C. M. Allan, S. Hill, S. Morvaridi, R. Saiki, J. S. Johnson et al., A conserved START domain coenzyme Q-binding polypeptide is required for efficient Q biosynthesis, respiratory electron transport, and antioxidant function in Saccharomyces cerevisiae, Biochimica et Biophysica Acta, vol.1831, issue.4, pp.776-791, 2013.

G. G. Anderson, J. J. Palermo, J. D. Schilling, R. Roth, J. Heuser et al., Intracellular bacterial biofilm-like pods in urinary tract infections, Science, vol.301, pp.105-107, 2003.

S. G. Andersson, A. Zomorodipour, J. O. Andersson, T. Sicheritz-pontén, U. C. Alsmark et al., The genome sequence of Rickettsia prowazekii and the origin of mitochondria, Nature, vol.396, issue.6707, pp.133-140, 1998.

Y. Anraku, Bacterial electron transport chains, Annual Review of Biochemistry, vol.57, pp.101-132, 1988.

D. Arndt, J. R. Grant, A. Marcu, T. Sajed, A. Pon et al., PHASTER: A better, faster version of the PHAST phage search tool, Nucleic Acids Research, vol.44, issue.W1, pp.16-21, 2016.

L. Aussel, L. Loiseau, M. Hajj-chehade, B. Pocachard, M. Fontecave et al., ubiJ, a new gene required for aerobic growth and proliferation in macrophage, is involved in coenzyme Q biosynthesis in Escherichia coli and Salmonella enterica serovar Typhimurium, Journal of Bacteriology, vol.196, issue.1, pp.70-79, 2014.
URL : https://hal.archives-ouvertes.fr/hal-00917119

A. M. Awad, M. C. Bradley, L. Fernandez-del-rio, A. Nag, H. S. Tsui et al., Coenzyme Q10 deficiencies: Pathways in yeast and humans, Essays in Biochemistry, vol.62, issue.3, pp.361-376, 2018.

N. Q. Balaban, S. Helaine, K. Lewis, M. Ackermann, B. Aldridge et al., Definitions and guidelines for research on antibiotic persistence, Nature Reviews Microbiology, vol.17, issue.7, pp.441-448, 2019.
URL : https://hal.archives-ouvertes.fr/pasteur-02558489

M. H. Barros, A. Johnson, P. Gin, B. N. Marbois, C. F. Clarke et al., The Saccharomyces cerevisiae COQ10 gene encodes a START domain protein required for function of coenzyme Q in respiration, Journal of Biological Chemistry, vol.280, issue.52, pp.42627-42635, 2005.

A. Battesti, N. Majdalani, and S. Gottesman, The RpoS-mediated general stress response in Escherichia coli, Annual Review of Microbiology, vol.65, pp.189-213, 2011.

M. G. Blango and M. A. Mulvey, Persistence of uropathogenic Escherichia coli in the face of multiple antibiotics, Antimicrobial Agents and Chemotherapy, vol.54, issue.5, pp.1855-1863, 2010.

K. Blank, M. Hensel, and R. G. Gerlach, Rapid and highly efficient method for scarless mutagenesis within the Salmonella enterica chromosome, PLoS One, vol.6, issue.1, 2011.

D. Castro-roa, A. Garcia-pino, S. De-gieter, N. A. Van-nuland, R. Loris et al., The Fic protein Doc uses an inverted substrate to phosphorylate and inactivate EF-Tu, Nature Chemical Biology, vol.9, issue.12, pp.811-817, 2013.

C. T. Chung, S. L. Niemela, and R. H. Miller, One-step preparation of competent Escherichia coli: Transformation and storage of bacterial cells in the same solution, Proceedings of the National Academy of Sciences of the United States of America, vol.86, pp.2172-2175, 1989.

T. Z. Cui and M. Kawamukai, Coq10, a mitochondrial coenzyme Q binding protein, is required for proper respiration in Schizosaccharomyces pombe, FEBS Journal, vol.276, issue.3, pp.748-759, 2009.

M. Day, Yeast petites and small colony variants: For everything there is a season, Advances in Applied Microbiology, vol.85, pp.1-41, 2013.

T. Dörr, M. Vulic, and K. Lewis, Ciprofloxacin causes persister formation by inducing the TisB toxin in Escherichia coli, PLoS Biology, vol.8, issue.2, 2010.

M. Fauvart, V. N. De-groote, and J. Michiels, Role of persister cells in chronic infections: Clinical relevance and perspectives on anti-persister therapies, Journal of Medical Microbiology, vol.60, pp.699-709, 2011.

A. L. Flores-mireles, J. N. Walker, M. Caparon, and S. J. Hultgren, Urinary tract infections: Epidemiology, mechanisms of infection and treatment options, Nature Reviews Microbiology, vol.13, issue.5, pp.269-284, 2015.

E. Germain, D. Castro-roa, N. Zenkin, and K. Gerdes, Molecular mechanism of bacterial persistence by HipA, Molecular Cell, vol.52, issue.2, pp.248-254, 2013.

M. Glover, C. G. Moreira, V. Sperandio, and P. Zimmern, Recurrent urinary tract infections in healthy and nonpregnant women, Urological Science, vol.25, issue.1, pp.1-8, 2014.

L. W. Goneau, N. S. Yeoh, K. W. Macdonald, P. A. Cadieux, J. P. Burton et al., Selective target inactivation rather than global metabolic dormancy causes antibiotic tolerance in uropathogens, Antimicrobial Agents and Chemotherapy, vol.58, issue.4, pp.2089-2097, 2014.

F. Goormaghtigh, N. Fraikin, M. Putrins, T. Hallaert, V. Hauryliuk et al., Reassessing the role of type II toxin-antitoxin systems in formation of Escherichia coli type II persister cells, Mbio, vol.9, issue.3, pp.640-658, 2018.

M. Gotfredsen and K. Gerdes, The Escherichia coli relBE genes belong to a new toxin-antitoxin gene family, Molecular Microbiology, vol.29, issue.4, pp.1065-1076, 1998.

M. Hajj-chehade, L. Pelosi, C. D. Fyfe, L. Loiseau, B. Rascalou et al., A soluble metabolon synthesizes the isoprenoid lipid ubiquinone, Cell Chemistry & Biology, vol.26, issue.4, p.1, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02071798

A. Harms, D. E. Brodersen, N. Mitarai, and K. Gerdes, Toxins, targets, and triggers: An overview of toxin-antitoxin biology, Molecular Cell, vol.70, issue.5, pp.768-784, 2018.

A. Harms, C. Fino, M. A. Sørensen, S. Semsey, and K. Gerdes, Prophages and growth dynamics confound experimental results with antibiotic-tolerant persister cells, Mbio, vol.8, issue.6, pp.1964-1981, 2017.

A. Harms, E. Maisonneuve, and K. Gerdes, Mechanisms of bacterial persistence during stress and antibiotic exposure, Science, vol.354, issue.6318, 2016.

S. Helaine, A. M. Cheverton, K. G. Watson, L. M. Faure, S. A. Matthews et al., Internalization of Salmonella by macrophages induces formation of nonreplicating persisters, Science, vol.343, issue.6167, pp.204-208, 2014.

K. Hirose, S. Chang, H. Yu, J. Wang, E. Barca et al., Loss of a novel striated muscle-enriched mitochondrial protein Coq10a enhances postnatal cardiac hypertrophic growth, 2019.

J. L. Hobman, C. W. Penn, and M. J. Pallen, Laboratory strains of Escherichia coli: Model citizens or deceitful delinquents growing old disgracefully?, Molecular Microbiology, vol.64, issue.4, pp.881-885, 2007.

A. J. Hryckowian, G. A. Baisa, K. J. Schwartz, and R. A. Welch, dsdA does not affect colonization of the murine urinary tract by Escherichia coli CFT073, PLoS One, vol.10, issue.9, 2015.

A. J. Hryckowian and R. A. Welch, RpoS contributes to phagocyte oxidase-mediated stress resistance during urinary tract infection by Escherichia coli CFT073, MBio, vol.4, issue.1, pp.23-36, 2013.

M. Jahn, C. Vorpahl, T. Hubschmann, H. Harms, and S. Muller, Copy number variability of expression plasmids determined by cell sorting and Droplet Digital PCR, Microbial Cell Factories, vol.15, issue.1, p.211, 2016.

M. Jastroch, A. S. Divakaruni, S. Mookerjee, J. R. Treberg, and M. D. Brand, Mitochondrial proton and electron leaks, Essays in Biochemistry, vol.47, pp.53-67, 2010.

L. A. Kelley, S. Mezulis, C. M. Yates, M. N. Wass, and M. J. Sternberg, The Phyre2 web portal for protein modeling, prediction and analysis, Nature Protocols, vol.10, issue.6, pp.845-858, 2015.

I. Keren, Y. Wu, J. Inocencio, L. R. Mulcahy, and K. Lewis, Killing by bactericidal antibiotics does not depend on reactive oxygen species, Science, vol.339, issue.6124, pp.1213-1216, 2013.

M. A. Kohanski, D. J. Dwyer, and J. J. Collins, How antibiotics kill bacteria: From targets to networks, Nature Reviews Microbiology, vol.8, issue.6, pp.423-435, 2010.

S. Koskiniemi, M. Pranting, E. Gullberg, J. Näsvall, and D. I. Andersson, Activation of cryptic aminoglycoside resistance in Salmonella enterica, Molecular Microbiology, vol.80, issue.6, pp.1464-1478, 2011.

K. M. Krause, A. W. Serio, T. R. Kane, and L. E. Connolly, Aminoglycosides: An overview. Cold Spring Harbor Perspectives in Medicine, vol.6, 2016.

E. Lee, D. Yu, J. Martinez-de-velasco, L. Tessarollo, D. A. Swing et al., A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA, Genomics, vol.73, issue.1, pp.56-65, 2001.

K. Lewis, Persister cells, Annual Review of Microbiology, vol.64, pp.357-372, 2010.

H. Liu and J. H. Naismith, An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol, BMC Biotechnology, vol.8, p.91, 2008.

Y. Liu and J. A. Imlay, Cell death from antibiotics without the involvement of reactive oxygen species, Science, vol.339, issue.6124, pp.1210-1213, 2013.

D. Lobato-marquez, I. Moreno-cordoba, V. Figueroa, R. Diaz-orejas, and F. Garcia-del-portillo, Distinct type I and type II toxin-antitoxin modules control Salmonella lifestyle inside eukaryotic cells, Scientific Reports, vol.5, p.9374, 2015.

L. Loiseau, C. Fyfe, L. Aussel, M. Hajj-chehade, S. B. Hernández et al., The UbiK protein is an accessory factor necessary for bacterial ubiquinone (UQ) biosynthesis and forms a complex with the UQ biogenesis factor UbiJ, Journal of Biological Chemistry, vol.292, issue.28, pp.11937-11950, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01615493

, Cold Spring Harbor Protocols, M9 minimal medium (standard) (2010), 2010.

C. Mao, K. Bhardwaj, S. M. Sharkady, R. I. Fish, T. Driscoll et al., Variations on the tmRNA gene, RNA Biology, vol.6, issue.4, pp.355-361, 2009.

M. G. Marinus and A. R. Poteete, High efficiency generalized transduction in Escherichia coli O157:H7. F1000Research, vol.2, 2013.

J. E. Michiels, B. Van-den-bergh, N. Verstraeten, M. Fauvart, and J. Michiels, In vitro emergence of high persistence upon periodic aminoglycoside challenge in the ESKAPE pathogens, Antimicrobial Agents and Chemotherapy, vol.60, issue.8, pp.757-773, 2016.

M. H. Miller, S. C. Edberg, L. J. Mandel, C. F. Behar, and N. H. Steigbigel, Gentamicin uptake in wild-type and aminoglycoside-resistant small-colony mutants of Staphylococcus aureus, Antimicrobial Agents and Chemotherapy, vol.18, issue.5, pp.722-729, 1980.

R. C. Molina-quiroz, D. W. Lazinski, A. Camilli, and S. B. Levy, Transposon-sequencing analysis unveils novel genes involved in the generation of persister cells in uropathogenic Escherichia coli, Antimicrobial Agents and Chemotherapy, vol.60, issue.11, pp.6907-6910, 2016.

K. C. Murphy and K. G. Campellone, Lambda Red-mediated recombinogenic engineering of enterohemorrhagic and enteropathogenic E. coli, BMC Molecular Biology, vol.4, p.11, 2003.

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, issue.6058, pp.982-986, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-00722468

A. Nitzschke and K. Bettenbrock, All three quinone species play distinct roles in ensuring optimal growth under aerobic and fermentative conditions in E. coli K12, PLoS One, vol.13, issue.4, 2018.

J. P. Norton and M. A. Mulvey, Toxin-antitoxin systems are important for niche-specific colonization and stress resistance of uropathogenic Escherichia coli, PLoS Path, vol.8, issue.10, 2012.

L. Pelosi, A. L. Ducluzeau, L. Loiseau, F. Barras, D. Schneider et al., Evolution of ubiquinone biosynthesis: Multiple proteobacterial enzymes with various regioselectivities to catalyze three contiguous aromatic hydroxylation reactions. mSystems, vol.1, pp.91-107, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01424513

L. Pelosi, C. D. Vo, S. S. Abby, L. Loiseau, B. Rascalou et al., Ubiquinone biosynthesis over the entire O2 range: Characterization of a conserved O2-independent pathway, Mbio, vol.10, issue.4, pp.1319-1338, 2019.
URL : https://hal.archives-ouvertes.fr/hal-02183791

M. H. Pontes and E. A. Groisman, Slow growth determines nonheritable antibiotic resistance in Salmonella enterica, Science Signalling, vol.12, issue.592, 2019.

W. W. Poon, D. E. Davis, H. T. Ha, T. Jonassen, P. N. Rather et al., Identification of Escherichia coli ubiB, a gene required for the first monooxygenase step in ubiquinone biosynthesis, Journal of Bacteriology, vol.182, issue.18, pp.5139-5146, 2000.

R. A. Proctor, A. Kriegeskorte, B. C. Kahl, K. Becker, B. Löffler et al., Staphylococcus aureus Small Colony Variants (SCVs): A road map for the metabolic pathways involved in persistent infections, 2014.

, Frontiers in Cellular and Infection Microbiology, vol.4, p.99

S. Ronneau and S. Helaine, Clarifying the link between toxin-antitoxin modules and bacterial persistence, Journal of Molecular Biology, vol.431, issue.18, pp.3462-3471, 2019.

A. Schmidt, K. Kochanowski, S. Vedelaar, E. Ahrné, B. Volkmer et al., The quantitative and condition-dependent Escherichia coli proteome, Nature Biotechnology, vol.34, issue.1, pp.104-110, 2015.

Y. Shan, A. Brown-gandt, S. E. Rowe, J. P. Deisinger, B. P. Conlon et al., ATP-dependent persister formation in Escherichia coli, Mbio, vol.8, issue.1, pp.2267-2283, 2017.

Y. Shan, D. Lazinski, S. Rowe, A. Camilli, and K. Lewis, Genetic basis of persister tolerance to aminoglycosides in Escherichia coli, Mbio, vol.6, issue.2, pp.78-93, 2015.

P. Sharma, M. J. Teixeira-de-mattos, K. J. Hellingwerf, and M. Bekker, On the function of the various quinone species in Escherichia coli, FEBS Journal, vol.279, issue.18, pp.3364-3373, 2012.

Y. Shen, S. Goldsmith-fischman, H. S. Atreya, T. Acton, L. C. Ma et al., NMR structure of the 18 kDa protein CC1736 from Caulobacter crescentus identifies a member of the START domain superfamily and suggests residues mediating substrate specificity, Proteins, vol.58, issue.3, pp.747-750, 2005.

M. Snoussi, J. P. Talledo, N. A. Rosario, S. Mohammadi, B. Y. Ha et al., Heterogeneous absorption of antimicrobial peptide LL37 in Escherichia coli cells enhances population survivability, Elife, vol.7, 2018.

B. Søballe and R. K. Poole, Ubiquinone limits oxidative stress in Escherichia coli, Microbiology, pp.287-146, 2000.

J. A. Stefely and D. J. Pagliarini, Biochemistry of mitochondrial coenzyme Q biosynthesis, Trends in Biochemical Sciences, vol.42, issue.10, pp.824-843, 2017.

D. Szklarczyk, A. L. Gable, D. Lyon, A. Junge, S. Wyder et al., STRING v11: Protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets, Nucleic Acids Research, vol.47, issue.D1, pp.607-613, 2018.

U. C. Tran and C. F. Clarke, Endogenous synthesis of coenzyme Q in eukaryotes, Mitochondrion, vol.7, pp.62-71, 2007.

H. S. Tsui, N. V. Pham, B. R. Amer, M. C. Bradley, J. E. Gosschalk et al., Human COQ10A and COQ10B are distinct lipid-binding START domain proteins required for coenzyme Q function, Journal of Lipid Research, vol.60, issue.7, pp.1293-1310, 2019.

B. Van-den-bergh, J. E. Michiels, T. Wenseleers, E. M. Windels, P. V. Boer et al., Frequency of antibiotic application drives rapid evolutionary adaptation of Escherichia coli persistence, Nature Microbiology, vol.1, 2016.

N. Verstraeten, W. J. Knapen, C. I. Kint, V. Liebens, B. Van-den-bergh et al., Obg and membrane depolarization are part of a microbial bet-hedging strategy that leads to antibiotic tolerance, Molecular Cell, vol.59, issue.1, pp.9-21, 2015.

Y. Wang and S. Hekimi, Understanding ubiquinone, Trends in Cell Biology, vol.26, issue.5, pp.367-378, 2016.

M. D. White, K. A. Payne, K. Fisher, S. A. Marshall, D. Parker et al., UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis, Nature, vol.522, issue.7557, pp.502-506, 2015.

H. Xia, X. Yang, Q. Tang, J. Ye, H. Wu et al., EsrE-A yigP locus-encoded transcript-Is a 3? UTR sRNA involved in the respiratory chain of E. coli, Frontiers in Microbiology, vol.8, 1658.

J. H. Yang, S. C. Bening, and J. J. Collins, Antibiotic efficacy-context matters, Current Opinion in Microbiology, vol.39, pp.73-80, 2017.

M. A. Zampol, C. Busso, F. Gomes, J. R. Ferreira-junior, A. Tzagoloff et al., Over-expression of COQ10 in Saccharomyces cerevisiae inhibits mitochondrial respiration, Biochemical and Biophysical Research Communications, vol.402, issue.1, pp.82-87, 2010.

A. Zaslaver, A. Bren, M. Ronen, S. Itzkovitz, I. Kikoin et al., A comprehensive library of fluorescent transcriptional reporters for Escherichia coli, Nature Methods, vol.3, issue.8, pp.623-628, 2006.

Y. Zhang, M. Inouye, C. Fino, M. Vestergaard, H. Ingmer et al., PasT of Escherichia coli sustains antibiotic tolerance and aerobic respiration as a bacterial homolog of mitochondrial Coq10, Molecular Microbiology, vol.79, issue.6, pp.1418-1429, 2011.