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).
References
Lederberg, J. (1952) Cell genetics and hereditary symbiosis. Physiol. Rev. 32, 403–430.
Summers, D. K. (1996) The Biology of Plasmids, Blackwell Science, Oxford.
Thomas, C. M. (ed.) (2000) The Horizontal Gene Pool. Harwood Academic, Amsterdam.
Cohen, S. N. (1993) Bacterial plasmids: their extraordinary contribution to molecular genetics. Gene 135, 67–76.
Lederberg, J. (1998) Plasmid (1952–1997). Plasmid 39, 1–9.
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.
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.
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.
Chan, P. T., Ohmori, H., Tomizawa, J., et al. (1985) Nucleotide sequence and gene organization of ColE1 DNA. J. Biol. Chem. 260, 8925–8935.
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.
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.
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.
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.
del Solar, G. and Espinosa, M. (2000) Plasmid copy number control: an ever-growing story. Mol. Microbiol. 37, 492–500.
Kobryn, K. and Chaconas, G. (2001) The circle is broken: telomere resolution in linear replicons. Curr. Opin. Microbiol. 4, 558–564.
Meinhardt, F., Schaffrath, R., and Larsen, M. (1997) Microbial linear plasmids. Appl. Microbiol. Biotechnol. 47, 329–336.
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.
Champoux, J. J. (2001) DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem. 70, 369–413.
Khan, S. A. and Novick, R. P. (1983) Complete nucleotide sequence of pT181, a tetracycline-resistance plasmid from Staphylococcus aureus. Plasmid 10, 251–259.
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.
Futcher, A. B. (1988) The 2μ circle plasmid of Saccharomyces cerevisiae. Yeast 4, 27–40.
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.
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.
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.
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.
Silver, S. and Phung, L. T. (1996) Bacterial heavy metal resistance: new surprises. Annu. Rev. Microbiol. 50, 753–789.
McClelland, M., Sanderson, K. E., Spieth, J., et al. (2001) Complete genome sequence of Salmonella enterica serovar typhimurium LT2. Nature 413, 852–856.
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.
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.
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.
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.
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.
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.
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.
Bush, K. and Miller, G. H. (1998) Bacterial enzymatic resistance: β-lactamases and aminoglycoside-modifying enzymes. Curr. Opin. Microbiol. 1, 509–515.
Craig, N. L., Craigie, R., Gellert, M., and Lambowitz, A. M. (eds.) (2002) Mobile DNA II, American Society for Microbiology, Washington DC.
Silver, S. (1996) Bacterial resistances to toxic metal ions—a review. Gene 179, 9–19.
Stephens, C. and Murray, W. (2001) Pathogen evolution: how good bacteria go bad. Curr. Biol. 11, R53–R56.
Tan, H. M. (1999) Bacterial catabolic transposons. Appl. Microbiol. Biotechnol. 51, 1–12.
James, R., Kleanthous, C., and Moore, G. R. (1996) The biology of E colicins: paradigms and paradoxes. Microbology 142, 1569–1580.
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.
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.
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.
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.
Burian, J., Guller, L., Macor, M., et al. (1997) Small crytic plasmids of multiplasmid, clinical Escherichia coli. Plasmid 37, 2–14.
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.
Chattoraj, D. K. (2000) Control of plasmid DNA replication by iterons: no longer paradoxical. Mol. Microbiol. 37, 467–476.
Messer, W. and Weigel, C. (1997) DnaA initiator—also a transcription factor. Mol. Microbiol. 24, 1–6.
Cesareni, G., Helmer-Citterich, M., and Castagnoli, L. (1991) Control of ColE1 plasmid replication by antisense RNA. Trends Genet. 7, 230–235.
Khan, S. A. (2000) Plasmid rolling-circle replication: recent developments. Mol. Microbiol. 37, 477–484.
te Riele, H., Michel, B., and Ehrlich, S. D. (1986) Are single-stranded circles intermediates in plasmid DNA replication? EMBO J. 5, 631–637.
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.
Bignell, C. and Thomas, C. M. (2001) The bacterial ParA–ParB partitioning proteins. J. Biotechnol. 91, 1–34.
Moller-Jensen, J., Jensen, R. B., and Gerdes, K. (2000) Plasmid and chromosome segregation in prokaryotes. Trends Microbiol. 8, 313–320.
Gordon, G.S. and Wright, A. (2000) DNA segregation in bacteria. Annu. Rev. Microbiol. 54, 681–708.
Arber, W. (2000) Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiol. Rev. 24, 1–7.
Summers, D. K., Beton, C. W., and Withers, H. L. (1993) Multicopy plasmid instability: the dimer catastrophe hypothesis. Mol. Microbiol. 8, 1031–1038.
van Duyne, G. D (2001) A structural view of Cre-loxp site-specific recombination. Annu. Rev. Biophys. Biomol. Struct. 30, 87–104.
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.
Engelberg-Kulka, H. and Glaser, G. (1999) Addiction modules and programmed cell death and antideath in bacterial cultures. Annu. Rev. Microbiol. 53, 43–70.
Gerdes, K. (2000) Toxin-antitoxin modules may regulate synthesis of macromolecules during nutritional stress. J. Bacteriol. 182, 561–572.
Gerdes, K., Gultyaev, A. P., Franch, T., et al. (1997) Antisense RNA-regulated programmed cell death. Annu. Rev. Genet. 31, 1–31.
Holcik, M. and Iyer, V. N. (1997) Conditionally lethal genes associated with bacterial plasmids. Microbiology 143, 3403–3416.
Couturier, M., Bahassi, el-M., and van Melderen, L. (1998) Bacterial death by DNA gyrase poisoning. Trends Microbiol. 6, 269–275.
Tortosa, P. and Dubnau, D. (1999) Competence for transformation: a matter of taste. Curr. Opin. Microbiol. 2, 588–592.
Sternberg, N. L. and Maurer, R. (1991) Bacteriophage-mediated generalized transduction in Escherichia coli and Salmonella typhimurium. Methods Enzymol. 204, 18–43.
Lanka, E. and Wilkins, B. M. (1995) DNA processing reactions in bacterial conjugation. Annu. Rev. Biochem. 64, 141–169.
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.
Charlebois, R. L., She, Q., Sprott, D. P., et al. (1998) Sulfolobus genome: from genomics to biology. Curr. Opin. Microbiol. 1, 584–588.
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.
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.
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.
Dunny, G. M. and Leonard, B. A. (1997) Cell–cell communication in gram-positive bacteria. Annu. Rev. Microbiol. 51, 527–564.
Byrd, D. R. and Matson, S. W. (1997) Nicking by transesterification: the reaction catalysed by a relaxase. Mol. Microbiol. 25, 1011–1022.
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.
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.
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.
Bingle, L. E. and Thomas, C. M. (2001) Regulatory circuits for plasmid survival. Curr. Opin. Microbiol. 4, 194–200.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2003 Humana Press Inc.
About this protocol
Cite this protocol
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
Download citation
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
eBook Packages: Springer Protocols