K. Ochiai, T. Yamanaka, K. Kimura, and O. Sawada, Inheritance of drug resistance (and its 397 transfer) between Shigella strains and between Shigella and E. coli strains, Hihon Iji, p.398

. Shimpor, , p.34, 1861.

L. Boto, Horizontal gene transfer in evolution: facts and challenges, Proc Biol Sci, vol.400, pp.819-846, 1683.

J. E. Mcdade, C. C. Shepard, D. W. Fraser, T. R. Tsai, M. A. Redus et al., Legionnaires' 402 disease: isolation of a bacterium and demonstration of its role in other respiratory 403 disease, N Engl J Med, vol.297, issue.22, pp.1197-203, 1977.

H. J. Newton, D. K. Ang, I. R. Van-driel, and E. L. Hartland, Molecular pathogenesis of infections 405 caused by Legionella pneumophila, Clin Microbiol Rev, vol.23, issue.2, pp.274-98, 2010.

T. J. Rowbotham, Preliminary report on the pathogenicity of Legionella pneumophila for 407 freshwater and soil amoebae, J Clin Pathol, vol.33, issue.12, pp.1179-83, 1980.

M. A. Horwitz and S. C. Silverstein, Legionnaires' disease bacterium (Legionella pneumophila) 409 multiples intracellularly in human monocytes, J Clin Invest, vol.66, issue.3, pp.441-50, 1980.

T. W. Nash, D. M. Libby, and M. A. Horwitz, Interaction between the legionnaires' disease 411 bacterium (Legionella pneumophila) and human alveolar macrophages. Influence of 412 antibody, lymphokines, and hydrocortisone, J Clin Invest, vol.74, issue.3, pp.771-82, 1984.

K. H. Berger and R. R. Isberg, Two distinct defects in intracellular growth complemented by a 414 single genetic locus in Legionella pneumophila, Mol Microbiol, vol.7, issue.1, pp.7-19, 1993.

A. Marra, S. J. Blander, M. A. Horwitz, and H. A. Shuman, Identification of a Legionella 416 pneumophila locus required for intracellular multiplication in human macrophages, Proc, vol.417

U. Natl-acad-sci, , vol.89, pp.9607-9618, 1992.

P. Escoll, M. Rolando, L. Gomez-valero, and C. Buchrieser, From Amoeba to Macrophages: 419 Exploring the Molecular Mechanisms of Legionella pneumophila Infection in Both Hosts

, Curr Top Microbiol Immunol, vol.376, pp.1-34, 2013.

A. Hubber and C. R. Roy, Modulation of host cell function by Legionella pneumophila type IV 422 effectors, Annu Rev Cell Dev Biol, vol.26, pp.261-83, 2010.

R. R. Isberg, T. J. O'connor, and M. Heidtman, The Legionella pneumophila replication vacuole: 424 making a cosy niche inside host cells, Nat Rev Microbiol, vol.7, issue.1, pp.13-24, 2009.

C. Cazalet, C. Rusniok, H. Bruggemann, N. Zidane, A. Magnier et al., , p.426

, Legionella pneumophila genome for exploitation of host cell functions and high genome 427 plasticity, Nat Genet, vol.36, issue.11, pp.1165-73, 2004.

H. Nagai, J. C. Kagan, X. Zhu, R. A. Kahn, and C. R. Roy, A bacterial guanine nucleotide exchange 429 factor activates ARF on Legionella phagosomes, Science, vol.295, issue.5555, pp.679-82, 2002.

M. Rolando and C. Buchrieser, Post-translational modifications of host proteins by Legionella 431 pneumophila: a sophisticated survival strategy, Future Microbiol, vol.7, issue.3, pp.369-81, 2012.

T. Kubori, A. Hyakutake, and H. Nagai, Legionella translocates an E3 ubiquitin ligase that has 433 multiple U-boxes with distinct functions, Mol Microbiol, vol.67, issue.6, pp.1307-1326, 2008.

C. T. Price, S. Al-khodor, T. Al-quadan, M. Santic, F. Habyarimana et al., Molecular 435 Mimicry by an F-Box Effector of Legionella pneumophila Hijacks a Conserved 436

, Polyubiquitination Machinery within Macrophages and Protozoa, PLoS Pathog, vol.437, issue.12, p.1000704, 2009.

S. S. Ivanov, G. Charron, H. C. Hang, and C. R. Roy, Lipidation by the host prenyltransferase 439 machinery facilitates membrane localization of Legionella pneumophila effector proteins

, J Biol Chem, vol.285, issue.45, pp.34686-98, 2010.

C. T. Price, T. Al-quadan, M. Santic, S. C. Jones, A. Kwaik et al., Exploitation of conserved 442 eukaryotic host cell farnesylation machinery by an F-box effector of Legionella 443 pneumophila, J Exp Med, vol.207, issue.8, pp.1713-1739, 2010.

S. Debroy, J. Dao, M. Soderberg, O. Rossier, and N. P. Cianciotto, Legionella pneumophila type 445 II secretome reveals unique exoproteins and a chitinase that promotes bacterial 446 persistence in the lung, Proc Natl Acad Sci, vol.103, issue.50, pp.19146-51, 2006.

Z. Lifshitz, D. Burstein, M. Peeri, T. Zusman, K. Schwartz et al., 448 Computational modeling and experimental validation of the Legionella and Coxiella 449 virulence-related type-IVB secretion signal, Proc Natl Acad Sci, vol.110, issue.8, pp.707-722, 2013.

W. Zhu, S. Banga, Y. Tan, C. Zheng, R. Stephenson et al., Comprehensive 452 Identification of Protein Substrates of the Dot/Icm Type IV Transporter of Legionella 453 pneumophila, PLoS One, vol.6, issue.3, p.17638, 2011.

E. Crabill, W. B. Schofield, H. J. Newton, A. L. Goodman, and C. R. Roy, , p.455

, Proteins Important for Biogenesis of the Coxiella burnetii-Containing Vacuole Identified 456 by Screening of an Effector Mutant Sublibrary, Infect Immun, vol.86, issue.4, 2018.

T. J. O'connor, Y. Adepoju, D. Boyd, and R. R. Isberg, Minimization of the Legionella 458 pneumophila genome reveals chromosomal regions involved in host range expansion

, Proc Natl Acad Sci U S A, vol.108, issue.36, pp.14733-14773, 2011.

R. Bacigalupe, D. Lindsay, G. Edwards, and J. R. Fitzgerald, Population Genomics of Legionella 461 longbeachae and Hidden Complexities of Infection Source Attribution, Emerg Infect Dis, vol.462, issue.5, pp.750-757, 2017.

C. Cazalet, L. Gomez-valero, C. Rusniok, M. Lomma, D. Dervins-ravault et al.,

, Analysis of the Legionella longbeachae genome and transcriptome uncovers unique 465 strategies to cause Legionnaires' disease, PLoS Genet, vol.6, issue.2, p.1000851, 2010.

D. Burstein, F. Amaro, T. Zusman, Z. Lifshitz, O. Cohen et al., Genomic analysis 467 of 38 Legionella species identifies large and diverse effector repertoires, Nat Genet, vol.468, issue.2, pp.167-75, 2016.

L. Gomez-valero, C. Rusniok, D. Carson, S. Mondino, A. E. Perez-cobas et al.,

, More than 18,000 effectors in the Legionella genus genome provide multiple, 471 independent combinations for replication in human cells, Proc Natl Acad Sci, 2019.

P. Riedmaier, F. M. Sansom, T. Sofian, T. Beddoe, R. Schuelein et al., Multiple 474 ecto-nucleoside triphosphate diphosphohydrolases facilitate intracellular replication of 475 Legionella pneumophila, Biochem J, vol.462, issue.2, pp.279-89, 2014.

E. L. Summers, M. H. Cumming, T. Oulavallickal, N. J. Roberts, and V. L. Arcus, Structures and 477 kinetics for plant nucleoside triphosphate diphosphohydrolases support a domain motion 478 catalytic mechanism, Protein Sci, vol.26, issue.8, pp.1627-1665, 2017.

M. Rolando, S. Sanulli, C. Rusniok, L. Gomez-valero, C. Bertholet et al., Legionella 480 pneumophila effector RomA uniquely modifies host chromatin to repress gene 481 expression and promote intracellular bacterial replication, Cell Host Microbe, vol.482, issue.4, pp.395-405, 2013.

K. S. De-felipe, S. Pampou, O. S. Jovanovic, C. D. Pericone, S. F. Ye et al.,

, Evidence for acquisition of Legionella type IV secretion substrates via interdomain 485 horizontal gene transfer, J Bacteriol, vol.187, issue.22, pp.7716-7742, 2005.

G. Valero, L. Runsiok, C. Cazalet, C. , and C. , , p.487

, Legionella identified eukaryotic like proteins as key players in host-pathogen 488 interactions, Front Microbiol, vol.2, 2011.

M. N. Lurie-weinberger, L. Gomez-valero, N. Merault, and G. Glockner, , p.490

, The origins of eukaryotic-like proteins in Legionella pneumophila, Int J Med Microbiol, vol.491, issue.7, pp.470-81, 2010.

A. W. Ensminger, Legionella pneumophila, armed to the hilt: justifying the largest arsenal 493 of effectors in the bacterial world, Curr Opin Microbiol, vol.29, pp.74-80, 2016.

P. Escoll, S. Mondino, M. Rolando, and C. Buchrieser, Targeting of host organelles by 495 pathogenic bacteria: a sophisticated subversion strategy, Nat Rev Microbiol, vol.496, issue.1, pp.5-19, 2016.

L. Gomez-valero, C. Rusniok, C. Cazalet, and C. Buchrieser, Comparative and functional 498 genomics of Legionella identified eukaryotic like proteins as key players in host-499 pathogen interactions, Front Microbiol, vol.2, p.208, 2011.

J. Qiu and Z. Q. Luo, Legionella and Coxiella effectors: strength in diversity and activity, Nat 501 Rev Microbiol, vol.15, issue.10, pp.591-605, 2017.

M. Rolando and C. Buchrieser, Legionella pneumophila type IV effectors hijack the 503 transcription and translation machinery of the host cell, Trends Cell Biol, vol.504, issue.12, pp.771-779, 2014.

K. Barlocher, A. Welin, and H. Hilbi, Formation of the Legionella Replicative Compartment at 506 the Crossroads of Retrograde Trafficking. Frontiers in cellular and infection microbiology, vol.507, p.482, 2017.

A. H. Merrill and K. Sandhoff, Sphingolipids: metabolism and cell signalling, p.509

J. E. Vance, Biochemistry of Lipids, Lipoproteins and Membranes, vol.36

, Science, pp.373-407

J. L. Heung, C. Luberto, and D. Poeta, Role of Sphingolipids in Microbial Pathogenesis

, Infect Immun, vol.74, issue.1, pp.28-39, 2006.

V. Shabardina, T. Kischka, H. Kmita, Y. Suzuki, and W. Makalowski, Environmental adaptation 514 of Acanthamoeba castellanii and Entamoeba histolytica at genome level as seen by 515 comparative genomic analysis, Int J Biol Sci, vol.14, issue.3, pp.306-326, 2018.

M. Rolando, P. Escoll, and C. Buchrieser, Legionella pneumophila restrains autophagy by 517 modulating the host's sphingolipid metabolism, Autophagy, vol.12, issue.6, pp.1053-1057, 2016.

M. Rolando, P. Escoll, T. Nora, J. Botti, V. Boitez et al., Legionella pneumophila, p.519

, S1P-lyase targets host sphingolipid metabolism and restrains autophagy, Proc Natl Acad, vol.520

U. Sci, , vol.113, pp.1901-1907, 2016.

E. Degtyar, T. Zusman, M. Ehrlich, and G. Segal, A Legionella effector acquired from protozoa 522 is involved in sphingolipids metabolism and is targeted to the host cell mitochondria, Cell, vol.523

. Microbiol, , vol.11, pp.1219-1254, 2009.

L. Gomez-valero and C. Buchrieser, Genome dynamics in Legionella: the basis of versatility 525 and adaptation to intracellular replication. Cold Spring Harbor perspectives in medicine, vol.526, 2013.

A. Choy, J. Dancourt, B. Mugo, T. J. O'connor, R. R. Isberg et al., The Legionella, vol.528

, effector RavZ inhibits host autophagy through irreversible Atg8 deconjugation, Science, vol.529, issue.6110, pp.1072-1078, 2012.

S. Schmitz-esser, P. Tischler, R. Arnold, J. Montanaro, M. Wagner et al., The 531 genome of the amoeba symbiont "Candidatus Amoebophilus asiaticus" reveals common 532 mechanisms for host cell interaction among amoeba-associated bacteria, J Bacteriol, vol.533, issue.4, pp.1045-57, 2010.

A. Casadevall, M. S. Fu, A. J. Guimaraes, and P. Albuquerque, The 'Amoeboid Predator-Fungal 535

, Animal Virulence' Hypothesis. J Fungi (Basel), vol.5, issue.1, 2019.

D. Raoult, S. Audic, C. Robert, C. Abergel, P. Renesto et al., The 1.2-megabase 537 genome sequence of Mimivirus, Science, vol.306, issue.5700, pp.1344-50, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00651656

D. Moreira and C. Brochier-armanet, Giant viruses, giant chimeras: the multiple evolutionary 539 histories of Mimivirus genes, BMC Evol Biol, vol.8, p.12, 2008.

H. Ogata, L. Scola, B. Audic, S. Renesto, P. Blanc et al., Genome sequence 541 of Rickettsia bellii illuminates the role of amoebae in gene exchanges between 542 intracellular pathogens, PLoS Genet, vol.2, issue.5, p.76, 2006.

L. Gomez-valero, N. Bonora, M. Gribaldo, S. Buchrieser, and C. ,

, Gene Transfer Shaped the Genomes of Legionella pneumophila and Legionella 545 longbeachae, pp.199-219, 2013.

E. Nyvltova, R. Sut'ak, V. Zarsky, K. Harant, I. Hrdy et al., Lateral gene transfer of p-548 cresol-and indole-producing enzymes from environmental bacteria to Mastigamoeba 549 balamuthi, Environ Microbiol, vol.19, issue.3, pp.1091-102, 2017.

T. Kaneko, P. J. Stogios, X. Ruan, C. Voss, E. Evdokimova et al., Identification 551 and characterization of a large family of superbinding bacterial SH2 domains, Nature 552 communications, vol.9, issue.1, p.4549, 2018.

K. S. De-felipe, R. T. Glover, X. Charpentier, O. R. Anderson, M. Reyes et al.,

, Legionella eukaryotic-like type IV substrates interfere with organelle trafficking, PLoS 555 Pathog, vol.4, issue.8, p.1000117, 2008.

G. Gimenez, C. Bertelli, C. Moliner, C. Robert, D. Raoult et al., Insight into 557 cross-talk between intra-amoebal pathogens, BMC Genomics, vol.12, p.542, 2011.

L. Gomez-valero, C. Rusniok, S. Jarraud, B. Vacherie, Z. Rouy et al., Extensive 559 recombination events and horizontal gene transfer shaped the Legionella pneumophila 560 genomes, BMC Genomics, vol.12, p.536, 2011.

Z. Wang and M. Wu, Comparative Genomic Analysis of Acanthamoeba Endosymbionts, vol.562

, Highlights the Role of Amoebae as a "Melting Pot" Shaping the Rickettsiales Evolution

, Genome Biol Evol, vol.9, issue.11, pp.3214-3238, 2017.

C. Bertelli and G. Greub, Lateral gene exchanges shape the genomes of amoeba-resisting 565 microorganisms. Frontiers in cellular and infection microbiology, vol.2, p.110, 2012.

C. Buchrieser and X. Charpentier, Induction of competence for natural transformation in 567

, Legionella pneumophila and exploitation for mutant construction, Methods Mol Biol, vol.568, pp.183-95, 2013.