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Genome Plasticity

Insertion Sequence Elements, Transposons and Integrons, and DNA Rearrangement
  • Peter M. Bennett
Part of the Methods in Molecular Biology™ book series (MIMB, volume 266)

Abstract

Living organisms are defined by the genes they possess. Control of expression of this gene set, both temporally and in response to the environment, determines whether an organism can survive changing conditions and can compete for the resources it needs to reproduce. Bacteria are no exception; changes to the genome will, in general, threaten the ability of the microbe to survive, but acquisition of new genes may enhance its chances of survival by allowing growth in a previously hostile environment. For example, acquisition of an antibiotic resistance gene by a bacterial pathogen can permit it to thrive in the presence of an antibiotic that would otherwise kill it; this may compromise clinical treatments. Many forces, chemical and genetic, can alter the genetic content of DNA by locally changing its nucleotide sequence. Notable for genetic change in bacteria are transposable elements and site-specific recombination systems such as integrons. Many of the former can mobilize genes from one replicon to another, including chromosome-plasmid translocation, thus establishing conditions for interspecies gene transfer. Balancing this, transposition activity can result in loss or rearrangement of DNA sequences. This chapter discusses bacterial DNA transfer systems, transposable elements and integrons, and the contributions each makes towards the evolution of bacterial genomes, particularly in relation to bacterial pathogenesis. It highlights the variety of phylogenetically distinct transposable elements, the variety of transposition mechanisms, and some of the implications of rearranging DNA, and addresses the effects of genetic change on the fitness of the microbe.

Key Words

Insertion sequence transposon integron gene cassette plasmid conjugation transduction transformation pathogenicity island transposition site-specific recombination 

References

  1. 1.
    Deng, W., Burland, V., Plunkett III, G., Boutin, A., Mayhew, G. F., Liss, P., et al. (2002) Genome sequence of Yersinia pestis KIM. J. Bacteriol. 184, 4601–4611.PubMedCrossRefGoogle Scholar
  2. 2.
    Welch, R. A., Burland, V., Plunkett III, G., Redford, P., Roesch, P., Rasko, D., et al. (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Nat. Acad. Sci. USA 99, 17,020–17,024.PubMedCrossRefGoogle Scholar
  3. 3.
    Hayashi, T., Makino, K., Ohnishi, M., Kurokawa, K., Ishii, K., Yokoyama, K., et al. (2001) Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K12. DNA Res. 8, 11–22.PubMedCrossRefGoogle Scholar
  4. 4.
    Parkhill, J., Dougan, G., James, K. D., Thomson, N. R., Pickard, D., Wain, J., et al. (2001) Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413, 848–852.PubMedCrossRefGoogle Scholar
  5. 5.
    Lawrence, J. G. and Roth, J. R. (1999) Genomic flux: genome evolution by gene loss and acquisition. In Organization of the Prokaryotic Genome (Charlebois, R. L., ed.), ASM Press, Washington, DC, pp. 263–289.Google Scholar
  6. 6.
    Waldor, M. and Mekalanos, J. (1996) Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272, 1910–1914.PubMedCrossRefGoogle Scholar
  7. 7.
    Waldor, M. K. (1998) Bacteriophage biology and bacterial virulence. Trend Microbiol. 6, 295–297.CrossRefGoogle Scholar
  8. 8.
    Thomas, C. M., ed. (2000) The Horizontal Gene Pool: Bacterial Plasmids and Gene Spread, Harwood Academic Publishers, The Netherlands.Google Scholar
  9. 9.
    Syvanen, M. and Kado, C. I., eds. (1998) Horizontal Gene Transfer, Chapman & Hall, London.Google Scholar
  10. 10.
    Broda, P., ed. (1979) Plasmids, W. H. Freeman & Co., Oxford.Google Scholar
  11. 11.
    Burrus, V., Pavlovic, G., Decaris, B., and Guédon, G. (2002) Conjugative transposons: the tip of the iceberg. Mol. Microbiol. 46, 601–610.PubMedCrossRefGoogle Scholar
  12. 12.
    Salyers, A. A., Shoemaker, N. B., Stevens, A. M., and Li, L. Y. (1995) Conjugative transposons: an unusual and diverse set of integrated gene transfer elements. Microbiol. Rev. 59, 579–590.PubMedGoogle Scholar
  13. 13.
    Scott, J. R. and Churchward, G. G. (1995) Conjugative transposition. Ann. Rev. Microbiol. 49, 367–397.CrossRefGoogle Scholar
  14. 14.
    Zechner, E. L., de la Cruz, F., Eisenbrandt, R., Grahn, A. M., Koraimann, G., Lanka, E., et al. (2000) Conjugative-DNA transfer processes, in The Horizontal Gene Pool: Bacterial Plasmids and Gene Spread (Thomas, C. M.,ed.), Harwood Academic Publishers, Amsterdam, pp. 87–174.Google Scholar
  15. 15.
    Wilkins, B. M. (1995) Gene transfer by bacterial conjugation: diversity of systems and functional specializations, in Society for General Microbiology Symposium 52, Population Genetics of Bacteria (Baumberg, S., Young, J. P. W., Wellington, E. M. H., and Saunders, J. R.,eds.), Cambridge University Press, pp. 59–88.Google Scholar
  16. 16.
    Masters, M. (1996) Generalized transduction, in Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed. (Neidhardt, F. C.,ed.), ASM Press, Washington, DC, pp. 2421–2441.Google Scholar
  17. 17.
    Weisberg, R. A. (1996) Specialized transduction, in Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed. (Neidhardt, F. C.,ed.), ASM Press, Washington, DC, pp. 2442–2448.Google Scholar
  18. 18.
    Dubnau, D. (1999) DNA uptake in bacteria. Ann. Rev. Microbiol. 53, 217–244.CrossRefGoogle Scholar
  19. 19.
    Griffith, F. (1928) Significance of pneumococcal types. J. Hyg. 27, 113–159.CrossRefGoogle Scholar
  20. 20.
    Lorenz, M. G. and Wackernagel, W. (1994) Bacterial gene transfer by natural genetic transformation in the environment. Microbiol. Rev. 58, 563–602.PubMedGoogle Scholar
  21. 21.
    Kowalczykowski, S. C., Dixon, D. A., Eggleston, A. K., Lauder, S. D., and Rehrauer, W. M. (1994) Biochemistry of homologous recombination in Escherichia coli. Microbiol. Rev. 58, 401–465.PubMedGoogle Scholar
  22. 22.
    Dowson, C. G., Coffey, T. J., and Spratt, B. G. (1994) Origin and molecular epidemiology of penicillin-binding-protein-mediated resistance to-lactam antibiotics. Trend. Microbiol. 2, 361–366.CrossRefGoogle Scholar
  23. 23.
    Stanisich, V. A., Bennett, P. M., and Ortiz, J. M. (1976) A molecular analysis of transductional marker rescue involving P-group plasmids in Pseudomonas aeruginosa. Mol. Gen. Genet. 143, 333–337.PubMedCrossRefGoogle Scholar
  24. 24.
    Craig, N. L. (1996) Transposition, in Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed. (Neidhardt, F. C.,ed.), ASM Press, Washington, DC, pp. 2339–2362.Google Scholar
  25. 25.
    Davies, D. R., Goryshin, I. Y., Reznikoff, W. S., and Rayment, I. (2000) Threedimensional structure of the Tn5 synaptic complex transposition intermediate. Science 289, 77–85.PubMedCrossRefGoogle Scholar
  26. 26.
    Savilahti, H., Rice, P. A., and Mizuuchi, K. (1995) The phage Mu transpososome core: DNA requirements for assembly and function. EMBO J. 14, 4893–4903.PubMedGoogle Scholar
  27. 27.
    Chandler, M. and Mahillon, J. (2002) Insertion sequences revisited, in Mobile DNA II (Craig, N. L., Craigie, R., Gellert, M., and Lambowitz, A. M.,eds.), ASM Press, Washington, DC, pp. 305–366.Google Scholar
  28. 27.
    Chandler, M. and Mahillion, J. (2000) Insertion sequence nomenclature. ASM News 66, 324.Google Scholar
  29. 28.
    Mahillon, J. and Chandler, M. (1998) Insertion sequences. Microbiol. Mol. Biol. Rev. 62, 725–774.PubMedGoogle Scholar
  30. 29.
    Toussaint, A. and Résibois, A. (1983) Phage Mu: transposition as a life-style, in Mobile Genetic Elements (Shapiro, J. A.,ed.), Academic Press, New York, pp. 103–158.Google Scholar
  31. 30.
    Grindley, N. D. F. (2002) The movement of Tn3-like elements: transposition and cointegrate resolution, in Mobile DNA II (Craig, N. L., Craigie, R., Gellert, M., and Lambowitz, A. M., eds.), ASM Press, Washington, DC, pp. 272–304.Google Scholar
  32. 31.
    Grinsted, J., de la Cruz, F., and Schmitt, R. (1990) The Tn21 subgroup of bacterial transposable elements. Plasmid 24, 163–189.PubMedCrossRefGoogle Scholar
  33. 32.
    Sherratt, D. (1989) Tn3 and related transposable elements: site-specific recombination and transposition, in Mobile DNA (Berg, D. and Howe, M.,eds.), ASM Press, Washington, DC, pp. 163–184.Google Scholar
  34. 33.
    Garcillán-Barcia, M. P., Bernales, I., Mendiola, V., and de la Cruz, F. (2002) IS91 rolling-circle transposition, in Mobile DNA II (Craig, N. L., Craigie, R., Gellert, M., and Lambowitz, A. M.,eds), ASM Press, Washington, DC, pp. 891–904.Google Scholar
  35. 34.
    Taylor, A. L. (1963) Bacteriophage-induced mutations in E. coli. Proc. Nat. Acad. Sci. USA 50, 1043–1051.CrossRefGoogle Scholar
  36. 35.
    McClintock, B. (1956) Controlling elements and the gene. Cold Spring Harb. Symp. Quant. Biol. 21, 197–216.PubMedGoogle Scholar
  37. 36.
    Hirsch, H. J., Saedler, H., and Starlinger, P. (1972) Insertion mutations in the control region of the galactose operon of E. coli II. Physical characterization of the mutations. Mol. Gen. Genet. 115, 266–276.PubMedCrossRefGoogle Scholar
  38. 37.
    Barth, P. T., Datta, N., Hedges, R. W., and Grinter, N. J. (1976) Transposition of a deoxyribonucleic acid sequence encoding trimethoprim and streptomycin resistances from R483 to other replicons. J. Bacteriol. 125, 800–810.PubMedGoogle Scholar
  39. 38.
    Berg, D. E., Davies, J., Allet, B., and Rochaix, J.-D. (1975) Transposition of R factor genes to bacteriophage λ. Proc. Nat. Acad. Sci. USA 72, 3628–3632.PubMedCrossRefGoogle Scholar
  40. 39.
    Foster, T. J., Howe, T. G. B., and Richmond, K. M. V. (1975) Translocation of the tetracycline resistance determinant from R100-1 to the Escherichia coli K12 chromosome. J. Bacteriol. 124, 1153–1158.PubMedGoogle Scholar
  41. 40.
    Kleckner, N., Chan, R. K., Tye, B.-K., and Botstein, D. (1975) Mutagenesis by insertion of a drug-resistance element carrying an inverted repetition. J. Mol. Biol. 97, 561–575.PubMedCrossRefGoogle Scholar
  42. 41.
    Hedges, R. W. and Jacob, A. (1974) Transposition of ampicillin resistance from RP4 to other replicons. Mol. Gen. Genet. 132, 31–40.PubMedCrossRefGoogle Scholar
  43. 42.
    Reznikoff, W. S. (2002) Tn5 transposition, in Mobile DNA II (Craig, N. L., Craigie, R., Gellert, M., and Lambowitz, A. M., eds.), ASM Press, Washington, DC, pp. 403–422.Google Scholar
  44. 43.
    Haniford, D. B. (2002) Transposon Tn10, in Mobile DNA II (Craig, N. L., Craigie, R., Gellert, M., and Lambowitz, A. M., eds.), ASM Press, Washington, DC, pp. 457–483.Google Scholar
  45. 44.
    Lorenzo, V de, Herrero, M., Jakubzik, U., and Timmis, K. N. (1990) Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in Gram-negative bacteria. J. Bacteriol. 172, 6568–6572.PubMedGoogle Scholar
  46. 45.
    Allmeier, H., Cresnar, B., Greck, M., and Schmitt, R. (1992) Complete nucleotide sequence of Tn1721: gene organization and a novel gene product with features of a chemotaxis protein. Gene 111, 11–20.PubMedCrossRefGoogle Scholar
  47. 46.
    Nakatsu, C., Ng, J., Singh, R., Straus, N., and Wyndham, C. (1991) Chlorobenzoate catabolic transposon Tn5271 is a composite class I element with flanking class II insertion sequences. Proc. Nat. Acad. Sci. USA 88, 8312–8316.PubMedCrossRefGoogle Scholar
  48. 47.
    Bennett, P. M. (1989) Bacterial transposons and transposition: flexibility and limitations, in Genetic Transformation and Expression (Butler, L. O., Harwood, C., and Moseley, B. E. B., eds.), Intercept, Andover, UK, pp. 283–303.Google Scholar
  49. 48.
    Dobritsa, A. P., Dobritsa, S. V., Popov, E. I., and Fedoseeva, V. B. (1981) Transposition of DNA fragment flanked by two inverted Tn1 sequences. Gene 14, 217–225.PubMedCrossRefGoogle Scholar
  50. 49.
    Lederberg, E. M. (1981) Plasmid reference centre registry of transposon (Tn) allocations through July 1981. Gene 16, 59–61.PubMedCrossRefGoogle Scholar
  51. 50.
    Jordan, E., Saedler, H., and Starlinger, P. (1968) 0° and strong polar mutations in the gal operon are insertions. Mol. Gen. Genet. 102, 353–365.PubMedCrossRefGoogle Scholar
  52. 51.
    Shapiro, J. A. (1969) Mutations caused by the insertion of genetic material into the galactose operon of E. coli. J. Mol. Biol. 40, 93–105.PubMedCrossRefGoogle Scholar
  53. 52.
    Malamy, M. H. (1970) Some properties of insertion mutations in the lac operon, in The Lactose Operon (Beckwith, J. R. and Zipser, D., eds.), Cold Spring Harbor Laboratory, p. 359.Google Scholar
  54. 53.
    Habermann, P. and Starlinger, P. (1982) Bidirectional deletions associated with IS4. Mol. Gen. Genet. 185, 216–222.PubMedCrossRefGoogle Scholar
  55. 54.
    Reif, H. J. and Saedler, H. (1975) IS1 is involved in deletion formation in the gal region of E. coli K12. Mol. Gen. Genet. 137, 17–28.PubMedGoogle Scholar
  56. 55.
    Saedler, H., Reif, H. J., Hu, S., and Davidson, N. (1974) IS2, a genetic element for turn-off and turn-on of gene activity in E. coli. Mol. Gen. Genet. 132, 265–289.CrossRefGoogle Scholar
  57. 56.
    Starlinger, P. (1980) IS elements and transposons. Plasmid 3, 241–259.PubMedCrossRefGoogle Scholar
  58. 57.
    Sekine, Y. and Ohtsubo, E. (1989) Frameshifting is required for production of the transposase encoded by insertion sequence 1. Proc. Nat. Acad. Sci. USA 86, 4609–4613.PubMedCrossRefGoogle Scholar
  59. 58.
    Sekine, Y., Eisaki, N., and Ohtsubo, E. (1994) Translational control in production of transposase and in transposition of insertion sequence IS 3. J Mol. Biol. 235, 1406–1420.PubMedCrossRefGoogle Scholar
  60. 59.
    Chalmers, R. M. and Kleckner, N. (1994) Tn10/IS10 transposase purification, activation, and in vitro reaction. J. Biol. Chem. 269, 8029–8035.PubMedGoogle Scholar
  61. 60.
    Weinreich, M. D., Mahnke-Braam, L., and Reznikoff, W. S. (1994) A functional analysis of the Tn5 transposase: identification of domains required for DNA binding and multimerization. J. Mol. Biol. 241, 166–177.PubMedCrossRefGoogle Scholar
  62. 61.
    Mendiola, M. V., Jubete, Y., and de la Cruz, F. (1992) DNA sequence of IS91 and identification of the transposase gene. J. Bacteriol. 174, 1345–1351.PubMedGoogle Scholar
  63. 62.
    Derbyshire, K. M. and Grindley, N. D. (1992) Binding of the IS903 transposase to its inverted repeat in vitro. EMBO J. 11, 3449–3455.PubMedGoogle Scholar
  64. 63.
    Johnsrud, L. (1979) DNA sequence of the transposable element IS1. Mol. Gen. Genet. 169, 213–218.PubMedCrossRefGoogle Scholar
  65. 64.
    Ohtsubo, H. and Ohtsubo, E. (1978) Nucleotide sequence of an insertion element, IS1. Proc. Nat. Acad. Sci. USA 75, 615–619.PubMedCrossRefGoogle Scholar
  66. 65.
    Escoubas, J. M., Prère, M. F., Fayet, O., Salvignol, I., Galas, D., Zerbib, D., et al. (1991) Translational control of transposition activity of the bacterial insertion sequence IS1. EMBO J. 10, 705–712.PubMedGoogle Scholar
  67. 66.
    Zerbib, D., Prentki, P., Gamas, P., Freund, E., Galas, D. J., and Chandler, M. (1990) Functional organization of the ends of IS1: specific binding site for an IS1-encoded protein. Mol. Microbiol. 4, 1477–1486.PubMedCrossRefGoogle Scholar
  68. 67.
    Machida, C. and Machida, Y. (1989) Regulation of IS1 transposition by the insA gene product. J. Mol. Biol. 208, 567–574.PubMedCrossRefGoogle Scholar
  69. 68.
    Chandler, M. and Fayet, O. (1993) Translational frameshifting in the control of transposition in bacteria. Mol. Microbiol. 7, 497–503.PubMedCrossRefGoogle Scholar
  70. 69.
    Grindley, N. D. (1978) IS1 insertion generates duplication of a nine base pair sequence at its target site. Cell 13, 419–426.PubMedCrossRefGoogle Scholar
  71. 70.
    Grindley, N. D. F. (1983) Transposition of Tn3 and related transposons. Cell 32, 3–5.PubMedCrossRefGoogle Scholar
  72. 71.
    Tavakoli, N., Comanducci, A., Dodd, H. M., Lett, M. C., Albiger, B., and Bennett, P. M. (2000) IS1294, a DNA element that transposes by RC transposition. Plasmid 44, 66–84.PubMedCrossRefGoogle Scholar
  73. 72.
    Mendiola, M. V., Bernales, I., and de la Cruz, F. (1994) Differential roles of the transposon termini in IS91 transposition. Proc. Nat. Acad. Sci. USA 91, 1922–1926.PubMedCrossRefGoogle Scholar
  74. 73.
    Craig, N. L. (1995) Unity in transposition reactions. Science 270, 253–254.PubMedCrossRefGoogle Scholar
  75. 74.
    Ton-Hoang, B., Polard, P., and Chandler, M. (1998) Efficient transposition of IS911 circles in vitro. EMBO J. 17, 1169–1181.PubMedCrossRefGoogle Scholar
  76. 75.
    Polard, P., Prère, M.-F., Fayet, O., and Chandler, M. (1992) Transposase-induced excision and circularization of the bacterial insertion sequence IS911. EMBO J. 11, 5079–5090.PubMedGoogle Scholar
  77. 76.
    Polard, P., Prère, M.-F., Chandler, M., and Fayet, O. (1991) Programmed translational frameshifting and initiation at an AUU codon in gene expression of bacterial insertion sequence IS911. J. Mol. Biol. 222, 465–477.PubMedCrossRefGoogle Scholar
  78. 77.
    Ton-Hoang, B., Betermier, M., Polard, P., and Chandler, M. (1997) Assembly of a strong promoter following IS911 circularization and the role of circles in transposition. EMBO J. 16, 3357–3371.PubMedCrossRefGoogle Scholar
  79. 78.
    Richter, G. Y., Björklöf, K., Romantschuk, M., and Mills, D. (1998) Insertion specificity and trans-activation of IS801. Mol. Gen. Genet. 260, 381–387.PubMedCrossRefGoogle Scholar
  80. 79.
    Díaz-Aroca, E., Mendiola, M. V., Zabala, J. C., and de la Cruz, F. (1987) Transposition of IS91 does not generate a target duplication. J. Bacteriol. 169, 442–443.PubMedGoogle Scholar
  81. 80.
    Mendiola, M. V. and de la Cruz, F. (1992) IS91 transposase is related to the rolling-circle-type replication proteins of the pUB110 family of plasmids. Nucl. Acids Res. 20, 3521.PubMedCrossRefGoogle Scholar
  82. 81.
    Comanducci, A., Dodd, H. M., and Bennett, P. M. (1989) pUB2380: an R plasmid encoding a unique, natural one-ended transposition system, in Genetic Transformation and Expression (Butler, L. O., Harwood, C., and Moseley, B. E. B., eds.), Intercept, Andover, UK, pp. 305–311.Google Scholar
  83. 82.
    Poirel, L., Decousser, J.-W., and Nordmann, P. (2003) Insertion sequence ISEcp1B is involved in expression and mobilization of a bla CTX-M β-lactamase gene. Antimicrob. Agents Chemother. 47, 2938–2945.PubMedCrossRefGoogle Scholar
  84. 83.
    Chalmers, R., Sewitz, K., Lipkow, K., and Crellin, P. (2000) Complete nucleotide sequence of Tn10. J. Bacteriol. 182, 2970–2972.PubMedCrossRefGoogle Scholar
  85. 84.
    Reznikoff, W. S. (1993) The Tn5 transposon. Ann. Rev. Microbiol. 47, 945–963.CrossRefGoogle Scholar
  86. 85.
    Oka, A., Sugisaki, H., and Takanami, M. (1981) Nucleotide sequence of the kanamycin resistance transposon Tn903. J. Mol. Biol. 147, 217–226.PubMedCrossRefGoogle Scholar
  87. 86.
    Grindley, N. D. and Joyce, C. M. (1980) Genetic and DNA sequence analysis of the kanamycin resistance transposon Tn903. Proc. Nat. Acad. Sci. USA 77, 7176–7180.PubMedCrossRefGoogle Scholar
  88. 87.
    Krebs, M. P. and Reznikoff, W. S. (1986) Transcriptional and translational sites of IS50. Control of transposase and inhibitor expression. J. Mol. Biol. 192, 781–791.PubMedCrossRefGoogle Scholar
  89. 88.
    Kleckner, N., Chalmers, R. M., Kwon, D., Sakai, J., and Bolland, S. (1996) Tn10 and IS10 transposition and chromosome rearrangements; mechanism and regulation in vivo and in vitro. Curr. Topic. Microbiol. Immunol. 204, 49–82.Google Scholar
  90. 89.
    Derbyshire, K. M., Kramer, M., and Grindley, N. D. (1990) Role of instability in the cis action of the insertion sequence IS903 transposase. Proc. Nat. Acad. Sci. USA 87, 4048–4052.PubMedCrossRefGoogle Scholar
  91. 90.
    Heffron, F., McCarthy, B. J., Ohtsubo, H., and Ohtsubo, E. (1979) DNA sequence analysis of the transposon Tn3: three genes and three sites involved in transposition of Tn3. Cell 18, 1153–1163.PubMedCrossRefGoogle Scholar
  92. 91.
    Mahillon, J. and Lereclus, D. (1988) Structural and functional analysis of Tn4430: identification of an integrase-like protein involved in the co-integrate resolution process. EMBO J. 7, 1515–1526.PubMedGoogle Scholar
  93. 92.
    Gill, R. E., Heffron, F., and Falkow, S. (1979) Identification of the protein encoded by the transposable element Tn3 which is required for its transposition. Nature 282, 797–801.PubMedCrossRefGoogle Scholar
  94. 93.
    Shapiro, J. A. (1979) Molecular model for the transposition and replication of bacteriophage Mu and other transposable elements. Proc. Nat. Acad. Sci. USA 76, 1933–1937.PubMedCrossRefGoogle Scholar
  95. 94.
    Arthur, A. and Sherratt, D. J. (1979) Dissection of the transposition process. Mol. Gen. Genet. 175, 267–274.PubMedCrossRefGoogle Scholar
  96. 95.
    Heritage, J. and Bennett, P. M. (1985) Plasmid fusions mediated by one end of TnA. J. Gen. Microbiol. 131, 1131–1140.Google Scholar
  97. 96.
    Avila, P., de la Cruz, F., Ward, E., and Grinsted, J. (1984) Plasmids containing one inverted repeat of Tn21 can fuse with other plasmids in the presence of Tn21 transposase. Mol. Gen. Genet. 195, 288–293.PubMedCrossRefGoogle Scholar
  98. 97.
    Mötsch, S. and Schmitt, R. (1984) Replicon fusion mediated by a single-ended derivative of transposon Tn1721. Mol. Gen. Genet. 195, 281–287.PubMedCrossRefGoogle Scholar
  99. 98.
    Robinson, M. K., Bennett, P. M., and Richmond, M. H. (1977) Inhibition of TnA translocation by TnA. J. Bacteriol. 129, 407–414.PubMedGoogle Scholar
  100. 99.
    Lee, C.-H., Bhagwhat, A., and Heffron, F. (1983) Identification of a transposon Tn3 sequence required for transposition immunity. Proc. Nat. Acad. Sci. USA 80, 6765–6769.PubMedCrossRefGoogle Scholar
  101. 100.
    Arciszewska, L. K., Drake, D., and Craig, N. L. (1989) Transposon Tn7 cis-acting sequences in transposition and transposition immunity. J. Mol. Biol. 207, 35–52.PubMedCrossRefGoogle Scholar
  102. 101.
    Mizuuchi, K. (1992) Transpositional recombination: mechanistic insights from studies of Mu and other elements. Ann. Rev. Biochem. 61, 1011–1051.PubMedCrossRefGoogle Scholar
  103. 102.
    Stokes, H. W. and Hall, R. M. (1989) A novel family of potentially mobile DNA elements encoding site-specific gene-integration functions: integrons. Mol. Microbiol. 3, 1669–1683.PubMedCrossRefGoogle Scholar
  104. 103.
    Recchia, G. D. and Hall, R. M. (1995) Gene cassettes: a new class of mobile element. Microbiol. 141, 3015–3027.CrossRefGoogle Scholar
  105. 104.
    Bennett, P. M. (1999) Integrons and gene cassettes: a genetic construction kit for bacteria. J. Antimicrob. Chemother. 43, 1–4.PubMedCrossRefGoogle Scholar
  106. 105.
    Stokes, H. W., Gorman, D. B., Recchia, G. D., Parsekhian, M., and Hall, R. M. (1997) Structure and function of 59-base element recombination sites associated with mobile gene cassettes. Mol. Microbiol. 26, 731–745.PubMedCrossRefGoogle Scholar
  107. 106.
    Naas, T., Mikami, Y., Imai, T., Poirel, L., and Nordmann, P. (2001) Characterization of In53, a class 1 plasmid-and composite-transposon-located integron of Escherichia coli which carries an unusual array of gene cassettes. J. Bacteriol. 183, 235–249.PubMedCrossRefGoogle Scholar
  108. 107.
    Rowe-Magnus, D. A., Guerout, A. M., and Mazel, D. (1999) Super-integrons. Res. Microbiol. 150, 641–651.PubMedCrossRefGoogle Scholar
  109. 108.
    Mazel, D., Dychinco, B., Webb, V. A., and Davies, J. (1998) A distinctive class of integron in the Vibrio cholerae genome. Science 280, 605–608.PubMedCrossRefGoogle Scholar
  110. 109.
    Nield, B. S., Holmes, A. J., Gillings, M. R., Recchia, G. D., Mabbutt, B. C., Nevalainen, et al. (2001) Recovery of new integron classes from environmental DNA. FEMS Microbiol. Lett. 195, 59–65.PubMedCrossRefGoogle Scholar
  111. 110.
    Rowe-Magnus, D. A., Guerout, A. M., Ploncard, P., Dychinco, B., Davies, J., and Mazel, D. (2001) The evolutionary history of chromosomal super-integrons provides an ancestry for multiresistant integrons. Proc. Nat. Acad. Sci. USA 98, 652–657.PubMedCrossRefGoogle Scholar
  112. 111.
    Vaisvila, R., Morgan, R. D., Posfai, J., and Raleigh, E. A. (2001) Discovery and distribution of super-integrons among pseudomonads. Mol. Microbiol. 42, 587–601.PubMedCrossRefGoogle Scholar
  113. 112.
    Hansson, K., Sundstrom, L., Pelletier, A., and Roy, P. H. (2002) IntI2 integron integrase in Tn7. J. Bacteriol. 184, 1712–1721.PubMedCrossRefGoogle Scholar
  114. 113.
    Collis, C. M., Kim, M. J., Partridge, S. R., Stokes, H. W., and Hall, R. M. (2002) Characterization of the class 3 integron and the site-specific recombination system it determines. J. Bacteriol. 184, 3017–3026.PubMedCrossRefGoogle Scholar
  115. 114.
    Walsh, T. R., Toleman, M. A., Hryniewicz, W., Bennett, P. M., and Jones, R. N. (2003) Evolution of an integron carrying bla VIM-2 in Eastern Europe: report from the SENTRY antimicrobial surveillance program. J. Antimicrob. Chemother. 52, 116–119.PubMedCrossRefGoogle Scholar
  116. 115.
    Clewell, D. B. and Gawron-Burke, C. (1986) Conjugative transposons and the dissemination of antibiotic resistance. Ann. Rev. Microbiol. 40, 635–659.CrossRefGoogle Scholar
  117. 116.
    Salyers, A. A., Shoemaker, N. B., and Li, L. Y. (1995) In the driver’s seat: the Bacteroides conjugative transposons and the elements they mobilize. J. Bacteriol. 177, 5727–5731.PubMedGoogle Scholar
  118. 117.
    Osborn, A. M. and Böltner, D. (2002) When Phage, plasmids, and transposons collide: genomic islands, and conjugative-and mobilizable-transposons as a mosaic continuum. Plasmid 48, 202–212.PubMedCrossRefGoogle Scholar
  119. 118.
    Böltner, D. and Osborn, A. M. (2004) Structural comparison of the integrative and conjugative elements R391, pMERPH, R997, and SXT. Plasmid 51, 12–23.PubMedCrossRefGoogle Scholar
  120. 119.
    Hochhut, B., Lotfi, Y., Mazel, D., Faruque, S. M., Woodgate, R., and Waldor, M. K. (2001) Molecular analysis of antibiotic resistance gene clusters in Vibrio cholerae O139 and O1 SXT constins. Antimicrob. Agents Chemother. 45, 2991–3000.PubMedCrossRefGoogle Scholar
  121. 120.
    Beaber, J. W., Burrus, V., Hochhut, B., and Waldor, M. K. (2002) Comparison of SXT and R391, two conjugative integrating elements: definition of a genetic backbone for the mobilization of resistance determinants. Cell. Molec. Life Sci. 59, 2065–2070.PubMedCrossRefGoogle Scholar
  122. 121.
    Franke, A. E. and Clewell, D. B. (1981) Evidence for a chromosome-borne resistance transposon (Tn916) in Streptococcus faecalis that is capable of conjugative transfer in the absence of a conjugative plasmid. J. Bacteriol. 145, 494–502.PubMedGoogle Scholar
  123. 122.
    Churchward, G. (2002) Conjugative transposons and related mobile elements, in Mobile DNA II (Craig, N. L., Craigie, R., Gellert, M., and Lambowitz, A. M, eds.), ASM Press, Washington, DC, pp. 177–191.Google Scholar
  124. 123.
    Flannagan, S. E., Zitzow, L. A., Su, Y. A., and Clewell, D. B. (1994) Nucleotide sequence of the 18-kb conjugative transposon Tn916 from Enterococcus faecalis. Plasmid 32, 350–354.PubMedCrossRefGoogle Scholar
  125. 124.
    Senghas, E., Jones, J. M., Yamamoto, M., Gawron-Burke, C., and Clewell, D. B. (1988) Genetic organization of the bacterial conjugative transposon Tn916. J. Bacteriol. 170, 245–249.PubMedGoogle Scholar
  126. 125.
    Storrs, M. J., Carlier, C., Poyart-Salmeron, C., Trieu-Cuot, P., and Courvalin, P. (1991) Conjugative transposition of Tn916 requires the excisive and integrative activities of the transposon-encoded integrase. J. Bacteriol. 173, 4347–4352.PubMedGoogle Scholar
  127. 126.
    Craig, N. L. (1988) The mechanism of conservative site-specific recombination. Ann. Rev. Genet. 22, 77–105.PubMedCrossRefGoogle Scholar
  128. 127.
    Nash, H. A. (1981) Integration and excision of bacteriophage lambda: the mechanism of conservative site specific recombination. Ann. Rev. Genet. 15, 143–167.PubMedCrossRefGoogle Scholar
  129. 128.
    Craig, N. L. (1997) Target site selection in transposition. Ann. Rev. Biochem. 66, 437–474.PubMedCrossRefGoogle Scholar
  130. 129.
    Craig, N. L. (1991) Tn7: a target site-specific transposon. Mol. Microbiol. 5, 2569–2573.PubMedCrossRefGoogle Scholar
  131. 130.
    Gay, N. J., Tybulewicz, V. L., and Walker, J. E. (1986) Insertion of transposon Tn7 into the Escherichia coli glmS transcriptional terminator. Biochem. J. 234, 111–117.PubMedGoogle Scholar
  132. 131.
    Craig, N. L. (2002) Tn7, in Mobile DNA II (Craig, N. L., Craigie, R., Gellert, M., and Lambowitz, A. M., eds.), ASM Press, Washington, DC, pp. 423–456.Google Scholar
  133. 132.
    Bainton, R. J., Kubo, K. M., Feng, J.-N., and Craig, N. L. (1993) Tn7 transposition: target DNA recognition is mediated by multiple Tn7-encoded proteins in a purified in vitro system. Cell 72, 931–943.PubMedCrossRefGoogle Scholar
  134. 133.
    Bainton, R., Gamas, P., and Craig, N. L. (1991) Tn7 transposition in vitro proceeds through an excised transposon intermediate generated by staggered breaks in DNA. Cell 65, 805–816.PubMedCrossRefGoogle Scholar
  135. 134.
    Stanisich, V. A., Arwas, R., Bennett, P. M., and de la Cruz, F. (1989) Characterization of Pseudomonas mercury-resistance transposon Tn502, which has a preferred insertion site in RP1. J. Gen. Microbiol. 135, 2909–2915.PubMedGoogle Scholar
  136. 135.
    Carmo de Freire Bastos, M. D. and Murphy, E. (1988) Transposon Tn544 encodes three products required for transposition. EMBO J. 7, 2935–2941.Google Scholar
  137. 136.
    Murphy, E. and Lofdahl, S. (1984) Transposition of Tn544 does not generate a target duplication. Nature 307, 292–295.PubMedCrossRefGoogle Scholar
  138. 137.
    Pato, M. L. (1989) Bacteriophage Mu, in Mobile DNA (Berg, D. E. and Howe, M. M., eds.), ASM Press, Washington, DC, pp. 23–52.Google Scholar
  139. 138.
    Hacker, J. and Kaper, J. B. (2000) Pathogenicity islands and the evolution of microbes. Ann. Rev. Microbiol. 54, 641–679.CrossRefGoogle Scholar
  140. 139.
    Davis, B. M. and Waldor, M. K. (2002) Mobile genetic elements and bacterial pathogenesis, in Mobile DNA II (Craig, N. L., Craigie, R., Gellert, M., and Lambowitz, A. M., eds.), ASM Press, Washington, DC, pp. 1040–1059.Google Scholar
  141. 140.
    Lindsay, J. A., Ruzin, A., Ross, H. F., Kurepina, N., and Novick, R. P. (1998) The gene for toxic shock toxin is carried by a family of mobile pathogenicity islands in Staphylococcus aureus. Mol. Microbiol. 29, 527–543.PubMedCrossRefGoogle Scholar
  142. 141.
    Karaolis, D. K. R., Somara, S., Maneval, D. R. Jr., Johnson, J. A., and Kaper, J. B. (1999) A bacteriophage encoding a pathogenicity island, a type IV pilus and a phage receptor in cholera bacteria. Nature 399, 375–379.PubMedCrossRefGoogle Scholar
  143. 142.
    Rankin, A., Schubert, S., Pelludat, C., Brem, D., and Hessemann, J. (1999) The high-pathogenicity island of Yersinia, in Pathogenicity Islands and Other Mobile Virulence Elements (Kaper, J. B. and Hacker, J., eds.), ASM Press, Washington, DC, pp. 77–90.Google Scholar
  144. 143.
    Hiramatsu, K., Cui, L., Kuroda, M., and Ito, T. (2001) The emergence and evolution of methicillin-resistant Staphylococcus aureus. Trends Microbiol. 9, 486–493.PubMedCrossRefGoogle Scholar
  145. 144.
    Ma, X. X., Ito, T., Tiensasitorn, C., Jamklang, M., Chongtrakool, P., Boyle-Vavra, S., et al. (2002) Novel type of staphylococcal cassette chromosome mec identified in community-acquired methicillin-resistant Staphylococcus aureus strains. Antimicrob. Agents Chemother. 46, 1147–1152.PubMedCrossRefGoogle Scholar
  146. 145.
    Katayama, Y., Ito, T., and Hiramatsu, K. (2000) A new class of genetic element, Staphylococcus Cassette Chromosome mec, encodes methicillin resistance in Staphylococcus aureus. Antimicrob. Agents Chemother. 44, 1549–1555.PubMedCrossRefGoogle Scholar
  147. 146.
    Katayama, Y., Takeuchi, F., Ito, T., Ma, X. X., Ui-Mizutani, Y., Kobayashi, I., and Hiramatsu, K. (2003) Identification in methicillin-susceptible Staphylococcus hominis of an active primordial mobile genetic element for the staphylococcal cassette chromosome mec of methicillin-resistant Staphylococcus aureus. J. Bacteriol. 185, 2711–2722.PubMedCrossRefGoogle Scholar
  148. 147.
    Groisman, E. A. and Casadaban, M. J. (1986) Mini-Mu bacteriophage with plasmid replicons for in vivo cloning and lac gene fusions. J. Bacteriol. 168, 357–364.PubMedGoogle Scholar
  149. 148.
    Van Gijsegem, F. and Toussaint, A. (1982) Chromosome transfer and R-prime formation by an RP4::mini-Mu derivative in Escherichia coli, Salmonella typhimurium, Klebsiella pneumoniae, and Proteus mirabilis. Plasmid 7, 30–44.PubMedCrossRefGoogle Scholar
  150. 149.
    Koch, C., Mertens, G., Rudt, F., Kahmann, R., Kanaar, R., Plasterk, R. H., et al. (1987) The invertible G segment, in Phage Mu (Symonds, N., Toussaint, A., van de Putte, P., and Howe, M. M., eds.), Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, pp. 75–91.Google Scholar
  151. 150.
    Toussaint, A., Lefebvre, N., Scott, J. R., Cowan, J. A., de Bruijn, F., and Bukhari, A. I. (1978) Relationships between temperate phages Mu and P1. Virology 89, 146–161.PubMedCrossRefGoogle Scholar
  152. 151.
    Zieg, J. and Simon, M. (1980) Analysis of the nucleotides sequence of an invertible controlling element. Proc. Nat. Acad. Sci. USA 77, 4196–4200.PubMedCrossRefGoogle Scholar
  153. 152.
    Sharp, P. A., Cohen, S. N., and Davidson, N. (1973) Electron microscope heteroduplex studies of sequence relations among plasmids of Escherichia coli II. Structure of drug resistance (R) factors and F factors. J. Mol. Biol. 75, 235–255.PubMedCrossRefGoogle Scholar
  154. 153.
    Rownd, R. and Mickel, S. (1971) Dissociation and reassociation of RTF and r-determinant of the R-factor NR1 in Proteus mirabilis. Nature New Biol. 234, 40–43.PubMedCrossRefGoogle Scholar
  155. 154.
    Clowes, R. C. (1972) Molecular structure of bacterial plasmids. Bacteriol. Rev. 36, 361–405.PubMedGoogle Scholar
  156. 155.
    Bennett, P. M. and Richmond, M. H. (1978) Plasmids and their possible influence on bacterial evolution, in The Bacteria: A Treatise on Structure and Function (Gunsalus, I. C., ed.), Academic Press, NY, pp. 1–69.Google Scholar

Copyright information

© Humana Press Inc. 2004

Authors and Affiliations

  • Peter M. Bennett
    • 1
  1. 1.Department of Pathology and MicrobiologyUniversity of Bristol, School of Medical SciencesUK

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