C. Pál and B. Papp, Evolution of complex adaptations in molecular systems, Nature 513 Ecol Evol, vol.1, p.1084, 2017.

H. Ochman, Lateral gene transfer and the nature of bacterial innovation. 515, Nature, vol.405, pp.299-304, 2000.

R. E. Lenski, Experimental evolution and the dynamics of adaptation and genome 517 evolution in microbial populations, ISME J, vol.11, pp.2181-2194, 2017.

L. Bobay and H. Ochman, Factors driving effective population size and pan-519 genome evolution in bacteria, BMC evolutionary biology, vol.18, p.153, 2018.

F. Jacob, Evolution and tinkering, Science, vol.196, pp.1161-1166, 1977.

J. L. Martínez, Antibiotics and antibiotic resistance genes in natural environments, 522 Science, vol.321, pp.365-367, 2008.

J. Wiedenbeck and F. M. Cohan, Origins of bacterial diversity through horizontal 524 genetic transfer and adaptation to new ecological niches, FEMS Microbiol Rev, vol.35, pp.957-976, 2011.

M. Touchon, The chromosomal accommodation and domestication of mobile 526 genetic elements, Curr Opin Microbiol, vol.22, pp.22-29, 2014.

S. J. Gould and E. S. Vrba, Exaptation-A Missing Term in the Science of Form, 528 Paleobiology, vol.8, pp.4-15, 1982.

T. Nogueira, Horizontal Gene Transfer of the Secretome Drives the Evolution 530 of Bacterial Cooperation and Virulence, Curr Biol, vol.19, pp.1683-91, 2009.

E. T. Granato, The evolution and ecology of bacterial warfare, Curr Biol, vol.29, pp.532-521, 2019.

M. Desvaux, Secretion and subcellular localizations of bacterial proteins: a 534 semantic awareness issue, Trends Microbiol, vol.17, pp.139-184, 2009.

R. E. Dalbey and A. Kuhn, Protein traffic in Gram-negative bacteria--how exported 536 and secreted proteins find their way, FEMS Microbiol Rev, vol.36, pp.1023-1068, 2012.

T. R. Costa, Secretion systems in Gram-negative bacteria: structural and 538 mechanistic insights, Nature Rev Microbiol, vol.13, pp.343-359, 2015.

P. J. Planet, Phylogeny of genes for secretion NTPases: identification of the 540 widespread tadA subfamily and development of a diagnostic key for gene classification, Natl Acad Sci U S A, vol.541, pp.2503-2511, 2001.

L. M. Iyer, Comparative genomics of the FtsK-HerA superfamily of pumping 543 ATPases: implications for the origins of chromosome segregation, cell division and viral 544 capsid packaging, Nucleic Acids Res, vol.32, pp.5260-79, 1991.

, Gene, vol.101, pp.33-44

R. Denise, Diversification of the type IV filament superfamily into machines 549 for adhesion, protein secretion, DNA uptake, and motility, PLoS Biol, vol.17, 2019.

S. S. Abby and E. P. Rocha, The non-flagellar type III secretion system evolved from 551 the bacterial flagellum and diversified into host-cell adapted systems, PLoS Genet, vol.8, p.1002983, 2012.

C. C. Ginocchio, Contact with epithelial cells induces the formation of surface 554 appendages on Salmonella typhimurium, Cell, vol.76, pp.717-741, 1994.

A. A. Weiss, Molecular characterization of an operon required for pertussis 556 toxin secretion, Proc Natl Acad Sci U S A, vol.90, pp.2970-2974, 1993.

E. Scanlan, A quantitative proteomic screen of the Campylobacter jejuni 605 flagellar-dependent secretome, J Proteomics, vol.152, pp.181-187, 2017.

K. Maezawa, Hundreds of flagellar basal bodies cover the cell surface of the 607 endosymbiotic bacterium Buchnera aphidicola sp. strain APS, J Bacteriol, vol.188, pp.6539-6582, 2006.

J. Ferreira, e al -proteobacteria eject their polar flagella under nutrient 609 depletion, retaining flagellar motor relic structures, PLoS Biol, vol.17, p.3000165

M. J. Pallen and N. J. Matzke, From The Origin of Species to the origin of bacterial 611 flagella, Nature Rev Microbiol, vol.4, pp.784-790, 2006.

J. E. Galán and G. Waksman, Protein-injection machines in bacteria, Cell, vol.172, pp.613-1306, 2018.

D. S. Guttman, Diversifying selection drives the evolution of the type III 615 secretion system pilus of Pseudomonas syringae, Mol Biol Evol, vol.23, pp.2342-2354, 2006.

P. Troisfontaines and G. R. Cornelis, Type III secretion: more systems than you 617 think, Physiology, vol.20, pp.326-365, 2005.

L. Nguyen, Phylogenetic analyses of the constituents of Type III protein 619 secretion systems, J Mol Microbiol Biotechnol, vol.2, pp.125-169, 2000.

U. Gophna, Bacterial type III secretion systems are ancient and evolved by 621 multiple horizontal-transfer events, Gene, vol.312, pp.151-163, 2003.

G. W. Sun and Y. H. Gan, Unraveling type III secretion systems in the highly 623 versatile Burkholderia pseudomallei, Trends Microbiol, vol.18, pp.561-569, 2010.

J. Berry, V. Pelicic, and M. Tomich, Exceptionally widespread nanomachines composed of 625 type IV pilins: the prokaryotic Swiss Army knives, Nature Reviews. Microbiology, vol.39, pp.363-375, 2007.

N. P. Cianciotto and R. C. White, Expanding role of type II secretion in bacterial 629 pathogenesis and beyond, Infection and immunity, vol.85, pp.14-17, 2017.

K. S. Makarova, Diversity and evolution of type IV pili systems in archaea, Frontiers Microbiol, vol.631, p.667, 2016.

N. Roux, Neglected but amazingly diverse type IVb pili, Res Microbiol, vol.163, pp.633-659, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01458245

A. Lopez-castilla, Structure of the calcium-dependent type 2 secretion 635 pseudopilus, Nature Microbiol, vol.2, p.1686, 2017.

R. Zöllner, Motor Properties of PilT-Independent Type 4 Pilus Retraction in 637 Gonococci, J Bacteriol, vol.201, pp.778-796, 2019.

D. W. Adams, The type IV pilus protein PilU functions as a PilT-dependent 639 retraction ATPase, PLoS Genet, vol.15, 2019.

J. L. Chlebek, PilT and PilU are homohexameric ATPases that coordinate to 641 retract type IVa pili, PLoS Genet, vol.15, 2019.

S. S. Abby, Identification of protein secretion systems in bacterial genomes, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01374967

, Sci Rep, vol.6, 23080.

S. Debroy, Legionella pneumophila type II secretome reveals unique 645 exoproteins and a chitinase that promotes bacterial persistence in the lung, Proc Natl Acad, p.646, 2006.

U. Sci, , pp.19146-51

K. V. Korotkov and M. Sandkvist, Architecture, function, and substrates of the 648 type II secretion system, EcoSal Plus, vol.8, 2019.

J. G. Lawrence and J. R. Roth, Selfish operons: horizontal transfer may drive the 650 evolution of gene clusters, Genetics, vol.143, pp.1843-1860, 1996.

J. D. Mougous, A virulence locus of Pseudomonas aeruginosa encodes a 652 protein secretion apparatus, Science, vol.312, pp.1526-1556, 2006.

R. D. Hood, A type VI secretion system of Pseudomonas aeruginosa targets a 654 toxin to bacteria, Cell host & microbe, vol.7, pp.25-37, 2010.

S. Borgeaud, The type VI secretion system of Vibrio cholerae fosters 656 horizontal gene transfer, Science, vol.347, pp.63-67, 2015.

P. G. Leiman, Type VI secretion apparatus and phage tail-associated protein 658 complexes share a common evolutionary origin, Proc Natl Acad Sci U S A, vol.106, pp.4154-4163, 2009.

L. G. Pell, The phage lambda major tail protein structure reveals a common 660 evolution for long-tailed phages and the type VI bacterial secretion system, Proc Natl Acad, p.661, 2009.

U. Sci, , vol.106, pp.4160-4165

N. S. Lossi, The HsiB1C1 (TssB-TssC) complex of the Pseudomonas aeruginosa 663 type VI secretion system forms a bacteriophage tail sheathlike structure, J Biol Chem, vol.288, pp.7536-7548, 2013.

M. Basler, Type VI secretion requires a dynamic contractile phage tail-like 666 structure, EMBO reports, vol.483, pp.735-741, 2008.

S. Schwarz, Burkholderia type VI secretion systems have distinct roles in 669 eukaryotic and bacterial cell interactions, PLoS Pathogens, vol.6, 2010.

J. S. Ludu, The Francisella pathogenicity island protein PdpD is required for 671 full virulence and associates with homologues of the type VI secretion system, J Bacteriol, vol.672, pp.4584-95, 2008.

A. B. Russell, Type VI secretion system effectors: poisons with a purpose, Nat 674 Rev Microbiol, vol.12, pp.137-185, 2014.

A. B. Russell, A type VI secretion-related pathway in Bacteroidetes mediates 676 interbacterial antagonism, Cell Host Microbe, vol.16, pp.227-263, 2014.

D. Böck, In situ architecture, function, and evolution of a contractile 678 injection system, Science, vol.357, pp.713-717, 2017.

M. Touchon, Genetic and life-history traits associated with the distribution 680 of prophages in bacteria, ISME J, vol.10, 2016.

T. Komano, The transfer region of IncI1 plasmid R64: similarities between 682 R64 tra and legionella icm/dot genes, Mol Microbiol, vol.35, pp.1348-59, 2000.

J. A. Jurcisek, Nontypeable Haemophilus influenzae releases DNA and DNABII 684 proteins via a T4SS-like complex and ComE of the type IV pilus machinery, Proc Natl Acad Sci, vol.685, pp.6632-6641, 2017.

O. Spitz, Type I Secretion Systems-One Mechanism for All? Microbiology 687 spectrum 7, 2019.

S. Bhattacharya, Pathogenic E. coli extracts nutrients from infected host cells 691 utilizing injectisome components, Cell reports, vol.689, pp.683-696, 2019.

M. J. Pallen, The ESAT-6/WXG100 superfamily and a new Gram-positive secretion 693 system?, Trends in microbiology, vol.10, pp.209-212, 2002.

M. I. Gröschel, ESX secretion systems: mycobacterial evolution to counter 695 host immunity, Nature Rev Microbiol, vol.14, p.677, 2016.

S. L. Rouse, A new class of hybrid secretion system is employed in 697 Pseudomonas amyloid biogenesis, Nature communications, vol.8, p.263, 2017.

C. Morlot and C. D. Rodrigues, The New Kid on the Block: a specialized secretion 699 system during bacterial sporulation, Trends in microbiology, vol.26, pp.663-676, 2018.

N. Gómez-santos, A TonB-dependent transporter is required for secretion of 701 protease PopC across the bacterial outer membrane, Nature communications, vol.10, p.77, 2018.

M. J. Mcbride, Bacteroidetes Gliding Motility and the Type IX Secretion System. 705 Microbiology spectrum, vol.7, 2019.

A. Blocker, The tripartite type III secreton of Shigella flexneri inserts IpaB and 707 IpaC into host membranes, J Cell Biol, vol.147, pp.683-693, 1999.

A. Hachani, Type VI secretion and anti-host effectors, Curr Opin Microbiol, vol.709, pp.81-93, 2016.

M. Kwak, Architecture of the type IV coupling protein complex of 711 Legionella pneumophila, Nature Microbiol, vol.2, p.17114, 2017.

A. Jamet and X. Nassif, New players in the toxin field: polymorphic toxin systems 713 in bacteria, MBio, vol.6, pp.285-300, 2015.

S. Matsuda, Export of a Vibrio parahaemolyticus toxin by the Sec and type III 715 secretion machineries in tandem, Nature Microbiol, vol.4, p.781, 2019.

D. M. Swain, A prophage tail-like protein is deployed by Burkholderia 717 bacteria to feed on fungi, Nature communications, vol.8, p.404, 2017.

T. Tobe, An extensive repertoire of type III secretion effectors in Escherichia 719 coli O157 and the role of lambdoid phages in their dissemination, Proc Natl Acad Sci U S A, vol.720, issue.103, pp.14941-14947, 2006.

C. Wandersman and P. Delepelaire, TolC, an Escherichia coli outer membrane 722 protein required for hemolysin secretion, Proc Natl Acad Sci, vol.87, pp.4776-4780, 1990.

J. W. Marsh and R. K. Taylor, Identification of the Vibrio cholerae type 4 prepilin 724 peptidase required for cholera toxin secretion and pilus formation, Mol Microbiol, vol.29, pp.1481-725, 1998.

A. Wilkin, The e ol ion of bricolage Trend in Gene ic, vol.727, pp.54-59

N. N. Nickerson, A Single Amino Acid Substitution Changes the Self-729 Assembly Status of a Type IV Piliation Secretin, J Bacteriol, vol.194, pp.4951-4958, 2012.

K. V. Korotkov, Secretins: dynamic channels for protein transport across 731 membranes, Trends Biochem Sci, vol.36, pp.433-476, 2011.

A. Crago, V. Koronaki, and . Salmonella, G form a ring like m l imer that 733 requires the InvH lipoprotein for outer membrane localization, vol.30, pp.47-56

K. Katoh and D. M. Standley, MAFFT multiple sequence alignment software 735 version 7: improvements in performance and usability, Algorithms Mol Biol, vol.30, p.7, 2008.

L. T. Nguyen, IQ-TREE: a fast and effective stochastic algorithm for 739 estimating maximum-likelihood phylogenies, Mol Biol Evol, vol.32, pp.268-74, 2015.

D. T. Hoang, UFBoot2: improving the ultrafast bootstrap approximation, 2017.

, Mol Biol Evol, vol.35, pp.518-522

K. V. Korotkov, The type II secretion system: biogenesis, molecular 743 architecture and mechanism, Nature Reviews. Microbiology, vol.10, pp.336-51, 2012.