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
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
Integrons: agents of bacterial evolution, Nature Reviews Microbiology, vol.91, issue.8, pp.608-620, 2006. ,
DOI : 10.1073/pnas.91.20.9218
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
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
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
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
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
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
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
Gene cassettes: a new class of mobile element, Microbiology, vol.141, issue.12, pp.3015-3027, 1995. ,
DOI : 10.1099/13500872-141-12-3015
The IntI1 integron integrase preferentially binds single-stranded DNA of the attC site, J Bacteriol, vol.181, pp.6844-6849, 1999. ,
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
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
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
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
recombination sites, Nucleic Acids Research, vol.173, issue.16, pp.7792-7803, 2016. ,
DOI : 10.1093/nar/gkq511
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
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
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
Replicative resolution of integron cassette insertion, Nucleic Acids Research, vol.155, issue.17, pp.8361-8370, 2012. ,
DOI : 10.1093/nar/gkm709
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
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
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
ABSTRACT, Journal of Bacteriology, vol.197, issue.13, pp.2171-217802455, 2015. ,
DOI : 10.1128/JB.02455-14
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
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
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
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
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
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
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
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
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
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
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
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
Topological domain structure of the Escherichia coli chromosome, Genes & Development, vol.18, issue.14, pp.1766-1779, 2004. ,
DOI : 10.1101/gad.1207504
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
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
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
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
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
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
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
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
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
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
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
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
Predicting RNA Structure: Advances and Limitations, Methods Mol Biol, vol.1086, pp.1-19, 2013. ,
DOI : 10.1007/978-1-62703-667-2_1