Chapter 26 : Second Chromosomes and Megaplasmids in Bacteria

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This chapter reviews some aspects of the many major secondary DNA replicons that have been characterized from organisms that possess multireplicon genomes. Nonprimary replicons are often referred to as secondary chromosomes if they are essential for cell viability or as megaplasmids. A modern source of ambiguity in genomic biology is whether certain replicons represent megaplasmids or second chromosomes. Multircplicon genomes in bacteria could conceivably arise by a number of mechanisms, but two general mechanisms seem most plausible. A major secondary replicon may derive from an ancestral chromosome via an excision event where the excised DNA possesses an origin of replication that is either a duplicated copy of the region or a second, redundant origin that was previously resident on that part of the ancestral chromosome. Chromosome I has an origin of replication typical of other bacterial chromosomes, and the region encodes the , , , and genes. A greater proportion of chromosome II is also devoted to genes encoding transporters and solute binding proteins and to genes encoding enzymes required in central intermediary metabolism. The linear chromosome encodes and other genes required for synthesis of several cell surface polysaccharides and also the cellulose synthesis genes that are required for host attachment. Copies of genes required for the synthesis of some amino acids and for certain enzyme cofactors are carried uniquely on the megaplasmid as are the flagellar genes.

Citation: MacLellan S, Sibley C, Finan T. 2004. Second Chromosomes and Megaplasmids in Bacteria, p 529-542. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch26
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Image of Figure 1.
Figure 1.

Cladogram of ParA ATPases. Amino acid sequences were obtained from tbe NCBI database and aligned using ClustalX. In the case of multiple ParA-like sequences on a replicon, the ParA sequence closest to the origin of replication was used. The maximum likelihood tree was generated with a quartet puzzling program, TreePuzzle 5.0. Branch lengths were computed using a model of substitution and rate heterogeneity ( ). Support for the internal branches of the quartet puzzling tree topology is shown in percent values at each node. Accession numbers are provided in the descending order they appear in the tree: NP_700354, NP_541070, NP_109505, NP_534416, AAB69096, NP_436589, NP_53616I, NP_535377, AAC83387, NP_436540, CAA62234, CAA28295, NP.233494, NP_763081, AAA99230, CAA28769, NP_085829, CAA62234, NP_720345, NP_387441, NP_532810, NP_699034, NP.538927, NP_105341, NP_76727l, NP_422547, NP_220452, NP_742172, NP_391977, NP_521445, NP_720272, NP_232399, NP_759973.

Citation: MacLellan S, Sibley C, Finan T. 2004. Second Chromosomes and Megaplasmids in Bacteria, p 529-542. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch26
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1. Allardet-Servent, A.,, S. Michaux-Charachon,, E. Jumas- Bilak,, L. Karayan,, and M. Ramuz. 1993. Presence of one linear and one circular chromosome in the Agrobacterium tumefaciens C58 genome.J. Bacteriol. 175:78697874.
2. Banfalvi, Z.,, E. Kondorosi,, and A. Kondorosi. 1985. Rbizobium meliloti carries two megaplasmids. Plasmid 13:129138.
3. Baril, C.,, C. Richaud,, G. Baranton,, and I. S. Saint Girons. 1989. Linear chromosome of Borrelia burgdorferi. Res. Microbiol. 140:507516.
4. Barnett, M. J.,, R. F. Fisher,, T. Jones,, C. Komp,, A. P. Abola,, F. Barloy-Hubler,, L. Bowser,, D. Capela,, F. Galibert,, J. Gouzy,, M. Gurjal,, A. Hong,, L. Huizar,, R. W. Hyman,, D. Kahn,, M. L. Kahn,, S. Kalman,, D. H. Keating,, C. Palm,, M. C. Peck,, R. Surzycki,, D. H. Wells,, K. C. Yeh,, R. W. Davis,, N. A. Federspiel,, and S. R. Long. 2001. Nucleotide sequence and predicted functions of the entire Sinorbizobium meliloti pSymA megaplasmid. Proc. Natl. Acad. Sci. USA 98:98839888.
5. Bartosik, D.,, M. Szymanik,, and E. Wysocka. 2001. Identification of the partitioning site within the repABC-type replicon of the composite Paracoccus versutus plasmid pTAVl. J. Bacteriol. 183:62346243.
6. Bentley, S. D.,, K. F. Chatcr,, A. M. Cerdeno-Tarraga,, G. L. Challis,, N. R. Thomson,, K. D. James,, D. E. Harris,, M. A. Quail,, H. Kieser,, D. Harper,, A. Bateman,, S. Brown,, G. Chandra,, C. W. Chen,, M. Collins,, A. Cronin,, A. Fraser,, A. Goble,, J. Hidalgo,, T. Hornsby,, S. Howarth,, C. H. Huang,, T. Kieser,, L. Larke,, L. Murphy,, K. Oliver,, S. O'Neil,, E. Rabbinowitsch,, M. A. Rajandream,, K. Rutherford,, S. Rutter,, K. Secger,, D. Saunders,, S. Sharp,, R. Squares,, S. Squares,, K. Taylor,, T. Warren,, A. Wietzorrek,, J. Woodward,, B. G. Barrell,, J. Parkhill,, and D. A. Hopwood. 2002. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141147.
7. Bignell, C.,, and C. M. Thomas. 2001. The bacterial ParAParB partitioning proteins.J. Bioteclynol. 91:134.
8. Brassinga, A. K.,, R. Siam,, W. McSween,, H. Winkler,, D. Wood,, and G. T. Marczynski. 2002. Conserved response regulator CtrA and IHF binding sites in the alpha-proteobacteria Caulobacter crescentus and Rickettsia prowazekii chromosomal replication origins.J. Bacteriol. 184:57895799.
9. Brumbley, S. M.,, B. F. Carney,, and T. P. Denny. 1993. Phenotype conversion in Pseudomonas solanacearum due to spontaneous inactivation of PhcA, a putative LysR transcriptional regulator.J. Bacteriol. 175:54775487.
10. Casjens, S. 1998. The diverse and dynamic structure of bacterial genomes. Annu. Rev. Genet. 32:339377.
11. Cevallos, M. A.,, H. Porta,, J. Izquierdo,, C. Tun-Garrido,, A. Garcia-de-los-Santos,, G. Davila,, and S. Brom. 2002. Rhizobium etli CFN42 contains at least three plasmids of the repABC family: a structural and evolutionary analysis. Plasmid 48:104116.
12. Chain, P. S.,, I. Hernandez-Lucas,, B. Golding,, and T. M. Finan. 2000. onT-directed cloning of defined large regions from bacterial genomes: identification of the Sinorbizobium meliloti pExo megaplasmid replicator region. J. Bacteriol. 182:54865494.
13. Charles, T. C.,, and T. M. Finan. 1991. Analysis of a 1600- kb Rhizobium meliloti megaplasmid using defined deletions generated in vivo. Genetics 127:520.
14. Chen, H.,, J. Higgins,, I. J. Oresnik,, M. F. Hynes,, S. Natera,, M. A. Djordjevic,, J. J. Weinman,, and B. G. Rolfe. 2000. Proteome analysis demonstrates complex replicon and luteolin interactions in pSyma-cured derivatives of Sinorbizobium meliloti strain 2011, Electrophoresis 21:38333842.
15. Chen, H. W.,, A. Kuspa,, I. M. Keseler,, and L. J. Shimkets. 1991. Physical map of the Myxococcus xanthus chromosome.J. Bacteriol 173:21092115.
16. Choudhary, M.,, C. Mackenzie,, K. Nereng,, E. Sodergren,, G. M. Weinstock,, and S. Kaplan. 1997. Low-resolution sequencing of Rhodobacter sphaeroides 2.4.IT: chromosome II is a true chromosome. Microbiology 143(Pt 10):30853099.
17. Choudhary, M.,, C. Mackenzie,, K. S. Nereng,, E. Sodergren,, G. M. Weinstock,, and S. Kaplan. 1994. Multiple chromosomes in bacteria: structure and function of chromosome II of Rhodobacter sphaeroides 2.4 I T.J. Bacteriol. 176:76947702.
18. Coenye, T.,, and P. Vandamme, 2003. Simple sequence repeats and compositional bias in the bipartite Ralstonia solanacearum GMI1000 genome. BMC Genomics 4:10.
19. DelVecchio, V. G.,, V. Kapatral,, R. J . Redkar,, G. Patra,, C. Mujer,, T. Los,, N. Ivanova,, L. Anderson,, A. Bhattacharyya,, A. Lykidis,, G. Reznik,, L. Jablonski,, N. Larson,, M. D'Souza,, A. Bernal,, M. Mazur,, E. Goltsman,, E. Sclkov,, P. H. Elzer,, S. Hagius,, D. O'Callaghan,, J. J. Letesson,, R. Haselkorn,, N. Kyrpides,, and R. Overbeek. 2002. The genome sequence of the facultative intracellular pathogen Brucella melitensis. Proc. Natl. Acad. Sci. USA 99:443448.
20. England, J. C., and J. W. Gober. 2001. Cell cycle control of cell morphogenesis in Caulobacter. Curr. Opin. Microbial 4:674680,
21. Errington, J . 2001. Septation and chromosome segregation during sporulation in Bacillus subtilis. Curr. Opin. Microbial 4:660666.
22. Finan, T. M.,, B. Kunkel,, G. F. De Vos,, and E. R. Signer. 1986. Second symbiotic megaplasmid in Rhizobium meliloti carrying exopolysaccharide and thiamine synthesis genes. J. Bacteriol 167:6672.
23. Finan, T. M.,, I. Oresnik,, and A. Bottacin. 1988. Mutants of Rhizobium meliloti defective in succinate metabolism. J. Bacteriol 170:33963403.
24. Finan, T. M.,, S. Weidner,, K. Wong,, J . Buhrmester,, P. Chain,, F. J . Vorholter,, I. Hernandez-Lucas,, A. Becker,, A. Cowic,, J. Gouzy,, B. Golding,, and A. Puhler, 2001. The complete sequence of the 1,683-kb pSymB megaplasmid from the N2- fixing endosymbiont Sinorbizobium meliloti. Proc. Natl. Acad. Sci. USA 98:98899894.
25. Finan, T.M.,, J. M. Wood,, and D.C. Jordan, 1983. Symbiotic properties of C4-dicarboxylic acid transport mutants of Rhizobium leguminosarum. J. Bacteriol. 154:14031413.
26. Fraser, C. M.,, J . D. Gocayne,, O. White,, M. D. Adams,, R. A. Clayton,, R. D. Fleisehmann,, C. J. Bult,, A. R. Kerlavage,, G. Sutton,, and J. M. Kelley. 1995. The minimal gene complement of Mycoplasma genitalium. Science 270:397403.
27. Freiberg, C.,, R. Fellay,, A. Bairoch,, W. J. Broughton, A. Rosenthal, and X . Perret. 1997. Molecular basis of symbiosis between Rhizobium and legumes. Nature 387:394401.
28. Fuqua, C.,, M. R. Parsek,, and E. P. Greenberg. 2001. Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing. Annu. Rev. Genet. 35:439468.
29. Galibert, F.,, T. M. Finan,, S. R. Long,, A. Puhler,, P. Abola,, F. Ampc,, F. Barloy-Hubler,, M. J . Barnett,, A. Becker,, P. Boistard,, G. Bothe,, M. Boutry,, L. Bowser,, J . Buhrmester,, E. Cadieu,, D. Capela,, P. Chain,, A. Cowie,, R. W. Davis,, S. Dreano,, N. A. Fcdcrspicl,, R. F. Fisher,, S. Gloux,, T. Godrie,, A. Goffeau,, B. Golding,, J . Gouzy,, M. Gurjal,, I. Hernandez-Lucas,, A. Hong,, L. Huizar,, R. W. Hyman,, T. Jones,, D. Kahn,, M. L. Kahn,, S. Kalman,, D. H. Keating,, E. Kiss,, C. Komp,, V. Lelaurc,, D. Masuy,, C. Palm,, M. C. Peck,, T. M. Pohl,, D. Portetelle,, B. Purnelle,, U. Ramspcrger,, R. Surzycki,, P. Thebault,, M. Vandenbol,, F. J. Vorholter,, S. Weidner,, D. H. Wells,, K. Wong,, K. C. Yeh,, and J. Batut. 2001. The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293:668672.
30. Gerdes, K.,, J. Moller-Jensen,, and J. R. Bugge. 2000. Plasmid and chromosome partitioning: surprises from phylogcny. Mol Microbiol 37:455166.
31. Gil, R.,, B. Sabater-Munoz,, A. Latorre,, F. J. Silva,, and A. Moya. 2002. Extreme genome reduction in Bucbnera spp.: toward rhe minimal genome needed for symbiotic life. Proc. Natl. Acad. Sci. USA 99:44544458.
32. Girard, M. L.,, M. Flores,, S. Brom,, D. Romero,, R. Palacios,, and G. Davila. 1991. Structural complexity of the symbiotic plasmid of Rhizobium leguminosarum bv. phaseoli. J . Bacterial 173:24112419.
33. Godfrin-Estevenon, A. M.,, F. Pasta,, and D. Lane. 2002. The parAB gene products of Pseudomonas putida exhibit partition activity in both P. putida and Escherichia coli. Mol. Microbiol 43:3949.
34. Goodner, B.,, G. Hinkle,, S. Gattung,, N. Miller,, M. Blanchard,, B. Qurollo,, B. S. Goldman,, Y. Cao,, M. Askcna2i,, C. Hailing,, L. Mullin,, K. Houmiel,, J . Gordon,, M. Vaudin,, O. Iartchouk,, A. Epp,, F. Liu,, C. Wollam,, M. Allinger,, D. Doughty,, C. Scott,, C. Lappas,, B. Markelz,, C. Flanagan,, C. Crowell,, J. Gurson,, C. Lomo,, C. Sear,, G. Strub,, C. Cielo,, and S. Slater. 2001. Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58. Science 294:23232328.
35. Goodner, B. W., B. P. Markelz,, M. C. Flanagan,, C. B. CrowellJr.,, J. L. Raccttc,, B. A. Schilling,, L. M. Halfon,, J. S. Mellors,, and G. Grabowski. 1999. Combined genetic and physical map of the complex genome of Agrobacterium tumefaciens.J. Bacteriol 181:51605166,
36. Heidelberg, J. F.,, J. A. Eisen,, W. C Nelson,, R. A. Clayton,, M. L. Gwinn,, R. J. Dodson,, D. H. Haft,, E. K. Hickey,, J. D. Peterson,, L. Umayam,, S. R. Gill,, K. E. Nelson,, T. D. Read,, H. Tcttclin,, D. Richardson,, M. D. Ermolaeva,, J . Vamathevan,, S. Bass,, H. Qin,, I. Dragoi,, P. Sellers,, L. McDonald,, T. Utterback,, R. D. Fteishmann,, W. C. Nierman,, and O. White. 2000. DNA sequence of both chromosomes of the cholera pathogen Vibrio cbolerae. Nature 406:477483.
37. Heidelberg, J. F.,, L. T. Paulsen,, K. E. Nelson,, E. J. Gaidos,, W. C. Nelson,, T. D. Read,, J. A. Eisen,, R. Seshadri,, N. Ward,, B. Mcthc,, R. A. Clayton,, T. Meyer,, A. Tsapin,, J. Scott,, M. Beanan,, L. Brinkac,, S. Daugherty,, R. T. Deboy,, R. J. Dodson,, A. S. Durkin,, D. H. Haft,, J. F. Kolonay,, R. Madupu,, J. D. Peterson,, L. A. Umayam,, O. White,, A. M. Wolf,, J. Vamathevan,, J. Weidman,, M. Impraim,, K. Lee,, K. Berry,, C. Lee,, J. Mueller,, H. Khouri,, J. Gill,, T. R. Utterback,, L. A. McDonald,, T. V. Fetdblyum,, H. O. Smith,, J. C. Venter,, K. H. Neatson,, and C. M. Frascr. 2002. Genome sequence of the dissimilatory metal ion-reducing bacterium Shetvanella oneidensis. Nat. Biotechnol. 20:11181123.
38. Hinnebusch, J.,, S. Bergstrom,, and A. G. Barbour. 1990. Cloning and sequence analysis of linear plasmid telomeres of the bacterium Borrelia burgdorferi. Mol. Microbiol 4:811820.
39. Honeycutt, R. J .,, M. McClelland,, and B. W. Sobral. 1993. Physical map of the genome of Rhizobium meliloti 1021. J . Bacteriol. 175:69456952.
40. Hutchison, C. A.,, S. N. Peterson,, S. R. Gill,, R. T. Clinc,, O. White,, C. M. Fraser,, H. O. Smith,, and J . C Venter, 1999. Global transposon mutagenesis and a minimal Mycoplasma genome. Science 286:21652169.
41. Hynes, M. F.,, and T. M. Finan,. 2003. General genetic knowledge, p. 2543. In H. P. Spaink,, A. Kondorosi,, and P. J. J. Hooykaas (ed.), The Rbizobiaceae—Molecular Biology of Model Plant-Associated Bacteria. Kluwer Academic Publishers, Dordrecht, The Netherlands.
42. Hynes, M. F.,, R. Simon,, P. Mullcr,, K. Niehaus,, M. Labes,, and A. Puhlcr. 1986. The two megaplasmids of Rhizobium meliloti are involved in the effective nodulation of alfalfa. Mol. Gen. Genet. 202:356362.
43. Jenal, U.,, and C. Stephens. 2002. The Caulobacter cell cycle: timing, spatial organization and checkpoints. Curr. Opin. Microbiol. 5:558563.
44. Jumas-Bilak, E.,, S. Michaux-Charachon,, G. Bourg,, D. O'Callaghan,, and M. Ramuz. 1998. Differences in chromosome number and genome rearrangements in the genus Brucella. Mol Microbiol 27:99106.
45. Jumas-Bilak, E.,, S. Michaux-Charachon,, G. Bourg,, M. Ramuz,, and A. Allardet-Servent, 1998. Unconventional genomic organization in the alpha subgroup of the Proteobacteria. J. Bacteriol. 180:27492755.
46. Kaneko, T.,, Y. Nakamura,, S. Sato,, E. Asamizu,, T. Kato,, S. Sasamoto,, A. Watanabe,, K. Idcsawa,, A. Ishikawa,, K. Kawashima,, T. Kimura,, Y. Kishida,, C. Kiyokawa,, M. Kohara,, M. Matsumoto,, A. Matsuno,, Y. Mochizuki,, S. Nakayama,, N. Nakazaki,, S. Shimpo,, M. Sugimoto,, C. Takeuchi,, M. Yamada,, and S. Tabata. 2000. Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti. DNA Res. 7:331338.
47. Kaneko, T.,, Y. Nakamura,, S. Sato,, K. Minamisawa,, T. Uchiumi,, S. Sasamoto,, A. Watanabe,, K. Idesawa,, M. Iriguchi,, K. Kawashima,, M. Kohara,, M. Matsumoto,, S. Shimpo,, H. Tsuruoka,, T. Wada,, M. Yamada,, and S. Tabata. 2002. Complete genomic sequence of nitrogen-fixing symbiotic bacterium Bradyrhizobium japonicum USDA110. DNA Res. 9:189197.
48. Kaneko, T.,, Y. Nakamura,, C. P. Wolk,, T. Kuritz,, S. Sasamoto,, A. Watanabe,, M. Iriguchi,, A. Ishikawa,, K. Kawashima,, T. Kimura,, Y. Kishida,, M. Kohara,, M. Matsumoto,, A. Matsuno,, A. Muraki,, N. Nakazaki,, S. Shimpo,, M. Sugimoto,, M. Takazawa,, M. Yamada,, M. Yasuda,, and S. Tabata. 2001. Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. DNA Res. 8:205213.
49. Karlin, S.,, J . Mrazek,, and A. M, Campbell. 1997. Compositional biases of bacterial genomes and evolutionary implications.;. Bacteriol. 179:38993913.
50. Kieser, H. M.,, T. Kieser,, and D. A. Hopwood. 1992. A combined genetic and physical map of the Streptomyces coelicolor A3(2)chromosome.J. Bacteriol. 174:54965507.
51. Kolsto, A. B. 1997. Dynamic bacterial genome organization. Mol. Microbiol. 24:241248.
52. Kolsto, A. B. 1999. Time for a fresh look at the bacterial chromosome. Trends Microbiol. 7:223226.
53. Koonin, E. V. 2000. How many genes can make a cell: the minimat-gene-set concept. Annu. Rev. Genomics Hum. Genet. 1:99116.
54. Kornberg, A. 2000. Ten commandments: lessons from the enzymology of DNA replication. J. Bacteriol. 182:36133618.
55. Leblond, P.,, M. Redenbach,, and J. Cullum. 1993. Physical map of the Streptomyces lividans 66 genome and comparison with that of the related strain Streptomyces coelicolor A3(2).J. Bacteriol. 175:34223429.
56. Levin, P. A.,, and A. D. Grossman. 1998. Cell cycle and sporulation in Bacillus subtilis. Curr. Opin. Microbiol. 1:630635.
57. Levin-Zaidman, S.,, J . Englander,, E. Shimoni,, A. K. Sharma,, K. W. Minton,, and A. Minsky. 2003. Ringlike structure of the Deinococcus radiodurans genome: a key to radio-resistant-? Science 299:254256.
58. Lewis, R. A.,, C. R. Bignell,, W. Zeng,, A. C. Jones,, and C. M. Thomas. 2002. Chromosome loss from par mutants of Pseudomonas putida depends on growth medium and phase of growth. Microbiology 148:537548.
59. Li, P. L.,, and S. K. Farrand. 2000. The replicator of the nopalinc-type Ti plasmid pTiC58 is a member of the repABC family and is influenced by the TraR-dependent quorumsensing regulatory system. J. Bacteriol. 182:179188.
60. Lin, Y . S.,, H. M. Kieser,, D. A. Hopwood,, and C. W. Chen. 1993. The chromosomal DNA of Streptomyces lividans 66 is linear. Mol. Microbiol 10:923933.
61. MacLellan, S. R.,, C. D. Sibley,, B. Golding,, and T. M. Finan,. 2002. The 1683 kb replicon of Sinorhizobium meliloti:. past and present investigations into the nature of a very large bacterial plasmid. p. 4145 In T. M. Finan,. M. R. O'Brian,, D. B. Layzell,, J. K. Vessey,, and A. Newton (ed.), Nitrogen Fixation: Global Perspectives. CAB1 Publishing, London, United Kingdom.
62. Maldonado, R.,, J. Jimenez,, and J. Casadesus. 1994. Changes of ploidy during the Azotobacter vinelandii growth cycle. J. Bacteriol 176:39113919.
63. Marezynski, G. T.,, and L. Shapiro. 1992. Cell-cycle control of a cloned chromosomal origin of replication from Caulobacter crescentus. J. Mol Biol 226:959977.
64. Mavingui, P.,, M. Flores,, X . Guo,, G. Davila,, X. Perret,, W. J. Broughton,, and R. Palacios. 2002. Dynamics of genome architecture in Rhizobium sp. strain NGR234, J. Bacteriol 184:171176.
65. Mcsser, W. 2002. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol Rev. 26:355374.
66. Michaux, S.,, J . Paillisson,, M. J . Carles-Nurit,, G. Bourg,, A. Allardet-Scrvcnt,, and M. Ramuz. 1993. Presence of two independent chromosomes in the Brucella melitensis 16M genome, J. Bacteriol 175:701705.
67. Michaux-Charachon, S.,, G. Bourg,, E. Jumas-Bilak,, P. Guigue-Talet,, A. Allardet-Servent,, D. O'Callaghan,, and M. Ramuz. 1997. Genome structure and phylogeny in the genus Brucella.J. Bacteriol. 179:32443249.
68. Miller, M. B.,, and B. L. Bassler. 2001. Quorum sensing in bacteria. Annu. Rev. Microbiol. 55:165199.
69. Moreno, E. 1998. Genome evolution within the alpha Proteobacteria: why do some bacteria not possess plasmids and others exhibit more than one different chromosome? FEMS Microbiol. Rev. 22:255275.
70. Moriguchi, K.,, Y. Macda,, M. Satou,, N. S. Hardayani,, M. Kataoka,, N. Tanaka,, and K. Yoshida. 2001. The complete nucleotide sequence of a plant root-inducing (Ri) plasmid indicates its chimeric structure and evolutionary relationship between tumor-inducing (Ti) and symbiotic (Sym) plasmids in Rhizobiaceae. J. Mol Biol. 307:771784.
71. Muller, T.,, and M. Vingron. 2000. Modeling amino acid replacement. J. Comput. Biol 7:761776.
72. Mushegian, A. R.,, and E. V. Koonin. 1996. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. NatL Acad. Sci. USA 93:1026810273.
73. Ng, W. V.,, S. A. Ciufo,, T. M. Smith,, R. E. Bumgarner,, D. Baskin,, J . Faust,, B. Hall,, C. Lorctz,, J . Seto,, J. Slagel,, L. Hood,, and S. DasSarma. 1998. Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or in in .chromosome? Genome Res. 8:11311141.
74. Ng, W. V.,, S. P. Kennedy,, G. G. Mahairas,, B. Berquist,, M. Pan,, H. D. Shukla,, S. R. Lasky,, N. S. Baliga,, V. Thorsson,, J . Sbrogna,, S. Swartzell,, D. Weir,, J . Hall,, T. A. Dahl,, R. Welti,, Y. A. Goo,, B. Leithauscr,, K. Keller,, R. Cruz,, M. J . Danson,, D. W. Hough,, D. G. Maddocks,, P. E. Jablonski,, M. P. Krebs,, C. M. Angevine,, H. Dale,, T. A. Isenbarger,, R. F. Peck,, M. Pohlschrodcr,, J. L. Spudich,, K. W. Jung,, M. Alam,, T. Freitas,, S. Hou,, C. J. Daniels,, P. P. Dennis,, A. D. Omcr,, H. Ebhardt,, T. M. Lowe,, P. Liang,, M. Riley,, L. Hood,, and S. DasSarma. 2000. Genome sequence of lialobacterium species NRC-I. Proc. NatL Acad. Sci. USA 97:1217612181.
75. Oresnik, I. J.,, S. L. Liu,, C. K. Yost,, and M. F. Hynes. 2000. Megaplasmid pRme201 la of Sinorbizobium meliloti is not required for viability.J. Bacteriol. 182:35823586.
76. Osteras, M.,, and U. Jcnal. 2000. Regulatory circuits in Caulobacter. Curr. Opin. Microbiol. 3:171176.
77. Parkhill, J .,, G. Dougan,, K. D. James,, N. R. Thomson,, D. Pickard,, J. Wain,, C. Churcher,, K. L. Mungall,, S. D. Bentley,, M. T. Holden,, M. Sebaihia,, S. Baker,, D. Basham,, K. Brooks,, T. Chillingworth,, P. Conncrton,, A. Cronin,, P. Davis,, R. M. Davies,, L. Dowd,, N. White,, J. Farrar,, T. Feltwell,, N. Hamlin,, A. Haquc,, T. T. Hien,, S. Holroyd,, K. Jagels,, A. Krogh,, T. S. Larsen,, S. Leather,, S. Moule,, P. O'Gaora,, C. Parry,, M. Quail,, K. Rutherford,, M. Simmonds,, J. Skelton,, K. Stevens,, S. Whitehead,, and B. G. Barrell. 2001. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413:848852.
78. Paulsen, I. T.,, R. Seshadri,, K. E. Nelson,, J. A. Eisen,, J . F. Heidelberg,, T. D. Read,, R. J. Dodson,, L. Umayam,, L. M. Brinkae,, M. J . Bcanan,, S. C Daugherty,, R. T. Deboy,, A. S. Durkin,, J. F. Kolonay,, R. Madupu,, W. C. Nelson,, B. Ayodcji,, M. Kraul,, J. Shetty,, J. Malek,, S. E. Van Aken,, S. Ricdmullcr,, H. Tcttclin,, S. R. Gill,, O. White,, S. L. Salzberg,, D. L. Hoover,, L. E. Lindler,, S. M. Hailing,, S. M. Boyle,, and C. M. Fraser. 2002. The Brucella suis genome reveals fundamental similarities between animal and plant pathogens and symbioms. Proc. Natl Acad. Sci. USA 99:1314813153,
79. Ramirez-Romero, M. A. N. Soberon, A. Perez-Oseguera, J . Tellez-Sosa, and M. A. Cevallos. 2000. Structural elements required for replication and incompatibility of the Rhizobium etli symbiotic plasmid. J. Bacteriol 182:31173124.
80. Redenbach, M.,, K. Ikeda,, M. Yamasaki,, and H. Kinashi. 1998. Cloning and physical mapping of the EcoRI fragments of the giant linear plasmid SCP1. J. Bacteriol 180:27962799.
81. Rodley, P. D.,, U. Romling,, and B. Tummler. 1995. A physical genome map of the Burkbolderia cepacia type strain. Mol Microbiol. 17:5767.
82. Rosenberg, C.,, F. Casse-Delbart,, I. Dusha,, M. David,, and C. Boucher. 1982. Megaplasmids in the plant-associated bacteria Rhizobium meliloti and Pseudomonas solanacearum. J. Bacteriol 150:402406.
83. Ryan, K. R.,, and L. Shapiro. 2003. Temporal and spatial regulation in prokaryotic cell cycle progression and development, Annu. Rev. Biochem. 72:367394.
84. Salanoubat, M.,, S. Genin,, F. Artiguenave,, J . Gouzy,, S. Mangenot,, M. Arlat,, A. Billault,, P. Brottier,, J . C. Camus,, L. Caaolico,, M. Chandler,, N. Choisne,, C. Claudel-Renard,, S. Cunnac,, N. Dcmange,, C. Gaspin,, M. Lavie,, A. Moisan,, C. Robert,, W. Saurin,, T. Schiex,, P. Siguier,, P. Thebault,, M. Whalen,, P. Wineker,, M. Levy,, J. Weissenbach,, and C. A. Boucher. 2002. Genome sequence of the plant pathogen Ralstonia solanacearum. Nature 415:497502.
85. Salmond, G. P.,, B. W. Bycroft,, G. S. Stewart,, and P. Williams. 1995. The bacterial 'enigma': cracking the code of cell-cell communication. Mol Microbiol 16:615624.
86. Schwartz, E.,, and B. Friedrich. 2001. A physical map of the megaplasmid pHGI, one of three genomic replicons in Ralstonia eutropha H16, FEMS Microbiol. Lett. 201:213219.
87. Shapiro, J. A. 1998. Thinking about bacterial populations as multicellular organisms. Annu. Rev. Microbiol. 52:81104.
88. Songsivilai, S.,, and T. Dharakul. 2000. Multiple replicons constitute the 6.5-megabase genome of Burkholderia pseudomallei. Acta Trop. 74:169179.
89. Su, C. J., , and J. B. Baseman. 1990. Genome size of Mycoplasma genitatium.J. Bacteriol 172:47054707.
90. Suwanto, A.,, and S. Kaplan. 1989. Physical and genetic mapping of the Rhodobacter sphaeroides 2.4.1 genome: presence of two unique circular chromosomes. J . Bacteriol 171:58505859.
91. Taghavi, S.,, M. Mergcay,, and D. van der Lelie. 1997. Genetic and physical maps of the Alcaligenes eutrophus CH34 megaplasmid pMOL28 and its derivative pMOL50 obtained after temperature-induced mutagenesis and mortality. Plasmid 37:2234.
92. Tagomori, K.,, T. Iida,, and T. Honda. 2002. Comparison of genome structures of vibrios, bacteria possessing two chromosomes. J . Bacteriol. 184:43514358.
93. Trucksis, M.,, J . Michalski,, Y. K. Deng,, and J. B. Kaper. 1998. The Vibrio cholerae genome contains two unique circular chromosomes. Proc. Natl. Acad. Sci. USA 95:1446414469.
94. Venkatesan, M. M.,, M. B. Goldberg,, D. J. Rose,, E. J. Grotbeck,, V. Burland,, and F. R. Blattner. 2001. Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri. Infect. Immun. 69:32713285.
95. Waldor, M. K.,, and D. R. Cbaudhuri. 2000. Treasure trove for cholera research. Nature 406:469470.
96. White, O.,, J . A. Eisen,, J . F. Heidelberg,, E. K. Hickey,, J . D. Peterson,, R. J . Dodson,, D. H. Haft,, M. L. Gwinn,, W. C. Nelson,, D. L. Richardson,, K. S. Moffat,, H. Qin,, L. Jiang,, W. Pamphilc,, M. Crosby,, M. Shen,, J. J. Vamathcvan,, P. Lam,, L. McDonald,, T. Utterback,, C. Zalewski,, K. S. Makarova,, L. Aravind,, M. J. Daly,, K. W. Minton,, R. D. Flcischmann,, K. A. Ketchum,, K. E. Nelson,, S. Salzberg,, H. O. Smith,, J. C. Venter,, and C. M. Fraser. 1999. Genome sequence of the radioresistant bacterium Deinococcus radiodurans Rl. Science 286:15711577.
97. Williams, S. G.,, and P. A. Manning. 1991. Transcription of the Vibrio cholerae haemolysin gene, hlyA, and cloning of a positive regulatory locus, hlyU. Mol. Microbiol. 5:20312038.
98. Winterstein, C., and B. Ludwig. 1998. Genes coding for respiratory complexes map on all three chromosomes of the Paracoccus denitrifleans genome. Arch. Microbiol. 169:275281.
99. Wong, K.,, T. M. Finan,, and G. B. Golding. 2002. Dinucleotide compositional analysis of Sinorhizobium meliloti using the genome signature: distinguishing chromosomes and plasmids. Funct. Integr. Genomics 2:274281.
100. Wood, D. W.,, J. C. Setubal,, R. Kaul,, D. E. Monks,, J . P. Kitajima,, V. K. Okura,, Y. Zhou,, L. Chen,, G. E. Wood,, N. F. AlmeidaJr.,, L. Woo,, Y. Chen,, I. T. Paulsen,, J. A. Eisen,, P. D. Karp,, D. BovccSr.,, P. Chapman,, J. Ctendenning,, G. Deatherage,, W. Gillet,, C. Grant,, T. Kutyavin,, R. Levy,, M. J. Li,, E. McClelland,, A. Palmieri,, C. Raymond,, G. Rouse,, C. Sacnphimmachak,, Z. Wu,, P. Romero,, D. Gordon,, S. Zhang,, H. Yoo,, Y. Tao,, P. Biddle,, M. Jung,, W. Krespan,, M. Perry,, B. Gordon-Kamm,, L. Liao,, S. Kim,, C. Hendrick,, Z. Y. Zhao,, M. Dolan,, F. Chumley,, S. V. Tingey,, J. F. Tomb,, M. P. Gordon,, M. V. Olson,, and E. W. Nester . 2001. The genome of the natural genetic engineer Agrobacterium tumefaciens C58. Science 294:23172323.
101. Yamaichi, Y.,, T. Iida,, K. S. Park,, K. Yamamoto,, and T. Honda. 1999. Physical and genetic map of the genome of Vibrio parahaemolyticus: presence of two chromosomes in Vibrio species. Mol. Microbiol. 31:15131521.
102. Yarosh, O. K.,, T. C. Charles,, and T. M. Finan. 1989. Analysis of C4-dicarboxylate transport genes in Rhizobium meliloti. Mol. Microbiol. 3:813823.
103. Yildiz, F. H.,, and G. K. Schoolnik. 1998. Role of rpoS in stress survival and virulence of Vibrio cholerae.J. Bacteriol. 180:773784.


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Table 1.

Examples of multipartite bacterial genomes

Citation: MacLellan S, Sibley C, Finan T. 2004. Second Chromosomes and Megaplasmids in Bacteria, p 529-542. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch26

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