K. Nath and A. L. Koch, Protein degradation in Escherichia coli. I. Measurement of rapidly and slowly decaying components, J Biol Chem. American Society for Biochemistry and Molecular Biology, vol.245, issue.11, p.4912536, 1970.

M. R. Maurizi, Proteases and protein degradation in Escherichia coli, Experientia. Birkhäuser-Verlag, vol.48, issue.2, pp.178-201, 1992.

S. Gottesman, Proteases and their Targets in Escherichia coli, P.O. Box, vol.10139, issue.1, pp.465-506, 2003.

E. Gur and R. T. Sauer, Recognition of misfolded proteins by Lon, a AAA(+) protease. Genes Dev. Cold Spring Harbor Lab, vol.22, p.18708584, 2008.

A. Bezawork-geleta, E. J. Brodie, D. A. Dougan, and K. N. Truscott, LON is the master protease that protects against protein aggregation in human mitochondria through direct degradation of misfolded proteins. Sci Rep, vol.5, p.14914, 2015.

E. Laskowska, K. Wi?nik, D. Skó-rko-glonek, J. Taylor, and A. , Degradation by proteases Lon, Clp and HtrA, of Escherichia coli proteins aggregated in vivo by heat shock; HtrA protease action in vivo and in vitro, Mol Microbiol. Blackwell Science Ltd, vol.22, issue.3, p.8939438, 1996.

S. Wickner, M. R. Maurizi, and S. Gottesman, Posttranslational Quality Control: Folding, Refolding, and Degrading Proteins, Science. American Association for the Advancement of Science, vol.286, issue.5446, p.10583944, 1999.

G. K. Fu, M. J. Smith, and D. M. Markovitz, Bacterial protease Lon is a site-specific DNA-binding protein, J Biol Chem. American Society for Biochemistry and Molecular Biology, vol.272, issue.1, p.8995294, 1997.

J. M. Flynn, S. B. Neher, Y. Kim, R. T. Sauer, and T. A. Baker, Proteomic Discovery of Cellular Substrates of the ClpXP Protease Reveals Five Classes of ClpX-Recognition Signals, Molecular Cell, vol.11, issue.3, p.12667450, 2003.

M. Kafri, E. Metzl-raz, J. G. Barkai, and N. , The Cost of Protein Production, Cell Reports, vol.14, issue.1, p.26725116, 2016.

A. Mugler, M. Kittisopikul, L. Hayden, J. Liu, C. H. Wiggins et al., Noise Expands the Response Range of the Bacillus subtilis Competence Circuit, PLoS Comput Biol. Public Library of Science, vol.12, issue.3, p.27003682, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01339378

E. K. Schrader, K. G. Harstad, and A. Matouschek, Targeting proteins for degradation, Nat Chem Biol, vol.5, issue.11, p.19841631, 2009.

A. J. Giaccia and M. B. Kastan, The complexity of p53 modulation: emerging patterns from divergent signals. Genes Dev. Cold Spring Harbor Lab, vol.12, p.9765199, 1998.

E. Mathes, O. Dea, E. L. Hoffmann, A. Ghosh, and G. , NF-?B dictates the degradation pathway of I?B?, EMBO J, vol.27, issue.9, p.18401342, 2008.

T. D. Gilmore, Introduction to NF-kappaB: players, pathways, perspectives. Oncogene, vol.25, p.17072321, 2006.

K. Tudelska, J. Markiewicz, M. Czyk, M. Czerkies, W. Prus et al., Information processing in the NF-?B pathway. Sci Rep, pp.1-14, 2017.

R. Christiano, N. Nagaraj, F. Frö-hlich, and T. C. Walther, Global Proteome Turnover Analyses of the Yeasts S. cerevisiae and S. pombe, Cell Reports, vol.9, issue.5, p.25466257, 2014.

E. Eden, N. Geva-zatorsky, I. Issaeva, A. Cohen, E. Dekel et al., Proteome Half-Life Dynamics in Living Human Cells, Science, vol.331, issue.6018, p.21233346, 2011.

K. L. Griffith, I. M. Shah, and R. Wolf, Proteolytic degradation of Escherichia coli transcription activators SoxS and MarA as the mechanism for reversing the induction of the superoxide (SoxRS) and multiple antibiotic resistance (Mar) regulons, Mol Microbiol. Blackwell Science Ltd, vol.51, issue.6, p.15009903, 2004.

M. Das, C. Bhaskarla, T. Verma, A. Kumar, D. Nandi et al., Roles of Lon protease and its substrate MarA during sodium salicylate-mediated growth reduction and antibiotic resistance in Escherichia coli, Microbiology, vol.162, issue.5, p.26944926, 2016.

T. M. Barbosa and S. B. Levy, Differential expression of over 60 chromosomal genes in Escherichia coli by constitutive expression of MarA, J Bacteriol, vol.182, issue.12, p.10852879, 2000.

R. G. Martin, W. K. Gillette, S. Rhee, and J. L. Rosner, Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: sequence, orientation and spatial relationship to the core promoter, Mol Microbiol, vol.34, issue.3, p.10564485, 1999.

L. M. Chubiz, G. D. Glekas, and C. V. Rao, Transcriptional cross talk within the mar-sox-rob regulon in Escherichia coli is limited to the rob and marRAB operons, J Bacteriol, vol.194, issue.18, p.22753060, 2012.

M. El, I. Siu, Y. Dunlop, and M. J. , Stochastic expression of a multiple antibiotic resistance activator confers transient resistance in single cells, Sci Rep, vol.6, 2016.

J. Garcia-bernardo and M. J. Dunlop, Tunable stochastic pulsing in the Escherichia coli multiple antibiotic resistance network from interlinked positive and negative feedback loops, PLoS Comput Biol. Public Library of Science, vol.9, issue.9, p.24086119, 2013.

G. Tkacik and A. M. Walczak, Information transmission in genetic regulatory networks: a review, J Phys: Condens Matter, vol.23, issue.15, pp.153102-153134, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00560319

N. A. Rossi and M. J. Dunlop, Customized Regulation of Diverse Stress Response Genes by the Multiple Antibiotic Resistance Activator MarA. Ioshikhes I, editor, PLoS Comput Biol. Public Library of Science

, , vol.13, p.28060821, 2017.

D. T. Gillespie, Exact numerical simulation of the Ornstein-Uhlenbeck process and its integral, Phys Rev E. American Physical Society, vol.54, issue.2, pp.2084-91, 1996.

M. J. Dunlop, R. S. Cox, J. H. Levine, R. M. Murray, and M. B. Elowitz, Regulatory activity revealed by dynamic correlations in gene expression noise, Nat Genet, vol.40, issue.12, p.19029898, 2008.

S. Hooshangi, S. Thiberge, and R. Weiss, Ultrasensitivity and noise propagation in a synthetic transcriptional cascade, Proceedings of the National Academy of Sciences. National Acad Sciences, vol.102, issue.10, pp.3581-3587, 2005.

L. S. Qi, M. H. Larson, L. A. Gilbert, J. A. Doudna, J. S. Weissman et al., Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression, Cell, vol.152, issue.5, p.23452860, 2013.

R. G. Martin, E. S. Bartlett, J. L. Rosner, and M. E. Wall, Activation of the Escherichia coli marA/soxS/rob Regulon in Response to Transcriptional Activator Concentration, Journal of Molecular Biology, vol.380, issue.2, p.18514222, 2008.

J. M. Schoemaker, R. C. Gayda, and A. Markovitz, Regulation of cell division in Escherichia coli: SOS induction and cellular location of the sulA protein, a key to lon-associated filamentation and death, J Bacteriol, vol.158, issue.2, p.6327610, 1984.

D. T. Gillespie, The chemical Langevin equation, The Journal of Chemical Physics. American Institute of Physics, vol.113, issue.1, pp.297-306, 2000.

J. B. Andersen, C. Sternberg, L. K. Poulsen, S. P. Bjorn, M. Givskov et al., New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria, Appl Environ Microbiol, vol.64, issue.6, p.9603842, 1998.

J. L. Rosner and J. L. Slonczewski, Dual regulation of inaA by the multiple antibiotic resistance (mar) and superoxide (soxRS) stress response systems of Escherichia coli, J Bacteriol, vol.176, issue.20, p.7928997, 1994.

D. Du, Z. Wang, N. R. James, J. E. Voss, E. Klimont et al., Structure of the AcrAB-TolC multidrug efflux pump, Nature. Europe PMC Funders, vol.509, issue.7501, p.24747401, 2014.

H. Okusu, D. Ma, and H. Nikaido, AcrAB efflux pump plays a major role in the antibiotic resistance phenotype of Escherichia coli multiple-antibiotic-resistance (Mar) mutants, J Bacteriol. American Society for Microbiology, vol.178, issue.1, p.8550435, 1996.

C. K. Smith, T. A. Baker, and R. T. Sauer, Lon and Clp family proteases and chaperones share homologous substrate-recognition domains, Proceedings of the National Academy of Sciences. National Acad Sciences, vol.96, issue.12, pp.6678-82, 1999.

F. Tostevin and P. R. Wolde-ten, Mutual Information between Input and Output Trajectories of Biochemical Networks, Phys Rev Lett. American Physical Society, vol.102, issue.21, p.19519137, 2009.

M. Stamatakis, R. M. Adams, and G. Balá-zsi, A common repressor pool results in indeterminacy of extrinsic noise. Chaos: An Interdisciplinary Journal of Nonlinear Science, vol.21, p.47523, 2011.

Z. Hao, H. Lou, R. Zhu, J. Zhu, D. Zhang et al., The multiple antibiotic resistance regulator MarR is a copper sensor in Escherichia coli, Nat Chem Biol, vol.10, issue.1, p.24185215, 2014.

U. Alon, Network motifs: theory and experimental approaches, Nat Rev Genet, vol.8, issue.6, p.17510665, 2007.

K. L. Griffith, I. M. Shah, and . Wolf-r, Proteolytic degradation of Escherichia coli transcription activators SoxS and MarA as the mechanism for reversing the induction of the superoxide (SoxRS) and multiple antibiotic resistance (Mar) regulons, Mol Microbiol, vol.51, issue.6, p.15009903, 2004.

T. S. Lee, R. A. Krupa, F. Zhang, M. Hajimorad, W. J. Holtz et al., BglBrick vectors and datasheets: A synthetic biology platform for gene expression, Journal of Biological Engineering, vol.5, issue.1, p.1, 2011.

S. Stylianidou, C. Brennan, S. B. Nissen, N. J. Kuwada, and P. A. Wiggins, SuperSegger: robust image segmentation, analysis and lineage tracking of bacterial cells, Mol Microbiol, vol.102, issue.4, p.27569113, 2016.

A. Kraskov, H. Stö-gbauer, and P. Grassberger, Estimating mutual information, Phys Rev E, vol.69, issue.6, pp.231-247, 2004.