A. Agarwal, C. Kahyaoglu, and D. B. Hansen, Characterization of HmqF, a protein involved in the biosynthesis of unsaturated quinolones produced by Burkholderia thailandensis, Biochemistry, vol.51, pp.1648-1657, 2012.

K. Agnoli, S. Schwager, S. Uehlinger, A. Vergunst, D. F. Viteri et al., Exposing the third chromosome of Burkholderia cepacia complex strains as a virulence plasmid, Mol. Microbiol, vol.83, pp.362-378, 2011.

C. Aguilar, I. Bertani, and V. Venturi, Quorum-sensing system and stationary-phase sigma factor (rpoS) of the onion pathogen Burkholderia cepacia genomovar I type strain, ATCC 25416.s, Appl. Environ. Microbiol, vol.69, pp.1739-1747, 2003.

C. Bertelli, M. R. Laird, K. P. Williams, B. Y. Lau, G. Hoad et al., IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets, Nucleic Acids Res, vol.45, 2017.

B. Buchfink, C. Xie, and D. H. Huson, Fast and sensitive protein alignment using DIAMOND, Nat. Methods, vol.12, pp.59-60, 2015.

A. Butt, N. Halliday, P. Williams, H. S. Atkins, G. J. Bancroft et al., Burkholderia pseudomallei kynB plays a role in AQ production, biofilm formation, bacterial swarming and persistence, Res. Microbiol, vol.167, pp.159-167, 2016.

A. Chapalain, M. Groleau, S. Le-guillouzer, A. Miomandre, L. Vial et al., Interplay between 4-hydroxy-3-methyl-2-alkylquinoline and N-acyl-homoserine lactone signaling in a, Burkholderia cepacia Complex Clinical Strain. Front. Microbiol, vol.8, p.1648, 2017.
URL : https://hal.archives-ouvertes.fr/pasteur-01574572

K. Choudhary, S. Hudaiberdiev, Z. Gelencsr, B. Gonalvescoutinho, V. Venturi et al., The organization of the quorum sensing luxI/R family genes in Burkholderia, Int. J. Mol. Sci, vol.14, pp.13727-13747, 2013.

A. E. Darling, B. Mau, and N. T. Perna, progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement, PLoS ONE, vol.5, p.11147, 2010.

E. Déziel, F. Lépine, S. Milot, J. He, M. N. Mindrinos et al., Analysis of Pseudomonas aeruginosa 4-hydroxy-2-alkylquinolines (HAQs) reveals a role for 4-hydroxy-2-heptylquinoline in cell-to-cell communication, Proc. Natl. Acad. Sci.U.S.A, vol.101, pp.1339-1344, 2004.

S. P. Diggle, P. Lumjiaktase, F. Dipilato, K. Winzer, M. Kunakorn et al., Functional genetic analysis reveals a 2-Alkyl-4-quinolone signaling system in the human pathogen Burkholderia pseudomallei and related bacteria, Chem. Biol, vol.13, pp.701-710, 2006.

S. Drees and S. Fetzner, PqsE of Pseudomonas aeruginosa acts as pathwayspecific thioesterase in the biosynthesis of alkylquinolone signaling molecules, Chem. Biol, vol.22, pp.611-618, 2015.

S. L. Drees, C. Li, F. Prasetya, M. Saleem, I. Dreveny et al., PqsBC, a condensing enzyme in the biosynthesis of the Pseudomonas aeruginosa quinolone signal: crystal structure, inhibition, and reaction mecanism, J. Biol. Chem, vol.291, pp.6610-6624, 2016.

C. E. Dulcey, V. Dekimpe, D. Fauvelle, S. Milot, M. Groleau et al., The end of an old hypothesis: the Pseudomonas signaling molecules 4-hydroxy-2-alkylquinolines derive from fatty acids, not 3-ketofatty acids, Chem. Biol, vol.20, pp.1481-1491, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01130934

L. Eberl and P. Vandamme, Members of the genus Burkholderia: good and bad guys. F1000Research, vol.5, p.1007, 2016.

N. El-banna and G. Winkelmann, Pyrrolnitrin from Burkholderia cepacia: antibiotic activity against fungi and novel activities against streptomycetes, J. Appl. Microbiol, vol.85, pp.69-78, 2002.

J. Farrow, Z. Sund, M. Ellison, D. Wade, J. Coleman et al., PqsE functions independently of PqsR-Pseudomonas quinolone signal and enhances the rhl quorum-sensing system, J. Bacteriol, vol.190, pp.7043-7051, 2008.

J. M. Farrow and E. C. Pesci, Distal and proximal promoters co-regulate pqsR expression in Pseudomonas aeruginosa, Mol. Microbiol, vol.104, pp.78-91, 2017.

B. Folch, E. Dziel, and N. Doucet, Systematic mutational analysis of the putative hydrolase PqsE: toward a deeper molecular understanding of virulence acquisition in Pseudomonas aeruginosa, PLoS ONE, vol.8, p.73727, 2013.
URL : https://hal.archives-ouvertes.fr/pasteur-01130955

C. Fuqua and E. Greenberg, Self perception in bacteria: quorum sensing with acylated homoserine lactones, Curr. Opin. Microbiol, vol.1, pp.183-189, 1998.

L. Gallagher, S. Mcknight, M. Kuznetsova, E. Pesci, and C. Manoil, Functions required for extracellular quinolone signaling by Pseudomonas aeruginosa, J. Bacteriol, vol.184, pp.6472-6480, 2002.

P. Gilligan, Microbiology of airway disease in patients with cystic fibrosis, Clin. Microbiol. Rev, vol.4, pp.35-51, 1991.

R. Gold, E. Jin, H. Levison, A. Isles, F. et al., Ceftazidime alone and in combination in patients with cystic fibrosis: lack of efficacy in treatment of severe respiratory infections caused by Pseudomonas cepacia, J. Antimicrob. Chemother, vol.12, pp.331-336, 1983.

J. Govan and V. Deretic, Microbial pathogenesis in cystic fibrosis: mucoid Pseudomonas aeruginosa and Burkholderia cepacia, Microbiol. Rev, vol.60, pp.539-574, 1996.

J. Govan, C. Doherty, J. Nelson, P. Brown, A. Greening et al., Evidence for transmission of Pseudomonas cepacia by social contact in cystic fibrosis, Lancet, vol.342, pp.15-19, 1993.

S. Heeb, M. Fletcher, S. Chhabra, S. Diggle, P. Williams et al., Quinolones: from antibiotics to autoinducers, FEMS Microbiol. Rev, vol.35, pp.247-274, 2011.

D. Hooi, B. Bycroft, S. Chhabra, P. Williams, and D. Pritchard, Differential immune modulatory activity of Pseudomonas aeruginosa quorum-sensing signal molecules, Infect. Immun, vol.72, pp.6463-6470, 2004.

B. Huber, K. Riedel, M. Hentzer, A. Heydorn, A. Gotschlich et al., The cep quorum-sensing system of Burkholderia cepacia H111 controls biofilm formation and swarming motility, Microbiology, vol.147, pp.2517-2528, 2001.

M. Johnson, I. Zaretskaya, Y. Raytselis, Y. Merezhuk, S. Mcginnis et al., NCBI BLAST: a better web interface, Nucleic Acids Res, vol.36, 2008.

M. Juhas, L. Eberl, and B. Tmmler, Quorum sensing: the power of cooperation in the world of Pseudomonas, Environ. Microbiol, vol.7, pp.459-471, 2005.

M. Juhas, J. R. Van-der-meer, M. Gaillard, R. M. Harding, D. W. Hood et al., Genomic islands: tools of bacterial horizontal gene transfer and evolution, Fems Microbiol. Rev, vol.33, pp.376-393, 2009.

Y. Kang, R. Carlson, W. Tharpe, and M. A. Schell, Characterization of genes involved in biosynthesis of a novel antibiotic from Burkholderia cepacia BC11 and their role in biological control of Rhizoctonia solani, Appl. Environ. Microbiol, vol.64, pp.3939-3947, 1998.

O. Kilani-feki, G. Culioli, and M. Ortalo, Environmental Burkholderia cepacia strain Cs5 acting by two analogous alkyl-quinolones and a didecylphthalate against a broad spectrum of phytopathogens fungi, Curr. Microbiol, vol.62, pp.1490-1495, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01361875

O. Kilani-feki, I. Zouari, G. Culioli, A. Ortalo-magne, N. Zouari et al., Correlation between synthesis variation of 2-alkylquinolones and the antifungal activity of a Burkholderia cepacia strain collection, World J. Microbiol. Biotechnol, vol.28, pp.275-281, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01362665

K. Kim, S. Kim, F. Lépine, Y. Cho, and G. R. Lee, Global gene expression analysis on the target genes of PQS and HHQ in J774A.1 monocyte/macrophage cells, Microb. Pathog, vol.49, pp.174-180, 2010.

K. Kim, Y. U. Kim, B. H. Koh, S. S. Hwang, S. H. Kim et al., HHQ and PQS, two Pseudomonas aeruginosa quorumsensing molecules, down-regulate the innate immune responses through the nuclear factor-kappaB pathway, Immunology, vol.129, pp.578-588, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-00819562

J. G. Lawrence and H. Ochman, Reconciling the many faces of lateral gene transfer, Trends Microbiol, vol.10, 2002.

F. Lépine, S. Milot, E. Déziel, J. He, R. et al., Electrospray/mass spectrometric identification and analysis of 4-hydroxy-2-alkylquinolines (HAQs) produced by Pseudomonas aeruginosa, J. Am. Soc. Mass Spectr, vol.15, pp.862-869, 2004.

S. Lewenza, B. Conway, E. P. Greenberg, and P. A. Sokol, Quorum sensing in Burkholderia cepacia: identification of the LuxRI homologs CepRI, J. Bacteriol, vol.181, pp.748-756, 1999.

S. Lewenza and P. A. Sokol, Regulation of ornibactin biosynthesis and N-acyl-L-homoserine lactone production by CepR in Burkholderia cepacia, J. Bacteriol, vol.183, pp.2212-2218, 2001.

D. Li, N. Oku, A. Hasada, M. Shimizu, and Y. Igarashi, Two new 2-alkylquinolones, inhibitory to the fish skin ulcer pathogen Tenacibaculum maritimum, 2018.

, Beilstein J. Org. Chem, vol.14, pp.1446-1451

J. Lipuma, Burkholderia cepacia: management issues and new insights, Clin. Chest Med, vol.19, pp.473-486, 1998.

E. J. Loveridge, C. Jones, M. Bull, S. Moody, M. Kahl et al., Reclassification of the specialized metabolite producer Pseudomonas mesoacidophila ATCC 31433 as a member of the Burkholderia cepacia complex, J. Bacteriol, vol.199, pp.125-00117, 2017.

E. Mahenthiralingam, L. Song, A. Sass, J. White, C. Wilmot et al., Enacyloxins are products of an unusual hybrid modular polyketide synthase encoded by a cryptic Burkholderia ambifaria Genomic Island, Chem. Biol, vol.18, pp.665-677, 2011.

D. Mao, L. B. Bushin, K. Moon, Y. Wu, and M. R. Seyedsayamdost, Discovery of scmR as a global regulator of secondary metabolism and virulence in Burkholderia thailandensis E264, Proc. Natl. Acad. Sci. U.S.A, vol.114, 2017.

D. Mckenney, K. Brown, A. , and D. , Influence of Pseudomonas aeruginosa exoproducts on virulence factor production in Burkholderia cepacia: evidence of interspecies communication, J. Bacteriol, vol.177, pp.6989-6992, 1995.

T. Mori, T. Yamashita, K. Furihata, K. Nagai, K. Suzuki et al., Burkholone, a new cytotoxic antibiotic against IGF-I dependent cells from Burkholderia sp, J. Antibiot, vol.60, pp.713-716, 2007.

B. K. Okada, Y. Wu, D. Mao, L. B. Bushin, and M. R. Seyedsayamdost, Mapping the trimethoprim-induced secondary metabolome of Burkholderia thailandensis, ACS Chem. Biol, vol.11, 2016.

E. C. Pesci, J. B. Milbank, J. P. Pearson, S. Mcknight, A. S. Kende et al., Quinolone signaling in the cell-to-cell communication system of Pseudomonas aeruginosa, Proc. Natl. Acad. Sci. U.S.A, vol.96, pp.11229-11234, 1999.

E. F. Pettersen, T. D. Goddard, C. C. Huang, G. S. Couch, D. M. Greenblatt et al., UCSF Chimera-a visualization system for exploratory research and analysis, J. Comput. Chem, vol.25, pp.1605-1612, 2004.

E. P. Price, L. T. Viberg, T. J. Kidd, S. C. Bell, B. J. Currie et al., Transcriptomic analysis of longitudinal Burkholderia pseudomallei infecting the cystic fibrosis lung, Microb. Genomics, vol.43, pp.465-414, 2018.

G. Rampioni, M. Falcone, S. Heeb, E. Frangipani, M. P. Fletcher et al., Unravelling the genome-wide contributions of specific 2-alkyl-4-quinolones and PqsE to quorum sensing in Pseudomonas aeruginosa, PLoS Pathog, vol.12, p.1006029, 2016.

G. Rampioni, C. Pustelny, M. P. Fletcher, V. J. Wright, M. Bruce et al., Transcriptomic analysis reveals a global alkyl-quinolone-independent regulatory role for PqsE in facilitating the environmental adaptation of Pseudomonas aeruginosa to plant and animal hosts, Environ. Microbiol, vol.12, pp.1659-1673, 2010.

M. Ravenhall, N. ?kunca, F. Lassalle, and C. Dessimoz, Inferring horizontal gene transfer, PLoS Comput. Biol, vol.11, p.1004095, 2015.

J. A. Richau, J. H. Leitão, M. Correia, L. Lito, M. J. Salgado et al., Molecular typing and exopolysaccharide biosynthesis of Burkholderia cepacia: isolates from a portuguese cystic fibrosis center, J. Clin. Microbiol, vol.38, pp.1651-1655, 2000.

A. Sawana, M. Adeolu, and R. S. Gupta, Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species, Front. Genet, vol.5, p.429, 2014.

P. Siguier, J. Perochon, L. Lestrade, J. Mahillon, C. et al., ISfinder: the reference centre for bacterial insertion sequences, Nucleic Acids Res, vol.34, pp.32-36, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00021179

M. E. Skindersoe, L. H. Zeuthen, S. Brix, L. N. Fink, J. Lazenby et al., Pseudomonas aeruginosa quorum-sensingsignal molecules interfere with dendritic cell-induced T-cell proliferation, FEMS Immunol. Med. Microbiol, vol.55, pp.335-345, 2009.

D. P. Speert, M. Bond, R. C. Woodman, and J. T. Curnutte, Infection with Pseudomonas cepacia in chronic granulomatous disease: role of nonoxidative killing by neutrophils in host defense, J. Infect. Dis, vol.170, pp.1524-1531, 1994.

P. S. Stewart and J. W. Costerton, Antibiotic resistance of bacteria in biofilms, Lancet, vol.358, pp.135-138, 2001.

Z. R. Surez-moreno, J. Caballero-mellado, B. G. Coutinho, L. Mendona-previato, E. K. James et al., Common features of environmental and potentially beneficial plant-associated Burkholderia, Microb. Ecol, vol.63, pp.249-266, 2012.

L. Vial, A. Chapalain, M. Groleau, and E. Déziel, The various lifestyles of the Burkholderia cepacia complex species: a tribute to adaptation, Environ. Microbiol, vol.13, pp.1-12, 2011.
URL : https://hal.archives-ouvertes.fr/pasteur-00722215

L. Vial, M. Groleau, V. Dekimpe, and E. Déziel, Burkholderia diversity and versatility: an inventory of the extracellular products, J. Microbiol. Biotechnol, vol.17, pp.1407-1429, 2007.

L. Vial, M. Groleau, M. G. Lamarche, G. Filion, J. Castonguay-vanier et al., Phase variation has a role in Burkholderia ambifaria niche adaptation, ISME J, vol.4, pp.49-60, 2009.
URL : https://hal.archives-ouvertes.fr/pasteur-00819527

L. Vial, F. Lépine, S. Milot, M. Groleau, V. Dekimpe et al., Burkholderia pseudomallei, B. thailandensis, and B. ambifaria produce 4-hydroxy-2-alkylquinoline analogues with a methyl group at the 3 position that is required for quorum-sensing regulation, J. Bacteriol, vol.190, pp.5339-5352, 2008.

D. S. Wade, M. W. Calfee, E. R. Rocha, E. A. Ling, E. Engstrom et al., Regulation of Pseudomonas quinolone signal synthesis in Pseudomonas aeruginosa, J. Bacteriol, vol.187, pp.4372-4380, 2005.

G. L. Winsor, B. Khaira, T. Van-rossum, R. Lo, M. D. Whiteside et al., The Burkholderia Genome Database: facilitating flexible queries and comparative analyses, Bioinformatics, vol.24, pp.2803-2804, 2008.

Y. Wu and M. R. Seyedsayamdost, Synergy and target promiscuity drive structural divergence in bacterial alkylquinolone biosynthesis, Cell Chem. Biol, vol.24, pp.1437-1444, 2017.

G. Xiao, E. Déziel, J. He, F. Lepine, B. Lesic et al., MvfR, a key Pseudomonas aeruginosa pathogenicity LTTRclass regulatory protein, has dual ligands, Mol. Microbiol, vol.62, pp.1689-1699, 2006.
URL : https://hal.archives-ouvertes.fr/pasteur-00820001

E. Yabuuchi, Y. Kosako, H. Oyaizu, I. Yano, H. Hotta et al., Proposal of Burkholderia gen. nov. and transfer of seven species of the genus Pseudomonas homology group II to the new genus, with the type species Burkholderia cepacia (Palleroni and Holmes 1981) comb. nov, Microbiol. Immunol, vol.36, pp.1251-1275, 1992.

Y. Zhang, M. W. Frank, K. Zhu, A. Mayasundari, and C. O. Rock, PqsD is responsible for the synthesis of 2,4-dihydroxyquinoline, an extracellular metabolite produced by Pseudomonas aeruginosa, J. Biol. Chem, vol.283, pp.28788-28794, 2008.