1887

Chapter 26 : Second Chromosomes and Megaplasmids in Bacteria

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in
Zoomout

Second Chromosomes and Megaplasmids in Bacteria, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817732/9781555812652_Chap26-1.gif /docserver/preview/fulltext/10.1128/9781555817732/9781555812652_Chap26-2.gif

Abstract:

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
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

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
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555817732.chap26
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: 7869 7874.
2. Banfalvi, Z.,, E. Kondorosi,, and A. Kondorosi. 1985. Rbizobium meliloti carries two megaplasmids. Plasmid 13: 129 138.
3. Baril, C.,, C. Richaud,, G. Baranton,, and I. S. Saint Girons. 1989. Linear chromosome of Borrelia burgdorferi. Res. Microbiol. 140: 507 516.
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: 9883 9888.
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: 6234 6243.
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: 141 147.
7. Bignell, C.,, and C. M. Thomas. 2001. The bacterial ParAParB partitioning proteins. J. Bioteclynol. 91: 1 34.
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: 5789 5799.
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: 5477 5487.
10. Casjens, S. 1998. The diverse and dynamic structure of bacterial genomes. Annu. Rev. Genet. 32: 339 377.
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: 104 116.
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: 5486 5494.
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: 5 20.
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: 3833 3842.
15. Chen, H. W.,, A. Kuspa,, I. M. Keseler,, and L. J. Shimkets. 1991. Physical map of the Myxococcus xanthus chromosome. J. Bacteriol 173: 2109 2115.
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): 3085 3099.
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: 7694 7702.
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: 443 448.
20. England, J. C., and J. W. Gober. 2001. Cell cycle control of cell morphogenesis in Caulobacter. Curr. Opin. Microbial 4: 674 680,
21. Errington, J . 2001. Septation and chromosome segregation during sporulation in Bacillus subtilis. Curr. Opin. Microbial 4: 660 666.
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: 66 72.
23. Finan, T. M.,, I. Oresnik,, and A. Bottacin. 1988. Mutants of Rhizobium meliloti defective in succinate metabolism. J. Bacteriol 170: 3396 3403.
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: 9889 9894.
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: 1403 1413.
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: 397 403.
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: 394 401.
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: 439 468.
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: 668 672.
30. Gerdes, K.,, J. Moller-Jensen,, and J. R. Bugge. 2000. Plasmid and chromosome partitioning: surprises from phylogcny. Mol Microbiol 37: 455 166.
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: 4454 4458.
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: 2411 2419.
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: 39 49.
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: 2323 2328.
35. Goodner, B. W., B. P. Markelz,, M. C. Flanagan,, C. B. Crowell Jr.,, 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: 5160 5166,
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: 477 483.
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: 1118 1123.
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: 811 820.
39. Honeycutt, R. J .,, M. McClelland,, and B. W. Sobral. 1993. Physical map of the genome of Rhizobium meliloti 1021. J . Bacteriol. 175: 6945 6952.
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: 2165 2169.
41. Hynes, M. F.,, and T. M. Finan,. 2003. General genetic knowledge, p. 25 43. 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: 356 362.
43. Jenal, U.,, and C. Stephens. 2002. The Caulobacter cell cycle: timing, spatial organization and checkpoints. Curr. Opin. Microbiol. 5: 558 563.
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: 99 106.
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: 2749 2755.
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: 331 338.
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: 189 197.
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: 205 213.
49. Karlin, S.,, J . Mrazek,, and A. M, Campbell. 1997. Compositional biases of bacterial genomes and evolutionary implications.;. Bacteriol. 179: 3899 3913.
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: 5496 5507.
51. Kolsto, A. B. 1997. Dynamic bacterial genome organization. Mol. Microbiol. 24: 241 248.
52. Kolsto, A. B. 1999. Time for a fresh look at the bacterial chromosome. Trends Microbiol. 7: 223 226.
53. Koonin, E. V. 2000. How many genes can make a cell: the minimat-gene-set concept. Annu. Rev. Genomics Hum. Genet. 1: 99 116.
54. Kornberg, A. 2000. Ten commandments: lessons from the enzymology of DNA replication. J. Bacteriol. 182: 3613 3618.
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: 3422 3429.
56. Levin, P. A.,, and A. D. Grossman. 1998. Cell cycle and sporulation in Bacillus subtilis. Curr. Opin. Microbiol. 1: 630 635.
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: 254 256.
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: 537 548.
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: 179 188.
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: 923 933.
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. 41 45 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: 3911 3919.
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: 959 977.
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: 171 176.
65. Mcsser, W. 2002. The bacterial replication initiator DnaA. DnaA and oriC, the bacterial mode to initiate DNA replication. FEMS Microbiol Rev. 26: 355 374.
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: 701 705.
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: 3244 3249.
68. Miller, M. B.,, and B. L. Bassler. 2001. Quorum sensing in bacteria. Annu. Rev. Microbiol. 55: 165 199.
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: 255 275.
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: 771 784.
71. Muller, T.,, and M. Vingron. 2000. Modeling amino acid replacement. J. Comput. Biol 7: 761 776.
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: 10268 10273.
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: 1131 1141.
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: 12176 12181.
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: 3582 3586.
76. Osteras, M.,, and U. Jcnal. 2000. Regulatory circuits in Caulobacter. Curr. Opin. Microbiol. 3: 171 176.
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: 848 852.
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: 13148 13153,
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: 3117 3124.
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: 2796 2799.
81. Rodley, P. D.,, U. Romling,, and B. Tummler. 1995. A physical genome map of the Burkbolderia cepacia type strain. Mol Microbiol. 17: 57 67.
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: 402 406.
83. Ryan, K. R.,, and L. Shapiro. 2003. Temporal and spatial regulation in prokaryotic cell cycle progression and development, Annu. Rev. Biochem. 72: 367 394.
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: 497 502.
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: 615 624.
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: 213 219.
87. Shapiro, J. A. 1998. Thinking about bacterial populations as multicellular organisms. Annu. Rev. Microbiol. 52: 81 104.
88. Songsivilai, S.,, and T. Dharakul. 2000. Multiple replicons constitute the 6.5-megabase genome of Burkholderia pseudomallei. Acta Trop. 74: 169 179.
89. Su, C. J., , and J. B. Baseman. 1990. Genome size of Mycoplasma genitatium. J. Bacteriol 172: 4705 4707.
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: 5850 5859.
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: 22 34.
92. Tagomori, K.,, T. Iida,, and T. Honda. 2002. Comparison of genome structures of vibrios, bacteria possessing two chromosomes. J . Bacteriol. 184: 4351 4358.
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: 14464 14469.
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: 3271 3285.
95. Waldor, M. K.,, and D. R. Cbaudhuri. 2000. Treasure trove for cholera research. Nature 406: 469 470.
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: 1571 1577.
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: 2031 2038.
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: 275 281.
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: 274 281.
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. Almeida Jr.,, L. Woo,, Y. Chen,, I. T. Paulsen,, J. A. Eisen,, P. D. Karp,, D. Bovcc Sr.,, 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: 2317 2323.
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: 1513 1521.
102. Yarosh, O. K.,, T. C. Charles,, and T. M. Finan. 1989. Analysis of C4-dicarboxylate transport genes in Rhizobium meliloti. Mol. Microbiol. 3: 813 823.
103. Yildiz, F. H.,, and G. K. Schoolnik. 1998. Role of rpoS in stress survival and virulence of Vibrio cholerae. J. Bacteriol. 180: 773 784.

Tables

Generic image for table
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

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error