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The Function and Organization of Plasmids

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E. coli Plasmid Vectors

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 235))

Abstract

In 1952, Joshua Lederberg coined the term plasmid to describe any bacterial genetic element that exists in an extrachromosomal state for at least part of its replication cycle (1). As this description included bacterial viruses, the definition of what constitutes a plasmid was subsequently refined to describe exclusively or predominantly extrachromosomal genetic elements that replicate autonomously. Plasmids are now known to be present in most species of Eubacteria that have been examined, as well as in Archaea and lower Eukarya (2).

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References

  1. Lederberg, J. (1952) Cell genetics and hereditary symbiosis. Physiol. Rev. 32, 403–430.

    PubMed  CAS  Google Scholar 

  2. Summers, D. K. (1996) The Biology of Plasmids, Blackwell Science, Oxford.

    Book  Google Scholar 

  3. Thomas, C. M. (ed.) (2000) The Horizontal Gene Pool. Harwood Academic, Amsterdam.

    Google Scholar 

  4. Cohen, S. N. (1993) Bacterial plasmids: their extraordinary contribution to molecular genetics. Gene 135, 67–76.

    Article  PubMed  CAS  Google Scholar 

  5. Lederberg, J. (1998) Plasmid (1952–1997). Plasmid 39, 1–9.

    Article  PubMed  CAS  Google Scholar 

  6. Casjens, S., Palmer, N., van Vugt, R., et al. (2000) A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi. Mol. Microbiol. 35, 490–516.

    Article  PubMed  CAS  Google Scholar 

  7. Muller, R. E., Ano, T., Imanaka, T., et al. (1986) Complete nucleotide sequences of Bacillus plasmids pUB110dB, pRBH1 and its copy mutants. Mol. Gen. Genet. 202, 169–171.

    Article  PubMed  CAS  Google Scholar 

  8. Barnett, M. J., Fisher, R. F., Jones, T., et al. (2001) Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid. Proc. Natl. Acad. Sci. USA 98, 9883–9888.

    Article  PubMed  CAS  Google Scholar 

  9. Chan, P. T., Ohmori, H., Tomizawa, J., et al. (1985) Nucleotide sequence and gene organization of ColE1 DNA. J. Biol. Chem. 260, 8925–8935.

    PubMed  CAS  Google Scholar 

  10. She, Q., Phan, H., Garrett, R. A., et al. (1998) Genetic profile of pNOB8 from Sulfolobus: the first conjugative plasmid from an archaeon. Extremophiles 2, 417–425.

    Article  PubMed  CAS  Google Scholar 

  11. Frost, L. S., Ippen-Ihler, K., and Skurray, R.A. (1994) Analysis of the sequence and gene products of the transfer region of the F sex factor. Microbiol. Rev. 58, 162–210.

    PubMed  CAS  Google Scholar 

  12. Yamasaki, M., Miyashita, K., Cullum, J., et al. (2000) A complex insertion sequence cluster at a point of interaction between the linear plasmid SCP1 and the linear chromosome of Streptomyces coelicolor A3(2). J. Bacteriol. 182, 3104–3110.

    Article  PubMed  CAS  Google Scholar 

  13. Kunnimalaiyaan, M., Stevenson, D. M., Zhou, Y., et al. (2001) Analysis of the replicon region and identification of an rRNA operon on pBM400 of Bacillus megaterium QM B1551. Mol. Microbiol. 39, 1010–1102.

    Article  PubMed  CAS  Google Scholar 

  14. del Solar, G. and Espinosa, M. (2000) Plasmid copy number control: an ever-growing story. Mol. Microbiol. 37, 492–500.

    Article  PubMed  Google Scholar 

  15. Kobryn, K. and Chaconas, G. (2001) The circle is broken: telomere resolution in linear replicons. Curr. Opin. Microbiol. 4, 558–564.

    Article  PubMed  CAS  Google Scholar 

  16. Meinhardt, F., Schaffrath, R., and Larsen, M. (1997) Microbial linear plasmids. Appl. Microbiol. Biotechnol. 47, 329–336.

    Article  PubMed  CAS  Google Scholar 

  17. Volff, J. N. and Altenbuchner, J. (2000) A new beginning with new ends: linearisation of circular chromosomes during bacterial evolution. FEMS Microbiol. Lett. 186, 143–150.

    Article  PubMed  CAS  Google Scholar 

  18. Champoux, J. J. (2001) DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem. 70, 369–413.

    Article  PubMed  CAS  Google Scholar 

  19. Khan, S. A. and Novick, R. P. (1983) Complete nucleotide sequence of pT181, a tetracycline-resistance plasmid from Staphylococcus aureus. Plasmid 10, 251–259.

    Article  PubMed  CAS  Google Scholar 

  20. Peng, X., Holz, I., Zillig, W., et al. (2000) Evolution of the family of pRN plasmids and their integrase-mediated insertion into the chromosome of the crenarchaeon Sulfolobus solfataricus. J. Mol. Biol. 303, 449–454.

    Article  PubMed  CAS  Google Scholar 

  21. Futcher, A. B. (1988) The 2μ circle plasmid of Saccharomyces cerevisiae. Yeast 4, 27–40.

    Article  PubMed  CAS  Google Scholar 

  22. Betlach, M., Hershfield, V., Chow, L., et al. (1976). A restriction endonuclease analysis of the bacterial plasmid controlling the EcoRI restriction and modification of DNA. Fed. Proc. 35, 2037–2043.

    PubMed  CAS  Google Scholar 

  23. Schickel, J., Helmig, C., and Meinhardt, F. (1996) Kluyveromyces lactis killer system: analysis of cytoplasmic promoters of the linear plasmids. Nucleic Acids Res. 24, 1879–1886.

    Article  PubMed  CAS  Google Scholar 

  24. Dunny, G. M. and Clewell, D. B. (1975) Transmissible toxin (hemolysin) plasmid in Streptococcus faecalis and its mobilization of a noninfectious drug resistance plasmid. J. Bacteriol. 124, 784–790.

    PubMed  CAS  Google Scholar 

  25. Berg, T., Firth, N., Apisiridej, S., et al. (1998) Complete nucleotide sequence of pSK41: evolution of staphylococcal conjugative multiresistance plasmids. J. Bacteriol. 180, 4350–4359.

    PubMed  CAS  Google Scholar 

  26. Silver, S. and Phung, L. T. (1996) Bacterial heavy metal resistance: new surprises. Annu. Rev. Microbiol. 50, 753–789.

    Article  PubMed  CAS  Google Scholar 

  27. McClelland, M., Sanderson, K. E., Spieth, J., et al. (2001) Complete genome sequence of Salmonella enterica serovar typhimurium LT2. Nature 413, 852–856.

    Article  PubMed  CAS  Google Scholar 

  28. Lindler, L. E., Plano, G. V., Burland, V., et al. (1998) Complete DNA sequence and detailed analysis of the Yersinia pestis KIM5 plasmid encoding murine toxin and capsular antigen. Infect. Immun. 66, 5731–5742.

    PubMed  CAS  Google Scholar 

  29. Martinez, B., Tomkins, J., Wackett, L. P., et al. (2001) Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J. Bacteriol. 183, 5684–5697.

    Article  PubMed  CAS  Google Scholar 

  30. Bertoni, G., Perez-Martin, J., and de Lorenzo, V. (1997) Genetic evidence of separate repressor and activator activities of the XylR regulator of the TOL plasmid, pWW0, of Pseudomonas putida. Mol. Microbiol. 23, 1221–1227.

    Article  PubMed  CAS  Google Scholar 

  31. Ben-Dov, E., Nissan, G., Pelleg, N., et al. (1999) Refined, circular restriction map of the Bacillus thuringiensis subsp. israelensis plasmid carrying the mosquito larvicidal genes. Plasmid 42, 186–191.

    Article  PubMed  CAS  Google Scholar 

  32. Okinaka, R. T., Cloud, K., Hampton, O., et al. (1999) Sequence and organization of pXO1, the large Bacillus anthracis plasmid harboring the anthrax toxin genes. J. Bacteriol. 181, 6509–6515.

    PubMed  CAS  Google Scholar 

  33. Nolling, J., Breton, G., Omelchenko, M. V., et al. (2001) Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J. Bacteriol. 183, 4823–4838.

    Article  PubMed  CAS  Google Scholar 

  34. Finan, T. M., Weidner, S., Wong, K., et al. (2001) The complete sequence of the 1,683-kb pSymB megaplasmid from the N2-fixing endosymbiont Sinorhizobium meliloti. Proc. Natl Acad. Sci. USA 98, 9889–9894.

    Article  PubMed  CAS  Google Scholar 

  35. Bush, K. and Miller, G. H. (1998) Bacterial enzymatic resistance: β-lactamases and aminoglycoside-modifying enzymes. Curr. Opin. Microbiol. 1, 509–515.

    Article  PubMed  CAS  Google Scholar 

  36. Craig, N. L., Craigie, R., Gellert, M., and Lambowitz, A. M. (eds.) (2002) Mobile DNA II, American Society for Microbiology, Washington DC.

    Google Scholar 

  37. Silver, S. (1996) Bacterial resistances to toxic metal ions—a review. Gene 179, 9–19.

    Article  PubMed  CAS  Google Scholar 

  38. Stephens, C. and Murray, W. (2001) Pathogen evolution: how good bacteria go bad. Curr. Biol. 11, R53–R56.

    Article  PubMed  CAS  Google Scholar 

  39. Tan, H. M. (1999) Bacterial catabolic transposons. Appl. Microbiol. Biotechnol. 51, 1–12.

    Article  PubMed  CAS  Google Scholar 

  40. James, R., Kleanthous, C., and Moore, G. R. (1996) The biology of E colicins: paradigms and paradoxes. Microbology 142, 1569–1580.

    Article  CAS  Google Scholar 

  41. Belogurov, A.A., Delver, E. P., Agafonova, O. V., et al. (2000) Antirestriction protein Ard (Type C) encoded by IncW plasmid pSa has a high similarity to the ‘protein transport’ domain of TraC1 primase of promiscuous plasmid RP4. J. Mol. Biol. 296, 969–977.

    Article  PubMed  CAS  Google Scholar 

  42. Helgason, E., Okstad, O. A., Caugant, D. A., et al. (2000) Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis—one species on the basis of genetic evidence. Appl. Environ. Microbiol. 66, 2627–2630.

    Article  PubMed  CAS  Google Scholar 

  43. del Solar, G., Giraldo, R., Ruiz-Echevarria, M. J., e al. (1998) Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 62, 434–464.

    PubMed  Google Scholar 

  44. Kelman, Z. and O’Donnell, M. (1995) DNA polymerase III holoenzyme: structure and function of a chromosomal replicating machine. Annu. Rev. Biochem. 64, 171–200.

    Article  PubMed  CAS  Google Scholar 

  45. Burian, J., Guller, L., Macor, M., et al. (1997) Small crytic plasmids of multiplasmid, clinical Escherichia coli. Plasmid 37, 2–14.

    Article  PubMed  CAS  Google Scholar 

  46. Caspi, R., Pacek, M., Consiglieri, G., et al. (2001) A broad host range replicon with different requirements for replication initiation in three bacterial species. EMBO J. 20, 3262–3271.

    Article  PubMed  CAS  Google Scholar 

  47. Chattoraj, D. K. (2000) Control of plasmid DNA replication by iterons: no longer paradoxical. Mol. Microbiol. 37, 467–476.

    Article  PubMed  CAS  Google Scholar 

  48. Messer, W. and Weigel, C. (1997) DnaA initiator—also a transcription factor. Mol. Microbiol. 24, 1–6.

    Article  PubMed  CAS  Google Scholar 

  49. Cesareni, G., Helmer-Citterich, M., and Castagnoli, L. (1991) Control of ColE1 plasmid replication by antisense RNA. Trends Genet. 7, 230–235.

    PubMed  CAS  Google Scholar 

  50. Khan, S. A. (2000) Plasmid rolling-circle replication: recent developments. Mol. Microbiol. 37, 477–484.

    Article  PubMed  CAS  Google Scholar 

  51. te Riele, H., Michel, B., and Ehrlich, S. D. (1986) Are single-stranded circles intermediates in plasmid DNA replication? EMBO J. 5, 631–637.

    Google Scholar 

  52. Pogliano, J., Ho, T. Q., Zhong, Z., and Helinski, D. R. (2001) Multicopy plasmids are clustered and localized in Escherichia coli. Proc. Natl Acad. Sci. USA 98, 4486–4491.

    Article  PubMed  CAS  Google Scholar 

  53. Bignell, C. and Thomas, C. M. (2001) The bacterial ParA–ParB partitioning proteins. J. Biotechnol. 91, 1–34.

    Article  PubMed  CAS  Google Scholar 

  54. Moller-Jensen, J., Jensen, R. B., and Gerdes, K. (2000) Plasmid and chromosome segregation in prokaryotes. Trends Microbiol. 8, 313–320.

    Article  PubMed  CAS  Google Scholar 

  55. Gordon, G.S. and Wright, A. (2000) DNA segregation in bacteria. Annu. Rev. Microbiol. 54, 681–708.

    Article  PubMed  CAS  Google Scholar 

  56. Arber, W. (2000) Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiol. Rev. 24, 1–7.

    Article  PubMed  CAS  Google Scholar 

  57. Summers, D. K., Beton, C. W., and Withers, H. L. (1993) Multicopy plasmid instability: the dimer catastrophe hypothesis. Mol. Microbiol. 8, 1031–1038.

    Article  PubMed  CAS  Google Scholar 

  58. van Duyne, G. D (2001) A structural view of Cre-loxp site-specific recombination. Annu. Rev. Biophys. Biomol. Struct. 30, 87–104.

    Article  PubMed  Google Scholar 

  59. Barre, F. X., Soballe, B., Michel, B., et al. (2001) Circles: the replication-recombination-chromosome segregation connection. Proc. Natl Acad. Sci. USA 98, 8189–8195.

    Article  PubMed  CAS  Google Scholar 

  60. Engelberg-Kulka, H. and Glaser, G. (1999) Addiction modules and programmed cell death and antideath in bacterial cultures. Annu. Rev. Microbiol. 53, 43–70.

    Article  PubMed  CAS  Google Scholar 

  61. Gerdes, K. (2000) Toxin-antitoxin modules may regulate synthesis of macromolecules during nutritional stress. J. Bacteriol. 182, 561–572.

    Article  PubMed  CAS  Google Scholar 

  62. Gerdes, K., Gultyaev, A. P., Franch, T., et al. (1997) Antisense RNA-regulated programmed cell death. Annu. Rev. Genet. 31, 1–31.

    Article  PubMed  CAS  Google Scholar 

  63. Holcik, M. and Iyer, V. N. (1997) Conditionally lethal genes associated with bacterial plasmids. Microbiology 143, 3403–3416.

    Article  PubMed  CAS  Google Scholar 

  64. Couturier, M., Bahassi, el-M., and van Melderen, L. (1998) Bacterial death by DNA gyrase poisoning. Trends Microbiol. 6, 269–275.

    Article  PubMed  CAS  Google Scholar 

  65. Tortosa, P. and Dubnau, D. (1999) Competence for transformation: a matter of taste. Curr. Opin. Microbiol. 2, 588–592.

    Article  PubMed  CAS  Google Scholar 

  66. Sternberg, N. L. and Maurer, R. (1991) Bacteriophage-mediated generalized transduction in Escherichia coli and Salmonella typhimurium. Methods Enzymol. 204, 18–43.

    Article  PubMed  CAS  Google Scholar 

  67. Lanka, E. and Wilkins, B. M. (1995) DNA processing reactions in bacterial conjugation. Annu. Rev. Biochem. 64, 141–169.

    Article  PubMed  CAS  Google Scholar 

  68. Zechner, E. L., de la Cruz, F., Eisenbrandt, R., et al. (2000) Conjugative-DNA transfer processes, in The Horizontal Gene Pool (Thomas, C. M., ed.), Harwood Academic, Amsterdam, pp. 87–174.

    Google Scholar 

  69. Charlebois, R. L., She, Q., Sprott, D. P., et al. (1998) Sulfolobus genome: from genomics to biology. Curr. Opin. Microbiol. 1, 584–588.

    Article  PubMed  CAS  Google Scholar 

  70. Trieu-Cuot, P., Derlot, E., and Courvalin, P. (1993) Enhanced conjugative transfer of plasmid DNA from Escherichia coli to Staphylococcus aureus and Listeria monocytogenes. FEMS Microbiol. Lett. 109, 19–23.

    Article  PubMed  CAS  Google Scholar 

  71. Bates, S., Cashmore, A. M., and Wilkins, B. M. (1998) IncP plasmids are unusually effective in mediating conjugation of Escherichia coli and Saccharomyces cerevisiae: involvement of the Tra2 mating system J. Bacteriol. 180, 6538–6543.

    PubMed  CAS  Google Scholar 

  72. Christie, P. J. (1997) Agrobacterium tumefaciens T-complex transport apparatus: a paradigm for a new family of multifunctional transporters in eubacteria. J. Bacteriol. 179, 3085–3094.

    PubMed  CAS  Google Scholar 

  73. Dunny, G. M. and Leonard, B. A. (1997) Cell–cell communication in gram-positive bacteria. Annu. Rev. Microbiol. 51, 527–564.

    Article  PubMed  CAS  Google Scholar 

  74. Byrd, D. R. and Matson, S. W. (1997) Nicking by transesterification: the reaction catalysed by a relaxase. Mol. Microbiol. 25, 1011–1022.

    Article  PubMed  CAS  Google Scholar 

  75. Harris, R. L., Sholl, K. A., Conrad, M. N., et al. (1999) Interaction between the F plasmid TraA (F-pilin) and TraQ proteins. Mol. Microbiol. 34, 780–791.

    Article  PubMed  CAS  Google Scholar 

  76. Osborn, M., Bron, S., Firth, N., et al. (2000) The evolution of bacterial plasmids, in The Horizontal Gene Pool (Thomas, C. M., ed.), Harwood Academic, Amsterdam, pp. 301–361.

    Google Scholar 

  77. Burland, V., Shao, Y., Perna, N. T., et al. (1998) The complete DNA sequence and analysis of the large virulence plasmid of Escherichia coli O157∶H7. Nucleic Acids Res. 26, 4196–4204.

    Article  PubMed  CAS  Google Scholar 

  78. Bingle, L. E. and Thomas, C. M. (2001) Regulatory circuits for plasmid survival. Curr. Opin. Microbiol. 4, 194–200.

    Article  PubMed  CAS  Google Scholar 

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Hayes, F. (2003). The Function and Organization of Plasmids. In: Casali, N., Preston, A. (eds) E. coli Plasmid Vectors. Methods in Molecular Biology™, vol 235. Humana Press. https://doi.org/10.1385/1-59259-409-3:1

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  • DOI: https://doi.org/10.1385/1-59259-409-3:1

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-151-6

  • Online ISBN: 978-1-59259-409-2

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