L. Bermudez and J. Goodman, Mycobacterium tuberculosis invades and replicates within type II alveolar cells, Infect Immun, vol.64, pp.1400-1406, 1996.

K. Bodnar, N. Serbina, and J. Flynn, Fate of Mycobacterium tuberculosis within Murine Dendritic Cells, Infection and Immunity, vol.69, issue.2, pp.800-809, 2001.
DOI : 10.1128/IAI.69.2.800-809.2001

S. Hickman, J. Chan, and P. Salgame, Mycobacterium tuberculosis Induces Differential Cytokine Production from Dendritic Cells and Macrophages with Divergent Effects on Naive T Cell Polarization, The Journal of Immunology, vol.168, issue.9, pp.4636-4642, 2002.
DOI : 10.4049/jimmunol.168.9.4636

X. Jiao, R. Lo-man, P. Guermonprez, L. Fiette, and E. Deriaud, Dendritic Cells Are Host Cells for Mycobacteria In Vivo That Trigger Innate and Acquired Immunity, The Journal of Immunology, vol.168, issue.3, pp.1294-1301, 2002.
DOI : 10.4049/jimmunol.168.3.1294

L. Tailleux, S. Waddell, M. Pelizzola, A. Mortellaro, and M. Withers, Probing Host Pathogen Cross-Talk by Transcriptional Profiling of Both Mycobacterium tuberculosis and Infected Human Dendritic Cells and Macrophages, PLoS ONE, vol.99, issue.1, p.1403, 2008.
DOI : 10.1371/journal.pone.0001403.s001

S. Cole and B. Barrell, Analysis of the genome of Mycobacterium tuberculosis H37Rv, Novartis Found Symp, vol.217, pp.160-172, 1998.

E. Perez, S. Samper, Y. Bordas, C. Guilhot, and B. Gicquel, An essential role for phoP in Mycobacterium tuberculosis virulence, Molecular Microbiology, vol.182, issue.1, pp.179-187, 2001.
DOI : 10.1046/j.1365-2958.2001.02500.x

C. Martin, A. Williams, R. Hernandez-pando, P. Cardona, and E. Gormley, The live Mycobacterium tuberculosis phoP mutant strain is more attenuated than BCG and confers protective immunity against tuberculosis in mice and guinea pigs, Vaccine, vol.24, issue.17, pp.3408-3419, 2006.
DOI : 10.1016/j.vaccine.2006.03.017

W. Frigui, D. Bottai, L. Majlessi, M. Monot, and E. Josselin, Control of M. tuberculosis ESAT-6 Secretion and Specific T Cell Recognition by PhoP, PLoS Pathogens, vol.74, issue.2, p.33, 2008.
DOI : 10.1371/journal.ppat.0040033.st002
URL : https://hal.archives-ouvertes.fr/pasteur-01370872

J. Lee, R. Krause, J. Schreiber, H. Mollenkopf, and J. Kowall, Mutation in the Transcriptional Regulator PhoP Contributes to Avirulence of Mycobacterium tuberculosis H37Ra Strain, Cell Host & Microbe, vol.3, issue.2, pp.97-103, 2008.
DOI : 10.1016/j.chom.2008.01.002

H. Zheng, L. Lu, B. Wang, S. Pu, and X. Zhang, Genetic Basis of Virulence Attenuation Revealed by Comparative Genomic Analysis of Mycobacterium tuberculosis Strain H37Ra versus H37Rv, PLoS ONE, vol.99, issue.6, p.2375, 2008.
DOI : 10.1371/journal.pone.0002375.s008

C. Birck, Y. Chen, F. Hulett, and J. Samama, The Crystal Structure of the Phosphorylation Domain in PhoP Reveals a Functional Tandem Association Mediated by an Asymmetric Interface, Journal of Bacteriology, vol.185, issue.1, pp.254-261, 2003.
DOI : 10.1128/JB.185.1.254-261.2003

E. Groisman, M. Cromie, Y. Shi, and T. Latifi, A Mg2+-responding RNA That Controls the Expression of a Mg2+ Transporter, Cold Spring Harbor Symposia on Quantitative Biology, vol.144, issue.0, pp.251-258, 2006.
DOI : 10.1073/pnas.0408238102

A. Aranda, C. Sj, W. Loomis, and S. Miller, Salmonella typhimurium activates virulence gene transcription within acidified macrophage phagosomes, Proc Natl Acad Sci U S A Nov, vol.1, issue.8921, pp.10079-10083, 1992.

N. Martin-orozco, N. Touret, . Zaharik, . Ml-kopelman, and S. Miller, Visualization of Vacuolar Acidification-induced Transcription of Genes of Pathogens inside Macrophages, Molecular Biology of the Cell, vol.17, issue.1, pp.498-510, 2006.
DOI : 10.1091/mbc.E04-12-1096

M. Bader, W. Navarre, W. Shiau, H. Nikaido, and J. Frye, Regulation of Salmonella typhimurium virulence gene expression by cationic antimicrobial peptides, Molecular Microbiology, vol.145, issue.1, pp.219-230, 2003.
DOI : 10.1046/j.1365-2958.2003.03675.x

M. Bader, S. Sanowar, M. Daley, A. Schneider, and U. Cho, Recognition of Antimicrobial Peptides by a Bacterial Sensor Kinase, Cell, vol.122, issue.3, pp.461-472, 2005.
DOI : 10.1016/j.cell.2005.05.030

S. Miller, W. Pulkkinen, M. Selsted, and J. Mekalanos, Characterization of defensin resistance phenotypes associated with mutations in the phoP virulence regulon of Salmonella typhimurium, Infect Immun, vol.58, pp.3706-3710, 1990.

J. Gonzalo-asensio, S. Mostowy, J. Harders-westerveen, K. Huygen, and R. Hernandez-pando, PhoP: A Missing Piece in the Intricate Puzzle of Mycobacterium tuberculosis Virulence, PLoS ONE, vol.393, issue.10, p.3496, 2008.
DOI : 10.1371/journal.pone.0003496.s004

S. Walters, E. Dubnau, I. Kolesnikova, F. Laval, and M. Daffe, The Mycobacterium tuberculosis PhoPR two-component system regulates genes essential for virulence and complex lipid biosynthesis, Molecular Microbiology, vol.178, issue.2, pp.312-330, 2006.
DOI : 10.1073/pnas.221272198

T. Sirakova, A. Thirumala, V. Dubey, H. Sprecher, and P. Kolattukudy, The Mycobacterium tuberculosis pks2 Gene Encodes the Synthase for the Hepta- and Octamethyl-branched Fatty Acids Required for Sulfolipid Synthesis, Journal of Biological Chemistry, vol.276, issue.20, pp.16833-16839, 2001.
DOI : 10.1074/jbc.M011468200

V. Dubey, T. Sirakova, and P. Kolattukudy, Disruption of msl3 abolishes the synthesis of mycolipanoic and mycolipenic acids required for polyacyltrehalose synthesis in Mycobacterium tuberculosis H37Rv and causes cell aggregation, Molecular Microbiology, vol.64, issue.5, pp.1451-1459, 2002.
DOI : 10.1046/j.1365-2958.2002.03119.x

L. Camacho, D. Ensergueix, E. Perez, B. Gicquel, and C. Guilhot, Identification of a virulence gene cluster of Mycobacterium tuberculosis by signature-tagged transposon mutagenesis, Molecular Microbiology, vol.33, issue.2, pp.257-267, 1999.
DOI : 10.1016/S0378-1097(97)00503-X

S. Gupta, A. Sinha, and D. Sarkar, PhoP involves recognition of novel direct repeat sequences in the regulatory region of the promoter, FEBS Letters, vol.185, issue.22, pp.5328-5338, 2006.
DOI : 10.1016/j.febslet.2006.09.004

B. Saviola, S. Woolwine, and W. Bishai, Isolation of Acid-Inducible Genes of Mycobacterium tuberculosis with the Use of Recombinase-Based In Vivo Expression Technology, Infection and Immunity, vol.71, issue.3, pp.1379-1388, 2003.
DOI : 10.1128/IAI.71.3.1379-1388.2003

A. Murray, N. Winter, M. Lagranderie, D. Hill, and J. Rauzier, Expression of Escherichia coli ?-galactosidase in Mycobacterium bovis BCG using an expression system isolated from Mycobacterium paratuberculosis which induced humoral and cellular immune responses, Molecular Microbiology, vol.82, issue.22, pp.3331-3342, 1992.
DOI : 10.1016/0378-1119(85)90120-9

M. Chesne-seck, N. Barilone, F. Boudou, G. Asensio, J. Kolattukudy et al., A Point Mutation in the Two-Component Regulator PhoP-PhoR Accounts for the Absence of Polyketide-Derived Acyltrehaloses but Not That of Phthiocerol Dimycocerosates in Mycobacterium tuberculosis H37Ra, Journal of Bacteriology, vol.190, issue.4, pp.1329-1334, 2008.
DOI : 10.1128/JB.01465-07

J. Gonzalo-asensio, C. Soto, A. Arbues, J. Sancho, C. Menendez et al., The Mycobacterium tuberculosis phoPR Operon Is Positively Autoregulated in the Virulent Strain H37Rv, Journal of Bacteriology, vol.190, issue.21, pp.7068-7078, 2008.
DOI : 10.1128/JB.00712-08

R. Goyal, A. Das, R. Singh, P. Singh, and S. Korpole, Phosphorylation of PhoP Protein Plays Direct Regulatory Role in Lipid Biosynthesis of Mycobacterium tuberculosis, Journal of Biological Chemistry, vol.286, issue.52, pp.45197-45208, 2011.
DOI : 10.1074/jbc.M111.307447

S. Gupta, A. Pathak, A. Sinha, and D. Sarkar, Mycobacterium tuberculosis PhoP Recognizes Two Adjacent Direct-Repeat Sequences To Form Head-to-Head Dimers, Journal of Bacteriology, vol.191, issue.24, pp.7466-7476, 2009.
DOI : 10.1128/JB.00669-09

C. Chang and R. Stewart, The Two-Component System, Plant Physiology, vol.117, issue.3, pp.723-731, 1998.
DOI : 10.1104/pp.117.3.723

J. Parkinson and E. Kofoid, Communication Modules in Bacterial Signaling Proteins, Annual Review of Genetics, vol.26, issue.1, pp.71-112, 1992.
DOI : 10.1146/annurev.ge.26.120192.000443

K. Makino, M. Amemura, T. Kawamoto, S. Kimura, and H. Shinagawa, DNA Binding of PhoB and its Interaction with RNA Polymerase, Journal of Molecular Biology, vol.259, issue.1, pp.15-26, 1996.
DOI : 10.1006/jmbi.1996.0298

S. Dove, S. Darst, and A. Hochschild, Region 4 of ?? as a target for transcription regulation, Molecular Microbiology, vol.105, issue.4, pp.863-874, 2003.
DOI : 10.1046/j.1365-2958.2003.03467.x

C. Alteri, J. Lindner, D. Reiss, S. Smith, and H. Mobley, The broadly conserved regulator PhoP links pathogen virulence and membrane potential in Escherichia coli, Molecular Microbiology, vol.102, issue.1, pp.145-163, 2011.
DOI : 10.1111/j.1365-2958.2011.07804.x

S. Snapper, R. Melton, S. Mustafa, T. Kieser, W. Jacobs et al., Isolation and characterization of efficient plasmid transformation mutants of Mycobacterium smegmatis, Molecular Microbiology, vol.3, issue.11, pp.1911-1919, 1990.
DOI : 10.1038/316450a0

J. Timm, E. Lim, and B. Gicquel, Escherichia coli-mycobacteria shuttle vectors for operon and gene fusions to lacZ: the pJEM series., Journal of Bacteriology, vol.176, issue.21, pp.6749-6753, 1994.
DOI : 10.1128/jb.176.21.6749-6753.1994

T. Bailey, M. Boden, F. Buske, M. Frith, and C. Grant, 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

G. Crooks, G. Hon, J. Chandonia, and S. Brenner, WebLogo: A Sequence Logo Generator, Genome Research, vol.14, issue.6, pp.1188-1190, 2004.
DOI : 10.1101/gr.849004
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC419797

T. Schneider and R. Stephens, Sequence logos: a new way to display consensus sequences, Nucleic Acids Research, vol.18, issue.20, pp.6097-6100, 1990.
DOI : 10.1093/nar/18.20.6097