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

A. Landy, The lambda integrase site-specific recombination pathway, Microbiol Spectr, vol.3, pp.3-0051, 2015.

J. W. Golden, S. J. Robinson, and R. Haselkorn, Rearrangement of nitrogen fixation genes during heterocyst differentiation in the cyanobacterium Anabaena, Nature, vol.8, issue.6010, pp.419-423, 1985.
DOI : 10.1038/314419a0

M. E. Val, O. Skovgaard, M. Ducos-galand, M. J. Bland, and D. Mazel, Genome Engineering in Vibrio cholerae: A Feasible Approach to Address Biological Issues, PLoS Genetics, vol.163, issue.1, p.1002472, 2012.
DOI : 10.1371/journal.pgen.1002472.s005
URL : https://hal.archives-ouvertes.fr/inserm-01285625

D. J. Sherratt and D. B. Wigley, Conserved Themes but Novel Activities in Recombinases and Topoisomerases, Cell, vol.93, issue.2, pp.149-152, 1998.
DOI : 10.1016/S0092-8674(00)81566-4

A. Toth-petroczy and D. S. Tawfik, The robustness and innovability of protein folds, Current Opinion in Structural Biology, vol.26, pp.131-138, 2014.
DOI : 10.1016/j.sbi.2014.06.007

D. Mazel, Integrons: agents of bacterial evolution, Nature Reviews Microbiology, vol.91, issue.8, pp.608-620, 2006.
DOI : 10.1038/nrmicro1462

G. D. Recchia and R. M. Hall, Gene cassettes: a new class of mobile element, Microbiology, vol.141, issue.12, pp.3015-3027, 1995.
DOI : 10.1099/13500872-141-12-3015

J. A. Escudero, C. Loot, A. Nivina, and D. Mazel, The Integron: Adaptation On Demand, Microbiology Spectrum, vol.3, issue.2, pp.3-0019, 2015.
DOI : 10.1128/microbiolspec.MDNA3-0019-2014
URL : https://hal.archives-ouvertes.fr/pasteur-01423322

D. A. Rowe-magnus, The evolutionary history of chromosomal super-integrons provides an ancestry for multiresistant integrons, Proc. Natl Acad. Sci. USA 98, pp.652-657, 2001.
DOI : 10.1073/pnas.98.2.652

D. A. Rowe-magnus and D. Mazel, The role of integrons in antibiotic resistance gene capture, International Journal of Medical Microbiology, vol.292, issue.2, pp.115-125, 2002.
DOI : 10.1078/1438-4221-00197

E. Martinez and F. De-la-cruz, Genetic elements involved in Tn21 site-specific integration, a novel mechanism for the dissemination of antibiotic resistance genes, EMBO J, vol.9, pp.1275-1281, 1990.

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

C. Frumerie, M. Ducos-galand, D. N. Gopaul, and D. Mazel, The relaxed requirements of the integron cleavage site allow predictable changes in integron target specificity, Nucleic Acids Research, vol.38, issue.2, pp.559-569, 2010.
DOI : 10.1093/nar/gkp990

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

G. Cambray, A. M. Guerout, D. Mazel, and . Integrons, 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

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 : 10.1038/nature04643
URL : https://hal.archives-ouvertes.fr/pasteur-00140781

C. Loot, M. Ducos-galand, J. A. Escudero, M. Bouvier, and D. Mazel, Replicative resolution of integron cassette insertion, Nucleic Acids Research, vol.40, issue.17, pp.8361-8370, 2012.
DOI : 10.1093/nar/gks620

S. E. Nunes-duby, H. J. Kwon, R. S. Tirumalai, T. Ellenberger, and A. Landy, Similarities and differences among 105 members of the Int family of site-specific recombinases, Nucleic Acids Research, vol.26, issue.2, pp.391-406, 1998.
DOI : 10.1093/nar/26.2.391

M. Toll-riera and M. M. Alba, Emergence of novel domains in proteins, BMC Evolutionary Biology, vol.13, issue.1, p.47, 2013.
DOI : 10.1093/molbev/msm088

R. Aroul-selvam, T. Hubbard, and R. Sasidharan, Domain Insertions in Protein Structures, Journal of Molecular Biology, vol.338, issue.4, pp.633-641, 2004.
DOI : 10.1016/j.jmb.2004.03.039

E. Guerin, The SOS Response Controls Integron Recombination, Science, vol.324, issue.5930, p.1034, 2009.
DOI : 10.1126/science.1172914
URL : https://hal.archives-ouvertes.fr/hal-00409031

A. Wagner, The molecular origins of evolutionary innovations, Trends in Genetics, vol.27, issue.10, pp.397-410, 2011.
DOI : 10.1016/j.tig.2011.06.002

G. Demarre, C. Frumerie, D. N. Gopaul, and D. Mazel, Identification of key structural determinants of the IntI1 integron integrase that influence attC x attI1 recombination efficiency, Nucleic Acids Research, vol.35, issue.19, pp.6475-6489, 2007.
DOI : 10.1093/nar/gkm709
URL : https://hal.archives-ouvertes.fr/pasteur-00180748

C. Loot, The Integron Integrase Efficiently Prevents the Melting Effect of Escherichia coli Single-Stranded DNA-Binding Protein on Folded attC Sites, Journal of Bacteriology, vol.196, issue.4
DOI : 10.1128/JB.01109-13
URL : https://hal.archives-ouvertes.fr/hal-01101080

C. M. Collis, M. J. Kim, H. W. Stokes, and R. M. Hall, Integron-encoded IntI integrases preferentially recognize the adjacent cognate attI site in recombination with a 59-be site, Molecular Microbiology, vol.5, issue.5, pp.1415-1427, 2002.
DOI : 10.1046/j.1365-2958.2002.03260.x

S. R. Partridge, Definition of the attI1 site of class 1 integrons, Microbiology, vol.146, issue.11, pp.2855-2864, 2000.
DOI : 10.1099/00221287-146-11-2855

N. Tokuriki and D. S. Tawfik, Protein Dynamism and Evolvability, Science, vol.324, issue.5924, pp.203-207, 2009.
DOI : 10.1126/science.1169375

R. G. Lloyd and G. J. Sharples, Dissociation of synthetic Holliday junctions by E. coli RecG protein, EMBO J, vol.12, pp.17-22, 1993.

I. R. Tsaneva, B. Muller, and S. C. West, ATP-dependent branch migration of holliday junctions promoted by the RuvA and RuvB proteins of E. coli, Cell, vol.69, issue.7, pp.1171-1180, 1992.
DOI : 10.1016/0092-8674(92)90638-S

B. Connolly, Resolution of Holliday junctions in vitro requires the Escherichia coli ruvC gene product., Proc. Natl Acad. Sci. USA, pp.6063-6067, 1991.
DOI : 10.1073/pnas.88.14.6063

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

Z. Baharoglu, D. Bikard, and D. Mazel, Conjugative DNA Transfer Induces the Bacterial SOS Response and Promotes Antibiotic Resistance Development through Integron Activation, PLoS Genetics, vol.310, issue.Pt 9, p.1001165, 2010.
DOI : 10.1371/journal.pgen.1001165.s006

K. Hansson, O. Skold, and L. Sundstrom, sites of integrons are capable of site-specific recombination with one another and with secondary targets, Molecular Microbiology, vol.26, issue.03, pp.441-453, 1997.
DOI : 10.1046/j.1365-2958.1997.5401964.x

A. Gravel, B. Fournier, and P. Roy, DNA complexes obtained with the integron integrase IntI1 at the attI1 site, Nucleic Acids Research, vol.26, issue.19, pp.4347-4355, 1998.
DOI : 10.1093/nar/26.19.4347

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

V. Dubois, C. Debreyer, S. Litvak, C. Quentin, and V. Parissi, A New In Vitro Strand Transfer Assay for Monitoring Bacterial Class 1 Integron Recombinase IntI1 Activity, PLoS ONE, vol.435, issue.12, p.1315, 2007.
DOI : 10.1371/journal.pone.0001315.g009
URL : https://hal.archives-ouvertes.fr/hal-00319126

B. Gonzalez-zorn, Genetic basis for dissemination of armA, Journal of Antimicrobial Chemotherapy, vol.56, issue.3, pp.583-585, 2005.
DOI : 10.1093/jac/dki246

D. Boyd, A. Cloeckaert, E. Chaslus-dancla, and M. R. Mulvey, Characterization of Variant Salmonella Genomic Island 1 Multidrug Resistance Regions from Serovars Typhimurium DT104 and Agona, Antimicrobial Agents and Chemotherapy, vol.46, issue.6, pp.1714-1722, 2002.
DOI : 10.1128/AAC.46.6.1714-1722.2002

M. Hamidian, K. E. Holt, and R. M. Hall, isolate, Journal of Antimicrobial Chemotherapy, vol.70, issue.9, pp.2519-2523, 2015.
DOI : 10.1093/jac/dkv137

Z. Baharoglu, E. Krin, and D. Mazel, Connecting Environment and Genome Plasticity in the Characterization of Transformation-Induced SOS Regulation and Carbon Catabolite Control of the Vibrio cholerae Integron Integrase, Journal of Bacteriology, vol.194, issue.7, pp.1659-1667, 2012.
DOI : 10.1128/JB.05982-11

M. Chandler, Breaking and joining single-stranded DNA: the HUH endonuclease superfamily, Nature Reviews Microbiology, vol.36, issue.8, pp.525-538, 2013.
DOI : 10.1038/nrmicro3067
URL : https://hal.archives-ouvertes.fr/hal-00944976

S. Millan and A. , amplification causing high-level carbapenem resistance, Journal of Antimicrobial Chemotherapy, vol.70, issue.11, pp.3000-3003, 2015.
DOI : 10.1093/jac/dkv222

M. E. Val, 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

M. Quinones, H. H. Kimsey, and M. K. Waldor, LexA Cleavage Is Required for CTX Prophage Induction, Molecular Cell, vol.17, issue.2, pp.291-300, 2005.
DOI : 10.1016/j.molcel.2004.11.046

B. Das, E. Martinez, C. Midonet, and F. Barre, Integrative mobile elements exploiting Xer recombination, Trends in Microbiology, vol.21, issue.1, pp.23-30, 2013.
DOI : 10.1016/j.tim.2012.10.003

C. Midonet and F. Barre, Xer Site-Specific Recombination: Promoting Vertical and Horizontal Transmission of Genetic Information, Microbiology Spectrum, vol.2, issue.6, pp.3-0056, 2014.
DOI : 10.1128/microbiolspec.MDNA3-0056-2014

M. K. Waldor and J. J. Mekalanos, Lysogenic Conversion by a Filamentous Phage Encoding Cholera Toxin, Science, vol.272, issue.5270, pp.1910-1914, 1996.
DOI : 10.1126/science.272.5270.1910

A. Campbell, A. Del-campillo-campbell, and M. L. Ginsberg, Specificity in DNA recognition by phage integrases, Gene, vol.300, issue.1-2, pp.13-18, 2002.
DOI : 10.1016/S0378-1119(02)00846-6

P. Gottfried, E. Yagil, and M. Kolot, Core-binding specificity of bacteriophage integrases, Molecular and General Genetics MGG, vol.263, issue.4, pp.619-624, 2000.
DOI : 10.1007/s004380051209

E. Yagil, L. Dorgai, and R. A. Weisberg, Identifying Determinants of Recombination Specificity: Construction and Characterization of Chimeric Bacteriophage Integrases, Journal of Molecular Biology, vol.252, issue.2, pp.163-177, 1995.
DOI : 10.1006/jmbi.1995.0485

D. S. Tawfik, Accuracy-rate tradeoffs: how do enzymes meet demands of selectivity and catalytic efficiency?, Current Opinion in Chemical Biology, vol.21, pp.73-80, 2014.
DOI : 10.1016/j.cbpa.2014.05.008

G. Demarre, 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

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

V. Dubois, C. Debreyer, C. Quentin, and V. Parissi, In Vitro Recombination Catalyzed by Bacterial Class 1 Integron Integrase IntI1 Involves Cooperative Binding and Specific Oligomeric Intermediates, PLoS ONE, vol.285, issue.4, p.5228, 2009.
DOI : 10.1371/journal.pone.0005228.g005
URL : https://hal.archives-ouvertes.fr/hal-00426323