue.5753, pp.1456-1460, 2005. ,
DOI : 10.1126/science.1114021
Bacterial type IV secretion: conjugation systems adapted to deliver effector molecules to host cells, Trends in Microbiology, vol.8, issue.8, pp.354-360, 2000. ,
DOI : 10.1016/S0966-842X(00)01792-3
Toward Automatic Reconstruction of a Highly Resolved Tree of Life, Science, vol.311, issue.5765, pp.1283-1287, 2006. ,
DOI : 10.1126/science.1123061
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments, BMC Evolutionary Biology, vol.10, issue.1, p.210, 2010. ,
DOI : 10.1186/1471-2148-10-210
Phylogenomic networks, Trends in Microbiology, vol.19, issue.10, pp.483-491, 2011. ,
DOI : 10.1016/j.tim.2011.07.001
ProtTest 3: fast selection of best-fit models of protein evolution, Bioinformatics, vol.27, issue.8, pp.1164-1165, 2011. ,
DOI : 10.1093/bioinformatics/btr088
Horizontal gene transfer and the origin of species: lessons from bacteria, Trends in Microbiology, vol.8, issue.3, pp.128-133, 2000. ,
DOI : 10.1016/S0966-842X(00)01703-0
Conjugative DNA metabolism in Gram-negative bacteria, FEMS Microbiology Reviews, vol.34, issue.1, pp.18-40, 2010. ,
DOI : 10.1111/j.1574-6976.2009.00195.x
Functional Dissection of the Conjugative Coupling Protein TrwB, Journal of Bacteriology, vol.192, issue.11, pp.2655-2669, 2010. ,
DOI : 10.1128/JB.01692-09
Functional interactions between type IV secretion systems involved in DNA transfer and virulence, Microbiology, vol.151, issue.11, pp.3505-3516, 2005. ,
DOI : 10.1099/mic.0.28410-0
Plasmid transfer systems in the rhizobia, Canadian Journal of Microbiology, vol.55, issue.8, pp.917-927, 2009. ,
DOI : 10.1139/W09-056
Accelerated Profile HMM Searches, PLoS Computational Biology, vol.21, issue.10, p.1002195, 2011. ,
DOI : 10.1371/journal.pcbi.1002195.g006
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004. ,
DOI : 10.1093/nar/gkh340
Parallel Evolution of a Type IV Secretion System in Radiating Lineages of the Host-Restricted Bacterial Pathogen Bartonella, PLoS Genetics, vol.52, issue.4, p.1001296 ,
DOI : 10.1371/journal.pgen.1001296.s011
Transfer of R388 Derivatives by a Pathogenesis-Associated Type IV Secretion System into both Bacteria and Human Cells, Journal of Bacteriology, vol.193, issue.22, pp.6257-6265, 2011. ,
DOI : 10.1128/JB.05905-11
Functional Divergence and Horizontal Transfer of Type IV Secretion Systems, Molecular Biology and Evolution, vol.22, issue.5, pp.1325-1336, 2005. ,
DOI : 10.1093/molbev/msi124
The structural biology of type IV secretion systems, Nature Reviews Microbiology, vol.179, issue.10, pp.703-714, 2009. ,
DOI : 10.1038/nrmicro2218
Mobile genetic elements: the agents of open source evolution, Nature Reviews Microbiology, vol.11, issue.9, pp.722-732, 2005. ,
DOI : 10.1093/nar/gkh059
Pilus Assembly by Agrobacterium T-DNA Transfer Genes, Science, vol.273, issue.5278, pp.1107-1109, 1996. ,
DOI : 10.1126/science.273.5278.1107
The diversity of conjugative relaxases and its application in plasmid classification, FEMS Microbiology Reviews, vol.33, issue.3, pp.657-687, 2009. ,
DOI : 10.1111/j.1574-6976.2009.00168.x
New algorithms and methods to estimate maximumlikelihood phylogenies: assessing the performance of PhyML 3.0, Syst Biol, vol.59, pp.307-321, 2010. ,
URL : https://hal.archives-ouvertes.fr/lirmm-00511784
Natural conjugative plasmids induce bacterial biofilm development, Nature, vol.143, issue.6845, pp.442-445, 2001. ,
DOI : 10.1038/35086581
Uncovering the Prevalence and Diversity of Integrating Conjugative Elements in Actinobacteria, PLoS ONE, vol.147, issue.Pt 3, p.27846, 2011. ,
DOI : 10.1371/journal.pone.0027846.s013
Contact with epithelial cells induces the formation of surface appendages on Salmonella typhimurium, Cell, vol.76, issue.4, pp.717-724, 1994. ,
DOI : 10.1016/0092-8674(94)90510-X
Prokaryotic Evolution in Light of Gene Transfer, Molecular Biology and Evolution, vol.19, issue.12, pp.2226-2238, 2002. ,
DOI : 10.1093/oxfordjournals.molbev.a004046
Complete Nucleotide Sequence of the pCTX-M3 Plasmid and Its Involvement in Spread of the Extended-Spectrum ??-Lactamase Gene blaCTX-M-3, Antimicrobial Agents and Chemotherapy, vol.51, issue.11, pp.3789-3795, 2007. ,
DOI : 10.1128/AAC.00457-07
Coupling Factors in Macromolecular Type-IV Secretion Machineries, Current Pharmaceutical Design, vol.10, issue.13, pp.1551-1565, 2004. ,
DOI : 10.2174/1381612043384817
Exaptation???a Missing Term in the Science of Form, Paleobiology, vol.76, issue.01, pp.4-15, 1982. ,
DOI : 10.2307/2412538
SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol.27, issue.2, pp.221-224, 2010. ,
DOI : 10.1093/molbev/msp259
URL : https://hal.archives-ouvertes.fr/lirmm-00705187
Conjugative Plasmid Transfer in Gram-Positive Bacteria, Microbiology and Molecular Biology Reviews, vol.67, issue.2, pp.277-301, 2003. ,
DOI : 10.1128/MMBR.67.2.277-301.2003
The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation, PLoS Genetics, vol.22, issue.8, p.1002222, 2011. ,
DOI : 10.1371/journal.pgen.1002222.s002
URL : https://hal.archives-ouvertes.fr/pasteur-00647077
Bacterial conjugation mediated by plasmid RP4: RSF1010 mobilization, donor-specific phage propagation, and pilus production require the same Tra2 core components of a proposed DNA transport complex., Journal of Bacteriology, vol.177, issue.16, pp.4779-4791, 1995. ,
DOI : 10.1128/jb.177.16.4779-4791.1995
Network analyses structure genetic diversity in independent genetic worlds, Proceedings of the National Academy of Sciences, vol.107, issue.1, pp.127-132, 2010. ,
DOI : 10.1073/pnas.0908978107
secretes chromosomal DNA via a novel type IV secretion system, Molecular Microbiology, vol.163, issue.Suppl. 1, pp.1704-1721, 2005. ,
DOI : 10.1111/j.1365-2958.2005.04521.x
Roles of Internal Cysteines in the Function, Localization, and Reactivity of the TraV Outer Membrane Lipoprotein Encoded by the F Plasmid, Journal of Bacteriology, vol.184, issue.11, pp.3126-3129, 2002. ,
DOI : 10.1128/JB.184.11.3126-3129.2002
Natural transformation competence in Helicobacter pylori is mediated by the basic components of a type IV secretion system, Molecular Microbiology, vol.63, issue.2, pp.379-391, 2001. ,
DOI : 10.1046/j.1365-2958.2001.02502.x
Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging, Nucleic Acids Research, vol.32, issue.17, pp.5260-5279, 2004. ,
DOI : 10.1093/nar/gkh828
Novel Type IV Secretion System Involved in Propagation of Genomic Islands, Journal of Bacteriology, vol.189, issue.3, pp.761-771, 2007. ,
DOI : 10.1128/JB.01327-06
Type IV secretion systems: tools of bacterial horizontal gene transfer and virulence, Cellular Microbiology, vol.63, issue.12, pp.2377-2386, 2008. ,
DOI : 10.1111/j.1462-5822.2008.01187.x
16 co-authors). 2007. Sequence and functional analyses of Haemophilus spp ,
Parallelization of the MAFFT multiple sequence alignment program, Bioinformatics, vol.26, issue.15, pp.1899-1900, 2010. ,
DOI : 10.1093/bioinformatics/btq224
The plasmid R64 thin pilus identified as a type IV pilus., Journal of Bacteriology, vol.179, issue.11, pp.3594-3603, 1997. ,
DOI : 10.1128/jb.179.11.3594-3603.1997
Transcriptional analysis of the flagellar regulon of Salmonella typhimurium., Journal of Bacteriology, vol.172, issue.2, pp.741-747, 1990. ,
DOI : 10.1128/jb.172.2.741-747.1990
Gene Recombination in Escherichia Coli, Nature, vol.158, issue.4016, p.558, 1946. ,
DOI : 10.1038/158558a0
Bacterial conjugation: a two-step mechanism for DNA transport, Molecular Microbiology, vol.174, issue.1, pp.1-8, 2002. ,
DOI : 10.1046/j.1365-2958.2000.02164.x
Conjugative coupling proteins interact with cognate and heterologous VirB10-like proteins while exhibiting specificity for cognate relaxosomes, Proceedings of the National Academy of Sciences, vol.100, issue.18, pp.10465-10470, 2003. ,
DOI : 10.1073/pnas.1830264100
Bioinformatics: sequence and genome analysis, Cold Spring Harbor, 2004. ,
Horizontal Gene Transfer of the Secretome Drives the Evolution of Bacterial Cooperation and Virulence, Current Biology, vol.19, issue.20, pp.1683-1691, 2009. ,
DOI : 10.1016/j.cub.2009.08.056
T-coffee: a novel method for fast and accurate multiple sequence alignment, Journal of Molecular Biology, vol.302, issue.1, pp.205-217, 2000. ,
DOI : 10.1006/jmbi.2000.4042
Diversifying Selection and Concerted Evolution of a Type IV Secretion System in Bartonella, Molecular Biology and Evolution, vol.25, issue.2, pp.287-300, 2008. ,
DOI : 10.1093/molbev/msm252
Examining bacterial species under the specter of gene transfer and exchange, Proceedings of the National Academy of Sciences, vol.102, issue.Supplement 1, pp.6595-6599, 2005. ,
DOI : 10.1073/pnas.0502035102
URL : https://hal.archives-ouvertes.fr/hal-00427799
TcpA, an FtsK/SpoIIIE Homolog, Is Essential for Transfer of the Conjugative Plasmid pCW3 in Clostridium perfringens, Journal of Bacteriology, vol.189, issue.21, pp.7782-7790, 2007. ,
DOI : 10.1128/JB.00783-07
The phage ?? major tail protein structure reveals a common evolution for long-tailed phages and the type VI bacterial secretion system, Proceedings of the National Academy of Sciences, vol.106, issue.11, pp.4160-4165, 2009. ,
DOI : 10.1073/pnas.0900044106
Autoinhibitory Regulation of TrwK, an Essential VirB4 ATPase in Type IV Secretion Systems, Journal of Biological Chemistry, vol.286, issue.19, pp.17376-17382, 2011. ,
DOI : 10.1074/jbc.M110.208942
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough, PLoS Biology, vol.25, issue.3, p.1000602, 2011. ,
DOI : 10.1371/journal.pbio.1000602.s019
URL : https://hal.archives-ouvertes.fr/hal-00594558
The ecological coherence of high bacterial taxonomic ranks, Nature Reviews Microbiology, vol.444, issue.7, pp.523-529, 2010. ,
DOI : 10.1038/nrmicro2367
Phylogeny of genes for secretion NTPases: Identification of the widespread tadA subfamily and development of a diagnostic key for gene classification, Proceedings of the National Academy of Sciences, vol.98, issue.5, pp.2503-2508, 2001. ,
DOI : 10.1073/pnas.051436598
The integrative element pSAM2 from Streptomyces: kinetics and mode of conjugal transfer, Molecular Microbiology, vol.264, issue.57, pp.159-166, 2001. ,
DOI : 10.1046/j.1365-2958.2001.02618.x
What traits are carried on mobile genetic elements, and why?, Heredity, vol.87, issue.1, pp.1-10, 2011. ,
DOI : 10.1046/j.1365-313X.2000.00808.x
The Integrase of the Conjugative Transposon Tn916 Directs Strand- and Sequence-Specific Cleavage of the Origin of Conjugal Transfer, oriT, by the Endonuclease Orf20, Journal of Bacteriology, vol.188, issue.6, pp.2207-2213, 2006. ,
DOI : 10.1128/JB.188.6.2207-2213.2006
Inference and Analysis of the Relative Stability of Bacterial Chromosomes, Molecular Biology and Evolution, vol.23, issue.3, pp.513-522, 2006. ,
DOI : 10.1093/molbev/msj052
A novel relaxase homologue is involved in chromosomal DNA processing for type IV secretion in Neisseria gonorrhoeae, Molecular Microbiology, vol.236, issue.4, pp.930-947, 2007. ,
DOI : 10.1074/jbc.M405120200
Conjugative DNA transfer into human cells by the VirB/VirD4 type IV secretion system of the bacterial pathogen Bartonella henselae, Proceedings of the National Academy of Sciences, vol.108, issue.35, pp.14643-14648, 2011. ,
DOI : 10.1073/pnas.1019074108
A bacterial conjugation machinery recruited for pathogenesis, Molecular Microbiology, vol.277, issue.5, pp.1253-1266, 2003. ,
DOI : 10.1046/j.1365-2958.2003.03650.x
Mobility of Plasmids, Microbiology and Molecular Biology Reviews, vol.74, issue.3, pp.434-452, 2010. ,
DOI : 10.1128/MMBR.00020-10
URL : https://hal.archives-ouvertes.fr/pasteur-01374958
Intermolecular disulfide bonds stabilize VirB7 homodimers and VirB7/VirB9 heterodimers during biogenesis of the Agrobacterium tumefaciens T-complex transport apparatus., Proceedings of the National Academy of Sciences, vol.93, issue.15, pp.7512-7517, 1996. ,
DOI : 10.1073/pnas.93.15.7512
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, pp.2688-2690, 2006. ,
DOI : 10.1093/bioinformatics/btl446
The Putative Coupling Protein TcpA Interacts with Other pCW3-Encoded Proteins To Form an Essential Part of the Conjugation Complex, Journal of Bacteriology, vol.191, issue.9, pp.2926-2933, 2009. ,
DOI : 10.1128/JB.00032-09
TrwB, the coupling protein involved in DNA transport during bacterial conjugation, is a DNA-dependent ATPase, Proceedings of the National Academy of Sciences, vol.102, issue.23, pp.8156-8161, 2005. ,
DOI : 10.1073/pnas.0503402102
Functional Characterization and Localization of the TcpH Conjugation Protein from Clostridium perfringens, Journal of Bacteriology, vol.190, issue.14, pp.5075-5086, 2008. ,
DOI : 10.1128/JB.00386-08
Horizontal gene pool: bacterial plasmids and gene spread, 2000. ,
DOI : 10.4324/9780203304334
B operon, Nucleic Acids Research, vol.16, issue.10, pp.4621-4636, 1988. ,
DOI : 10.1093/nar/16.10.4621
Genomic islands and the evolution of catabolic pathways in bacteria, Current Opinion in Biotechnology, vol.14, issue.3, pp.248-254, 2003. ,
DOI : 10.1016/S0958-1669(03)00058-2
Conjugative Transfer by the Virulence System of Legionella pneumophila, Science, vol.279, issue.5352, pp.873-876, 1998. ,
DOI : 10.1126/science.279.5352.873
resembles bacterial chromosome segregation by FtsK/SpoIIIE, The EMBO Journal, vol.180, issue.11, pp.2246-2254, 2011. ,
DOI : 10.1038/emboj.2011.121
Membrane Lipids in Cyanobacteria, Lipids in photosynthesis: structure, function and genetics, pp.65-81, 1998. ,
DOI : 10.1007/0-306-48087-5_4
Structure of the VirB4 ATPase, alone and bound to the core complex of a type IV secretion system, Proceedings of the National Academy of Sciences, vol.109, issue.28, pp.11348-11353, 2012. ,
DOI : 10.1073/pnas.1201428109
Characterization of the virB operon from an Agrobacterium tumefaciens Ti plasmid, J Biol Chem, vol.263, pp.5804-5814, 1988. ,
Molecular characterization of an operon required for pertussis toxin secretion., Proceedings of the National Academy of Sciences, vol.90, issue.7, pp.2970-2974, 1993. ,
DOI : 10.1073/pnas.90.7.2970
Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow, Nature Reviews Microbiology, vol.5, issue.8, pp.552-563, 2010. ,
DOI : 10.1038/nrmicro2382