J. B. Lyczak, C. L. Cannon, and G. B. Pier, Establishment of Pseudomonas aeruginosa infection: lessons from a versatile opportunist, Microbes Infect, vol.2, pp.1051-1060, 2000.

C. K. Stover, Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen, Nature, vol.406, pp.959-964, 2000.

A. Staron, The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family, Mol Microbiol, vol.74, pp.557-581, 2009.

S. Chevalier, Extracytoplasmic function sigma factors in Pseudomonas aeruginosa, Biochim Biophys Acta, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01788719

E. Bouffartigues, Sucrose favors Pseudomonas aeruginosa pellicle production through the extracytoplasmic function sigma factor SigX, FEMS Microbiol Lett, vol.356, pp.193-200, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00998403

E. Bouffartigues, The absence of the Pseudomonas aeruginosa OprF protein leads to increased biofilm formation through variation in c-di-GMP level, Front Microbiol, vol.6, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01166905

E. Bouffartigues, Transcription of the oprF gene of Pseudomonas aeruginosa is dependent mainly on the SigX sigma factor and is sucrose induced, J Bacteriol, vol.194, pp.4301-4311, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01137659

G. Gicquel, The extra-cytoplasmic function sigma factor SigX modulates biofilm and virulence-related properties in Pseudomonas aeruginosa, PLoS One, vol.8, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01131037

A. Blanka, Identification of the alternative sigma factor SigX regulon and its implications for Pseudomonas aeruginosa pathogenicity, J Bacteriol, vol.196, pp.345-356, 2014.

S. Schulz, Elucidation of sigma factor-associated networks in Pseudomonas aeruginosa reveals a modular architecture with limited and function-specific crosstalk, PLoS Pathog, vol.11, 2015.

A. L. Boechat, G. H. Kaihami, M. J. Politi, F. Lepine, and R. L. Baldini, A novel role for an ECF sigma factor in fatty acid biosynthesis and membrane fluidity in Pseudomonas aeruginosa, PLoS One, vol.8, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01130270

W. Nicholson, Increased competitive fitness of Bacillus subtilis under nonsporulating conditions via inactivation of pleiotropic regulators AlsR, SigD, and SigW, Appl Environ Microbiol, vol.78, pp.3500-3503, 2012.

R. Duchesne, A proteomic approach of SigX function in Pseudomonas aeruginosa outer membrane composition, J Proteomics, vol.94, pp.451-459, 2013.

G. Sezonov, D. Joseleau-petit, and R. D'-ari, Escherichia coli physiology in Luria-Bertani broth, J Bacteriol, vol.189, pp.8746-8749, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00184125

L. F. Wood and D. E. Ohman, Use of cell wall stress to characterize sigma 22 (AlgT/U) activation by regulated proteolysis and its regulon in Pseudomonas aeruginosa, Mol Microbiol, vol.72, pp.183-201, 2009.

G. L. Winsor, Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database, Nucleic Acids Res, vol.44, pp.646-653, 2016.

S. Chevalier, Structure, function and regulation of Pseudomonas aeruginosa porins, FEMS Microbiol Rev, vol.41, pp.698-722, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01969453

G. M. Teitzel, Survival and growth in the presence of elevated copper: transcriptional profiling of copper-stressed Pseudomonas aeruginosa, J Bacteriol, vol.188, pp.7242-7256, 2006.

R. C. Fowler and N. D. Hanson, The OpdQ porin of Pseudomonas aeruginosa is regulated by environmental signals associated with cystic fibrosis including nitrate-induced regulation involving the NarXL two-component system, vol.4, pp.967-982, 2015.

S. K. Kim, S. J. Im, D. H. Yeom, and J. H. Lee, AntR-mediated bidirectional activation of antA and antR, anthranilate degradative genes in Pseudomonas aeruginosa, Gene, vol.505, pp.146-152, 2012.

J. J. Kukor, R. H. Olsen, and D. P. Ballou, Cloning and expression of the catA and catBC gene clusters from Pseudomonas aeruginosa PAO, J Bacteriol, vol.170, pp.4458-4465, 1988.

S. P. Diggle, The Pseudomonas aeruginosa 4-quinolone signal molecules HHQ and PQS play multifunctional roles in quorum sensing and iron entrapment, Chem Biol, vol.14, pp.87-96, 2007.

B. Hoschle, V. Gnau, and D. Jendrossek, Methylcrotonyl-CoA and geranyl-CoA carboxylases are involved in leucine/isovalerate utilization (Liu) and acyclic terpene utilization (Atu), and are encoded by liuB/liuD and atuC/atuF, in Pseudomonas aeruginosa, Microbiology, vol.151, pp.3649-3656, 2005.

X. X. Zhang and P. Rainey, Genetic analysis of the histidine utilization (hut) genes in Pseudomonas fluorescens SBW25, Genetics, vol.176, pp.2165-2176, 2007.

H. Arai, Regulation and Function of Versatile Aerobic and Anaerobic Respiratory Metabolism in Pseudomonas aeruginosa, Front Microbiol, vol.2, 2011.

T. Osamura, T. Kawakami, R. Kido, M. Ishii, and H. Arai, Specific expression and function of the A-type cytochrome c oxidase under starvation conditions in Pseudomonas aeruginosa, PLoS One, vol.12, 2017.

N. E. Van-alst, L. A. Sherrill, B. H. Iglewski, and C. G. Haidaris, Compensatory periplasmic nitrate reductase activity supports anaerobic growth of Pseudomonas aeruginosa PAO1 in the absence of membrane nitrate reductase, Can J Microbiol, vol.55, pp.1133-1144, 2009.

K. Schreiber, The anaerobic regulatory network required for Pseudomonas aeruginosa nitrate respiration, J Bacteriol, vol.189, pp.4310-4314, 2007.

R. Scientific, , vol.8, 2018.

Y. Jiang, H. Tang, G. Wu, and P. Xu, Functional Identification of a Novel Gene, moaE, for 3-Succinoylpyridine Degradation in Pseudomonas putida S16, Sci Rep, vol.5, 2015.

S. Perinet, Molybdate transporter ModABC is important for Pseudomonas aeruginosa chronic lung infection, BMC Res Notes, vol.9, 2016.

E. Sonnleitner and U. Blasi, Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa carbon catabolite repression, PLoS Genet, vol.10, 2014.

L. Rosa, R. Behrends, V. Williams, H. D. Bundy, J. G. Rojo et al., Influence of the Crc regulator on the hierarchical use of carbon sources from a complete medium in Pseudomonas, Environ Microbiol, vol.18, pp.807-818, 2016.

E. Sonnleitner, A. Romeo, and U. Blasi, Small regulatory RNAs in Pseudomonas aeruginosa, RNA Biol, vol.9, pp.364-371, 2012.

E. Sonnleitner, K. Prindl, and U. Blasi, The Pseudomonas aeruginosa CrcZ RNA interferes with Hfq-mediated riboregulation, PLoS One, vol.12, 2017.

J. F. Linares, The global regulator Crc modulates metabolism, susceptibility to antibiotics and virulence in Pseudomonas aeruginosa, Environ Microbiol, vol.12, pp.3196-3212, 2010.

E. Sonnleitner, Novel targets of the CbrAB/Crc carbon catabolite control system revealed by transcript abundance in Pseudomonas aeruginosa, PLoS One, vol.7, p.44637, 2012.

M. Valentini and K. Lapouge, Catabolite repression in Pseudomonas aeruginosa PAO1 regulates the uptake of C4 -dicarboxylates depending on succinate concentration, Environ Microbiol, vol.15, pp.1707-1716, 2013.

T. Milojevic, I. Grishkovskaya, E. Sonnleitner, K. Djinovic-carugo, and U. Blasi, The Pseudomonas aeruginosa catabolite repression control protein Crc is devoid of RNA binding activity, PLoS One, vol.8, 2013.

E. Sonnleitner, Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa, Nucleic Acids Res, vol.46, pp.1470-1485, 2018.

E. Sonnleitner, M. Schuster, T. Sorger-domenigg, E. P. Greenberg, and U. Blasi, Hfq-dependent alterations of the transcriptome profile and effects on quorum sensing in Pseudomonas aeruginosa, Mol Microbiol, vol.59, pp.1542-1558, 2006.

T. K. Kambara, K. M. Ramsey, and S. L. Dove, Pervasive Targeting of Nascent Transcripts by Hfq, Cell Rep, vol.23, pp.1543-1552, 2018.

E. Sonnleitner, L. Abdou, and D. Haas, Small RNA as global regulator of carbon catabolite repression in Pseudomonas aeruginosa, Proc Natl Acad Sci, vol.106, pp.21866-21871, 2009.

L. Abdou, H. Chou, D. Haas, and C. Lu, Promoter recognition and activation by the global response regulator CbrB in Pseudomonas aeruginosa, J Bacteriol, vol.193, pp.2784-2792, 2011.

Y. Itoh, T. Nishijyo, and Y. Nakada, Histidine catabolism and catabolic regulation, vol.5, pp.371-395, 2007.

O. Rojas-rosas, J. Villafana-rojas, F. A. Lopez-dellamary, J. Nungaray-arellano, and O. Gonzalez-reynoso, Production and characterization of polyhydroxyalkanoates in Pseudomonas aeruginosa ATCC 9027 from glucose, an unrelated carbon source, Can J Microbiol, vol.53, pp.840-851, 2007.

L. Rosa, R. De-la-pena, F. Prieto, M. A. Rojo, and F. , The Crc protein inhibits the production of polyhydroxyalkanoates in Pseudomonas putida under balanced carbon/nitrogen growth conditions, Environ Microbiol, vol.16, pp.278-290, 2014.

E. P. Briczinski, A. T. Phillips, and R. F. Roberts, Transport of glucose by Bifidobacterium animalis subsp. lactis occurs via facilitated diffusion, Appl Environ Microbiol, vol.74, pp.6941-6948, 2008.

P. Fonseca, R. Moreno, and F. Rojo, Pseudomonas putida growing at low temperature shows increased levels of CrcZ and CrcY sRNAs, le ading to reduced Crc-dep endent cat ab olite repression, Env iron Microbiol, vol.15, pp.24-35, 2013.

C. Baysse, Modulation of quorum sensing in Pseudomonas aeruginosa through alteration of membrane properties, Microbiology, vol.151, pp.2529-2542, 2005.

W. B. Terzaghi, Manipulating membrane Fatty Acid compositions of whole plants with tween-Fatty Acid esters, Plant Physiol, vol.91, pp.203-212, 1989.

D. De-mendoza, Temperature sensing by membranes, Annu Rev Microbiol, vol.68, pp.101-116, 2014.

K. R. Pandit and J. B. Klauda, Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain, Biochim Biophys Acta, vol.1818, pp.1205-1210, 2012.

D. Poger and A. E. Mark, A ring to rule them all: the effect of cyclopropane Fatty acids on the fluidity of lipid bilayers, J Phys Chem B, vol.119, pp.5487-5495, 2015.

D. W. Grogan and J. E. Cronan, Cyclopropane ring formation in membrane lipids of bacteria, Microbiol Mol Biol Rev, vol.61, pp.429-441, 1997.

A. W. Kingston, C. Subramanian, C. O. Rock, and J. D. Helmann, A sigmaW-dependent stress response in Bacillus subtilis that reduces membrane fluidity, Mol Microbiol, vol.81, pp.69-79, 2011.

R. E. Hancock, G. M. Decad, and H. Nikaido, Identification of the protein producing transmembrane diffusion pores in the outer membrane of Pseudomonas aeruginosa PA01, Biochim Biophys Acta, vol.554, pp.323-331, 1979.

M. Guyard-nicodeme, Outer membrane modifications of Pseudomonas fluorescens MF37 in response to hyperosmolarity, J Proteome Res, vol.7, pp.1218-1225, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00846221

R. A. Irizarry, Exploration, normalization, and summaries of high density oligonucleotide array probe level data, Biostatistics, vol.4, pp.249-264, 2003.

G. W. Wright and R. M. Simon, A random variance model for detection of differential gene expression in small microarray experiments, Bioinformatics, vol.19, pp.2448-2455, 2003.

T. Clamens, The aliphatic amidase AmiE is involved in regulation of Pseudomonas aeruginosa virulence, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01623395

M. Vincent, L. S. England, and J. T. Trevors, Cytoplasmic membrane polarization in Gram-positive and Gram-negative bacteria grown in the absence and presence of tetracycline, Biochim Biophys Acta, vol.1672, pp.131-134, 2004.

J. R. Lakowicz, Principles of Fluorescence Spectroscopy, 2006.

W. R. Morrison and L. M. Smith, Preparation of Fatty Acid Methyl Esters and Dimethylacetals from Lipids with Boron Fluoride-Methanol, J Lipid Res, vol.5, pp.600-608, 1964.

H. J. Heipieper, G. Meulenbeld, Q. Van-oirschot, and J. De-bont, Effect of Environmental Factors on the trans/cis Ratio of Unsaturated Fatty Acids in Pseudomonas putida S12, Appl Environ Microbiol, vol.62, pp.2773-2777, 1996.

F. Lépine, E. Deziel, S. Milot, and L. G. Rahme, A stable isotope dilution assay for the quantification of the Pseudomonas quinolone signal in Pseudomonas aeruginosa cultures, Biochim Biophys Acta, vol.1622, pp.36-41, 2003.

H. Chen and P. C. Boutros, VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R, BMC Bioinformatics, 2011.

M. D. Whiteside, G. L. Winsor, M. R. Laird, and F. S. Brinkman, OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis, Nucleic Acids Res, pp.366-76, 2013.

R. Scientific, , vol.8, 2018.