J. Courcelle, A. Khodursky, B. Peter, P. Brown, and P. Hanawalt, Comparative gene expression profiles following UV exposure in wild-type and SOS-deficient Escherichia coli, Genetics, vol.158, pp.41-64, 2001.

I. Erill, S. Campoy, and J. Barbe, Aeons of distress: an evolutionary perspective on the bacterial SOS response, FEMS Microbiology Reviews, vol.31, issue.6, pp.637-656, 2007.
DOI : 10.1111/j.1574-6976.2007.00082.x

G. Mazon, I. Erill, S. Campoy, P. Cortes, E. Forano et al., Reconstruction of the evolutionary history of the LexA-binding sequence, Microbiology, vol.150, issue.11, pp.3783-3795, 2004.
DOI : 10.1099/mic.0.27315-0

J. Wade, N. Reppas, G. Church, and K. Struhl, Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites, Genes & Development, vol.19, issue.21, pp.2619-2630, 2005.
DOI : 10.1101/gad.1355605

N. Au, E. Kuester-schoeck, V. Mandava, L. Bothwell, S. Canny et al., Genetic Composition of the Bacillus subtilis SOS System, Journal of Bacteriology, vol.187, issue.22, pp.7655-7666, 2005.
DOI : 10.1128/JB.187.22.7655-7666.2005

M. Butala, S. Sonjak, S. Kamensek, M. Hodoscek, D. Browning et al., promoter by two repressors prevents premature colicin expression and cell lysis, Molecular Microbiology, vol.38, issue.1, pp.129-139, 2012.
DOI : 10.1111/j.1365-2958.2012.08179.x

M. Quinones, H. Kimsey, and M. 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

S. Da-re, F. Garnier, E. Guerin, S. Campoy, F. Denis et al., The SOS response promotes qnrB quinolone-resistance determinant expression, EMBO reports, vol.112, issue.8, pp.929-933, 2009.
DOI : 10.1128/AAC.00339-07

URL : https://hal.archives-ouvertes.fr/inserm-00533078

E. Guerin, G. Cambray, N. Sanchez-alberola, S. Campoy, I. Erill et al., 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

C. Ubeda, E. Maiques, E. Knecht, I. Lasa, R. Novick et al., Antibiotic-induced SOS response promotes horizontal dissemination of pathogenicity island-encoded virulence factors in staphylococci, Molecular Microbiology, vol.181, issue.3, pp.836-844, 2005.
DOI : 10.1111/j.1365-2958.2005.04584.x

J. Beaber, B. Hochhut, and M. Waldor, SOS response promotes horizontal dissemination of antibiotic resistance genes, Nature, vol.427, issue.6969, pp.72-74, 2004.
DOI : 10.1038/nature02241

A. Goranov, E. Kuester-schoeck, J. Wang, and A. Grossman, Characterization of the Global Transcriptional Responses to Different Types of DNA Damage and Disruption of Replication in Bacillus subtilis, Journal of Bacteriology, vol.188, issue.15, pp.5595-5605, 2006.
DOI : 10.1128/JB.00342-06

M. Rupnik, M. Wilcox, and D. Gerding, Clostridium difficile infection: new developments in epidemiology and pathogenesis, Nature Reviews Microbiology, vol.36, issue.7, pp.526-536, 2009.
DOI : 10.1016/S0140-6736(97)08062-8

D. Gebhart, S. Williams, K. Bishop-lilly, G. Govoni, K. Willner et al., Novel High-Molecular-Weight, R-Type Bacteriocins of Clostridium difficile, Journal of Bacteriology, vol.194, issue.22, pp.6240-6247, 2012.
DOI : 10.1128/JB.01272-12

J. Johnston, J. Sloan, J. Fyfe, J. Davies, and J. Rood, The recA gene from Clostridium perfringens is induced by methyl methanesulphonate and contains an upstream Cheo box, Microbiology, vol.143, issue.3, pp.143885-890, 1997.
DOI : 10.1099/00221287-143-3-885

S. Nuyts, L. Van-mellaert, S. Barbe, E. Lammertyn, J. Theys et al., Insertion or Deletion of the Cheo Box Modifies Radiation Inducibility of Clostridium Promoters, Applied and Environmental Microbiology, vol.67, issue.10, pp.4464-4470, 2001.
DOI : 10.1128/AEM.67.10.4464-4470.2001

J. Cornish, F. Matthews, J. Thomas, and I. Erill, Inference of self-regulated transcriptional networks by comparative genomics, Evol Bioinform Online, vol.8, pp.449-461, 2012.

A. Walker, D. Eyre, D. Wyllie, K. Dingle, D. Griffiths et al., Relationship Between Bacterial Strain Type, Host Biomarkers, and Mortality in Clostridium difficile Infection, Clinical Infectious Diseases, vol.56, issue.11, pp.1589-1600, 2013.
DOI : 10.1093/cid/cit127

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3641870

M. Rupnik, toxinotypes, FEMS Microbiology Reviews, vol.32, issue.3, pp.541-555, 2008.
DOI : 10.1111/j.1574-6976.2008.00110.x

G. Marsden, I. Davis, V. Wright, M. Sebaihia, E. Kuijper et al., Array comparative hybridisation reveals a high degree of similarity between UK and European clinical isolates of hypervirulent Clostridium difficile, BMC Genomics, vol.11, issue.1, p.389, 2010.
DOI : 10.1186/1471-2164-11-389

R. Stabler, M. He, L. Dawson, M. Martin, E. Valiente et al., Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium, Genome Biology, vol.10, issue.9, p.102, 2009.
DOI : 10.1186/gb-2009-10-9-r102

R. Stabler, L. Dawson, E. Valiente, M. Cairns, M. Martin et al., Macro and Micro Diversity of Clostridium difficile Isolates from Diverse Sources and Geographical Locations, PLoS ONE, vol.178, issue.3, p.31559, 2012.
DOI : 10.1371/journal.pone.0031559.s013

C. Knetsch, M. Hensgens, C. Harmanus, M. Van-der-bijl, P. Savelkoul et al., Genetic markers for Clostridium difficile lineages linked to hypervirulence, Microbiology, vol.157, issue.11, pp.3113-3123, 2011.
DOI : 10.1099/mic.0.051953-0

I. Erill, O. Neill, and M. , A reexamination of information theory-based methods for DNA-binding site identification, BMC Bioinformatics, vol.10, issue.1, p.57, 2009.
DOI : 10.1186/1471-2105-10-57

M. Butala, D. Klose, V. Hodnik, A. Rems, Z. Podlesek et al., Interconversion between bound and free conformations of LexA orchestrates the bacterial SOS response, Nucleic Acids Research, vol.39, issue.15, pp.6546-6557, 2011.
DOI : 10.1093/nar/gkr265

E. Meouche, I. Peltier, J. Monot, M. Soutourina, O. Pestel-caron et al., Characterization of the SigD Regulon of C. difficile and Its Positive Control of Toxin Production through the Regulation of tcdR, PLoS ONE, vol.4, issue.12, p.83748, 2013.
DOI : 10.1371/journal.pone.0083748.s004

URL : https://hal.archives-ouvertes.fr/pasteur-01370779

M. Aldape, A. Packham, D. Nute, A. Bryant, and D. Stevens, Effects of ciprofloxacin on the expression and production of exotoxins by Clostridium difficile, Journal of Medical Microbiology, vol.62, issue.Pt_5, pp.741-747, 2013.
DOI : 10.1099/jmm.0.056218-0

M. Butala, D. Zgur-bertok, and S. Busby, The bacterial LexA transcriptional repressor, Cellular and Molecular Life Sciences, vol.66, issue.1, pp.82-93, 2009.
DOI : 10.1007/s00018-008-8378-6

L. Simmons, A. Goranov, H. Kobayashi, B. Davies, D. Yuan et al., Comparison of Responses to Double-Strand Breaks between Escherichia coli and Bacillus subtilis Reveals Different Requirements for SOS Induction, Journal of Bacteriology, vol.191, issue.4, pp.1152-1161, 2009.
DOI : 10.1128/JB.01292-08

L. Geer, A. Marchler-bauer, R. Geer, L. Han, J. He et al., The NCBI BioSystems database, Nucleic Acids Research, vol.38, issue.Database, pp.492-496, 2010.
DOI : 10.1093/nar/gkp858

M. Monot, C. Boursaux-eude, M. Thibonnier, D. Vallenet, I. Moszer et al., Reannotation of the genome sequence of Clostridium difficile strain 630, Journal of Medical Microbiology, vol.60, issue.8, pp.1193-1199, 2011.
DOI : 10.1099/jmm.0.030452-0

URL : https://hal.archives-ouvertes.fr/pasteur-01370838

D. Huson, D. Richter, C. Rausch, T. Dezulian, M. Franz et al., Dendroscope: An interactive viewer for large phylogenetic trees, BMC Bioinformatics, vol.8, issue.1, p.460, 2007.
DOI : 10.1186/1471-2105-8-460

T. Bailey, M. Boden, F. Buske, M. Frith, C. Grant et al., MEME SUITE: tools for motif discovery and searching, Nucleic Acids Research, vol.37, issue.Web Server, pp.202-208, 2009.
DOI : 10.1093/nar/gkp335

URL : http://doi.org/10.1093/nar/gkp335

K. Giese, C. Michalowski, and J. Little, RecA-Dependent Cleavage of LexA Dimers, Journal of Molecular Biology, vol.377, issue.1, pp.148-161, 2008.
DOI : 10.1016/j.jmb.2007.12.025

. Walter, The LexA regulated genes of the Clostridium difficile, BMC Microbiology, vol.14, issue.1, p.88, 2014.
DOI : 10.1016/j.jmb.2007.12.025

URL : https://hal.archives-ouvertes.fr/pasteur-00976526