J. M. Auchtung, C. A. Lee, R. E. Monson, A. P. Lehman, and A. D. Grossman, Regulation of a Bacillus subtilis mobile genetic element by intercellular signaling and the global DNA damage response, Proc. Natl. Acad, 2005.
DOI : 10.1099/mic.0.25737-0

M. Bacic, A. C. Parker, J. Stagg, H. P. Whitley, W. G. Wells et al., Genetic and Structural Analysis of the Bacteroides Conjugative Transposon CTn341, Journal of Bacteriology, vol.187, issue.8, pp.2858-2869, 2005.
DOI : 10.1128/JB.187.8.2858-2869.2005

J. W. Beaber, B. Hochhut, and M. K. Waldor, SOS response promotes horizontal dissemination of antibiotic resistance genes, Nature, vol.53, issue.6969, pp.72-74, 2004.
DOI : 10.1073/pnas.120163297

S. D. Bentley, K. F. Chater, A. M. Cerdeno-tarraga, G. L. Challis, N. R. Thomson et al., Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2), Complete genome sequence of the model actinomycete Streptomyces coelicolor A3, pp.141-147, 2002.
DOI : 10.1073/pnas.85.8.2444

I. Biswas, A. Gruss, S. D. Ehrlich, and E. Maguin, High-efficiency gene inactivation and replacement system for gram-positive bacteria., Journal of Bacteriology, vol.175, issue.11, pp.3628-3635, 1993.
DOI : 10.1128/jb.175.11.3628-3635.1993
URL : http://jb.asm.org/content/175/11/3628.full.pdf

G. T. Bonheyo, B. D. Hund, N. B. Shoemaker, and A. A. Salyers, Transfer Region of a Bacteroides Conjugative Transposon Contains Regulatory as Well as Structural Genes, Plasmid, vol.46, issue.3, pp.202-209, 2001.
DOI : 10.1006/plas.2001.1545

H. Brüssow and A. Bruttin, Characterization of a Temperate Streptococcus therrnophilus Bacteriophage and Its Genetic Relationship with Lyric Phages, Virology, vol.212, issue.2, pp.632-640, 1995.
DOI : 10.1006/viro.1995.1521

V. Burrus, G. Pavlovic, B. Decaris, and G. Guédon, Conjugative transposons: the tip of the iceberg, Molecular Microbiology, vol.67, issue.3, pp.601-610, 2002.
DOI : 10.1128/jb.175.9.2713-2719.1993
URL : https://hal.archives-ouvertes.fr/hal-01659089

V. Burrus, G. Pavlovic, B. Decaris, and G. Guédon, The ICESt1 element of Streptococcus thermophilus belongs to a large family of integrative and conjugative elements that exchange modules and change their specificity of integration, Plasmid, vol.48, issue.2, p.77, 2002.
DOI : 10.1016/S0147-619X(02)00102-6
URL : https://hal.archives-ouvertes.fr/hal-01659496

V. Burrus, Y. Roussel, B. Decaris, and G. Guédon, Characterization of a Novel Integrative Element, ICESt1, in the Lactic Acid Bacterium Streptococcus thermophilus, Applied and Environmental Microbiology, vol.66, issue.4, pp.1749-1753, 2000.
DOI : 10.1128/AEM.66.4.1749-1753.2000
URL : https://hal.archives-ouvertes.fr/hal-01659518

D. B. Clewell, D. D. Jaworski, S. E. Flannagan, L. A. Zitzow, and Y. A. Su, The conjugative transposon Tn916 of Enterococcus faecalis: structural analysis and some key factors involved in movement, Dev. Biol. Stand, vol.85, pp.11-17, 1995.

I. B. Dodd, K. E. Shearwin, A. J. Perkins, T. Burr, A. Hochschild et al., Cooperativity in long-range gene regulation by the ?? CI repressor, Genes & Development, vol.18, issue.3, pp.344-354, 2004.
DOI : 10.1101/gad.1167904

M. Gaillard, T. Vallaeys, F. J. Vorholter, M. Minoia, C. Werlen et al., The clc Element of Pseudomonas sp. Strain B13, a Genomic Island with Various Catabolic Properties, Journal of Bacteriology, vol.188, issue.5, pp.1999-2013, 2006.
DOI : 10.1128/JB.188.5.1999-2013.2006

A. H. Johansen, L. Brondsted, and K. Hammer, Identification of operator sites of the CI repressor of phage TP901-1: evolutionary link to other phages, Virology, vol.311, issue.1, pp.144-156, 2003.
DOI : 10.1016/S0042-6822(03)00169-7

K. D. Larbig, A. Christmann, A. Johann, J. Klockgether, T. Hartsch et al., Gene Islands Integrated into tRNAGly Genes Confer Genome Diversity on a Pseudomonas aeruginosa Clone, Journal of Bacteriology, vol.184, issue.23, pp.6665-6680, 2002.
DOI : 10.1128/JB.184.23.6665-6680.2002

P. L. Madsen, A. H. Johansen, K. Hammer, and L. Brondsted, The genetic switch regulating activity of early promoters of the temperate lactococcal bacteriophage TP901-1, J. Bacteriol, vol.181, pp.7430-7438, 1999.

E. Maguin, H. Prévost, S. D. Ehrlich, and A. Gruss, Efficient insertional mutagenesis in lactococci and other gram-positive bacteria., Journal of Bacteriology, vol.178, issue.3, pp.931-935, 1996.
DOI : 10.1128/jb.178.3.931-935.1996

B. M. Mcgrath, J. A. O-'halloran, and J. T. Pembroke, dependent, FEMS Microbiology Letters, vol.243, issue.2, pp.461-465, 2005.
DOI : 10.1016/j.femsle.2005.01.013
URL : https://hal.archives-ouvertes.fr/jpa-00226229

Z. Mohd-zain, S. L. Turner, A. M. Cerdeno-tarraga, A. K. Lilley, T. J. Inzana et al., Transferable Antibiotic Resistance Elements in Haemophilus influenzae Share a Common Evolutionary Origin with a Diverse Family of Syntenic Genomic Islands, Journal of Bacteriology, vol.186, issue.23, pp.8114-8122, 2004.
DOI : 10.1128/JB.186.23.8114-8122.2004

G. Pavlovic, V. Burrus, B. Gintz, B. Decaris, and G. Guédon, Evolution of genomic islands by deletion and tandem accretion by site-specific recombination: ICESt1-related elements from Streptococcus thermophilus, Microbiology, vol.150, issue.4, pp.759-774, 2004.
DOI : 10.1099/mic.0.26883-0
URL : https://hal.archives-ouvertes.fr/hal-01659488

N. D. Rawlings and A. J. Barrett, [13] Evolutionary families of metallopeptidases, Methods Enzymol, vol.248, pp.183-228, 1995.
DOI : 10.1016/0076-6879(95)48015-3

V. Sentchilo, R. Ravatn, C. Werlen, A. J. Zehnder, and J. R. Van-der-meer, Unusual Integrase Gene Expression on the clc Genomic Island in Pseudomonas sp. Strain B13, Journal of Bacteriology, vol.185, issue.15, pp.4530-4538, 2003.
DOI : 10.1128/JB.185.15.4530-4538.2003

G. Sezonov, C. Possoz, A. Friedmann, J. L. Pernodet, and M. Guérineau, KorSA from the Streptomyces Integrative Element pSAM2 Is a Central Transcriptional Repressor: Target Genes and Binding Sites, Journal of Bacteriology, vol.182, issue.5, pp.1243-1250, 2000.
DOI : 10.1128/JB.182.5.1243-1250.2000

A. Toussaint, C. Merlin, S. Monchy, M. A. Benotmane, R. Leplae et al., The Biphenyl- and 4-Chlorobiphenyl-Catabolic Transposon Tn4371, a Member of a New Family of Genomic Islands Related to IncP and Ti Plasmids, Applied and Environmental Microbiology, vol.69, issue.8, pp.4837-4845, 2003.
DOI : 10.1128/AEM.69.8.4837-4845.2003

J. R. Van-der-meer and V. Sentchilo, Genomic islands and the evolution of catabolic pathways in bacteria, Current Opinion in Biotechnology, vol.14, issue.3, pp.1-7, 2003.
DOI : 10.1016/S0958-1669(03)00058-2