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, 2012.
URL : https://hal.archives-ouvertes.fr/hal-02381171

L. Akman, A. Yamashita, H. Watanabe, K. Oshima, T. Shiba et al., Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia, Nat. Genet, vol.32, pp.402-407, 2002.

A. Allardet-servent, S. Michaux-charachon, E. Jumas-bilak, L. Karayan, and M. Ramuz, Presence of one linear and one circular chromosome in the Agrobacterium tumefaciens C58 genome, J. Bacteriol, vol.175, pp.7869-7874, 1993.

D. Ausiannikava, L. Mitchell, H. Marriott, V. Smith, M. Hawkins et al., Evolution of genome architecture in Archaea: spontaneous generation of a new chromosome in Haloferax volcanii, Mol. Biol. Evol, 2018.

J. H. Baek and D. K. Chattoraj, Chromosome I controls chromosome II replication in Vibrio cholerae, PLoS Genet, vol.10, p.1004184, 2014.

C. Baril, C. Richaud, G. Baranton, and I. S. Girons, Linear chromosome of Borrelia burgdorferi, Res. Microbiol, vol.140, issue.89, pp.90083-90084, 1989.

A. Bavishi, L. Lin, K. Schroeder, A. Peters, H. Cho et al., The prevalence of gene duplications and their ancient origin in Rhodobacter sphaeroides 2.4.1, BMC Microbiol, vol.10, p.331, 2010.

S. Brantl, Plasmid replication control by antisense RNAs, Microbiol. Spectr, vol.2, 2014.

M. Brilli, M. Fondi, R. Fani, A. Mengoni, L. Ferri et al., The diversity and evolution of cell cycle regulation in alpha-proteobacteria: a comparative genomic analysis, BMC Syst. Biol, vol.4, p.52, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00682798

C. Buchrieser, P. Glaser, C. Rusniok, H. Nedjari, H. D'hauteville et al., The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri, Mol. Microbiol, vol.38, pp.760-771, 2000.

S. Castillo-ramírez, J. F. Vázquez-castellanos, V. González, and M. A. Cevallos, Horizontal gene transfer and diverse functional constrains within a common replication-partitioning system in Alphaproteobacteria: the repABC operon, BMC Genomics, vol.10, p.536, 2009.

R. Cervantes-rivera, F. Pedraza-lópez, G. Pérez-segura, and M. A. Cevallos, The replication origin of a repABC plasmid, BMC Microbiol, vol.11, p.158, 2011.

R. Cervantes-rivera, C. Romero-lópez, A. Berzal-herranz, and M. A. Cevallos, Analysis of the mechanism of action of the antisense RNA that controls the replication of the repABC plasmid p42d, J. Bacteriol, vol.192, pp.3268-3278, 2010.

M. A. Cevallos, R. Cervantes-rivera, and R. M. Gutiérrez-ríos, The repABC plasmid family, Plasmid, vol.60, pp.19-37, 2008.

Y. Chai and S. C. Winans, A small antisense RNA downregulates expression of an essential replicase protein of an Agrobacterium tumefaciens Ti plasmid, Mol. Microbiol, vol.56, pp.1574-1585, 2005.

Y. Chai and S. C. Winans, RepB protein of an Agrobacterium tumefaciens Ti plasmid binds to two adjacent sites between repA and repB for plasmid partitioning and autorepression, Mol. Microbiol, vol.58, pp.1114-1129, 2005.

M. C. Chao, J. R. Pritchard, Y. J. Zhang, E. J. Rubin, J. Livny et al., High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data, Nucleic Acids Res, vol.41, pp.9033-9048, 2013.

D. K. Chattoraj, Control of plasmid DNA replication by iterons: no longer paradoxical, Mol. Microbiol, vol.37, pp.467-476, 2000.

J. Cheng, C. D. Sibley, R. Zaheer, and T. M. Finan, A Sinorhizobium meliloti minE mutant has an altered morphology and exhibits defects in legume symbiosis, Microbiology, vol.153, pp.375-387, 2007.

H. Cho and S. C. Winans, VirA and VirG activate the Ti plasmid repABC operon, elevating plasmid copy number in response to wound-released chemical signals, Proc. Natl. Acad. Sci. U.S.A, vol.102, pp.14843-14848, 2005.

M. Choudhary, C. Mackenzie, K. Nereng, E. Sodergren, G. M. Weinstock et al., Low-resolution sequencing of Rhodobacter sphaeroides 2.4.1T: chromosome II is a true chromosome, Microbiology, vol.143, pp.3085-3099, 1997.

J. Collier, Regulation of chromosomal replication in Caulobacter crescentus, Plasmid, vol.67, pp.76-87, 2012.

M. Deghelt, C. Mullier, J. Sternon, N. Francis, G. Laloux et al., G1-arrested newborn cells are the predominant infectious form of the pathogen Brucella abortus, Nat. Commun, vol.5, p.4366, 2014.

G. Del-solar, R. Giraldo, M. J. Ruiz-echevarría, M. Espinosa, and R. Díaz-orejas, Replication and control of circular bacterial plasmids. Microbiol, Mol. Biol. Rev, vol.62, pp.434-464, 1998.

G. Demarre and D. K. Chattoraj, DNA adenine methylation is required to replicate both Vibrio cholerae chromosomes once per cell cycle, PLoS Genet, vol.6, p.1000939, 2010.

T. Díaz-lópez, M. Lages-gonzalo, A. Serrano-lópez, C. Alfonso, G. Rivas et al., Structural changes in RepA, a plasmid replication initiator, upon binding to origin DNA, J. Biol. Chem, vol.278, pp.18606-18616, 2003.

G. Dicenzo, B. Milunovic, J. Cheng, and T. M. Finan, The tRNA arg gene and engA are essential genes on the 1.7-Mb pSymB megaplasmid of Sinorhizobium meliloti and were translocated together from the chromosome in an ancestral strain, J. Bacteriol, vol.195, pp.202-212, 2013.

G. C. Dicenzo and T. M. Finan, Genetic redundancy is prevalent within the 6.7 Mb Sinorhizobium meliloti genome, Mol. Genet. Genomics, vol.290, pp.1345-1356, 2015.

G. C. Dicenzo and T. M. Finan, The divided bacterial genome: structure, function, and evolution. Microbiol, Mol. Biol. Rev, vol.81, pp.19-36, 2017.

W. Du, N. Dubarry, F. M. Passot, A. Kamgoué, H. Murray et al., Orderly replication and segregation of the four replicons of Burkholderia cenocepacia J2315, PLoS Genet, vol.12, p.1006172, 2016.

Y. Duan, J. D. Huey, and J. K. Herman, The DnaA inhibitor SirA acts in the same pathway as Soj (ParA) to facilitate oriC segregation during Bacillus subtilis sporulation, Mol. Microbiol, vol.102, pp.530-544, 2016.

S. Duigou, K. G. Knudsen, O. Skovgaard, E. S. Egan, A. Løbner-olesen et al., Independent control of replication initiation of the two Vibrio cholerae chromosomes by DnaA and RctB, J. Bacteriol, vol.188, pp.6419-6424, 2006.

L. Dziewit, J. Czarnecki, D. Wibberg, M. Radlinska, P. Mrozek et al., Architecture and functions of a multipartite genome of the methylotrophic bacterium Paracoccus aminophilus JCM 7686, containing primary and secondary chromids, BMC Genomics, vol.15, p.124, 2014.

E. S. Egan, S. Duigou, and M. K. Waldor, Autorepression of RctB, an initiator of Vibrio cholerae chromosome II replication, J. Bacteriol, vol.188, pp.789-793, 2006.

E. S. Egan, M. A. Fogel, and M. K. Waldor, Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes, Mol. Microbiol, vol.56, pp.1129-1138, 2005.

E. S. Egan, A. Løbner-olesen, and M. K. Waldor, Synchronous replication initiation of the two Vibrio cholerae chromosomes, Curr. Biol, vol.14, pp.501-502, 2004.

E. S. Egan and M. K. Waldor, Distinct replication requirements for the two Vibrio cholerae chromosomes, Cell, vol.114, pp.521-530, 2003.

M. Felletti, D. J. Omnus, J. , and K. , Regulation of the replication initiator DnaA in Caulobacter crescentus, Biochim. Biophys. Acta, 2018.

A. Fioravanti, C. Fumeaux, S. S. Mohapatra, C. Bompard, M. Brilli et al., DNA binding of the cell cycle transcriptional regulator GcrA depends on N6-adenosine methylation in Caulobacter crescentus and other Alphaproteobacteria, PLoS Genet, vol.9, p.1003541, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01110809

B. Frage, J. Döhlemann, M. Robledo, D. Lucena, P. Sobetzko et al., Spatiotemporal choreography of chromosome and megaplasmids in the Sinorhizobium meliloti cell cycle, Mol. Microbiol, vol.100, pp.808-823, 2016.

N. Francis, K. Poncin, A. Fioravanti, V. Vassen, K. Willemart et al., CtrA controls cell division and outer membrane composition of the pathogen Brucella abortus, Mol. Microbiol, vol.103, pp.780-797, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01640044

O. Frank, M. Göker, S. Pradella, and J. Petersen, Ocean's Twelve: flagellar and biofilm chromids in the multipartite genome of Marinovum algicola DG898 exemplify functional compartmentalization, Environ. Microbiol, vol.17, pp.4019-4034, 2015.

O. Frank, V. Michael, O. Päuker, C. Boedeker, C. Jogler et al., Plasmid curing and the loss of grip-the 65-kb replicon of Phaeobacter inhibens DSM 17395 is required for biofilm formation, motility and the colonization of marine algae, Syst. Appl. Microbiol, vol.38, pp.120-127, 2015.

D. I. Friedman, E. R. Olson, C. Georgopoulos, K. Tilly, I. Herskowitz et al., Interactions of bacteriophage and host macromolecules in the growth of bacteriophage lambda, Microbiol. Rev, vol.48, pp.299-325, 1984.

K. Fujimitsu, T. Senriuchi, and T. Katayama, Specific genomic sequences of E. coli promote replicational initiation by directly reactivating ADP-DnaA, Genes Dev, vol.23, pp.1221-1233, 2009.

H. Gaimster and D. Summers, Plasmids in the driving seat: the regulatory RNA Rcd gives plasmid ColE1 control over division and growth of its E. coli host, Plasmid, vol.78, pp.59-64, 2015.

M. Galardini, F. Pini, M. Bazzicalupo, E. G. Biondi, and A. Mengoni, , 2013.

, Replicon-dependent bacterial genome evolution: the case of Sinorhizobium meliloti, Genome Biol. Evol, vol.5, pp.542-558

F. Galibert, T. M. Finan, S. R. Long, A. Puhler, P. Abola et al., The composite genome of the legume symbiont Sinorhizobium meliloti, Science, vol.293, pp.668-672, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00427172

. García-de-los, A. Santos, E. López, C. A. Cubillas, K. D. Noel et al., Requirement of a plasmid-encoded catalase for survival of Rhizobium etli CFN42 in a polyphenol-rich environment, Appl. Environ. Microbiol, vol.74, pp.2398-2403, 2008.

M. A. Gerding, M. C. Chao, B. M. Davis, and M. K. Waldor, Molecular dissection of the essential features of the origin of replication of the second Vibrio cholerae chromosome, vol.6, p.973, 2015.

R. Giraldo, C. Fernández-tornero, P. R. Evans, R. Díaz-orejas, and A. Romero, A conformational switch between transcriptional repression and replication initiation in the RepA dimerization domain, Nat. Struct. Biol, vol.10, pp.565-571, 2003.

D. Gonzalez, J. B. Kozdon, H. H. Mcadams, L. Shapiro, and J. Collier, The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach, Nucleic Acids Res, vol.42, pp.3720-3735, 2014.

B. Goodner, G. Hinkle, S. Gattung, N. Miller, M. Blanchard et al., Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58, Science, vol.294, pp.2323-2328, 2001.

H. Guo, S. Sun, B. Eardly, T. Finan, and J. Xu, Genome variation in the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti, Genome, vol.52, pp.862-875, 2009.

F. G. Hansen, A. , and T. , The DnaA tale, Front. Microbiol, vol.9, p.319, 2018.

P. W. Harrison, R. P. Lower, N. K. Kim, and J. P. Young, Introducing the bacterial "chromid": not a chromosome, not a plasmid, Trends Microbiol, vol.18, pp.141-148, 2010.

A. L. Hartman, C. Norais, J. H. Badger, S. Delmas, S. Haldenby et al., The complete genome sequence of Haloferax volcanii DS2, a model archaeon, PLoS One, vol.5, p.9605, 2010.

M. Hase, T. Yoshimi, Y. Ishikawa, A. Ohba, L. Guo et al., , 1998.

, Site-directed mutational analysis for the membrane binding of DnaA protein. Identification of amino acids involved in the functional interaction between DnaA protein and acidic phospholipids, J. Biol. Chem, vol.273, pp.28651-28656

J. F. Heidelberg, J. A. Eisen, W. C. Nelson, R. A. Clayton, M. L. Gwinn et al., DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae, Nature, vol.406, pp.477-483, 2000.

H. Hirochika and K. Sakaguchi, Analysis of linear plasmids isolated from Streptomyces: association of protein with the ends of the plasmid DNA, Plasmid, vol.7, pp.59-65, 1982.

J. K. Jha, G. Demarre, T. Venkova-canova, and D. K. Chattoraj, Replication regulation of Vibrio cholerae chromosome II involves initiator binding to the origin both as monomer and as dimer, Nucleic Acids Res, vol.40, pp.6026-6038, 2012.

J. K. Jha, R. Ghirlando, and D. K. Chattoraj, Initiator protein dimerization plays a key role in replication control of Vibrio cholerae chromosome 2, Nucleic Acids Res, vol.42, pp.10538-10549, 2014.

J. K. Jha, M. Li, R. Ghirlando, L. M. Miller-jenkins, A. Wlodawer et al., The DnaK chaperone uses different mechanisms to promote and inhibit replication of Vibrio cholerae chromosome 2, vol.8, pp.427-444, 2017.

E. Jumas-bilak, S. Michaux-charachon, G. Bourg, D. O'callaghan, and M. Ramuz, Differences in chromosome number and genome rearrangements in the genus Brucella, Mol. Microbiol, vol.27, pp.99-106, 1998.

R. Kadoya, J. H. Baek, A. Sarker, and D. K. Chattoraj, Participation of chromosome segregation protein ParAI of Vibrio cholerae in chromosome replication, J. Bacteriol, vol.193, pp.1504-1514, 2011.

L. S. Kahng and L. Shapiro, The CcrM DNA methyltransferase of Agrobacterium tumefaciens is essential, and its activity is cell cycle regulated, J. Bacteriol, vol.183, pp.3065-3075, 2001.

L. S. Kahng and L. Shapiro, Polar localization of replicon origins in the multipartite genomes of Agrobacterium tumefaciens and Sinorhizobium meliloti, J. Bacteriol, vol.185, pp.3384-3391, 2003.

K. Kasho and T. Katayama, DnaA binding locus datA promotes DnaA-ATP hydrolysis to enable cell cycle-coordinated replication initiation, Proc. Natl. Acad. Scci. U.S.A, vol.110, pp.936-941, 2013.

T. Katayama, S. Ozaki, K. Keyamura, and K. Fujimitsu, Regulation of the replication cycle: conserved and diverse regulatory systems for DnaA and oriC, Nat. Rev. Microbiol, vol.8, pp.163-170, 2010.

H. Kawakami, K. Keyamura, and T. Katayama, Formation of an ATP-DnaA-specific initiation complex requires DnaA Arginine 285, a conserved motif in the AAA+ protein family, J. Biol. Chem, vol.280, pp.27420-27430, 2005.

F. S. Kemter, S. J. Messerschmidt, N. Schallopp, P. Sobetzko, E. Lang et al., Synchronous termination of replication of the two chromosomes is an evolutionary selected feature in Vibrionaceae, PLoS Genet, vol.14, p.1007251, 2018.

R. Kitagawa, T. Ozaki, S. Moriya, and T. Ogawa, Negative control of replication initiation by a novel chromosomal locus exhibiting exceptional affinity for Escherichia coli DnaA protein, Genes Dev, vol.12, pp.3032-3043, 1998.

B. Koch, X. Ma, and A. Løbner-olesen, Replication of Vibrio cholerae chromosome I in Escherichia coli: dependence on dam methylation, J. Bacteriol, vol.192, pp.3903-3914, 2010.

B. Koch, X. Ma, and A. Løbner-olesen, rctB mutations that increase copy number of Vibrio cholerae oriCII in Escherichia coli, Plasmid, vol.68, pp.159-169, 2012.

H. Komori, F. Matsunaga, Y. Higuchi, M. Ishiai, C. Wada et al., Crystal structure of a prokaryotic replication initiator protein bound to DNA at 2.6 A resolution, EMBO J, vol.18, pp.4597-4607, 1999.

P. Koper, K. ?ebracki, M. Marczak, A. Skorupska, and A. Mazur, RepB proteins of the multipartite Rhizobium leguminosarum bv. trifolii genome discriminate between centromere-like parS sequences for plasmid segregational stability, Mol. Microbiol, vol.102, pp.446-466, 2016.

C. Landeta, A. Dávalos, M. Á. Cevallos, O. Geiger, S. Brom et al., Plasmids with a chromosome-like role in rhizobia, J. Bacteriol, vol.193, pp.1317-1326, 2011.

B. Lesic, M. Zouine, M. Ducos-galand, C. Huon, M. Rosso et al., A natural system of chromosome transfer in Yersinia pseudotuberculosis, PLoS Genet, vol.8, p.1002529, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01136644

Y. B. Lu, H. J. Datta, and D. Bastia, Mechanistic studies of initiatorinitiator interaction and replication initiation, EMBO J, vol.17, pp.5192-5200, 1998.

A. M. Maclean, T. M. Finan, and M. J. Sadowsky, Genomes of the symbiotic nitrogen-fixing bacteria of legumes, Plant Physiol, vol.144, pp.615-622, 2007.

S. R. Maclellan, L. A. Smallbone, C. D. Sibley, and T. M. Finan, The expression of a novel antisense gene mediates incompatibility within the large repABC family of alpha-proteobacterial plasmids, Mol. Microbiol, vol.55, pp.611-623, 2005.

S. R. Maclellan, R. Zaheer, A. L. Sartor, A. M. Maclean, and T. M. Finan, Identification of a megaplasmid centromere reveals genetic structural diversity within the repABC family of basic replicons, Mol. Microbiol, vol.59, pp.1559-1575, 2006.

M. Marchetti, D. Capela, M. Glew, S. Cruveiller, B. Chane-woon-ming et al., Experimental evolution of a plant pathogen into a legume symbiont, PLoS Biol, vol.8, p.1000280, 2010.
URL : https://hal.archives-ouvertes.fr/hal-02665813

G. T. Marczynski, Chromosome methylation and measurement of faithful, once and only once per cell cycle chromosome replication in Caulobacter crescentus, J. Bacteriol, vol.181, 1984.

G. T. Marczynski and L. Shapiro, Control of chromosome replication in Caulobacter crescentus, Annu. Rev. Microbiol, vol.56, pp.625-656, 2002.

S. J. Messerschmidt, F. S. Kemter, D. Schindler, and T. Waldminghaus, Synthetic secondary chromosomes in Escherichia coli based on the replication origin of chromosome II in Vibrio cholerae, Biotechnol. J, vol.10, pp.302-314, 2015.

S. Michaux, J. Paillisson, M. J. Carles-nurit, G. Bourg, A. Allardet-servent et al., Presence of two independent chromosomes in the Brucella melitensis 16M genome, J. Bacteriol, vol.175, pp.701-705, 1993.

S. S. Mohapatra, A. Fioravanti, and E. G. Biondi, DNA methylation in Caulobacter and other Alphaproteobacteria during cell cycle progression, Trends Microbiol, vol.22, pp.528-535, 2014.

E. Moreno, Genome evolution within the alpha Proteobacteria: why do some bacteria not possess plasmids and others exhibit more than one different chromosome?, FEMS Microbiol. Rev, vol.22, pp.255-275, 1998.

H. Murray and J. Errington, Dynamic control of the DNA replication initiation protein DnaA by Soj/ParA, Cell, vol.135, pp.74-84, 2008.

A. Nakamura, C. Wada, M. , and K. , Structural basis for regulation of bifunctional roles in replication initiator protein, Proc. Natl. Acad. Sci. U.S.A, vol.104, pp.18484-18489, 2007.

C. Norais, M. Hawkins, A. L. Hartman, J. A. Eisen, H. Myllykallio et al., Genetic and physical mapping of DNA replication origins in Haloferax volcanii, PLoS Genet, vol.3, p.77, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00195310

K. Nordström and S. Dasgupta, Copy-number control of the Escherichia coli chromosome: a plasmidologist's view, EMBO Rep, vol.7, pp.484-489, 2006.

Y. Ogura, N. Ogasawara, E. J. Harry, and S. Moriya, Increasing the ratio of Soj to Spo0J promotes replication initiation in Bacillus subtilis, J. Bacteriol, vol.185, pp.6316-6324, 2003.

R. Ohbayashi, S. Watanabe, S. Ehira, Y. Kanesaki, T. Chibazakura et al., Diversification of DnaA dependency for DNA replication in cyanobacterial evolution, ISME J, vol.10, pp.1113-1121, 2016.

K. Okada, T. Iida, K. Kita-tsukamoto, and T. Honda, Vibrios commonly possess two chromosomes, J. Bacteriol, vol.187, pp.752-757, 2005.

N. Orlova, M. Gerding, O. Ivashkiv, P. D. Olinares, B. T. Chait et al., The replication initiator of the cholera pathogen's second chromosome shows structural similarity to plasmid initiators, Nucleic Acids Res, vol.45, pp.3724-3737, 2017.

D. Pal, T. Venkova-canova, P. Srivastava, and D. K. Chattoraj, , 2005.

, Multipartite regulation of rctB, the replication initiator gene of Vibrio cholerae chromosome II, J. Bacteriol, vol.187, pp.7167-7175

K. M. Palmer, S. L. Turner, and J. P. Young, Sequence diversity of the plasmid replication gene repC in the Rhizobiaceae, Plasmid, vol.44, pp.209-219, 2000.

K. M. Pappas and S. C. Winans, A LuxR-type regulator from Agrobacterium tumefaciens elevates Ti plasmid copy number by activating transcription of plasmid replication genes, Mol. Microbiol, vol.48, pp.1059-1073, 2003.

K. M. Pappas and S. C. Winans, The RepA and RepB autorepressors and TraR play opposing roles in the regulation of a Ti plasmid repABC operon, Mol. Microbiol, vol.49, pp.441-455, 2003.

G. N. Pastorino, V. Martinez-alcántara, and P. A. Balatti, Identification of fast and slow growing rhizobia nodulating soybean (Glycine max [L.] Merr) by a multiplex PCR reaction, FEMS Microbiol. Lett, vol.229, issue.03, pp.796-797, 2003.

J. Petersen, H. Brinkmann, and S. Pradella, Diversity and evolution of repABC type plasmids in Rhodobacterales, Environ. Microbiol, vol.11, pp.2627-2638, 2009.

J. Petersen, O. Frank, M. Göker, and S. Pradella, Extrachromosomal, extraordinary and essential-the plasmids of the Roseobacter clade, Appl. Microbiol. Biotechnol, vol.97, pp.2805-2815, 2013.

F. Pini, N. J. De-nisco, L. Ferri, J. Penterman, A. Fioravanti et al., Cell cycle control by the master regulator CtrA in Sinorhizobium meliloti, PLoS Genet, vol.11, p.1005232, 2015.

U. M. Pinto, A. L. Flores-mireles, E. D. Costa, and S. C. Winans, RepC protein of the octopine-type Ti plasmid binds to the probable origin of replication within repC and functions only in cis, Mol. Microbiol, vol.81, pp.1593-1606, 2011.

U. M. Pinto, K. M. Pappas, and S. C. Winans, The ABCs of plasmid replication and segregation, Nat. Rev. Microbiol, vol.10, pp.755-765, 2012.

R. H. Pritchard, M. G. Chandler, C. , and J. , Independence of F replication and chromosome replication in Escherichia coli, Mol. Gen. Genet, vol.138, pp.143-155, 1975.

A. A. Prozorov, Additional chromosomes in bacteria: properties and origin, Mikrobiologiia, vol.77, pp.437-447, 2008.

K. C. Quon, G. T. Marczynski, and L. Shapiro, Cell cycle control by an essential bacterial two-component signal transduction protein, Cell, vol.84, pp.83-93, 1996.

M. Rajewska, K. Wegrzyn, and I. Konieczny, AT-rich region and repeated sequences -the essential elements of replication origins of bacterial replicons, FEMS Microbiol. Rev, vol.36, pp.408-434, 2012.

R. Ramachandran, P. N. Ciacca, T. A. Filsuf, J. K. Jha, and D. K. Chattoraj, Chromosome 1 licenses chromosome 2 replication in Vibrio cholerae by doubling the crtS gene dosage, PLoS Genet, vol.14, p.1007426, 2018.

M. A. Ramírez-romero, N. Soberón, A. Pérez-oseguera, J. Téllez-sosa, and M. A. Cevallos, Structural elements required for replication and incompatibility of the Rhizobium etli symbiotic plasmid, J. Bacteriol, vol.182, pp.3117-3124, 2000.

M. A. Ramírez-romero, J. Téllez-sosa, H. Barrios, A. Pérez-oseguera, V. Rosas et al., RepA negatively autoregulates the transcription of the repABC operon of the Rhizobium etli symbiotic plasmid basic replicon, Mol. Microbiol, vol.42, pp.195-204, 2001.

T. Rasmussen, R. B. Jensen, and O. Skovgaard, The two chromosomes of Vibrio cholerae are initiated at different time points in the cell cycle, EMBO J, vol.26, pp.3124-3131, 2007.

R. Reyes-lamothe, E. Nicolas, and D. J. Sherratt, Chromosome replication and segregation in bacteria, Annu. Rev. Genet, vol.46, pp.121-143, 2012.

G. T. Robertson, A. Reisenauer, R. Wright, R. B. Jensen, A. Jensen et al., The Brucella abortus CcrM DNA methyltransferase is essential for viability, and its overexpression attenuates intracellular replication in murine macrophages, J. Bacteriol, vol.182, pp.3482-3489, 2000.

C. Rosenberg, F. Casse-delbart, I. Dusha, M. David, and C. Boucher, Megaplasmids in the plant-associated bacteria Rhizobium meliloti and Pseudomonas solanacearum, J. Bacteriol, vol.150, pp.402-406, 1982.

N. Schallopp, S. Milbredt, T. Sperlea, F. S. Kemter, M. Bruhn et al., Establishing a system for testing replication inhibition of the Vibrio cholerae secondary chromosome in Escherichia coli, Antibiotics, vol.7, p.3, 2017.

R. Schekman, A. Weiner, and A. Kornberg, Multienzyme systems of DNA replication, Science, vol.186, pp.987-993, 1974.

G. Scholefield, J. Errington, M. , and H. , Soj/ParA stalls DNA replication by inhibiting helix formation of the initiator protein DnaA, EMBO J, vol.31, pp.1542-1555, 2012.

A. J. Silva and J. A. Benitez, Vibrio cholerae biofilms and cholera pathogenesis, PLoS Negl. Trop. Dis, vol.10, p.4330, 2016.

N. Soberón, T. Venkova-canova, M. A. Ramírez-romero, J. Téllez-sosa, and M. A. Cevallos, Incompatibility and the partitioning site of the repABC basic replicon of the symbiotic plasmid from Rhizobium etli, Plasmid, vol.51, pp.203-216, 2004.

M. Soora, J. Tomasch, H. Wang, V. Michael, J. Petersen et al., Oxidative stress and starvation in Dinoroseobacter shibae: the role of extrachromosomal elements, Front. Microbiol, vol.6, p.233, 2015.

C. Stephens, A. Reisenauer, R. Wright, and L. Shapiro, A cell cycle-regulated bacterial DNA methyltransferase is essential for viability, Proc. Natl. Acad. Sci. U.S.A, vol.93, pp.1210-1214, 1996.

A. Suwanto and S. Kaplan, Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: presence of two unique circular chromosomes, J. Bacteriol, vol.171, pp.5850-5859, 1989.

M. K. Swan, D. Bastia, and C. Davies, Crystal structure of pi initiator protein-iteron complex of plasmid R6K: implications for initiation of plasmid DNA replication, Proc. Natl. Acad. Sci. U.S.A, vol.103, pp.18481-18486, 2006.

M. Szymanik, R. Welc-faleciak, D. Bartosik, and M. W?odarczyk, Replication system of plasmid pMTH4 of Paracoccus methylutens DM12 contains an enhancer, Pol. J. Microbiol, vol.55, pp.261-270, 2006.

M. Touchon and E. P. Rocha, Coevolution of the organization and structure of prokaryotic genomes, Cold Spring Harb. Perspect. Biol, vol.8, p.18168, 2016.

M. Trucksis, J. Michalski, Y. K. Deng, and J. B. Kaper, The Vibrio cholerae genome contains two unique circular chromosomes, Proc. Natl. Acad. Sci. U.S.A, vol.95, pp.14464-14469, 1998.

M. Val, S. P. Kennedy, M. El-karoui, L. Bonné, F. Chevalier et al., FtsK-dependent dimer resolution on multiple chromosomes in the pathogen Vibrio cholerae, PLoS Genet, vol.4, p.1000201, 2008.
URL : https://hal.archives-ouvertes.fr/inserm-01285588

M. Val, S. P. Kennedy, A. J. Soler-bistué, V. Barbe, C. Bouchier et al., Fuse or die: how to survive the loss of Dam in Vibrio cholerae, Mol. Microbiol, vol.91, pp.665-678, 2014.
URL : https://hal.archives-ouvertes.fr/inserm-01285641

M. Val, M. Marbouty, F. De-lemos-martins, S. P. Kennedy, H. Kemble et al., A checkpoint control orchestrates the replication of the two chromosomes of Vibrio cholerae, Sci. Adv, vol.2, p.1501914, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01309592

M. Val, O. Skovgaard, M. Ducos-galand, M. J. Bland, and D. Mazel, , 2012.

, Genome engineering in Vibrio cholerae: a feasible approach to address biological issues, PLoS Genet, vol.8, p.1002472

T. Venkova-canova, J. H. Baek, P. C. Fitzgerald, M. Blokesch, and D. K. Chattoraj, Evidence for two different regulatory mechanisms linking replication and segregation of Vibrio cholerae chromosome II, PLoS Genet, vol.9, p.1003579, 2013.

T. Venkova-canova and D. K. Chattoraj, Transition from a plasmid to a chromosomal mode of replication entails additional regulators, Proc. Natl. Acad. Sci. U.S.A, vol.108, pp.6199-6204, 2011.

T. Venkova-canova, A. Saha, and D. K. Chattoraj, A 29-mer site regulates transcription of the initiator gene as well as function of the replication origin of Vibrio cholerae chromosome II, Plasmid, vol.67, pp.102-110, 2012.

T. Venkova-canova, N. E. Soberón, M. A. Ramírez-romero, and M. A. Cevallos, Two discrete elements are required for the replication of a repABC plasmid: an antisense RNA and a stem-loop structure, Mol. Microbiol, vol.54, pp.1431-1444, 2004.

T. Venkova-canova, P. Srivastava, and D. K. Chattoraj, Transcriptional inactivation of a regulatory site for replication of Vibrio cholerae chromosome II, Proc. Natl. Acad. Sci. U.S.A, vol.103, pp.12051-12056, 2006.

K. E. Wegrzyn, M. Gross, U. Uciechowska, and I. Konieczny, Replisome assembly at bacterial chromosomes and iteron plasmids, Front. Mol. Biosci, vol.3, p.39, 2016.

S. Wickner, J. Hoskins, and K. Mckenney, Monomerization of RepA dimers by heat shock proteins activates binding to DNA replication origin, Proc. Natl. Acad. Sci. U.S.A, vol.88, pp.7903-7907, 1991.

D. R. Williams and C. M. Thomas, Active partitioning of bacterial plasmids, J. Gen. Microbiol, vol.138, pp.1-16, 1992.

D. Wion and J. Casadesús, N6-methyl-adenine: an epigenetic signal for DNA-protein interactions, Nat. Rev. Microbiol, vol.4, pp.183-192, 2006.
URL : https://hal.archives-ouvertes.fr/inserm-00390766

M. Wola?ski, D. Jakimowicz, and J. Zakrzewska-czerwi?ska, Fifty years after the replicon hypothesis: cell-specific master regulators as new players in chromosome replication control, J. Bacteriol, vol.196, pp.1706-1720, 2014.

R. Wright, C. Stephens, and L. Shapiro, The CcrM DNA methyltransferase is widespread in the alpha subdivision of proteobacteria, and its essential functions are conserved in Rhizobium meliloti and Caulobacter crescentus, J. Bacteriol, vol.179, pp.5869-5877, 1997.

Q. Xu, M. Dziejman, and J. J. Mekalanos, Determination of the transcriptome of Vibrio cholerae during intraintestinal growth and midexponential phase in vitro, Proc. Natl. Acad. Sci. U.S.A, vol.100, pp.1286-1291, 2003.

Y. Yamaichi, M. A. Fogel, S. M. Mcleod, M. P. Hui, and M. K. Waldor, Distinct centromere-like parS sites on the two chromosomes of Vibrio spp, J. Bacteriol, vol.189, pp.5314-5324, 2007.

Y. Yamaichi, M. A. Gerding, B. M. Davis, and M. K. Waldor, Regulatory cross-talk links Vibrio cholerae chromosome II replication and segregation, PLoS Genet, vol.7, p.1002189, 2011.

Y. Yamaichi, T. Iida, K. S. Park, K. Yamamoto, and T. Honda, Physical and genetic map of the genome of Vibrio parahaemolyticus: presence of two chromosomes in Vibrio species, Mol. Microbiol, vol.31, pp.1513-1521, 1999.

Y. Yao, S. Enkhtsetseg, I. Odsbu, L. Fan, and M. Morigen, Mutations of DnaA-boxes in the oriR region increase replication frequency of the MiniR1-1 plasmid, BMC Microbiol, vol.18, p.27, 2018.

K. Zebracki, P. Koper, M. Marczak, A. Skorupska, and A. Mazur, Plasmidencoded RepA proteins specifically autorepress individual repABC operons in the multipartite Rhizobium leguminosarum bv. trifolii Genome, PLoS One, vol.10, p.131907, 2015.

J. Zeuthen and M. L. Pato, Replication of the F'lac sex factor in the cell cycle of Escherichia coli, Mol. Gen. Genet, vol.111, pp.242-255, 1971.

Z. Zhong, D. Helinski, and A. Toukdarian, A specific region in the N terminus of a replication initiation protein of plasmid RK2 is required for recruitment of Pseudomonas aeruginosa DnaB helicase to the plasmid origin, J. Biol. Chem, vol.278, pp.45305-45310, 2003.

R. L. Zuerner, J. L. Herrmann, and I. Girons, Comparison of genetic maps for two Leptospira interrogans serovars provides evidence for two chromosomes and intraspecies heterogeneity, J. Bacteriol, vol.175, pp.5445-5451, 1993.