G. Cambray, A. M. Guerout, and D. Mazel, Integrons, Annual Review of Genetics, vol.44, issue.1, pp.141-166, 2010.
DOI : 10.1146/annurev-genet-102209-163504
URL : https://hal.archives-ouvertes.fr/hal-00535771

E. Martinez and F. De-la-cruz, Transposon Tn21 encodes a RecA-independent site-specific integration system, Molecular and General Genetics MGG, vol.181, issue.2, pp.320-325, 1988.
DOI : 10.1007/BF00330610

C. Levesque, S. Brassard, J. Lapointe, and P. H. Roy, Diversity and relative strength of tandem promoters for the antibiotic-resistance genes of several integron, Gene, vol.142, issue.1, pp.49-54, 1994.
DOI : 10.1016/0378-1119(94)90353-0

T. Jove, S. Da-re, F. Denis, D. Mazel, and M. C. Ploy, Inverse Correlation between Promoter Strength and Excision Activity in Class 1 Integrons, PLoS Genetics, vol.314, issue.1, p.1000793, 2010.
DOI : 10.1371/journal.pgen.1000793.s004
URL : https://hal.archives-ouvertes.fr/inserm-00533193

D. Mazel, Integrons: agents of bacterial evolution, Nature Reviews Microbiology, vol.91, issue.8, pp.608-620, 2006.
DOI : 10.1073/pnas.91.20.9218

H. W. Stokes and R. M. Hall, A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons, Molecular Microbiology, vol.9, issue.12, pp.1669-1683, 1989.
DOI : 10.1007/BF00337818

C. M. Collis, G. Grammaticopoulos, J. Briton, H. W. Stokes, and R. M. Hall, Site-specific insertion of gene cassettes into integrons, Molecular Microbiology, vol.3, issue.1, pp.41-52, 1993.
DOI : 10.1007/BF00339581

C. M. Collis and R. M. Hall, Gene cassettes from the insert region of integrons are excised as covalently closed circles, Molecular Microbiology, vol.217, issue.19, pp.2875-2885, 1992.
DOI : 10.1016/0378-1119(85)90120-9

H. W. Stokes, D. B. O-'gorman, G. D. Recchia, M. Parsekhian, and R. M. Hall, Structure and function of 59-base element recombination sites associated with mobile gene cassettes, Molecular Microbiology, vol.26, issue.04, pp.731-745, 1997.
DOI : 10.1046/j.1365-2958.1997.6091980.x

M. V. Francia, J. C. Zabala, F. De-la-cruz, and J. M. Garcia-lobo, The IntI1 integron integrase preferentially binds single-stranded DNA of the attC site, J. Bacteriol, vol.181, pp.6844-6849, 1999.

M. Bouvier, G. Demarre, and D. Mazel, Integron cassette insertion: a recombination process involving a folded single strand substrate, The EMBO Journal, vol.91, issue.24, pp.4356-4367, 2005.
DOI : 10.1038/sj.emboj.7600434
URL : http://emboj.embopress.org/content/embojnl/24/24/4356.full.pdf

M. Bouvier, M. Ducos-galand, C. Loot, D. Bikard, and D. Mazel, Structural Features of Single-Stranded Integron Cassette attC Sites and Their Role in Strand Selection, PLoS Genetics, vol.155, issue.9, p.1000632, 2009.
DOI : 10.1371/journal.pgen.1000632.s002

D. Macdonald, G. Demarre, M. Bouvier, D. Mazel, and D. N. Gopaul, Structural basis for broad DNA-specificity in integron recombination, Nature, vol.54, issue.7088, pp.1157-1162, 2006.
DOI : 10.1107/S0907444998003254
URL : https://hal.archives-ouvertes.fr/pasteur-00140781

R. M. Hall, D. E. Brookes, and H. W. Stokes, Site-specific insertion of genes into integrons: role of the 59-base element and determination of the recombination cross-over point, Molecular Microbiology, vol.9, issue.8, pp.1941-1959, 1991.
DOI : 10.1016/0378-1119(85)90120-9

D. A. Rowe-magnus, A. M. Guerout, L. Biskri, P. Bouige, and D. Mazel, Comparative Analysis of Superintegrons: Engineering Extensive Genetic Diversity in the Vibrionaceae, Genome Research, vol.13, issue.3, pp.428-442, 2003.
DOI : 10.1101/gr.617103

D. Mazel, B. Dychinco, V. A. Webb, and J. Davies, A Distinctive Class of Integron in the Vibrio cholerae Genome, Science, vol.280, issue.5363, pp.605-608, 1998.
DOI : 10.1126/science.280.5363.605

N. D. Grindley, K. L. Whiteson, and P. A. Rice, Mechanisms of Site-Specific Recombination, Annual Review of Biochemistry, vol.75, issue.1, pp.567-605, 2006.
DOI : 10.1146/annurev.biochem.73.011303.073908

C. Loot, D. Bikard, A. Rachlin, and D. Mazel, Cellular pathways controlling integron cassette site folding, The EMBO Journal, vol.257, issue.15, pp.2623-2634, 2010.
DOI : 10.1093/nar/gkg595
URL : http://emboj.embopress.org/content/embojnl/29/15/2623.full.pdf

J. Sambrook, E. F. Fritsch, and T. Maniatis, Molecular Cloning: A Laboratory Manual, 1989.

L. Biskri, M. Bouvier, A. M. Guerout, S. Boisnard, and D. Mazel, Comparative Study of Class 1 Integron and Vibrio cholerae Superintegron Integrase Activities, Journal of Bacteriology, vol.187, issue.5, pp.1740-1750, 2005.
DOI : 10.1128/JB.187.5.1740-1750.2005

P. J. Pukkila, J. Peterson, G. Herman, P. Modrich, and M. Meselson, Effects of high levels of DNA adenine methylation on methyl-directed mismatch repair in Escherichia coli, Genetics, vol.104, pp.571-582, 1983.

S. C. West, ABC PROTEINS, Annual Review of Genetics, vol.31, issue.1, pp.213-244, 1997.
DOI : 10.1146/annurev.genet.31.1.213

C. A. Parsons, A. Stasiak, R. J. Bennett, and S. C. West, Structure of a multisubunit complex that promotes DNA branch migration, Nature, vol.374, issue.6520, pp.375-378, 1995.
DOI : 10.1038/374375a0

X. Yu, S. C. West, and E. H. Egelman, Structure and subunit composition of theRuvAB-holliday junction complex 1 1Edited by P. E. Wright, Journal of Molecular Biology, vol.266, issue.2, pp.217-222, 1997.
DOI : 10.1006/jmbi.1996.0799

A. K. Eggleston and S. C. West, RuvABC Complex, Journal of Biological Chemistry, vol.269, issue.34, pp.26467-26476, 2000.
DOI : 10.1016/0022-2836(77)90028-6

P. Mcglynn and R. G. Lloyd, Genome stability and the processing of damaged replication forks by RecG, Trends in Genetics, vol.18, issue.8, pp.413-419, 2002.
DOI : 10.1016/S0168-9525(02)02720-8

P. Mcglynn and R. G. Lloyd, Rescue of stalled replication forks by RecG: Simultaneous translocation on the leading and lagging strand templates supports an active DNA unwinding model of fork reversal and Holliday junction formation, Proc. Natl. Acad. Sci. USA, pp.8227-8234, 2001.
DOI : 10.1073/pnas.121007798

A. V. Gregg, P. Mcglynn, R. P. Jaktaji, and R. G. Lloyd, Direct Rescue of Stalled DNA Replication Forks via the Combined Action of PriA and RecG Helicase Activities, Molecular Cell, vol.9, issue.2, pp.241-251, 2002.
DOI : 10.1016/S1097-2765(02)00455-0

N. Messier and P. H. Roy, Integron Integrases Possess a Unique Additional Domain Necessary for Activity, Journal of Bacteriology, vol.183, issue.22, pp.6699-6706, 2001.
DOI : 10.1128/JB.183.22.6699-6706.2001
URL : http://jb.asm.org/content/183/22/6699.full.pdf

T. Tanaka, T. Mizukoshi, K. Sasaki, D. Kohda, and H. Masai, PriA Protein, Two Modes of DNA Binding and Activation of ATP Hydrolysis, Journal of Biological Chemistry, vol.1764, issue.27, pp.19917-19927, 2007.
DOI : 10.1016/S1097-2765(02)00455-0

G. Grompone, S. D. Ehrlich, and B. Michel, Replication restart in gyrB Escherichia coli mutants, Molecular Microbiology, vol.275, issue.3, pp.845-854, 2003.
DOI : 10.1016/S0167-4781(98)00126-2
URL : http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2003.03480.x/pdf

A. M. Gestal, H. W. Stokes, S. R. Partridge, and R. M. Hall, Recombination between the dfrA12-orfF-aadA2 Cassette Array and an aadA1 Gene Cassette Creates a Hybrid Cassette, aadA8b, Antimicrobial Agents and Chemotherapy, vol.49, issue.11, pp.4771-4774, 2005.
DOI : 10.1128/AAC.49.11.4771-4774.2005

C. Turlan and M. Chandler, Playing second fiddle: second-strand processing and liberation of transposable elements from donor DNA, Trends in Microbiology, vol.8, issue.6, pp.268-274, 2000.
DOI : 10.1016/S0966-842X(00)01757-1

M. E. Val, M. Bouvier, J. Campos, D. Sherratt, F. Cornet et al., The Single-Stranded Genome of Phage CTX Is the Form Used for Integration into the Genome of Vibrio cholerae, Molecular Cell, vol.19, issue.4, pp.559-566, 2005.
DOI : 10.1016/j.molcel.2005.07.002
URL : https://hal.archives-ouvertes.fr/inserm-01285606

C. Guynet, A. B. Hickman, O. Barabas, F. Dyda, M. Chandler et al., In Vitro Reconstitution of a Single-Stranded Transposition Mechanism of IS608, Molecular Cell, vol.29, issue.3, pp.302-312, 2008.
DOI : 10.1016/j.molcel.2007.12.008
URL : https://hal.archives-ouvertes.fr/hal-00268914

G. Demarre, A. M. Guerout, C. Matsumoto-mashimo, D. A. Rowe-magnus, P. Marliè-re et al., A new family of mobilizable suicide plasmids based on broad host range R388 plasmid (IncW) and RP4 plasmid (IncP??) conjugative machineries and their cognate Escherichia coli host strains, Research in Microbiology, vol.156, issue.2, pp.245-255, 2005.
DOI : 10.1016/j.resmic.2004.09.007

B. R. Palmer and M. G. Marinus, The dam and dcm strains of Escherichia coli ??? a review, Gene, vol.143, issue.1, pp.1-12, 1994.
DOI : 10.1016/0378-1119(94)90597-5

G. Demarre, C. Frumerie, D. N. Gopaul, and D. Mazel, Identification of key structural determinants of the IntI1 integron integrase that influence attC??attI1 recombination efficiency, Nucleic Acids Research, vol.98, issue.19, pp.6475-6489, 2007.
DOI : 10.1073/pnas.98.2.652
URL : https://hal.archives-ouvertes.fr/pasteur-00180748

C. Matsumoto-mashimo, A. M. Guerout, and D. Mazel, A new family of conditional replicating plasmids and their cognate Escherichia coli host strains, Research in Microbiology, vol.155, issue.6, pp.455-461, 2004.
DOI : 10.1016/j.resmic.2004.03.001