F. D. Lowy, Infections, New England Journal of Medicine, vol.339, issue.8, pp.520-532, 1998.
DOI : 10.1056/NEJM199808203390806

A. Van-belkum, N. J. Verkaik, C. P. De-vogel, H. A. Boelens, J. Verveer et al., Nasal Carriage Types, The Journal of Infectious Diseases, vol.199, issue.12, pp.1820-1826, 2009.
DOI : 10.1086/599119

H. F. Chambers and F. R. Deleo, Waves of resistance: Staphylococcus aureus in the antibiotic era, Nature Reviews Microbiology, vol.346, issue.9, pp.629-641, 2009.
DOI : 10.1038/nrmicro2200

N. K. Priest, J. K. Rudkin, E. J. Feil, J. M. Van-den-elsen, A. Cheung et al., From genotype to phenotype: can systems biology be used to predict Staphylococcus aureus virulence?, Nature Reviews Microbiology, vol.193, issue.11, pp.791-797, 2012.
DOI : 10.1038/nrmicro2880

M. S. Thomas and S. Wigneshweraraj, Regulation of virulence gene expression, Virulence, vol.181, issue.8, pp.832-834, 2014.
DOI : 10.1016/S0966-842X(00)88960-X

A. L. Cheung and G. Zhang, Global regulation of virulence determinants in Staphylococcus Aureus by the SarA protein family, Frontiers in Bioscience, vol.7, issue.4, pp.1825-1842, 2002.
DOI : 10.2741/A882

D. F. Browning and S. J. Busby, The regulation of bacterial transcription initiation, Nature Reviews Microbiology, vol.57, issue.1, pp.57-65, 2004.
DOI : 10.1128/JB.182.15.4129-4136.2000

A. Ballal and A. C. Manna, Control of Thioredoxin Reductase Gene (trxB) Transcription by SarA in Staphylococcus aureus, Journal of Bacteriology, vol.192, issue.1, pp.336-345, 2010.
DOI : 10.1128/JB.01202-09

A. L. Cheung, K. Nishina, and A. C. Manna, SarA of Staphylococcus aureus Binds to the sarA Promoter To Regulate Gene Expression, Journal of Bacteriology, vol.190, issue.6, pp.2239-2243, 2008.
DOI : 10.1128/JB.01826-07

Y. Liu, A. C. Manna, C. H. Pan, I. A. Kriksunov, D. J. Thiel et al., Structural and function analyses of the global regulatory protein SarA from Staphylococcus aureus, Proceedings of the National Academy of Sciences, vol.103, issue.7, pp.2392-2397, 2006.
DOI : 10.1073/pnas.0510439103

A. C. Manna and A. L. Cheung, Transcriptional regulation of the agr locus and the identification of DNA binding residues of the global regulatory protein SarR in Staphylococcus aureus, Molecular Microbiology, vol.12, issue.5, pp.1289-1301, 2006.
DOI : 10.1046/j.1365-2958.2000.01853.x

A. L. Cheung, M. G. Bayer, and J. H. Heinrichs, sar Genetic determinants necessary for transcription of RNAII and RNAIII in the agr locus of Staphylococcus aureus., Journal of Bacteriology, vol.179, issue.12, pp.3963-3971, 1997.
DOI : 10.1128/jb.179.12.3963-3971.1997

A. L. Cheung, J. M. Koomey, C. A. Butler, S. J. Projan, and V. A. Fischetti, Regulation of exoprotein expression in Staphylococcus aureus by a locus (sar) distinct from agr., Proceedings of the National Academy of Sciences, vol.89, issue.14, pp.6462-6466, 1992.
DOI : 10.1073/pnas.89.14.6462

A. L. Cheung, K. A. Nishina, M. P. Trotonda, and S. Tamber, The SarA protein family of Staphylococcus aureus, The International Journal of Biochemistry & Cell Biology, vol.40, issue.3, pp.355-361, 2008.
DOI : 10.1016/j.biocel.2007.10.032

P. M. Dunman, E. Murphy, S. Haney, D. Palacios, G. Tucker-kellogg et al., Transcription Profiling-Based Identification of Staphylococcus aureus Genes Regulated by the agr and/or sarA Loci, Journal of Bacteriology, vol.183, issue.24, pp.7341-7353, 2001.
DOI : 10.1128/JB.183.24.7341-7353.2001

J. S. Blevins, A. F. Gillaspy, T. M. Rechtin, B. K. Hurlburt, and M. S. Smeltzer, The staphylococcal accessory regulator (sar ) represses transcription of the Staphylococcus aureus collagen adhesin gene (cna ) in an agr-independent manner, Molecular Microbiology, vol.173, issue.2, pp.317-326, 1999.
DOI : 10.1046/j.1365-2958.1999.01474.x

Y. Chien, A. C. Manna, S. J. Projan, and A. L. Cheung, SarA, a Global Regulator of Virulence Determinants inStaphylococcus aureus, Binds to a Conserved Motif Essential for sar-dependent Gene Regulation, Journal of Biological Chemistry, vol.274, issue.52, pp.37169-37176, 1999.
DOI : 10.1074/jbc.274.52.37169

A. C. Manna, S. S. Ingavale, M. Maloney, W. Van-wamel, and A. L. Cheung, Identification of sarV (SA2062), a New Transcriptional Regulator, Is Repressed by SarA and MgrA (SA0641) and Involved in the Regulation of Autolysis in Staphylococcus aureus, Journal of Bacteriology, vol.186, issue.16, pp.5267-5280, 2004.
DOI : 10.1128/JB.186.16.5267-5280.2004

T. M. Rechtin, A. F. Gillaspy, M. A. Schumacher, R. G. Brennan, M. S. Smeltzer et al., Characterization of the SarA virulence gene regulator of Staphylococcus aureus, Molecular Microbiology, vol.34, issue.2, pp.307-316, 1999.
DOI : 10.1006/abio.1993.1155

J. Guillet, M. Hallier, and B. Felden, Emerging Functions for the Staphylococcus aureus RNome, PLoS Pathogens, vol.71, issue.12, p.1003767, 2013.
DOI : 10.1371/journal.ppat.1003767.t001
URL : https://hal.archives-ouvertes.fr/inserm-00924091

M. Sassi, Y. Augagneur, T. Mauro, L. Ivain, S. Chabelskaya et al., regulatory RNA database, RNA, vol.21, issue.5, pp.1005-1017, 2015.
DOI : 10.1261/rna.049346.114
URL : https://hal.archives-ouvertes.fr/inserm-01136506

C. Pichon and B. Felden, From The Cover: Small RNA genes expressed from Staphylococcus aureusgenomic and pathogenicity islands with specific expression among pathogenic strains, Proceedings of the National Academy of Sciences, vol.102, issue.40, pp.14249-14254, 2005.
DOI : 10.1073/pnas.0503838102

S. Chabelskaya, O. Gaillot, and B. Felden, A Staphylococcus aureus Small RNA Is Required for Bacterial Virulence and Regulates the Expression of an Immune-Evasion Molecule, PLoS Pathogens, vol.164, issue.6, p.1000927, 2010.
DOI : 10.1371/journal.ppat.1000927.s009
URL : https://hal.archives-ouvertes.fr/inserm-00697384

C. Romilly, C. Lays, A. Tomasini, I. Caldelari, Y. Benito et al., A Non-Coding RNA Promotes Bacterial Persistence and Decreases Virulence by Regulating a Regulator in Staphylococcus aureus, PLoS Pathogens, vol.197, issue.3, p.1003979, 2014.
DOI : 10.1371/journal.ppat.1003979.s010
URL : https://hal.archives-ouvertes.fr/hal-00965591

R. L. Koenig, J. L. Ray, S. J. Maleki, M. S. Smeltzer, and B. K. Hurlburt, Staphylococcus aureus AgrA Binding to the RNAIII-agr Regulatory Region, Journal of Bacteriology, vol.186, issue.22, pp.7549-7555, 2004.
DOI : 10.1128/JB.186.22.7549-7555.2004

D. Reyes, D. O. Andrey, A. Monod, W. L. Kelley, G. Zhang et al., Coordinated Regulation by AgrA, SarA, and SarR To Control agr Expression in Staphylococcus aureus, Journal of Bacteriology, vol.193, issue.21, pp.6020-6031, 2011.
DOI : 10.1128/JB.05436-11

T. Xue, X. Zhang, H. Sun, and B. Sun, ArtR, a novel sRNA of Staphylococcus aureus, regulates ??-toxin expression by targeting the 5??? UTR of sarT mRNA, Medical Microbiology and Immunology, vol.79, issue.6, pp.1-12, 2014.
DOI : 10.1007/s00430-013-0307-0

S. Boisset, T. Geissmann, E. Huntzinger, P. Fechter, N. Bendridi et al., Staphylococcus aureus RNAIII coordinately represses the synthesis of virulence factors and the transcription regulator Rot by an antisense mechanism, Genes & Development, vol.21, issue.11, pp.1353-1366, 2007.
DOI : 10.1101/gad.423507
URL : https://hal.archives-ouvertes.fr/hal-00167517

E. Geisinger, R. P. Adhikari, R. Jin, H. F. Ross, and R. P. Novick, Inhibition of rot translation by RNAIII, a key feature of agr function, Molecular Microbiology, vol.12, issue.4, pp.1038-1048, 2006.
DOI : 10.1128/JB.186.24.8407-8423.2004

R. K. Gupta, T. T. Luong, and C. Y. Lee, system activates global regulator MgrA by stabilizing mRNA, Proceedings of the National Academy of Sciences, vol.112, issue.45, pp.14036-14041, 2015.
DOI : 10.1073/pnas.1509251112

L. Pabic, H. Germain-amiot, N. Bordeau, V. Felden, and B. , A bacterial regulatory RNA attenuates virulence, spread and human host cell phagocytosis, Nucleic Acids Res, vol.43, pp.9232-9248, 2015.
URL : https://hal.archives-ouvertes.fr/inserm-01194696

K. L. Krausz and J. L. Bose, Bacteriophage Transduction in Staphylococcus aureus: Broth-Based Method, Methods Mol. Biol, vol.1373, pp.63-68, 2016.
DOI : 10.1007/7651_2014_185

S. Herbert, A. K. Ziebandt, K. Ohlsen, T. Schafer, M. Hecker et al., Repair of Global Regulators in Staphylococcus aureus 8325 and Comparative Analysis with Other Clinical Isolates, Infection and Immunity, vol.78, issue.6, pp.2877-2889, 2010.
DOI : 10.1128/IAI.00088-10

B. N. Kreiswirth, S. Lofdahl, M. J. Betley, M. O-'reilly, P. M. Schlievert et al., The toxic shock syndrome exotoxin structural gene is not detectably transmitted by a prophage, Nature, vol.72, issue.5936, pp.709-712, 1983.
DOI : 10.1038/305709a0

E. Charpentier, A. I. Anton, P. Barry, B. Alfonso, Y. Fang et al., Novel Cassette-Based Shuttle Vector System for Gram-Positive Bacteria, Applied and Environmental Microbiology, vol.70, issue.10, pp.6076-6085, 2004.
DOI : 10.1128/AEM.70.10.6076-6085.2004

M. L. Pinel-marie, R. Brielle, and B. Felden, Dual Toxic-Peptide-Coding Staphylococcus aureus RNA under Antisense Regulation Targets Host Cells and Bacterial Rivals Unequally, Cell Reports, vol.7, issue.2, pp.424-435, 2014.
DOI : 10.1016/j.celrep.2014.03.012
URL : https://hal.archives-ouvertes.fr/inserm-00976764

A. Eyraud, P. Tattevin, S. Chabelskaya, and B. Felden, A small RNA controls a protein regulator involved in antibiotic resistance in Staphylococcus aureus, Nucleic Acids Research, vol.42, issue.8, pp.4892-4905, 2014.
DOI : 10.1093/nar/gku149
URL : https://hal.archives-ouvertes.fr/inserm-00951043

M. F. Carey, C. L. Peterson, and S. T. Smale, DNase I Footprinting, Cold Spring Harbor Protocols, vol.2013, issue.5, pp.469-478, 2013.
DOI : 10.1101/pdb.prot074328

B. E. Slatko, L. M. Albright, S. Tabor, and J. Ju, DNA Sequencing by the Dideoxy Method, Curr. Protoc. Mol. Biol, vol.2, issue.1, 2001.
DOI : 10.1002/0471142727.mb0704as47

J. J. Faith, B. Hayete, J. T. Thaden, I. Mogno, J. Wierzbowski et al., Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles, PLoS Biology, vol.280, issue.1, p.8, 2007.
DOI : 10.1371/journal.pbio.0050008.sd001

A. Manna and A. L. Cheung, Characterization of sarR, a Modulator of sar Expression in Staphylococcus aureus, Infection and Immunity, vol.69, issue.2, pp.885-896, 2001.
DOI : 10.1128/IAI.69.2.885-896.2001

K. A. Schmidt, A. C. Manna, S. Gill, and A. L. Cheung, SarT, a Repressor of ??-Hemolysin in Staphylococcus aureus, Infection and Immunity, vol.69, issue.8, pp.4749-4758, 2001.
DOI : 10.1128/IAI.69.8.4749-4758.2001

B. P. Howden, M. Beaume, P. F. Harrison, D. Hernandez, J. Schrenzel et al., Analysis of the Small RNA Transcriptional Response in Multidrug-Resistant Staphylococcus aureus after Antimicrobial Exposure, Antimicrobial Agents and Chemotherapy, vol.57, issue.8, pp.3864-3874, 2013.
DOI : 10.1128/AAC.00263-13

U. Mader, P. Nicolas, M. Depke, J. Pane-farre, M. Debarbouille et al., Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions, PLOS Genetics, vol.80, issue.Suppl 5, p.1005962, 2016.
DOI : 10.1371/journal.pgen.1005962.s013

J. Oscarsson, A. Kanth, K. Tegmark-wisell, and S. Arvidson, SarA Is a Repressor of hla (??-Hemolysin) Transcription in Staphylococcus aureus: Its Apparent Role as an Activator of hla in the Prototype Strain NCTC 8325 Depends on Reduced Expression of sarS, Journal of Bacteriology, vol.188, issue.24, pp.8526-8533, 2006.
DOI : 10.1128/JB.00866-06

R. Mondal, T. Ganguly, P. K. Chanda, A. Bandhu, B. Jana et al., Stabilization of the primary sigma factor of Staphylococcus aureus by core RNA polymerase, BMB Reports, vol.43, issue.3, pp.176-181, 2010.
DOI : 10.5483/BMBRep.2010.43.3.176

A. Belcheva, V. Verma, A. Korenevsky, M. Fridman, K. Kumar et al., Roles of DNA Sequence and Sigma A Factor in Transcription of the vraSR Operon, Journal of Bacteriology, vol.194, issue.1, pp.61-71, 2012.
DOI : 10.1128/JB.06143-11

E. G. Wagner and P. Romby, Small RNAs in Bacteria and Archaea, Adv. Genet, vol.90, pp.133-208, 2015.
DOI : 10.1016/bs.adgen.2015.05.001

K. E. Beenken, J. S. Blevins, and M. S. Smeltzer, Mutation of sarA in Staphylococcus aureus Limits Biofilm Formation, Infection and Immunity, vol.71, issue.7, pp.4206-4211, 2003.
DOI : 10.1128/IAI.71.7.4206-4211.2003

J. S. Blevins, M. O. Elasri, S. D. Allmendinger, K. E. Beenken, R. A. Skinner et al., Role of sarA in the Pathogenesis of Staphylococcus aureus Musculoskeletal Infection, Infection and Immunity, vol.71, issue.1, pp.516-523, 2003.
DOI : 10.1128/IAI.71.1.516-523.2003

J. Valle, A. Toledo-arana, C. Berasain, J. M. Ghigo, B. Amorena et al., SarA and not ??B is essential for biofilm development by Staphylococcus aureus, Molecular Microbiology, vol.32, issue.4, pp.1075-1087, 2003.
DOI : 10.1046/j.1365-2958.2003.03493.x

D. O. Andrey, A. Renzoni, A. Monod, D. P. Lew, A. L. Cheung et al., Control of the Staphylococcus aureus Toxic Shock tst Promoter by the Global Regulator SarA, Journal of Bacteriology, vol.192, issue.22, pp.6077-6085, 2010.
DOI : 10.1128/JB.00146-10

Y. Zhao, V. Verma, A. Belcheva, A. Singh, M. Fridman et al., Staphylococcus aureus Methicillin-Resistance Factor fmtA Is Regulated by the Global Regulator SarA, PLoS ONE, vol.7, issue.8, p.43998, 2012.
DOI : 10.1371/journal.pone.0043998.t001

K. M. Sterba, S. G. Mackintosh, J. S. Blevins, B. K. Hurlburt, and M. S. Smeltzer, Characterization of Staphylococcus aureus SarA Binding Sites, Journal of Bacteriology, vol.185, issue.15, pp.4410-4417, 2003.
DOI : 10.1128/JB.185.15.4410-4417.2003

D. F. Fujimoto, R. H. Higginbotham, K. M. Sterba, S. J. Maleki, A. M. Segall et al., Staphylococcus aureus SarA is a regulatory protein responsive to redox and pH that can support bacteriophage lambda integrase-mediated excision/recombination, Molecular Microbiology, vol.279, issue.2, pp.1445-1458, 2009.
DOI : 10.1111/j.1365-2958.2009.06942.x

S. Bronner, H. Monteil, and G. Prevost, : complexity and applications, FEMS Microbiology Reviews, vol.28, issue.2, pp.183-200, 2004.
DOI : 10.1016/j.femsre.2003.09.003

M. A. Schumacher, B. K. Hurlburt, and R. G. Brennan, Crystal structures of SarA, a pleiotropic regulator of virulence genes in S. aureus, Nature, vol.409, issue.6817, pp.215-219, 2001.
DOI : 10.1038/35051623

L. Stenz, P. Francois, K. Whiteson, C. Wolz, P. Linder et al., The CodY pleiotropic repressor controls virulence in gram-positive pathogens, FEMS Immunology & Medical Microbiology, vol.62, issue.2, pp.123-139, 2011.
DOI : 10.1111/j.1574-695X.2011.00812.x

K. B. Decker and D. M. Hinton, Transcription Regulation at the Core: Similarities Among Bacterial, Archaeal, and Eukaryotic RNA Polymerases, Annual Review of Microbiology, vol.67, issue.1, pp.113-139, 2013.
DOI : 10.1146/annurev-micro-092412-155756

F. Sun, Y. Ding, Q. Ji, Z. Liang, X. Deng et al., Protein cysteine phosphorylation of SarA/MgrA family transcriptional regulators mediates bacterial virulence and antibiotic resistance, Proceedings of the National Academy of Sciences, vol.109, issue.38, pp.15461-15466, 2012.
DOI : 10.1073/pnas.1205952109