D. O. Serra and R. Hengge, Stress responses go three dimensional-the spatial order of physiological differentiation in bacterial macrocolony biofilms, Environ Microbiol, vol.16, pp.1455-1471, 2014.

S. P. Bernier, D. Lebeaux, A. S. Defrancesco, A. Valomon, G. Soubigou et al., Starvation, together with the SOS response, mediates high biofilm-specific tolerance to the fluoroquinolone ofloxacin, PLoS Genet, vol.9, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01385427

D. Nguyen, A. Joshi-datar, F. Lepine, E. Bauerle, O. Olakanmi et al., Active starvation responses mediate antibiotic tolerance in biofilms and nutrient-limited bacteria, Science, vol.334, pp.982-986, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-00722468

D. Lebeaux, J. M. Ghigo, and C. Beloin, Biofilm-related infections: bridging the gap between clinical management and fundamental aspects of recalcitrance toward antibiotics, Microbiol Mol Biol Rev, vol.78, pp.510-543, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01370744

S. J. Pamp, M. Gjermansen, H. K. Johansen, and T. Tolker-nielsen, Tolerance to the antimicrobial peptide colistin in Pseudomonas aeruginosa biofilms is linked to metabolically active cells, and depends on the pmr and mexAB-oprM genes, Mol Microbiol, vol.68, pp.223-240, 2008.

J. Penterman, D. Nguyen, A. E. Staudinger, B. J. Greenberg, E. P. Lam et al., Rapid evolution of culture-impaired bacteria during adaptation to biofilm growth, Cell Rep, vol.6, pp.293-300, 2014.

S. Chalabaev, A. Chauhan, A. Novikov, P. Iyer, M. Szczesny et al., Biofilms formed by gram-negative bacteria undergo increased lipid A palmitoylation, enhancing in vivo survival, mBio, vol.5, pp.1116-1130, 2014.
URL : https://hal.archives-ouvertes.fr/pasteur-01381821

R. E. Bishop, H. S. Gibbons, T. Guina, M. S. Trent, S. I. Miller et al., Transfer of palmitate from phospholipids to lipid A in outer membranes of gram-negative bacteria, EMBO J, vol.19, pp.5071-5080, 2000.

R. E. Bishop, The lipid A palmitoyltransferase PagP: molecular mechanisms and role in bacterial pathogenesis, Mol Microbiol, vol.57, pp.900-912, 2005.

Z. Zhou, S. Lin, R. J. Cotter, and C. R. Raetz, Lipid A modifications characteristic of Salmonella typhimurium are induced by NH4VO3 in Escherichia coli K12. Detection of 4-amino-4-deoxy-L-arabinose, phosphoethanolamine and palmitate, J Biol Chem, vol.274, pp.18503-18514, 1999.

Y. Eguchi, T. Okada, S. Minagawa, T. Oshima, H. Mori et al., Signal transduction cascade between EvgA/EvgS and PhoP/PhoQ two-component systems of Escherichia coli, J Bacteriol, vol.186, pp.3006-3014, 2004.
DOI : 10.1128/jb.186.10.3006-3014.2004
URL : http://jb.asm.org/content/186/10/3006.full.pdf

W. Jia, E. Zoeiby, A. Petruzziello, T. N. Jayabalasingham, B. Seyedirashti et al., Lipid trafficking controls endotoxin acylation in outer membranes of Escherichia coli, J Biol Chem, vol.279, pp.44966-44975, 2004.
DOI : 10.1074/jbc.m404963200
URL : http://www.jbc.org/content/279/43/44966.full.pdf

R. E. Bishop, Structural biology of membrane-intrinsic beta-barrel enzymes: sentinels of the bacterial outer membrane, Biochim Biophys Acta, vol.1778, pp.1881-1896, 2008.

N. Majdalani, D. Hernandez, and S. Gottesman, Regulation and mode of action of the second small RNA activator of RpoS translation, RprA. Mol Microbiol, vol.46, pp.813-826, 2002.

X. P. Guo and Y. C. Sun, New insights into the non-orthodox two component Rcs phosphorelay system, Front Microbiol, vol.8, 2014.
DOI : 10.3389/fmicb.2017.02014
URL : https://www.frontiersin.org/articles/10.3389/fmicb.2017.02014/pdf

N. Majdalani and S. Gottesman, The Rcs phosphorelay: a complex signal transduction system, Annu Rev Microbiol, vol.59, pp.379-405, 2005.
DOI : 10.1146/annurev.micro.59.050405.101230

W. J. Belden and S. I. Miller, Further characterization of the PhoP regulon: identification of new PhoP-activated virulence loci, Infect Immun, vol.62, pp.5095-5101, 1994.

J. M. Ghigo, Natural conjugative plasmids induce bacterial biofilm development, Nature, vol.412, pp.442-445, 2001.
DOI : 10.1038/35086581

M. E. Laubacher and S. E. Ades, The Rcs phosphorelay is a cell envelope stress response activated by peptidoglycan stress and contributes to intrinsic antibiotic resistance, J Bacteriol, vol.190, pp.2065-2074, 2008.
DOI : 10.1128/jb.01740-07
URL : http://jb.asm.org/content/190/6/2065.full.pdf

D. D. Sledjeski and S. Gottesman, Osmotic shock induction of capsule synthesis in Escherichia coli K-12, J Bacteriol, vol.178, pp.1204-1206, 1996.
DOI : 10.1128/jb.178.4.1204-1206.1996
URL : http://jb.asm.org/content/178/4/1204.full.pdf

N. Majdalani, M. Heck, V. Stout, and S. Gottesman, Role of RcsF in signaling to the Rcs phosphorelay pathway in Escherichia coli, J Bacteriol, vol.187, pp.6770-6778, 2005.

C. E. Fredericks, S. Shibata, S. Aizawa, S. A. Reimann, and A. J. Wolfe, Acetyl phosphate-sensitive regulation of flagellar biogenesis and capsular biosynthesis depends on the Rcs phosphorelay, Mol Microbiol, vol.61, pp.734-747, 2006.

L. I. Hu, B. K. Chi, M. L. Kuhn, E. V. Filippova, A. J. Walker-peddakotla et al., Acetylation of the response regulator RcsB controls transcription from a small RNA promoter, J Bacteriol, vol.195, pp.4174-4186, 2013.

D. Pannen, M. Fabisch, L. Gausling, and K. Schnetz, Interaction of the RcsB response regulator with auxiliary transcription regulators in Escherichia coli, 2016.

, J Biol Chem, vol.291, pp.2357-2370

G. R. Venkatesh, K. Koungni, F. C. Paukner, A. Stratmann, T. Blissenbach et al., BglJ-RcsB heterodimers relieve repression of the Escherichia coli bgl operon by H-NS, J Bacteriol, vol.192, pp.6456-6464, 2010.

M. P. Castanié-cornet, C. K. Bastiat, B. Cros, A. Bordes, P. Gutierrez et al., Acid stress response in Escherichia coli: mechanism of regulation of gadA transcription by RcsB and GadE, Nucleic Acids Res, vol.38, pp.3546-3554, 2010.

P. S. Stewart and M. J. Franklin, Physiological heterogeneity in biofilms, Nat Rev. Microbiol, vol.6, pp.199-210, 2008.
DOI : 10.1038/nrmicro1838

L. A. Laimins, D. B. Rhoads, and W. Epstein, Osmotic control of kdp operon expression in Escherichia coli, Proc Natl Acad Sci U S A, vol.78, pp.464-468, 1981.

E. Perozo, D. M. Cortes, P. Sompornpisut, A. Kloda, and B. Martinac, Open channel structure of MscL and the gating mechanism of mechanosensitive channels, Nature, vol.418, pp.942-948, 2002.

Z. Ma, S. Gong, H. Richard, D. L. Tucker, T. Conway et al., GadE (YhiE) activates glutamate decarboxylase-dependent acid resistance in Escherichia coli K-12, Mol Microbiol, vol.49, pp.1309-1320, 2003.

C. R. Raetz and C. Whitfield, Lipopolysaccharide endotoxins, Annu Rev Biochem, vol.71, pp.635-700, 2002.

A. E. Smith, S. H. Kim, F. Liu, W. Jia, E. Vinogradov et al., PagP activation in the outer membrane triggers R3 core oligosaccharide truncation in the cytoplasm of Escherichia coli O157:H7, J Biol Chem, vol.283, pp.4332-4343, 2008.

P. M. Hwang, W. Y. Choy, E. I. Lo, L. Chen, J. D. Forman-kay et al., Solution structure and dynamics of the outer membrane enzyme PagP by NMR, Proc Natl Acad Sci U S A, vol.99, pp.13560-13565, 2002.

C. Beloin, J. Valle, P. Latour-lambert, P. Faure, M. Kzreminski et al., Global impact of mature biofilm lifestyle on Escherichia coli K-12 gene expression, Mol Microbiol, vol.51, pp.659-674, 2004.
URL : https://hal.archives-ouvertes.fr/pasteur-02080937

N. Majdalani and S. Gottesman, Genetic dissection of signaling through the Rcs phosphorelay, Methods Enzymol, vol.423, pp.23016-23018, 2007.

D. J. Clarke, The Rcs phosphorelay: more than just a two-component pathway, Future Microbiol, vol.5, pp.1173-1184, 2010.

D. L. Tucker, N. Tucker, and T. Conway, Gene expression profiling of the pH response in Escherichia coli, J Bacteriol, vol.184, pp.6551-6558, 2002.

W. Ebel, G. J. Vaughn, H. K. Peters, . Iii, and J. E. Trempy, Inactivation of mdoH leads to increased expression of colanic acid capsular polysaccharide in Escherichia coli, J Bacteriol, vol.179, pp.6858-6861, 1997.

M. P. Castanié-cornet, C. K. Jacq, and A. , RcsF is an outer membrane lipoprotein involved in the RcsCDB phosphorelay signaling pathway in Escherichia coli, J Bacteriol, vol.188, pp.4-06, 2006.

L. Ferrières and D. J. Clarke, The RcsC sensor kinase is required for normal biofilm formation in Escherichia coli K-12 and controls the expression of a regulon in response to growth on a solid surface, Mol Microbiol, vol.50, pp.1665-1682, 2003.

S. L. Salscheider, A. Jahn, and K. Schnetz, Transcriptional regulation by BglJ-RcsB, a pleiotropic heteromeric activator in Escherichia coli, Nucleic Acids Res, vol.42, pp.2999-3008, 2014.

M. Giangrossi, S. Zattoni, A. Tramonti, D. De-biase, and M. Falconi, Antagonistic role of H-NS and GadX in the regulation of the glutamate decarboxylase-dependent acid resistance system in Escherichia coli, J Biol Chem, vol.280, pp.21498-21505, 2005.

M. A. Schembri, K. Kjaergaard, and P. Klemm, Global gene expression in Escherichia coli biofilms, Mol Microbiol, vol.48, pp.253-267, 2003.

S. Gottesman, P. Trisler, and A. Torres-cabassa, Regulation of capsular polysaccharide synthesis in Escherichia coli K-12: characterization of three regulatory genes, J Bacteriol, vol.162, pp.1111-1119, 1985.

F. Hommais, E. Krin, C. Laurent-winter, O. Soutourina, A. Malpertuy et al., Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS, Mol Microbiol, vol.40, pp.20-36, 2001.

C. Ueguchi, T. Ohta, C. Seto, T. Suzuki, and T. Mizuno, The leuO gene product has a latent ability to relieve bgl silencing in Escherichia coli, J Bacteriol, vol.180, pp.190-193, 1998.

T. Shimada, A. Bridier, R. Briandet, and A. Ishihama, Novel roles of LeuO in transcription regulation of E. coli genome: antagonistic interplay with the universal silencer H-NS, Mol Microbiol, vol.82, pp.378-397, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01000634

T. A. Lehti, J. Heikkinen, T. K. Korhonen, and B. Westerlund-wikström, The response regulator RcsB activates expression of Mat fimbriae in meningitic Escherichia coli, J Bacteriol, vol.194, pp.3475-3485, 2012.

D. Sledjeski and S. Gottesman, A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli, Proc Natl Acad Sci U S A, vol.92, 1995.

T. Stratmann, S. Madhusudan, and K. Schnetz, Regulation of the yjjQ-bglJ operon, encoding LuxR-type transcription factors, and the divergent yjjP gene by H-NS and LeuO, J Bacteriol, vol.190, pp.926-935, 2008.

A. K. Sayed and J. W. Foster, A 750 bp sensory integration region directs global control of the Escherichia coli GadE acid resistance regulator, Mol Microbiol, vol.71, pp.1435-1450, 2009.

R. T. Dame, C. Wyman, and N. Goosen, Structural basis for preferential binding of H-NS to curved DNA, Biochimie, vol.83, pp.231-234, 2001.

H. Yamada, S. Muramatsu, and T. Mizuno, An Escherichia coli protein that preferentially binds to sharply curved DNA, J Biochem, vol.108, pp.420-425, 1990.

R. Amit, A. B. Oppenheim, and J. Stavans, Increased bending rigidity of single DNA molecules by H-NS, a temperature and osmolarity sensor, Biophys J, vol.84, pp.75051-75057, 2003.

R. D. Sleator and C. Hill, Bacterial osmoadaptation: the role of osmolytes in bacterial stress and virulence, FEMS Microbiol Rev, vol.26, pp.49-71, 2002.

J. H. Chang, S. M. Coleman, and T. Schellenberg-beaver, Differential effects of sucrose or NaCl osmotic shock on-galactosidase activity in Escherichia coli BW25993 is dependent on normalization method by total viable count or total protein content, J Expt Microbiol Immunol, vol.18, pp.54-59, 2014.

S. Bontemps-gallo, E. Madec, J. Dondeyne, B. Delrue, C. Robbe-masselot et al., Concentration of osmoregulated periplasmic glucans (OPGs) modulates the activation level of the RcsCD RcsB phosphorelay in the phytopathogen bacteria Dickeya dadantii, Environ Microbiol, vol.15, pp.881-894, 2013.

J. Lloret, L. Bolanos, M. M. Lucas, J. M. Peart, N. J. Brewin et al., Ionic stress and osmotic pressure induce different alterations in the lipopolysaccharide of a Rhizobium meliloti strain, Appl Environ Microbiol, vol.61, pp.3701-3704, 1995.

N. Hachicho, A. Birnbaum, and H. J. Heipieper, Osmotic stress in colony and planktonic cells of Pseudomonas putida mt-2 revealed significant differences in adaptive response mechanisms, AMB Express, vol.7, 2017.

H. Nikaido, Molecular basis of bacterial outer membrane permeability revisited, Microbiol Mol Biol Rev, vol.67, pp.593-656, 2003.

T. Baba, T. Ara, M. Hasegawa, Y. Takai, Y. Okumura et al., Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Mol Syst Biol, vol.2, 2006.

M. K. Chaveroche, J. M. Ghigo, and C. Enfert, A rapid method for efficient gene replacement in the filamentous fungus Aspergillus nidulans, Nucleic Acids Res, vol.28, 2000.

K. A. Datsenko and B. L. Wanner, One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products, Proc Natl Acad Sci U S A, vol.97, pp.6640-6645, 2000.

P. P. Cherepanov and W. Wackernagel, Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant, Gene, vol.158, p.193, 1995.

A. J. Lesse, A. A. Campagnari, W. E. Bittner, and M. A. Apicella, Increased resolution of lipopolysaccharides and lipooligosaccharides utilizing Tricinesodium dodecyl sulfate-polyacrylamide gel electrophoresis, J Immunol Methods, vol.126, pp.109-117, 1990.

C. M. Tsai and C. E. Frasch, A sensitive silver stain for detecting lipopolysaccharides in polyacrylamide gels, Anal Biochem, vol.119, pp.115-119, 1982.

E. Hamidi, A. Tirsoaga, A. Novikov, A. Hussein, A. Caroff et al., Microextraction of bacterial lipid A: easy and rapid method for mass spectrometric characterization, J Lipid Res, vol.46, pp.1773-1778, 2005.

A. Tirsoaga, A. Hamidi, M. B. Perry, M. Caroff, and A. Novikov, A rapid, small-scale procedure for the structural characterization of lipid A applied to Citrobacter and Bordetella strains: discovery of a new structural element, J Lipid Res, vol.48, pp.2419-2427, 2007.

H. Therisod, V. Labas, and M. Caroff, Direct microextraction and analysis of rough-type lipopolysaccharides by combined thin-layer chromatography and MALDI mass spectrometry, Anal Chem, vol.73, pp.3804-3807, 2001.
DOI : 10.1021/ac010313s

J. H. Miller and . Szczesny, A short course in bacterial genetics: a laboratory manual and handbook for Escherichia coli and related bacteria, 1992.