H. Stokes and R. 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

A. Fluit and F. Schmitz, Resistance integrons and super-integrons, Clinical Microbiology and Infection, vol.10, issue.4, pp.272-288, 2004.
DOI : 10.1111/j.1198-743X.2004.00858.x

URL : https://doi.org/10.1111/j.1198-743x.2004.00858.x

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

Y. Boucher, O. Cordero, A. Takemura, D. Hunt, K. Schliep et al., Local Mobile Gene Pools Rapidly Cross Species Boundaries To Create Endemicity within Global Vibrio cholerae Populations, mBio, vol.2, issue.2, pp.335-345, 2011.
DOI : 10.1128/mBio.00335-10

URL : http://mbio.asm.org/content/2/2/e00335-10.full.pdf

G. Cambray, A. 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

R. Rapa and M. Labbate, The function of integron-associated gene cassettes in Vibrio species: the tip of the iceberg, Frontiers in Microbiology, vol.4, p.385, 2013.
DOI : 10.3389/fmicb.2013.00385

J. 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

S. Partridge, G. Tsafnat, E. Coiera, and J. Iredell, Gene cassettes and cassette arrays in mobile resistance integrons, FEMS Microbiology Reviews, vol.16, issue.4, pp.757-784, 2009.
DOI : 10.1128/AAC.01313-08

URL : https://academic.oup.com/femsre/article-pdf/33/4/757/18141700/33-4-757.pdf

T. Naas, Y. Mikami, T. Imai, L. Poirel, and P. Nordmann, Characterization of In53, a Class 1 Plasmid- and Composite Transposon-Located Integron of Escherichia coli Which Carries an Unusual Array of Gene Cassettes, Journal of Bacteriology, vol.183, issue.1, pp.235-249, 2001.
DOI : 10.1128/JB.183.1.235-249.2001

J. Cury, T. Jové, M. Touchon, B. Néron, and E. Rocha, Identification and analysis of integrons and cassette arrays in bacterial genomes, Nucleic Acids Research, vol.43, issue.10, pp.4539-4550, 2016.
DOI : 10.1101/gr.849004

URL : https://hal.archives-ouvertes.fr/pasteur-01374968

G. Recchia and R. 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

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

C. Johansson, M. Kamali-moghaddam, and L. Sundström, Integron integrase binds to bulged hairpin DNA, Nucleic Acids Research, vol.32, issue.13, pp.4033-4043, 2004.
DOI : 10.1093/nar/gkh730

URL : https://academic.oup.com/nar/article-pdf/32/13/4033/7037154/gkh730.pdf

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

J. Escudero, C. Loot, V. Parissi, A. Nivina, C. Bouchier et al., Unmasking the ancestral activity of integron integrases reveals a smooth evolutionary transition during functional innovation, Nature Communications, vol.42, 2016.
DOI : 10.1021/bi0272306

URL : https://hal.archives-ouvertes.fr/pasteur-01292328

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, 2009.
DOI : 10.1371/journal.pgen.1000632.s002

A. Nivina, J. Escudero, C. Vit, D. Mazel, and C. Loot, recombination sites, Nucleic Acids Research, vol.173, issue.16, pp.7792-7803, 2016.
DOI : 10.1093/nar/gkq511

C. Frumerie, M. Ducos-galand, D. Gopaul, and D. Mazel, The relaxed requirements of the integron cleavage site allow predictable changes in integron target specificity, Nucleic Acids Research, vol.98, issue.2, pp.559-569, 2010.
DOI : 10.1073/pnas.98.2.652

H. Stokes, O. Gorman, D. Recchia, G. Parsekhian, M. Hall et al., 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

D. Mazel, B. Dychinco, V. 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

C. Loot, M. Ducos-galand, J. Escudero, M. Bouvier, and D. Mazel, Replicative resolution of integron cassette insertion, Nucleic Acids Research, vol.155, issue.17, pp.8361-8370, 2012.
DOI : 10.1093/nar/gkm709

C. Collis and R. Hall, Expression of antibiotic resistance genes in the integrated cassettes of integrons, Antimicrobial Agents and Chemotherapy, vol.39, issue.1, pp.155-162, 1995.
DOI : 10.1128/AAC.39.1.155

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

URL : https://doi.org/10.1371/journal.pgen.1001165

D. Hocquet, C. Llanes, M. Thouverez, H. Kulasekara, X. Bertrand et al., Evidence for Induction of Integron-Based Antibiotic Resistance by the SOS Response in a Clinical Setting, PLoS Pathogens, vol.47, issue.6, 2012.
DOI : 10.1371/journal.ppat.1002778.s008

URL : https://hal.archives-ouvertes.fr/hal-00802793

O. Barraud and M. Ploy, ABSTRACT, Journal of Bacteriology, vol.197, issue.13, pp.2171-217802455, 2015.
DOI : 10.1128/JB.02455-14

E. Guerin, G. Cambray, N. Sanchez-alberola, S. Campoy, I. Erill et al., The SOS Response Controls Integron Recombination, Science, vol.9, issue.5, 1034.
DOI : 10.1016/j.mib.2006.07.002

URL : https://hal.archives-ouvertes.fr/hal-00409031

G. Cambray, N. Sanchez-alberola, S. Campoy, E. Guerin, S. Da-re et al., Prevalence of SOSmediated control of integron integrase expression as an adaptive trait of chromosomal and mobile integrons, Mob DNA, vol.2, issue.6, pp.1759-8753, 2011.
URL : https://hal.archives-ouvertes.fr/inserm-00598347

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.1659-166705982, 2012.
DOI : 10.1128/JB.05982-11

D. Bikard, C. Loot, Z. Baharoglu, and D. Mazel, Folded DNA in Action: Hairpin Formation and Biological Functions in Prokaryotes, Microbiology and Molecular Biology Reviews, vol.74, issue.4, pp.570-588, 2010.
DOI : 10.1128/MMBR.00026-10

C. Loot, V. Parissi, J. Escudero, J. Amarir-bouhram, D. Bikard et al., 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, pp.762-77101109, 2014.
DOI : 10.1128/JB.01109-13

URL : https://hal.archives-ouvertes.fr/hal-01101080

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. Wolfson and D. Dressler, Regions of Single-Stranded DNA in the Growing Points of Replicating Bacteriophage T7 Chromosomes, Proceedings of the National Academy of Sciences, vol.69, issue.9, pp.2682-2686, 1972.
DOI : 10.1073/pnas.69.9.2682

A. Moura, M. Soares, C. Pereira, N. Leitão, I. Henriques et al., INTEGRALL: a database and search engine for integrons, integrases and gene cassettes, Bioinformatics, vol.4, issue.4, pp.1096-1098, 2009.
DOI : 10.1371/journal.pcbi.1000059

A. Sigel, B. Operschall, and H. Sigel, Comparison of the ??-stacking properties of purine versus pyrimidine residues. Some generalizations regarding selectivity, JBIC Journal of Biological Inorganic Chemistry, vol.111, issue.200, pp.691-703, 2014.
DOI : 10.1021/cr100415s

D. Rowe-magnus, A. Guerout, P. Ploncard, B. Dychinco, J. Davies et al., The evolutionary history of chromosomal super-integrons provides an ancestry for multiresistant integrons, Proceedings of the National Academy of Sciences, vol.96, issue.5, pp.652-657, 2001.
DOI : 10.1073/pnas.96.5.2192

M. Gillings, M. Holley, H. Stokes, and A. Holmes, Integrons in Xanthomonas: A source of species genome diversity, Proceedings of the National Academy of Sciences, vol.33, issue.2, pp.4419-4424, 2005.
DOI : 10.1093/nar/gki206

L. Poirel, T. Naas, and P. Nordmann, Diversity, Epidemiology, and Genetics of Class D ??-Lactamases, Antimicrobial Agents and Chemotherapy, vol.54, issue.1, pp.24-38, 2010.
DOI : 10.1128/AAC.01512-08

L. Postow, C. Hardy, J. Arsuaga, and N. Cozzarelli, Topological domain structure of the Escherichia coli chromosome, Genes & Development, vol.18, issue.14, pp.1766-1779, 2004.
DOI : 10.1101/gad.1207504

L. Shlyakhtenko, P. Hsieh, M. Grigoriev, V. Potaman, R. Sinden et al., A cruciform structural transition provides a molecular switch for chromosome structure and dynamics 1 1Edited by I. Tinoco, Journal of Molecular Biology, vol.296, issue.5, pp.1169-1173, 2000.
DOI : 10.1006/jmbi.2000.3542

A. Johnson, O. Donnell, and M. , CELLULAR DNA REPLICASES: Components and Dynamics at the Replication Fork, Annual Review of Biochemistry, vol.74, issue.1, pp.283-315, 2005.
DOI : 10.1146/annurev.biochem.73.011303.073859

B. Ton-hoang, C. Pasternak, P. Siguier, C. Guynet, A. Hickman et al., Single-Stranded DNA Transposition Is Coupled to Host Replication, Cell, vol.142, issue.3, pp.398-408, 2010.
DOI : 10.1016/j.cell.2010.06.034

URL : https://hal.archives-ouvertes.fr/hal-00557930

A. Soler-bistué, J. Mondotte, M. Bland, M. Val, M. Saleh et al., Genomic Location of the Major Ribosomal Protein Gene Locus Determines Vibrio cholerae Global Growth and Infectivity, PLOS Genetics, vol.26, issue.24, 2015.
DOI : 10.1371/journal.pgen.1005156.s023

M. Val, M. Marbouty, F. De-lemos-martins, S. Kennedy, H. Kemble et al., A checkpoint control orchestrates the replication of the two chromosomes of Vibrio cholerae, Science Advances, vol.2, issue.4, 2016.
DOI : 10.1126/sciadv.1501914

URL : https://hal.archives-ouvertes.fr/pasteur-01309592

L. Feng, P. Reeves, R. Lan, Y. Ren, C. Gao et al., A Recalibrated Molecular Clock and Independent Origins for the Cholera Pandemic Clones, PLoS ONE, vol.13, issue.12, p.4053, 2008.
DOI : 10.1371/journal.pone.0004053.s016

J. Chun, C. Grim, N. Hasan, J. Lee, S. Choi et al., Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae, Proceedings of the National Academy of Sciences, vol.9, issue.4, pp.15442-15447, 2009.
DOI : 10.1093/bib/bbn017

D. Rowe-magnus, A. Guerout, and D. Mazel, Bacterial resistance evolution by recruitment of super-integron gene cassettes, Molecular Microbiology, vol.43, issue.6, pp.1657-1669, 2002.
DOI : 10.1099/00222615-46-5-398

J. Engelstädter, K. Harms, and P. Johnsen, The evolutionary dynamics of integrons in changing environments, The ISME Journal, vol.165, issue.6, pp.1296-1307, 2016.
DOI : 10.1016/j.ijantimicag.2004.03.007

F. Gao, H. Luo, and C. Zhang, DoriC 5.0: an updated database of oriC regions in both bacterial and archaeal genomes, Nucleic Acids Research, vol.37, issue.D1, pp.90-93, 2013.
DOI : 10.1093/nar/gkp335

R. Lorenz, S. Bernhart, H. Zu-siederdissen, C. Tafer, H. Flamm et al., ViennaRNA Package 2.0, Algorithms for Molecular Biology, vol.6, issue.1, pp.1748-7188, 2011.
DOI : 10.1016/0005-2795(75)90109-9

URL : https://almob.biomedcentral.com/track/pdf/10.1186/1748-7188-6-26?site=almob.biomedcentral.com

D. Mathews, M. Disney, J. Childs, S. Schroeder, M. Zuker et al., Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure, Proceedings of the National Academy of Sciences, vol.4, issue.9, pp.7287-7292, 2004.
DOI : 10.1017/S1355838298980670

I. Hofacker and R. Lorenz, Predicting RNA Structure: Advances and Limitations, Methods Mol Biol, vol.1086, pp.1-19, 2013.
DOI : 10.1007/978-1-62703-667-2_1