F. D. Lowy, Staphylococcus aureus infections, N Engl J Med, vol.339, pp.520-552, 1998.

H. F. Wertheim, D. C. Melles, M. C. Vos, W. Van-leeuwen, A. Van-belkum et al., The role of nasal carriage in Staphylococcus aureus infections, Lancet Infect Dis, vol.5, pp.751-62, 2005.

M. Kuroda, T. Ohta, I. Uchiyama, T. Baba, H. Yuzawa et al., Whole genome sequencing of meticillin-resistant Staphylococcus aureus, Lancet, vol.357, pp.1225-1265, 2001.

A. T. Giraudo, A. Calzolari, A. A. Cataldi, C. Bogni, and R. Nagel, The sae locus of Staphylococcus aureus encodes a two-component regulatory system, FEMS Microbiol Lett, vol.177, pp.15-22, 1999.

R. P. Novick, Autoinduction and signal transduction in the regulation of staphylococcal virulence, Mol Microbiol, vol.48, pp.1429-1478, 2003.

A. Delauné, S. Dubrac, C. Blanchet, O. Poupel, U. Mader et al., The WalKR system controls major staphylococcal virulence genes and is involved in triggering the host inflammatory response, Infect Immun, vol.80, p.22825451, 2012.

Q. Liu, W. S. Yeo, and T. Bae, The SaeRS two-component system of Staphylococcus aureus, Genes, vol.7, 2016.

A. F. Haag and F. Bagnoli, The role of two-component signal transduction systems in Staphylococcus aureus virulence regulation, Curr Top Microbiol Immunol, vol.2016, pp.1-54

S. Dubrac and T. Msadek, Identification of genes controlled by the essential YycG/YycF two-component system of Staphylococcus aureus, J Bacteriol, vol.186, pp.1175-81, 2004.

A. Toledo-arana, N. Merino, M. Vergara-irigaray, M. Debarbouille, J. R. Penades et al., Staphylococcus aureus develops an alternative, ica-independent biofilm in the absence of the arlRS two-component system, J Bacteriol, vol.187, pp.5318-5347, 2005.

S. Dubrac, P. Bisicchia, K. M. Devine, and T. Msadek, A matter of life and death: cell wall homeostasis and the WalKR (YycGF) essential signal transduction pathway, Mol Microbiol, vol.70, p.19019149, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00332455

A. Y. Mitrophanov and E. A. Groisman, Signal integration in bacterial two-component regulatory systems, Genes Dev, vol.22, pp.2601-2612, 2008.

D. R. Buelow and T. L. Raivio, Three (and more) component regulatory systems-auxiliary regulators of bacterial histidine kinases, Mol Microbiol, vol.75, pp.547-66, 2010.

J. F. Hess, K. Oosawa, N. Kaplan, and M. I. Simon, Phosphorylation of three proteins in the signaling pathway of bacterial chemotaxis, Cell, vol.53, pp.79-87, 1988.

K. L. Ohlsen, J. K. Grimsley, and J. A. Hoch, Deactivation of the sporulation transcription factor Spo0A by the Spo0E protein phosphatase, Proceedings of the National Academy of Sciences of the United States of America, vol.91, pp.1756-60, 1994.

M. Perego, P. Glaser, and J. A. Hoch, Aspartyl-phosphate phosphatases deactivate the response regulator components of the sporulation signal transduction system in Bacillus subtilis, Mol Microbiol, vol.19, pp.1151-1158, 1996.

L. Wang, R. Grau, M. Perego, and J. A. Hoch, A novel histidine kinase inhibitor regulating development in Bacillus subtilis, Genes Dev, vol.11, pp.2569-79, 1997.

K. A. Cunningham and W. F. Burkholder, The histidine kinase inhibitor Sda binds near the site of autophosphorylation and may sterically hinder autophosphorylation and phosphotransfer to Spo0F, Mol Microbiol, vol.71, pp.659-77, 2009.

A. M. Garnerone, D. Cabanes, M. Foussard, P. Boistard, and J. Batut, Inhibition of the FixL sensor kinase by the FixT protein in Sinorhizobium meliloti, J Biol Chem, vol.274, pp.32500-32506, 1999.

T. Mascher, Bacterial (intramembrane-sensing) histidine kinases: signal transfer rather than stimulus perception, Trends Microbiol, vol.22, pp.559-65, 2014.

A. Hiron, M. Falord, J. Valle, M. Debarbouille, and T. Msadek, Bacitracin and nisin resistance in Staphylococcus aureus: a novel pathway involving the BraS/BraR two-component system (SA2417/SA2418) and both the BraD/BraE and VraD/VraE ABC transporters, Mol Microbiol, vol.81, p.21696458, 2011.

M. Falord, G. Karimova, A. Hiron, and T. Msadek, GraXSR proteins interact with the VraFG ABC transporter to form a five-component system required for cationic antimicrobial peptide sensing and resistance in Staphylococcus aureus, Antimicrob Agents Chemother, vol.56, pp.1047-58, 2012.

R. Alves and M. A. Savageau, Comparative analysis of prototype two-component systems with either bifunctional or monofunctional sensors: differences in molecular structure and physiological function, Mol Microbiol, vol.48, pp.25-51, 2003.

J. Keener and S. Kustu, Protein kinase and phosphoprotein phosphatase activities of nitrogen regulatory proteins NTRB and NTRC of enteric bacteria: roles of the conserved amino-terminal domain of NTRC, Proc Natl Acad Sci USA, vol.85, pp.4976-80, 1988.

A. Firon, A. Tazi, D. Cunha, V. Brinster, S. Sauvage et al., The Abi-domain protein Abx1 interacts with the CovS histidine kinase to control virulence gene expression in group B Streptococcus, PLoS Pathog, vol.9, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01300159

D. W. Jeong, H. Cho, M. B. Jones, K. Shatzkes, F. Sun et al., The auxiliary protein complex SaePQ activates the phosphatase activity of sensor kinase SaeS in the SaeRS two-component system of Staphylococcus aureus, Mol Microbiol, vol.86, p.22882143, 2012.

H. Szurmant, M. A. Mohan, P. M. Imus, and J. A. Hoch, YycH and YycI interact to regulate the essential YycFG two-component system in Bacillus subtilis, J Bacteriol, vol.189, pp.3280-3289, 2007.

H. Szurmant, L. Bu, C. L. Brooks, and J. A. Hoch, An essential sensor histidine kinase controlled by transmembrane helix interactions with its auxiliary proteins, Proc Natl Acad Sci USA, vol.105, pp.5891-5897, 2008.

T. Fukushima, I. Furihata, R. Emmins, R. A. Daniel, J. A. Hoch et al., A role for the essential YycG sensor histidine kinase in sensing cell division, Mol Microbiol, vol.79, p.21219466, 2011.

O. Poupel, M. Moyat, J. Groizeleau, L. Antunes, S. Gribaldo et al., Transcriptional analysis and subcellular protein localization reveal specific features of the essential WalKR system in Staphylococcus aureus, PLoS One, vol.11, p.151449, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-02445692

M. B. Frankel, B. M. Wojcik, A. C. Dedent, D. M. Missiakas, and O. Schneewind, ABI domain-containing proteins contribute to surface protein display and cell division in Staphylococcus aureus, Mol Microbiol, vol.78, pp.238-52, 2010.

B. Kneidinger, K. O'riordan, J. Li, J. R. Brisson, J. C. Lee et al., Three highly conserved proteins catalyze the conversion of UDP-N-acetyl-D-glucosamine to precursors for the biosynthesis of O antigen in Pseudomonas aeruginosa O11 and capsule in Staphylococcus aureus type 5. Implications for the UDP-Nacetyl-L-fucosamine biosynthetic pathway, J Biol Chem, vol.278, pp.3615-3642, 2003.

A. F. Gillaspy, V. Worrell, J. Orvis, B. A. Roe, D. W. Dyer et al., The Staphylococcus aureus NCTC 8325

V. A. Fischetti, R. P. Novick, J. J. Ferretti, D. A. Portnoy, and J. I. Rood, Gram-Positive Pathogens, pp.381-412, 2006.

C. Y. Lee, J. Lee, V. A. Fischetti, R. P. Novick, J. J. Ferretti et al., Staphylococcal capsule, Gram-Positive Pathogens, pp.456-63, 2006.

G. Karimova, J. Pidoux, A. Ullmann, and D. Ladant, A bacterial two-hybrid system based on a reconstituted signal transduction pathway, Proc Natl Acad Sci USA, vol.95, pp.5752-5758, 1998.

D. Raychaudhuri and A. N. Chatterjee, Use of resistant mutants to study the interaction of Triton X-100 with Staphylococcus aureus, J Bacteriol, vol.164, pp.1337-1386, 1985.

C. A. Schindler and V. T. Schuhardt, Lysostaphin: a new bacteriolytic agent for the Staphylococcus, Proc Natl Acad Sci USA, vol.51, pp.414-435, 1964.

J. M. Voyich, C. Vuong, M. Dewald, T. K. Nygaard, S. Kocianova et al., The SaeR/S gene regulatory system is essential for innate immune evasion by Staphylococcus aureus, J Infect Dis, vol.199, pp.1698-706, 2009.

M. Mainiero, C. Görke, T. Geiger, C. Gonser, S. Herbert et al., Differential target gene activation by the Staphylococcus aureus two-component system saeRS, J Bacteriol, vol.192, pp.613-636, 2010.

F. Sun, C. Li, D. Jeong, C. Sohn, C. He et al., In the Staphylococcus aureus two-component system sae, the response regulator SaeR binds to a direct repeat sequence and DNA binding requires phosphorylation by the sensor kinase SaeS, J Bacteriol, vol.192, pp.2111-2138, 2010.

M. Y. Galperin, A. N. Nikolskaya, and E. V. Koonin, Novel domains of the prokaryotic two-component signal transduction systems, FEMS Microbiol Lett, vol.203, pp.11-21, 2001.

E. C. Kofoid and J. S. Parkinson, Transmitter and receiver modules in bacterial signaling proteins, Proc Natl Acad Sci USA, vol.85, pp.4981-4986, 1988.

J. S. Parkinson and E. C. Kofoid, Communication modules in bacterial signaling proteins, Annu Rev Genet, vol.26, pp.71-112, 1992.

R. Dutta, L. Qin, and M. Inouye, Histidine kinases: diversity of domain organization, Mol Microbiol, vol.34, pp.633-673, 1999.

T. Mascher, Intramembrane-sensing histidine kinases: a new family of cell envelope stress sensors in Firmicutes bacteria, FEMS Microbiol Lett, vol.264, p.17064367, 2006.

A. Grundling, D. M. Missiakas, and O. Schneewind, Staphylococcus aureus mutants with increased lysostaphin resistance, J Bacteriol, vol.188, pp.6286-97, 2006.

S. Dubrac, I. G. Boneca, O. Poupel, and T. Msadek, New insights into the WalK/WalR (YycG/YycF) essential signal transduction pathway reveal a major role in controlling cell wall metabolism and biofilm formation in Staphylococcus aureus, J Bacteriol, vol.189, pp.8257-69, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00189231

T. Fukushima, H. Szurmant, E. J. Kim, M. Perego, and J. A. Hoch, A sensor histidine kinase co-ordinates cell wall architecture with cell division in Bacillus subtilis, Mol Microbiol, vol.69, p.18573169, 2008.

M. G. Pinho and J. Errington, Dispersed mode of Staphylococcus aureus cell wall synthesis in the absence of the division machinery, Mol Microbiol, vol.50, pp.871-81, 2003.

K. J. Wayne, S. Li, K. M. Kazmierczak, H. C. Tsui, and M. E. Winkler, Involvement of WalK (VicK) phosphatase activity in setting WalR (VicR) response regulator phosphorylation level and limiting cross-talk in Streptococcus pneumoniae D39 cells, Mol Microbiol, vol.86, pp.645-60, 2012.

A. D. Gutu, K. J. Wayne, L. T. Sham, and M. E. Winkler, Kinetic characterization of the WalRKSpn (VicRK) twocomponent system of Streptococcus pneumoniae: dependence of WalKSpn (VicK) phosphatase activity on its PAS domain, J Bacteriol, vol.192, pp.2346-58, 2010.

S. Maria, J. P. Sadaka, A. Moussa, S. H. Brown, S. Zhang et al., Compound-gene interaction mapping reveals distinct roles for Staphylococcus aureus teichoic acids, Proc Natl Acad Sci USA, vol.111, pp.12510-12515, 2014.

M. Schlag, R. Biswas, B. Krismer, T. Kohler, S. Zoll et al., Role of staphylococcal wall teichoic acid in targeting the major autolysin Atl, Mol Microbiol, vol.75, pp.864-73, 2010.

J. Pei, D. A. Mitchell, J. E. Dixon, and N. V. Grishin, Expansion of type II CAAX proteases reveals evolutionary origin of gamma-secretase subunit APH-1, J Mol Biol, vol.410, pp.18-26, 2011.

M. Wang and P. J. Casey, Protein prenylation: unique fats make their mark on biology, Nat Rev Mol Cell Biol, vol.17, pp.110-132, 2016.

C. N. Krute, R. K. Carroll, F. E. Rivera, A. Weiss, R. M. Young et al., The disruption of prenylation leads to pleiotropic rearrangements in cellular behavior in Staphylococcus aureus, Mol Microbiol, vol.95, pp.819-851, 2015.

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, Infect Immun, vol.78, pp.2877-89, 2010.

J. Sambrook, E. F. Fritsch, and T. Maniatis, Molecular cloning: a laboratory manual, 1989.

M. Arnaud, A. Chastanet, and M. Debarbouille, New vector for efficient allelic replacement in naturally nontransformable, low-GC-content, gram-positive bacteria, Appl Environ Microbiol, vol.70, pp.6887-91, 2004.

C. Archambaud, E. Gouin, J. Pizarro-cerda, P. Cossart, and O. Dussurget, Translation elongation factor EF-Tu is a target for Stp, a serine-threonine phosphatase involved in virulence of Listeria monocytogenes

, Mol Microbiol, vol.56, pp.383-96, 2005.

K. L. Krausz and J. L. Bose, Bacteriophage transduction in Staphylococcus aureus: broth-based method, pp.63-71, 2016.

M. Falord, U. Mader, A. Hiron, M. Debarbouille, and T. Msadek, Investigation of the Staphylococcus aureus GraSR regulon reveals novel links to virulence, stress response and cell wall signal transduction pathways, PLoS One, vol.6, 2011.

M. A. Sullivan, R. E. Yasbin, and F. E. Young, New shuttle vectors for Bacillus subtilis and Escherichia coli which allow rapid detection of inserted fragments, Gene, vol.29, pp.21-27, 1984.

J. H. Miller, Assay of ?-Galactosidase. Experiments in molecular genetics, pp.352-357, 1972.

M. Bradford, A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding, Anal Biochem, vol.72, pp.248-54, 1976.

S. Even, P. Burguiere, S. Auger, O. Soutourina, A. Danchin et al., Global control of cysteine metabolism by CymR in Bacillus subtilis, J Bacteriol, vol.188, pp.2184-97, 2006.

B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol, vol.10, 2009.

S. Anders, P. T. Pyl, and W. Huber, HTSeq-a Python framework to work with high-throughput sequencing data, Bioinformatics, vol.31, pp.166-175, 2015.

. R-core-team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2014.

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.25516281, 2014.

Y. Benjamini and Y. Hiochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, J R Statist Soc B, vol.57, pp.289-300, 1995.

N. Dautin, G. Karimova, A. Ullmann, and D. Ladant, Sensitive genetic screen for protease activity based on a cyclic AMP signaling cascade in Escherichia coli, J Bacteriol, vol.182, pp.7060-7066, 2000.
URL : https://hal.archives-ouvertes.fr/hal-02539702

C. A. Schneider, W. S. Rasband, and K. W. Eliceiri, NIH Image to ImageJ: 25 years of image analysis, Nat Meth, vol.9, pp.671-676, 2012.

A. Delauné, O. Poupel, A. Mallet, Y. M. Coic, T. Msadek et al., Peptidoglycan crosslinking relaxation plays an important role in Staphylococcus aureus WalKR-dependent cell viability, PLoS One, vol.6, 2011.

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.305, pp.709-721, 1983.