D. and T. F. Meyer, A novel determinant (comA) essential for natural, 1993.

. Le-marquage-est-réalisé-dans-un, ADN, 2 µl de Terminal Transférase (40 unités) (Biolabs), de Tampon 4 1X (Biolabs), 0.25 mM de CoCl2 et 2 µl d'ATP-alpha-P32 à 5000Ci/mmol a été incubé 1 h à 37°C. Une fois la réaction de marquage terminée, l'ADN est purifié sur colonne d'exclusion Probquant G-50 micro columns (GE Healthcare) selon le protocole du fabricant

J. L. Alloway, . The, . In, . Vitro-of-r-pneumococci, . Into et al., THE TRANSFORMATION IN VITRO OF R PNEUMOCOCCI INTO S FORMS OF DIFFERENT SPECIFIC TYPES BY THE USE OF FILTERED PNEUMOCOCCUS EXTRACTS, Journal of Experimental Medicine, vol.55, issue.1, pp.91-99, 1932.
DOI : 10.1084/jem.55.1.91

R. A. Alm, L. S. Ling, D. T. Moir, B. L. King, E. D. Brown et al., Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori, Nature, vol.179, issue.6715, pp.176-1801016495, 1038.
DOI : 10.1128/jb.179.22.7135-7155.1997

T. Ando, D. A. Israel, K. Kusugami, and M. J. Blaser, HP0333, a member of the dprA family, is involved in natural transformation in Helicobacter pylori, J. Bacteriol, vol.181, pp.5572-5580, 1999.

E. S. Antonova and B. K. Hammer, Quorum-sensing autoinducer molecules produced by members of a multispecies biofilm promote horizontal gene transfer to Vibrio cholerae, FEMS Microbiology Letters, vol.322, issue.1, pp.68-76, 2011.
DOI : 10.1111/j.1574-6968.2011.02328.x

R. A. Aras, A. J. Small, T. Ando, and M. J. Blaser, Helicobacter pylori interstrain restriction-modification diversity prevents genome subversion by chromosomal DNA from competing strains, Nucleic Acids Research, vol.30, issue.24, pp.5391-5397, 2002.
DOI : 10.1093/nar/gkf686
URL : https://academic.oup.com/nar/article-pdf/30/24/5391/3752823/gkf686.pdf

L. Aravind, K. S. Makarova, and E. V. Koonin, SURVEY AND SUMMARY: Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories, Nucleic Acids Research, vol.28, issue.18, pp.3417-3432, 2000.
DOI : 10.1093/nar/28.18.3417

A. Asahi, T. Nishimoto, Y. Okazaki, H. Suzuki, T. Masaoka et al., Helicobacter pylori eradication shifts monocyte Fcgamma receptor balance toward inhibitory FcgammaRIIB in immune thrombocytopenic purpura patients, J. Clin. Invest, vol.118, pp.2939-294910, 1172.
DOI : 10.1172/jci34496
URL : http://www.jci.org/articles/view/34496/files/pdf

D. A. Baltrus and K. Guillemin, growth cycle, FEMS Microbiology Letters, vol.255, issue.1, pp.148-155, 2006.
DOI : 10.1111/j.1574-6968.2005.00066.x

D. A. Baltrus, K. Guillemin, and P. C. Phillips, NATURAL TRANSFORMATION INCREASES THE RATE OF ADAPTATION IN THE HUMAN PATHOGEN HELICOBACTER PYLORI, Evolution, vol.54, issue.12, 2008.
DOI : 10.1073/pnas.95.21.12619

F. Barany, M. E. Kahn, and H. O. Smith, Directional transport and integration of donor DNA in Haemophilus influenzae transformation., Proceedings of the National Academy of Sciences, vol.80, issue.23, pp.7274-7278, 1983.
DOI : 10.1073/pnas.80.23.7274

M. J. Bergé, A. Kamgoué, B. Martin, P. Polard, N. Campo et al., Midcell Recruitment of the DNA Uptake and Virulence Nuclease, EndA, for Pneumococcal Transformation, PLoS Pathogens, vol.152, issue.9, 2013.
DOI : 10.1371/journal.ppat.1003596.s009

M. Bergé, I. Mortier-barrière, B. Martin, and J. Claverys, Transformation of Streptococcus pneumoniae relies on DprA- and RecA-dependent protection of incoming DNA single strands, Molecular Microbiology, vol.20, issue.2, pp.527-536, 2003.
DOI : 10.1128/jb.165.3.689-695.1986

L. J. Bessa, R. Grande, D. Iorio, D. , D. Giulio et al., free-living and biofilm modes of growth: behavior in response to different culture media, APMIS, vol.45, issue.6, pp.549-560, 2013.
DOI : 10.1097/MCG.0b013e31822be4d6

B. Björkholm, M. Sjölund, P. G. Falk, O. G. Berg, L. Engstrand et al., Mutation frequency and biological cost of antibiotic resistance in Helicobacter pylori, Proceedings of the National Academy of Sciences, vol.108, issue.3, pp.14607-14612, 2001.
DOI : 10.1093/ajcp/108.3.284

M. Blokesch and G. K. Schoolnik, The Extracellular Nuclease Dns and Its Role in Natural Transformation of Vibrio cholerae, Journal of Bacteriology, vol.190, issue.21, pp.7232-7240, 2008.
DOI : 10.1128/JB.00959-08

M. Blokesch and G. K. Schoolnik, Serogroup Conversion of Vibrio cholerae in Aquatic Reservoirs, PLoS Pathogens, vol.184, issue.6, 2007.
DOI : 10.1371/journal.ppat.0030081.st002

S. Borgeaud, L. C. Metzger, T. Scrignari, and M. Blokesch, The type VI secretion system of Vibrio cholerae fosters horizontal gene transfer, Science, vol.109, issue.1, pp.63-67, 2015.
DOI : 10.1016/0378-1119(91)90604-A

K. Briley-jr, P. Prepiak, M. J. Dias, J. Hahn, and D. Dubnau, Maf acts downstream of ComGA to arrest cell division in competent cells of B. subtilis, Molecular Microbiology, vol.174, issue.1, 2011.
DOI : 10.1128/jb.174.21.6729-6742.1992

A. D. Cameron, M. Volar, L. A. Bannister, and R. J. Redfield, RNA secondary structure regulates the translation of sxy and competence development in Haemophilus influenzae, Nucleic Acids Research, vol.36, issue.1, pp.10-20, 2008.
DOI : 10.1093/nar/gkm915

C. A. Carlson, L. S. Pierson, J. J. Rosen, and J. L. Ingraham, Pseudomonas stutzeri and related species undergo natural transformation, J Bacteriol, vol.153, pp.93-99, 1983.

A. Cehovin, P. J. Simpson, M. A. Mcdowell, D. R. Brown, R. Noschese et al., Specific DNA recognition mediated by a type IV pilin, Proceedings of the National Academy of Sciences, vol.84, issue.5, pp.3065-3070, 2013.
DOI : 10.1111/j.1365-2958.2012.08062.x
URL : http://www.pnas.org/content/110/8/3065.full.pdf

L. Cellini, : A chameleon-like approach to life, World Journal of Gastroenterology, vol.20, issue.19, pp.5575-5582, 2014.
DOI : 10.3748/wjg.v20.i19.5575
URL : http://doi.org/10.3748/wjg.v20.i19.5575

M. S. Chandler, The gene encoding cAMP receptor protein is required for competence development in Haemophilus influenzae Rd., Proceedings of the National Academy of Sciences, vol.89, issue.5, pp.1626-1630, 1992.
DOI : 10.1073/pnas.89.5.1626

K. C. Chang, Y. C. Yeh, T. L. Lin, and J. T. Wang, Identification of Genes Associated with Natural Competence in Helicobacter pylori by Transposon Shuttle Random Mutagenesis, Biochemical and Biophysical Research Communications, vol.288, issue.4, pp.961-9685877, 2001.
DOI : 10.1006/bbrc.2001.5877

X. Charpentier, E. Kay, D. Schneider, and H. A. Shuman, Antibiotics and UV Radiation Induce Competence for Natural Transformation in Legionella pneumophila, Journal of Bacteriology, vol.193, issue.5, pp.1114-1121, 2011.
DOI : 10.1128/JB.01146-10
URL : https://hal.archives-ouvertes.fr/hal-00800691

X. Charpentier, P. Polard, and J. Claverys, Induction of competence for genetic transformation by antibiotics: convergent evolution of stress responses in distant bacterial species lacking SOS?, Current Opinion in Microbiology, vol.15, issue.5, pp.570-576, 2012.
DOI : 10.1016/j.mib.2012.08.001
URL : https://hal.archives-ouvertes.fr/hal-00787606

I. Chen and D. Dubnau, DNA uptake during bacterial transformation, Nature Reviews Microbiology, vol.180, issue.3, pp.241-249, 2004.
DOI : 10.1016/S0966-842X(02)02314-4

J. Claverys, M. Prudhomme, and B. Martin, Induction of Competence Regulons as a General Response to Stress in Gram-Positive Bacteria, Annual Review of Microbiology, vol.60, issue.1, pp.451-475, 2006.
DOI : 10.1146/annurev.micro.60.080805.142139
URL : https://hal.archives-ouvertes.fr/hal-00119281

J. M. Coticchia, C. Sugawa, V. R. Tran, J. Gurrola, E. Kowalski et al., Presence and Density of Helicobacter pylori Biofilms in Human Gastric Mucosa in Patients With Peptic Ulcer Disease, Journal of Gastrointestinal Surgery, vol.10, issue.6, pp.883-889, 2006.
DOI : 10.1016/j.gassur.2005.12.009

N. J. Croucher, S. R. Harris, C. Fraser, M. A. Quail, J. Burton et al., Rapid Pneumococcal Evolution in Response to Clinical Interventions, Science, vol.7, issue.47, pp.430-434, 2011.
DOI : 10.1098/rsif.2009.0400
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3648787/pdf

C. Stewart-goodwin, Transfer of Campylobacter pylori and Campylobacter mustelae to Helicobacter gen. nov as Helicobacter pylori comb . nov. and Helicobacter mustelae comb. nov., Respectively p, pp.397-405, 1989.

P. P. Damke, R. Dhanaraju, S. Marsin, J. P. Radicella, and D. N. Rao, ???MutS2, Molecular Microbiology, vol.27, issue.6, pp.1240-1256, 2015.
DOI : 10.1093/nar/27.21.4200

D. B. Danner, R. A. Deich, K. L. Sisco, and H. O. Smith, An eleven-base-pair sequence determines the specificity of DNA uptake in Haemophilus transformation, Gene, vol.11, issue.3-4, pp.311-318, 1980.
DOI : 10.1016/0378-1119(80)90071-2

D. B. Danner, H. O. Smith, and S. A. Narang, Construction of DNA recognition sites active in Haemophilus transformation., Proceedings of the National Academy of Sciences, vol.79, issue.7, pp.2393-2397, 1982.
DOI : 10.1073/pnas.79.7.2393

M. S. Dillingham and S. C. Kowalczykowski, RecBCD Enzyme and the Repair of Double-Stranded DNA Breaks, Microbiology and Molecular Biology Reviews, vol.72, issue.4, pp.642-671, 2008.
DOI : 10.1128/MMBR.00020-08

M. P. Dore, A. R. Sepulveda, H. El-zimaity, Y. Yamaoka, M. S. Osato et al., Isolation of Helicobacter pylori from sheep-implications for transmission to humans, Am. J. Gastroenterol, vol.96, pp.1396-1401, 2001.

M. S. Dorer, J. Fero, and N. R. Salama, DNA Damage Triggers Genetic Exchange in Helicobacter pylori, PLoS Pathogens, vol.24, issue.7, 2010.
DOI : 10.1371/journal.ppat.1001026.s008
URL : https://doi.org/10.1371/journal.ppat.1001026

D. Dubnau, DNA Uptake in Bacteria, Annual Review of Microbiology, vol.53, issue.1, pp.217-244, 1999.
DOI : 10.1146/annurev.micro.53.1.217

P. M. Duffin and H. S. Seifert, DNA Uptake Sequence-Mediated Enhancement of Transformation in Neisseria gonorrhoeae Is Strain Dependent, Journal of Bacteriology, vol.192, issue.17, pp.4436-4444, 2010.
DOI : 10.1128/JB.00442-10

G. R. Dwivedi, E. Sharma, and D. N. Rao, Helicobacter pylori DprA alleviates restriction barrier for incoming DNA, Nucleic Acids Research, vol.41, issue.5, pp.3274-3288, 2013.
DOI : 10.1093/nar/gkt024
URL : https://academic.oup.com/nar/article-pdf/41/5/3274/16946967/gkt024.pdf

C. Elkins, C. E. Thomas, H. S. Seifert, and P. F. Sparling, Species-specific uptake of DNA by gonococci is mediated by a 10-base-pair sequence., Journal of Bacteriology, vol.173, issue.12, pp.3911-3913, 1991.
DOI : 10.1128/jb.173.12.3911-3913.1991

D. Falush, C. Kraft, N. S. Taylor, P. Correa, J. G. Fox et al., Recombination and mutation during long-term gastric colonization by Helicobacter pylori: Estimates of clock rates, recombination size, and minimal age, Proceedings of the National Academy of Sciences, vol.181, issue.1, pp.15056-15061, 2001.
DOI : 10.1086/315173

P. L. Foster, Stress responses and genetic variation in bacteria, Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis, vol.569, issue.1-2, 2005.
DOI : 10.1016/j.mrfmmm.2004.07.017
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2729700/pdf

A. L. Gagne, K. E. Stevens, M. Cassone, A. Pujari, O. E. Abiola et al., Competence in Streptococcus pneumoniae Is a Response to an Increasing Mutational Burden, PLoS ONE, vol.331, issue.8, 2013.
DOI : 10.1371/journal.pone.0072613.s003

H. Gangel, C. Hepp, S. Müller, E. R. Oldewurtel, F. E. Aas et al., Concerted Spatio-Temporal Dynamics of Imported DNA and ComE DNA Uptake Protein during Gonococcal Transformation, PLoS Pathogens, vol.63, issue.4, 2014.
DOI : 10.1371/journal.ppat.1004043.s015
URL : http://doi.org/10.1371/journal.ppat.1004043

M. García-ortíz, S. Marsin, M. E. Arana, D. Gasparutto, R. Guérois et al., Unexpected Role for Helicobacter pylori DNA Polymerase I As a Source of Genetic Variability, PLoS Genetics, vol.278, issue.6, 2011.
DOI : 10.1371/journal.pgen.1002152.s006

M. F. Go, V. Kapur, D. Y. Graham, and J. M. Musser, Population genetic analysis of Helicobacter pylori by multilocus enzyme electrophoresis: extensive allelic diversity and recombinational population structure., Journal of Bacteriology, vol.178, issue.13, pp.3934-3938, 1996.
DOI : 10.1128/jb.178.13.3934-3938.1996

S. H. Goodgal and M. Mitchell, Uptake of heterologous DNA by Haemophilus influenzae, J Bacteriol, vol.157, pp.785-788, 1984.

C. S. Goodwin and J. A. Armstrong, Microbiological aspects of Helicobacter pylori (Campylobacter pylori). Eur, J. Clin. Microbiol. Infect. Dis, vol.9, pp.1-13, 1990.

D. Y. Graham, A. R. Opekun, M. S. Osato, H. M. El-zimaity, C. K. Lee et al., Challenge model for Helicobacter pylori infection in human volunteers, Gut, vol.53, issue.9, pp.1235-1243, 2004.
DOI : 10.1136/gut.2003.037499
URL : http://gut.bmj.com/content/gutjnl/53/9/1235.full.pdf

R. Grande, D. Giulio, M. Bessa, L. J. , D. Campli et al., Extracellular DNA in Helicobacter pylori biofilm: a backstairs rumour, Journal of Applied Microbiology, vol.15, issue.2, pp.490-498, 2011.
DOI : 10.1186/1471-2180-9-197
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2672.2010.04911.x/pdf

S. Graupner and W. Wackernagel, Pseudomonas stutzeri Has Two Closely Related pilA Genes (Type IV Pilus Structural Protein) with Opposite Influences on Natural Genetic Transformation, Journal of Bacteriology, vol.183, issue.7, 2001.
DOI : 10.1128/JB.183.7.2359-2366.2001
URL : http://jb.asm.org/content/183/7/2359.full.pdf

F. Griffith, The Significance of Pneumococcal Types, Journal of Hygiene, vol.27, issue.02, pp.113-159, 1928.
DOI : 10.1017/S0022172400031879

F. Guerrini and M. S. Fox, Effects of DNA repair in transformation-heterozygotes of pneumococcus., Proceedings of the National Academy of Sciences, vol.59, issue.4, pp.1116-1123, 1968.
DOI : 10.1073/pnas.59.4.1116

S. Guiral, T. J. Mitchell, B. Martin, and J. Claverys, From The Cover: Competence-programmed predation of noncompetent cells in the human pathogen Streptococcus pneumoniae: Genetic requirements, Proceedings of the National Academy of Sciences, vol.64, issue.2, pp.8710-8715, 2005.
DOI : 10.1128/IAI.69.4.2477-2486.2001

J. Hahn, B. Maier, B. J. Haijema, M. Sheetz, and D. Dubnau, Transformation Proteins and DNA Uptake Localize to the Cell Poles in Bacillus subtilis, Cell, vol.122, issue.1, pp.59-71, 2005.
DOI : 10.1016/j.cell.2005.04.035

B. J. Haijema, J. Hahn, J. Haynes, and D. Dubnau, A ComGA-dependent checkpoint limits growth during the escape from competence, Molecular Microbiology, vol.177, issue.1, pp.52-64, 2001.
DOI : 10.1128/jb.177.19.5711-5715.1995

H. L. Hamilton and J. P. Dillard, Natural transformation of Neisseria gonorrhoeae: from DNA donation to homologous recombination, Molecular Microbiology, vol.59, 2006.

H. L. Hamilton, N. M. Domínguez, K. J. Schwartz, K. T. Hackett, and J. P. Dillard, Neisseria gonorrhoeae secretes chromosomal DNA via a novel type IV secretion system, Molecular Microbiology, vol.55, 2005.
DOI : 10.1111/j.1365-2958.2005.04521.x
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2005.04521.x/pdf

B. K. Hammer and B. L. Bassler, Quorum sensing controls biofilm formation in Vibrio cholerae, Molecular Microbiology, vol.99, issue.1, pp.101-104, 2003.
DOI : 10.1128/jb.173.13.4039-4048.1991
URL : http://onlinelibrary.wiley.com/doi/10.1046/j.1365-2958.2003.03688.x/pdf

L. K. Handt, J. G. Fox, F. E. Dewhirst, G. J. Fraser, B. J. Paster et al., Helicobacter pylori isolated from the domestic cat: public health implications, Infect. Immun, vol.62, pp.2367-2374, 1994.

L. S. Håvarstein, B. Martin, O. Johnsborg, C. Granadel, and J. Claverys, New insights into the pneumococcal fratricide: relationship to clumping and identification of a novel immunity factor, Molecular Microbiology, vol.105, issue.4, pp.1297-1307, 2006.
DOI : 10.1093/nar/gkf418

M. A. Hoelzer and R. E. Michod, DNA Repair and the Evolution of Transformation in Bacillus Subtilis. III. Sex with Damaged DNA, Genetics, vol.128, pp.215-223, 1991.

D. Hofreuter, S. Odenbreit, and R. Haas, Natural transformation competence in Helicobacter pylori is mediated by the basic components of a type IV secretion system, Molecular Microbiology, vol.63, issue.2, pp.379-391, 2001.
DOI : 10.1038/41483

D. Hofreuter, S. Odenbreit, G. Henke, and R. Haas, Natural competence for DNA transformation in Helicobacter pylori : identification and genetic characterization of the comB locus, Molecular Microbiology, vol.263, issue.5, pp.1027-1038, 1998.
DOI : 10.1016/0140-6736(93)91409-F

X. Huang, X. Qu, W. Yan, Y. Huang, M. Cai et al., Iron deficiency anaemia can be improved after eradication of Helicobacter pylori, Postgraduate Medical Journal, vol.86, issue.1015, pp.272-278089987, 2009.
DOI : 10.1136/pgmj.2009.089987
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981025/pdf

O. Humbert, M. S. Dorer, and N. R. Salama, Characterization of Helicobacter pylori factors that control transformation frequency and integration length during inter-strain DNA recombination, Molecular Microbiology, vol.141, issue.2, pp.387-401, 2011.
DOI : 10.1073/pnas.94.18.9786
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2010.07456.x/pdf

J. J. Ipsaro, A. D. Haase, S. R. Knott, L. Joshua-tor, and G. J. Hannon, The structural biochemistry of Zucchini implicates it as a nuclease in piRNA biogenesis, Nature, vol.103, issue.7423, pp.279-28310, 1038.
DOI : 10.1063/1.470117

C. Johnston, B. Martin, G. Fichant, P. Polard, and J. Claverys, Bacterial transformation: distribution, shared mechanisms and divergent control, Nature Reviews Microbiology, vol.16, issue.3, pp.181-19610, 1038.
DOI : 10.1093/oxfordjournals.molbev.a026201
URL : https://hal.archives-ouvertes.fr/hal-01117850

C. Johnston, B. Martin, P. Polard, and J. Claverys, Postreplication targeting of transformants by bacterial immune systems?, Trends in Microbiology, vol.21, issue.10, 2013.
DOI : 10.1016/j.tim.2013.08.002
URL : https://hal.archives-ouvertes.fr/hal-00946765

M. E. Kahn, F. Barany, and H. O. Smith, Transformasomes: specialized membranous structures that protect DNA during Haemophilus transformation., Proceedings of the National Academy of Sciences, vol.80, issue.22, pp.6927-6931, 1983.
DOI : 10.1073/pnas.80.22.6927
URL : http://www.pnas.org/content/80/22/6927.full.pdf

A. Karnholz, C. Hoefler, S. Odenbreit, W. Fischer, D. Hofreuter et al., Functional and Topological Characterization of Novel Components of the comB DNA Transformation Competence System in Helicobacter pylori, Journal of Bacteriology, vol.188, issue.3, pp.882-893, 2006.
DOI : 10.1128/JB.188.3.882-893.2006

D. Kidane, S. Ayora, J. B. Sweasy, P. L. Graumann, and J. C. Alonso, The cell pole: the site of cross talk between the DNA uptake and genetic recombination machinery, Critical Reviews in Biochemistry and Molecular Biology, vol.194, issue.6, pp.531-555, 2012.
DOI : 10.1128/JB.00346-12

D. Kidane, B. Carrasco, C. Manfredi, K. Rothmaier, S. Ayora et al., Evidence for Different Pathways during Horizontal Gene Transfer in Competent Bacillus subtilis Cells, PLoS Genetics, vol.239, issue.9, 2009.
DOI : 10.1371/journal.pgen.1000630.s004
URL : https://doi.org/10.1371/journal.pgen.1000630

E. J. Kuipers, D. A. Israel, J. G. Kusters, and M. J. Blaser, Evidence for a conjugation-like mechanism of DNA transfer in Helicobacter pylori, J. Bacteriol, vol.180, pp.2901-2905, 1998.

S. Kulick, C. Moccia, X. Didelot, D. Falush, C. Kraft et al., Mosaic DNA Imports with Interspersions of Recipient Sequence after Natural Transformation of Helicobacter pylori, PLoS ONE, vol.61, issue.11, 2008.
DOI : 10.1371/journal.pone.0003797.s009

J. G. Kusters, A. H. Van-vliet, and E. J. Kuipers, Pathogenesis of Helicobacter pylori Infection, Clinical Microbiology Reviews, vol.19, issue.3, pp.449-490, 2006.
DOI : 10.1128/CMR.00054-05

E. M. Lai and C. I. Kado, The T-pilus of Agrobacterium tumefaciens, Trends in Microbiology, vol.8, issue.8, pp.361-369, 2000.
DOI : 10.1016/S0966-842X(00)01802-3

G. W. Liechti and J. B. Goldberg, Helicobacter pylori Salvages Purines from Extracellular Host Cell DNA Utilizing the Outer Membrane-Associated Nuclease NucT, Journal of Bacteriology, vol.195, issue.19, pp.4387-4398, 2013.
DOI : 10.1128/JB.00388-13
URL : http://jb.asm.org/content/195/19/4387.full.pdf

E. A. Lin, X. Zhang, S. M. Levine, S. R. Gill, D. Falush et al., Natural Transformation of Helicobacter pylori Involves the Integration of Short DNA Fragments Interrupted by Gaps of Variable Size, PLoS Pathogens, vol.45, issue.3, 2009.
DOI : 10.1371/journal.ppat.1000337.s002

L. Lin, J. Posfai, R. J. Roberts, and H. Kong, Comparative genomics of the restriction-modification systems in Helicobacter pylori, Proceedings of the National Academy of Sciences, vol.95, issue.21, pp.2740-2745, 2001.
DOI : 10.1073/pnas.95.21.12619

B. Linz and S. C. Schuster, Genomic diversity in Helicobacter and related organisms, Research in Microbiology, vol.158, issue.10, pp.737-744, 2007.
DOI : 10.1016/j.resmic.2007.09.006

P. Lopez, M. Espinosa, D. L. Stassi, and S. A. Lacks, Facilitation of plasmid transfer in Streptococcus pneumoniae by chromosomal homology, J. Bacteriol, vol.150, pp.692-701, 1982.

M. G. Lorenz and W. Wackernagel, Bacterial gene transfer by natural genetic transformation in the environment, Microbiol. Rev, vol.58, pp.563-602, 1994.

M. G. Lorenz and W. Wackernagel, High Frequency of Natural Genetic Transformation of Pseudomonas stutzeri in Soil Extract Supplemented with a Carbon/Energy and Phosphorus Source, Appl. Environ. Microbiol, vol.57, pp.1246-1251, 1991.

M. G. Lorenz and W. Wackernagel, Natural genetic transformation of Pseudomonas stutzeri by sand-adsorbed DNA, Archives of Microbiology, vol.6, issue.4, pp.380-385, 1990.
DOI : 10.1016/0006-291X(62)90337-6

C. Luo, P. Chiou, C. Yang, and N. Lin, Genome, Integration, and Transduction of a Novel Temperate Phage of Helicobacter pylori, Journal of Virology, vol.86, issue.16, pp.8781-879200446, 2012.
DOI : 10.1128/JVI.00446-12

H. Maamar and D. Dubnau, K-state (competence) system requires a positive feedback loop, Molecular Microbiology, vol.17, issue.3, pp.615-624, 2005.
DOI : 10.1093/emboj/17.22.6730
URL : http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2005.04592.x/pdf

B. Maier, I. Chen, D. Dubnau, and M. P. Sheetz, DNA transport into Bacillus subtilis requires proton motive force to generate large molecular forces, Nature Structural & Molecular Biology, vol.28, issue.7, pp.643-64910, 1038.
DOI : 10.1038/375809a0
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3832999/pdf

H. M. Malaty and D. Y. Graham, Importance of childhood socioeconomic status on the current prevalence of Helicobacter pylori infection., Gut, vol.35, issue.6, pp.742-745, 1994.
DOI : 10.1136/gut.35.6.742

B. J. Marshall, J. A. Armstrong, D. B. Mcgechie, and R. J. Glancy, Attempt to fulfil Koch's postulates for pyloric Campylobacter, Med. J. Aust, vol.142, pp.436-439, 1985.

B. J. Marshall and J. R. Warren, UNIDENTIFIED CURVED BACILLI IN THE STOMACH OF PATIENTS WITH GASTRITIS AND PEPTIC ULCERATION, The Lancet, vol.323, issue.8390, pp.1311-1315, 1984.
DOI : 10.1016/S0140-6736(84)91816-6

S. Marsin, A. Lopes, A. Mathieu, E. Dizet, E. Orillard et al., Genetic dissection of Helicobacter pylori AddAB role in homologous recombination, FEMS Microbiology Letters, vol.311, issue.1, pp.44-50, 2010.
DOI : 10.1111/j.1574-6968.2010.02077.x

S. Marsin, A. Mathieu, T. Kortulewski, R. Guérois, and J. P. Radicella, Unveiling Novel RecO Distant Orthologues Involved in Homologous Recombination, PLoS Genetics, vol.49, issue.8, 2008.
DOI : 10.1371/journal.pgen.1000146.s004
URL : https://hal.archives-ouvertes.fr/hal-00311931

B. Martin, A. Soulet, N. Mirouze, M. Prudhomme, I. Mortier-barrière et al., ComE/ComE???P interplay dictates activation or extinction status of pneumococcal X-state (competence), Molecular Microbiology, vol.4, issue.2, pp.394-411, 2013.
DOI : 10.1046/j.1365-2958.1999.01528.x
URL : https://hal.archives-ouvertes.fr/hal-01004510

A. Mathieu, E. J. O-'rourke, and J. P. Radicella, Helicobacter pylori Genes Involved in Avoidance of Mutations Induced by 8-Oxoguanine, Journal of Bacteriology, vol.188, issue.21, pp.7464-7469, 2006.
DOI : 10.1128/JB.00851-06

K. L. Meibom, M. Blokesch, N. A. Dolganov, C. Wu, and G. K. Schoolnik, Chitin Induces Natural Competence in Vibrio cholerae, Science, vol.310, issue.5755, pp.1824-1827, 2005.
DOI : 10.1126/science.1120096

P. Meier, C. Berndt, N. Weger, and W. Wackernagel, Natural transformation of Pseudomonas stutzeri by single-stranded DNA requires type IV pili, competence state and comA, FEMS Microbiology Letters, vol.0, issue.0, 2002.
DOI : 10.1016/S0378-1097(01)90507-5

V. Méjean and J. P. Claverys, DNA processing during entry in transformation of Streptococcus pneumoniae, J. Biol. Chem, vol.268, pp.5594-5599, 1993.

B. Michel, H. Boubakri, Z. Baharoglu, M. Lemasson, and R. Lestini, Recombination proteins and rescue of arrested replication forks, DNA Repair, vol.6, issue.7, 2007.
DOI : 10.1016/j.dnarep.2007.02.016
URL : https://hal.archives-ouvertes.fr/hal-00167418

R. E. Michod, M. F. Wojciechowski, and M. A. Hoelzer, DNA Repair and the Evolution of Transformation in the Bacterium Bacillus Subtilis, Genetics, vol.118, pp.31-39, 1988.

N. Mirouze, M. A. Bergé, A. Soulet, I. Mortier-barrière, Y. Quentin et al., Direct involvement of DprA, the transformation-dedicated RecA loader, in the shut-off of pneumococcal competence, Proceedings of the National Academy of Sciences, vol.181, issue.16, pp.1035-1044, 2013.
DOI : 10.1128/JB.00687-07
URL : https://hal.archives-ouvertes.fr/hal-01001538

N. Mirouze, Y. Desai, A. Raj, and D. Dubnau, Spo0A???P Imposes a Temporal Gate for the Bimodal Expression of Competence in Bacillus subtilis, PLoS Genetics, vol.283, issue.3, 2012.
DOI : 10.1371/journal.pgen.1002586.s013

J. A. Mongold, DNA repair and the evolution of transformation in Haemophilus influenzae, Genetics, vol.132, pp.893-898, 1992.

I. Mortier-barrière, M. Velten, P. Dupaigne, N. Mirouze, O. Piétrement et al., A Key Presynaptic Role in Transformation for a Widespread Bacterial Protein: DprA Conveys Incoming ssDNA to RecA, Cell, vol.130, issue.5, pp.824-836, 2007.
DOI : 10.1016/j.cell.2007.07.038

P. Nedenskov-sørensen, G. Bukholm, and K. Bøvre, Natural Competence for Genetic Transformation in Campylobacter pylori, Journal of Infectious Diseases, vol.161, issue.2, pp.365-366, 1990.
DOI : 10.1093/infdis/161.2.365

H. Nishimasu, H. Ishizu, K. Saito, S. Fukuhara, M. K. Kamatani et al., Structure and function of Zucchini endoribonuclease in piRNA biogenesis, Nature, vol.66, issue.7423, pp.284-28710, 1038.
DOI : 10.1107/S0907444909042589

E. Orillard, J. P. Radicella, and S. Marsin, Biochemical and Cellular Characterization of Helicobacter pylori RecA, a Protein with High-Level Constitutive Expression, Journal of Bacteriology, vol.193, issue.23, pp.6490-6497, 2011.
DOI : 10.1128/JB.05646-11

E. J. O-'rourke, A. V. Pinto, E. A. Petroni, M. E. Tolmasky, and L. Ielpi, Evidence for the Active Role of a Novel Nuclease from Helicobacter pylori in the Horizontal Transfer of Genetic Information, Journal of Bacteriology, vol.186, issue.9, pp.2586-2593, 2004.
DOI : 10.1128/JB.186.9.2586-2593.2004

O. A. Oyarzabal, R. Rad, and S. Backert, Conjugative Transfer of Chromosomally Encoded Antibiotic Resistance from Helicobacter pylori to Campylobacter jejuni, Journal of Clinical Microbiology, vol.45, issue.2, pp.402-408, 2007.
DOI : 10.1128/JCM.01456-06

V. Papastergiou, S. D. Georgopoulos, and S. Karatapanis, Treatment of Helicobacter pylori infection: Past, present and future, World J Gastrointest Pathophysiol, vol.5, 2014.

J. R. Parrish, J. Yu, G. Liu, J. A. Hines, J. E. Chan et al., A proteomewide protein interaction map for Campylobacter jejuni, Genome Biol, vol.8, 2007.
DOI : 10.1186/gb-2007-8-7-r130
URL : https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2007-8-7-r130?site=genomebiology.biomedcentral.com

G. G. Perron, A. E. Lee, Y. Wang, W. E. Huang, and T. G. Barraclough, Bacterial recombination promotes the evolution of multi-drug-resistance in functionally diverse populations, Proceedings of the Royal Society B: Biological Sciences, vol.10, issue.9, pp.1477-1484, 1933.
DOI : 10.1016/S1473-3099(10)70143-2

A. V. Pinto, A. Mathieu, S. Marsin, X. Veaute, L. Ielpi et al., Suppression of Homologous and Homeologous Recombination by the Bacterial MutS2 Protein, Molecular Cell, vol.17, issue.1, pp.113-120, 2005.
DOI : 10.1016/j.molcel.2004.11.035

R. Provvedi, I. Chen, and D. Dubnau, NucA is required for DNA cleavage during transformation of Bacillus subtilis, Molecular Microbiology, vol.170, issue.3, pp.634-644, 2001.
DOI : 10.1128/jb.170.8.3703-3710.1988

S. Quevillon-cheruel, N. Campo, N. Mirouze, I. Mortier-barrière, M. A. Brooks et al., Structure-function analysis of pneumococcal DprA protein reveals that dimerization is crucial for loading RecA recombinase onto DNA during transformation, Proceedings of the National Academy of Sciences, vol.130, issue.5, pp.2466-2475
DOI : 10.1016/j.cell.2007.07.038
URL : https://hal.archives-ouvertes.fr/hal-01004530

R. J. Redfield, Do bacteria have sex?, Nature Reviews Genetics, vol.870, issue.8, pp.634-639, 2001.
DOI : 10.1111/j.1749-6632.1999.tb08870.x

R. J. Redfield, A. D. Cameron, Q. Qian, J. Hinds, T. R. Ali et al., A Novel CRP-dependent Regulon Controls Expression of Competence Genes in Haemophilus influenzae, Journal of Molecular Biology, vol.347, issue.4, pp.735-747, 2005.
DOI : 10.1016/j.jmb.2005.01.012

R. J. Roberts, T. Vincze, J. Posfai, and D. Macelis, REBASE???a database for DNA restriction and modification: enzymes, genes and genomes, Nucleic Acids Research, vol.43, issue.D1, pp.298-299, 2015.
DOI : 10.1093/nar/gku1046
URL : https://academic.oup.com/nar/article-pdf/38/suppl_1/D234/11217809/gkp874.pdf

S. Rohrer, L. Holsten, E. Weiss, M. Benghezal, W. Fischer et al., Multiple Pathways of Plasmid DNA Transfer in Helicobacter pylori, PLoS ONE, vol.7, issue.9, 2012.
DOI : 10.1371/journal.pone.0045623.s001

N. Saito, K. Konishi, F. Sato, M. Kato, H. Takeda et al., Plural Transformation-Processes from Spiral to Coccoid Helicobacter pylori and its Viability, Journal of Infection, vol.46, issue.1, pp.49-55, 2003.
DOI : 10.1053/jinf.2002.1047

M. Scrudato, . Lo, and M. Blokesch, The Regulatory Network of Natural Competence and Transformation of Vibrio cholerae, PLoS Genetics, vol.2, issue.6, 2012.
DOI : 10.1371/journal.pgen.1002778.s009

P. Seitz and M. Blokesch, DNA Transport across the Outer and Inner Membranes of Naturally Transformable Vibrio cholerae Is Spatially but Not Temporally Coupled, mBio, vol.5, issue.4, 2014.
DOI : 10.1128/mBio.01409-14

P. Seitz and M. Blokesch, Cues and regulatory pathways involved in natural competence and transformation in pathogenic and environmental Gram-negative bacteria, FEMS Microbiology Reviews, vol.37, issue.3, 2013.
DOI : 10.1111/j.1574-6976.2012.00353.x
URL : https://academic.oup.com/femsre/article-pdf/37/3/336/18142743/37-3-336.pdf

S. Sinha, J. C. Mell, and R. J. Redfield, Seventeen Sxy-Dependent Cyclic AMP Receptor Protein Site-Regulated Genes Are Needed for Natural Transformation in Haemophilus influenzae, Journal of Bacteriology, vol.194, issue.19, pp.5245-5254, 2012.
DOI : 10.1128/JB.00671-12
URL : http://jb.asm.org/content/194/19/5245.full.pdf

S. Sinha, J. Mell, and R. Redfield, The availability of purine nucleotides regulates natural competence by controlling translation of the competence activator Sxy, Molecular Microbiology, vol.65, issue.6, pp.1106-1119, 2013.
DOI : 10.1007/s00018-008-8295-8

J. Slager, M. Kjos, L. Attaiech, and J. Veening, Antibiotic-Induced Replication Stress Triggers Bacterial Competence by Increasing Gene Dosage near the Origin, Cell, vol.157, issue.2, pp.395-406, 2014.
DOI : 10.1016/j.cell.2014.01.068
URL : https://doi.org/10.1016/j.cell.2014.01.068

L. C. Smeets and J. G. Kusters, Natural transformation in Helicobacter pylori: DNA transport in an unexpected way, Trends in Microbiology, vol.10, issue.4, pp.159-162, 2002.
DOI : 10.1016/S0966-842X(02)02314-4

M. Specht, F. Dempwolff, S. Schätzle, R. Thomann, and B. Waidner, Localization of FtsZ in Helicobacter pylori and Consequences for Cell Division, Journal of Bacteriology, vol.195, issue.7, pp.1411-1420, 2013.
DOI : 10.1128/JB.01490-12

K. Stingl, S. Müller, G. Scheidgen-kleyboldt, M. Clausen, and B. Maier, Composite system mediates two-step DNA uptake into Helicobacter pylori, Proceedings of the National Academy of Sciences, vol.176, issue.15, pp.1184-1189, 2010.
DOI : 10.1128/jb.176.15.4642-4645.1994
URL : http://www.pnas.org/content/107/3/1184.full.pdf

G. Suckow, P. Seitz, and M. Blokesch, Quorum Sensing Contributes to Natural Transformation of Vibrio cholerae in a Species-Specific Manner, Journal of Bacteriology, vol.193, issue.18, pp.4914-4924, 2011.
DOI : 10.1128/JB.05396-11

S. Suerbaum and C. Josenhans, Helicobacter pylori evolution and phenotypic diversification in a changing host, Nature Reviews Microbiology, vol.5, issue.6, pp.441-452, 1658.
DOI : 10.1086/515601

S. Suerbaum, J. M. Smith, K. Bapumia, G. Morelli, N. H. Smith et al., Free recombination within Helicobacter pylori, Proceedings of the National Academy of Sciences, vol.32, issue.1, pp.12619-12624, 1998.
DOI : 10.3109/00365529709025059
URL : http://www.pnas.org/content/95/21/12619.full.pdf

N. Takeuchi, K. Kaneko, and E. V. Koonin, Horizontal Gene Transfer Can Rescue Prokaryotes from Muller???s Ratchet: Benefit of DNA from Dead Cells and Population Subdivision, G3: Genes|Genomes|Genetics, vol.4, issue.2, pp.325-339, 2013.
DOI : 10.1534/g3.113.009845

T. L. Testerman and J. Morris, Beyond the stomach: An updated view of Helicobacter pylori pathogenesis, diagnosis, and treatment, World J Gastroenterol, vol.20, 2014.

C. M. Waters and B. L. Bassler, QUORUM SENSING: Cell-to-Cell Communication in Bacteria, Annual Review of Cell and Developmental Biology, vol.21, issue.1, pp.319-346, 2005.
DOI : 10.1146/annurev.cellbio.21.012704.131001

D. L. Weeks, S. Eskandari, D. R. Scott, and G. Sachs, A H+-Gated Urea Channel: The Link Between Helicobacter pylori Urease and Gastric Colonization, Science, vol.287, issue.5452, pp.482-485, 2000.
DOI : 10.1126/science.287.5452.482

E. M. Wise, S. P. Alexander, and M. Powers, Adenosine 3':5'-Cyclic Monophosphate as a Regulator of Bacterial Transformation, Proceedings of the National Academy of Sciences, vol.70, issue.2, pp.471-474, 1973.
DOI : 10.1073/pnas.70.2.471

S. Yamamoto, H. Izumiya, J. Mitobe, M. Morita, E. Arakawa et al., Identification of a Chitin-Induced Small RNA That Regulates Translation of the tfoX Gene, Encoding a Positive Regulator of Natural Competence in Vibrio cholerae, Journal of Bacteriology, vol.193, issue.8, pp.1953-19651001340, 1128.
DOI : 10.1128/JB.01340-10

Y. Yeh, T. Lin, K. Chang, and J. Wang, Characterization of a ComE3 Homologue Essential for DNA Transformation in Helicobacter pylori, Infection and Immunity, vol.71, issue.9, pp.5427-5431, 2003.
DOI : 10.1128/IAI.71.9.5427-5431.2003

X. Zhang and M. J. Blaser, DprB Facilitates Inter- and Intragenomic Recombination in Helicobacter pylori, Journal of Bacteriology, vol.194, issue.15, pp.3891-3903, 2012.
DOI : 10.1128/JB.00346-12
URL : http://jb.asm.org/content/194/15/3891.full.pdf

J. Zhu, M. B. Miller, R. E. Vance, M. Dziejman, B. L. Bassler et al., Quorum-sensing regulators control virulence gene expression in Vibrio cholerae, Proceedings of the National Academy of Sciences, vol.180, issue.19, pp.3129-3134, 2002.
DOI : 10.1016/S0378-1119(00)00117-7
URL : http://www.pnas.org/content/99/5/3129.full.pdf

A. Zullo, C. Hassan, F. Cristofari, A. Andriani, V. De-francesco et al., Effects of Helicobacter pylori Eradication on Early Stage Gastric Mucosa???Associated Lymphoid Tissue Lymphoma, Clinical Gastroenterology and Hepatology, vol.8, issue.2, pp.105-110, 2010.
DOI : 10.1016/j.cgh.2009.07.017