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Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria

Key Points

  • Mutation and horizontal gene transfer (HGT) continually give rise to new bacterial genotypes. Infrequently, such new bacterial genotypes establish and spread in the larger population through either positive selection or random genetic drift. Therefore, bacterial genomes are in a constant state of flux, and any segment of DNA in a large bacterial population might have the opportunity to be horizontally transferred.

  • Three main mechanisms of HGT have been described: natural transformation, the uptake of free DNA in competent bacteria, exhibited by about 1% of validly described bacterial species; transduction, the transfer of bacterial DNA between a bacteriophage-infected bacterium and a bacteriophage-susceptible bacterium; and conjugation, the transfer of mobile genetic elements by pili structures assembled between two adjacently located bacteria.

  • A number of factors limit the transfer, uptake and stabilization of foreign DNA molecules acquired by bacteria. These include limited release and stability of adaptive DNA in the environment; limits on competence development; limits on host range of the transfer and maintenance mechanism of mobile genetic elements; recipient restriction enzyme activity; and limited ability of foreign DNA to integrate into a replicating genetic element owing to a lack of DNA sequence similarity.

  • Homologous recombination depends on the incoming DNA containing regions between 25 and 200 bp in length, depending on the system, of high similarity to the recipient genome. Dependence on DNA sequence similarity for recombination between species is relaxed in some mutator strains. DNA acquisition through double-stranded breaks and end-joining — illegitimate recombination — applies more to integration of circular DNA than linear fragments.

  • Most of the understanding of the processes facilitating HGT and their frequencies of occurrence have come from well designed laboratory studies of a few model bacterial species. These studies have proven suited to resolve the basic biological mechanisms involved, but fail to encompass the environmental variables involved. We have still to develop a quantitative and qualitative understanding of ongoing gene-transfer processes occurring under natural conditions. Biologically significant gene-transfer processes might occur at temporospatial scales that current methodology do not allow us to monitor.


Bacteria evolve rapidly not only by mutation and rapid multiplication, but also by transfer of DNA, which can result in strains with beneficial mutations from more than one parent. Transformation involves the release of naked DNA followed by uptake and recombination. Homologous recombination and DNA-repair processes normally limit this to DNA from similar bacteria. However, if a gene moves onto a broad-host-range plasmid it might be able to spread without the need for recombination. There are barriers to both these processes but they reduce, rather than prevent, gene acquisition.

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Figure 1: The process of horizontal gene transfer.
Figure 2: The natural transformation of recipient bacteria and selection of transformants.
Figure 3: Overview of plasmids and conjugative transfer in the horizontal spread of genes.


  1. 1

    Griffith, F. The significance of pneumococcal types. J. Hyg. 27, 113–159 (1928).

    CAS  PubMed  Google Scholar 

  2. 2

    Thomas, C. M. (ed.) The Horizontal Gene Pool: Bacterial Plasmids and Gene Spread (Harwood Academic Publishers, Amsterdam, 2000).

    Google Scholar 

  3. 3

    Nakamura, Y., Itoh, T., Matsuda, H. & Gojobori, T. Biased function of horizontally transferred genes in prokaryotic genomes. Nature Genet. 36, 760–766 (2004).

    CAS  PubMed  Google Scholar 

  4. 4

    Jain, R., Rivera, M. C. & Lake, J. A. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl Acad. Sci. USA 96, 3801–3806 (1999).

    CAS  Google Scholar 

  5. 5

    Nielsen, K. M. & Townsend, J. P. Monitoring and modeling horizontal gene transfer. Nature Biotechnol. 22, 1110–1114 (2004).

    CAS  Google Scholar 

  6. 6

    Cohan, F. M., Roberts, M. S. & King, E. C. The potential for genetic exchange by transformation within a natural population of Bacillus subtilis. Evolution 45, 1383–1421 (1991).

    Google Scholar 

  7. 7

    Jonas, D. A. et al. Safety considerations of DNA in food. Ann. Nutr. Metab. 45, 235–254 (2001).

    CAS  PubMed  Google Scholar 

  8. 8

    Paget, E. & Simonet, P. On the track of natural transformation in soil. FEMS Microbiol. Ecol. 15, 109–117 (1994).

    CAS  Google Scholar 

  9. 9

    Lorenz, M. G. & Wackernagel, W. Bacterial gene-transfer by natural genetic-transformation in the environment. Microbiol. Rev. 58, 563–602 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. 10

    Moscoso, M. & Claverys, J. P. Release of DNA into the medium by competent Streptococcus pneumoniae: kinetics, mechanism and stability of the liberated DNA. Mol. Microbiol. 54, 783–794 (2004).

    CAS  PubMed  Google Scholar 

  11. 11

    Lorenz, M. G., Gerjets, D. & Wackernagel, W. Release of transforming plasmid and chromosomal DNA from 2 cultured soil bacteria. Arch. Microbiol. 156, 319–326 (1991).

    CAS  PubMed  Google Scholar 

  12. 12

    Ueda, S. & Hara, T. Studies on nucleic acid production and application. I. production of extracellular DNA by Pseudomonas sp. KYU-1. J. Appl. Biochem. 3, 1–10 (1981).

    CAS  Google Scholar 

  13. 13

    Whitchurch, C. B., Tolker-Nielsen, T., Ragas, P. C. & Mattick, J. S. Extracellular DNA required for bacterial biofilm formation. Science 295, 1487–1487 (2002).

    CAS  PubMed  Google Scholar 

  14. 14

    Palmen, R. & Hellingwerf, K. J. Acinetobacter calcoaceticus liberates chromosomal DNA during induction of competence by cell lysis. Curr. Microbiol. 30, 7–10 (1995).

    CAS  PubMed  Google Scholar 

  15. 15

    Friedlander, A. M. DNA release as a direct measure of microbial killing. J. Immunol. 115, 1404–1408 (1975).

    CAS  PubMed  Google Scholar 

  16. 16

    Connolly, J. H., Herriott, R. M. & Gupta, S. Deoxyribonuclease in human blood and platelets. Br. J. Exp. Pathol. 43, 392–408 (1962).

    CAS  PubMed  PubMed Central  Google Scholar 

  17. 17

    Rozenberg-Arska, M., Salters, E. C., Vanstrijp, J. A., Hoekstra, W. P. M. & Verhoef, J. Degradation of Escherichia coli chromosomal and plasmid DNA in serum. J. Gen. Microbiol. 130, 217–222 (1984).

    CAS  PubMed  Google Scholar 

  18. 18

    Doerfler, W. Foreign DNA in Mammalian Systems. (Wiley-VCH Verlag GmbH, Weinheim, 2000).

    Google Scholar 

  19. 19

    Worthey, A. L., Kane, J. F. & Orvos, D. R. Fate of pBR322 DNA in a wastewater matrix. J. Ind. Microbiol. Biotechnol. 22, 164–166 (1999).

    CAS  Google Scholar 

  20. 20

    Widmer, F., Seidler, R. J. & Watrud, L. S. Sensitive detection of transgenic plant marker gene persistence in soil microcosms. Mol. Ecol. 5, 603–613 (1996).

    CAS  Google Scholar 

  21. 21

    Widmer, F., Seidler, R. J., Donegan, K. K. & Reed, G. L. Quantification of transgenic plant marker gene persistence in the field. Mol. Ecol. 6, 1–7 (1997).

    CAS  Google Scholar 

  22. 22

    Romanowski, G., Lorenz, M. G., Sayler, G. S. & Wackernagel, W. Persistence of free plasmid DNA in soil monitored by various methods, including a transformation assay. Appl. Environ. Microbiol. 58 3012–3019 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. 23

    Romanowski, G., Lorenz, M. G. & Wackernagel, W. Plasmid DNA in a groundwater aquifer microcosm — adsorption, DNAase resistance and natural genetic transformation of Bacillus subtilis. Mol. Ecol. 2, 171–181 (1993).

    CAS  PubMed  Google Scholar 

  24. 24

    Landweber, L. in Genetics and the Extinction of Species: DNA and the Conservation of Biodiversity. (eds Landweber, L. & Dobson, A. P.) 163–186 (Princeton University Press, Princeton, 1999).

    Google Scholar 

  25. 25

    Hofreiter, M., Serre, D., Poinar, H. N., Kuch, M. & Paabo, S. Ancient DNA. Nature Rev. Genet. 2, 353–359 (2001).

    CAS  Google Scholar 

  26. 26

    Ogram, A., Sayler, G. S. & Barkay, T. The extraction and purification of microbial DNA from sediments. J. Microbiol. Methods 7, 57–66 (1987).

    CAS  Google Scholar 

  27. 27

    DeFlaun, M. F. & Paul, J. H. Detection of exogenous gene sequences in dissolved DNA from aquatic environments. Microb. Ecol. 18, 21–28 (1989).

    CAS  PubMed  Google Scholar 

  28. 28

    Karl, D. M. & Bailiff, M. D. The measurement and distribution of dissolved nucleic acids in aquatic environments. Limnol. Oceanogr. 34, 543–558 (1989).

    CAS  Google Scholar 

  29. 29

    Schubbert, R., Renz, D., Schmitz, B. & Doerfler, W. Foreign (M13) DNA ingested by mice reaches peripheral leukocytes, spleen, and liver via the intestinal wall mucosa and can be covalently linked to mouse DNA. Proc. Natl Acad. Sci. USA 94, 961–966 (1997).

    CAS  PubMed  Google Scholar 

  30. 30

    Einspanier, R. et al. The fate of forage plant DNA in farm animals: a collaborative case-study investigating cattle and chicken fed recombinant plant material. Eur. Food Res. Technol. 212, 129–134 (2001).

    CAS  Google Scholar 

  31. 31

    Chiter, A., Forbes, J. M. & Blair, G. E. DNA stability in plant tissues: implications for the possible transfer of genes from genetically modified food. FEBS Lett. 481, 164–168 (2000).

    CAS  PubMed  Google Scholar 

  32. 32

    Paget, E., Lebrun, M., Freyssinet, G. & Simonet, P. The fate of recombinant plant DNA in soil. Eur. J. Soil Biol. 34, 81–88 (1998).

    CAS  Google Scholar 

  33. 33

    Gebhard, F. & Smalla, K. Monitoring field releases of genetically modified sugar beets for persistence of transgenic plant DNA and horizontal gene transfer. FEMS Microbiol. Ecol. 28, 261–272 (1999).

    CAS  Google Scholar 

  34. 34

    Ceccherini, M. et al. Degradation and transformability of DNA from transgenic leaves. Appl. Environ. Microbiol. 69, 673–678 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  35. 35

    Graham, J. B. & Istock, C. A. Gene exchange and natural selection cause Bacillus subtilis to evolve in soil culture. Science 204, 637–639 (1979).

    CAS  PubMed  Google Scholar 

  36. 36

    Nielsen, K. M., Bones, A. M. & van Elsas, J. D. Induced natural transformation of Acinetobacter calcoaceticus in soil microcosms. Appl. Environ. Microbiol. 63, 3972–3977 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. 37

    Frischer, M. E., Stewart, G. J. & Paul, J. H. Plasmid transfer to indigenous marine bacterial-populations by natural transformation. FEMS Microbiol. Ecol. 15, 127–135 (1994).

    CAS  Google Scholar 

  38. 38

    Baur, B., Hanselman, K., Schlimme, W. & Jenni, B. Genetic transformation in freshwater: Escherichia coli is able to develop natural competence. Appl. Environ. Microbiol. 62, 3673–3678 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  39. 39

    Mercer, D. K., Scott, K. P., Melville, C. M., Glover, L. A. & Flint, H. J. Transformation of an oral bacterium via chromosomal integration of free DNA in the presence of human saliva. FEMS Microbiol. Lett. 200, 163–167 (2001).

    CAS  PubMed  Google Scholar 

  40. 40

    Duggan, P. S., Chambers, P. A., Heritage, J. & Forbes, J. M. Survival of free DNA encoding antibiotic resistance from transgenic maize and the transformation activity of DNA in ovine saliva, ovine rumen fluid and silage effluent. FEMS Microbiol. Lett. 191, 71–77 (2000).

    CAS  PubMed  Google Scholar 

  41. 41

    Brautigaum, M., Hertel, C. & Hammes, W. P. Evidence for natural transformation of Bacillus subtilis in foodstuffs. FEMS Microbiol. Lett. 155, 93–98 (1997).

    Google Scholar 

  42. 42

    Bauer, F., Hertel, C. & Hammes, W. P. Transformation of Escherichia coli in foodstuffs. Syst. Appl. Microbiol. 22 (1999).

  43. 43

    Palmen, R. & Hellingwerf, K. J. Uptake and processing of DNA by Acinetobacter calcoaceticus — a review. Gene 192, 179–190 (1997).

    CAS  PubMed  Google Scholar 

  44. 44

    Dubnau, D. DNA uptake in bacteria. Annu. Rev. Microbiol. 53, 217–244 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. 45

    Dreiseikelmann, B. Translocation of DNA across bacterial-membranes. Microbiol. Rev. 58, 293–316 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. 46

    Puyet, A., Greenberg, B. & Lacks, S. A. Genetic and structural characterization of EndA — a membrane-bound nuclease required for transformation of Streptococcus pneumoniae. J. Mol. Biol. 213, 727–738 (1990).

    CAS  PubMed  Google Scholar 

  47. 47

    Chen, I. & Dubnau, D. DNA uptake during natural transformation. Nature Rev. Microbiol. 2, 241–249 (2004).

    CAS  Google Scholar 

  48. 48

    Nielsen, K. M. et al. Natural transformation and availability of transforming DNA to Acinetobacter calcoaceticus in soil microcosms. Appl. Environ. Microbiol. 63, 1945–1952 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. 49

    Mejean, V. & Claverys, J. P. DNA processing during entry in transformation of Streptococcus pneumoniae. J. Biol. Chem. 268, 5594–5599 (1993).

    CAS  PubMed  Google Scholar 

  50. 50

    Berndt, C., Meier, P. & Wackernagel, W. DNA restriction is a barrier to natural transformation in Pseudomonas stutzeri JM300. Microbiology 149, 895–901 (2003).

    CAS  PubMed  Google Scholar 

  51. 51

    Maynard Smith, J., Feil, E. J. & Smith, N. H. Population structure and evolutionary dynamics of pathogenic bacteria. BioEssays 22, 1115–1122 (2000).

    Google Scholar 

  52. 52

    Feil, E. J. & Spratt, B. G. Recombination and the population structures of bacterial pathogens. Annu. Rev. Microbiol. 55, 561–590 (2001).

    CAS  PubMed  Google Scholar 

  53. 53

    Townsend, J. P., Nielsen, K. M., Fisher, D. S. & Hartl, D. L. Horizontal acquisition of divergent chromosomal DNA in bacteria: effects of mutator phenotypes. Genetics 164, 13–21 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  54. 54

    Matic, I. et al. Highly variable mutation rates in commensal and pathogenic Escherichia coli. Science 277, 1833–1834 (1997).

    CAS  PubMed  Google Scholar 

  55. 55

    Vulic, M., Dionisio, F., Taddei, F. & Radman, M. Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. Proc. Natl Acad. Sci. USA 94, 9763–9767 (1997).

    CAS  PubMed  Google Scholar 

  56. 56

    de Vries, J., Meier, P. & Wackernagel, W. The natural transformation of the soil bacteria Pseudomonas stutzeri and Acinetobacter sp by transgenic plant DNA strictly depends on homologous sequences in the recipient cells. FEMS Microbiol. Lett. 195, 211–215 (2001).

    CAS  PubMed  Google Scholar 

  57. 57

    Majewski, J. & Cohan, F. M. The effect of mismatch repair and heteroduplex formation on sexual isolation in Bacillus. Genetics 148, 13–18 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. 58

    Majewski, J., Zawadzki, P., Pickerill, P., Cohan, F. M. & Dowson, C. G. Barriers to genetic exchange between bacterial species: Streptococcus pneumoniae transformation. J. Bacteriol. 182, 1016–1023 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. 59

    Heinemann, J. A. & Traavik, T. Problems in monitoring horizontal gene transfer in field trials of transgenic plants. Nature Biotechnol. 22, 1105–1109 (2004).

    CAS  Google Scholar 

  60. 60

    Ikeda, H., Shiraishi, K. & Ogata, Y. Illegitimate recombination mediated by double-strand break and end-joining in Escherichia coli. Adv. Biophys. 38, 3–20 (2004).

    CAS  PubMed  Google Scholar 

  61. 61

    Ehrlich, S. D. et al. Mechanisms of illegitimate recombination. Gene 135, 161–166 (1993).

    CAS  PubMed  Google Scholar 

  62. 62

    Nielsen, K. M. An assessment of factors affecting the likelihood of horizontal transfer of recombinant plant DNA to bacterial recipients in the soil and rhizosphere. Collection of Biosafety Reviews (Italy) 1, 96–149 (2003).

    Google Scholar 

  63. 63

    Kurland, C. G. What tangled web: barriers to rampant horizontal gene transfer. BioEssays 27, 741–747 (2005).

    CAS  PubMed  Google Scholar 

  64. 64

    Dempsey, L. A. & Dubnau, D. A. Identification of plasmid and Bacillus subtilis chromosomal recombination sites used for pE194 integration. J. Bacteriol. 171, 2856–2865 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  65. 65

    Lovett, S. T., Hurley, R. L., Sutera, V. A., Aubuchon, R. H. & Lebedeva, M. A. Crossing over between regions of limited homology in Escherichia coli: RecA-dependent and RecA-independent pathways. Genetics 160, 851–859 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. 66

    Shen, P. & Huang, H. V. Homologous recombination in Escherichia coli — dependence on substrate length and homology. Genetics 112, 441–457 (1986).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. 67

    Majewski, J. & Cohan, F. M. DNA sequence similarity requirements for interspecific recombination in Bacillus. Genetics 153, 1525–1533 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. 68

    Meier, P. & Wackernagel, W. Mechanisms of homology-facilitated illegitimate recombination for foreign DNA acquisition in transformable Pseudomonas stutzeri. Mol. Microbiol. 48, 1107–1118 (2003).

    CAS  PubMed  Google Scholar 

  69. 69

    de Vries, J., Herzfeld, T. & Wackernagel, W. Transfer of plastid DNA from tobacco to the soil bacterium Acinetobacter sp. by natural transformation. Mol. Microbiol. 53, 323–334 (2004).

    CAS  PubMed  Google Scholar 

  70. 70

    de Vries, J. & Wackernagel, W. Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination. Proc. Natl Acad. Sci. USA 99, 2094–2099 (2002).

    CAS  PubMed  Google Scholar 

  71. 71

    Prudhomme, M., Libante, V. & Claverys, J. P. Homologous recombination at the border: insertion-deletions and the trapping of foreign DNA in Streptococcus pneumoniae. Proc. Natl Acad. Sci. USA 99, 2100–2105 (2002).

    CAS  PubMed  Google Scholar 

  72. 72

    Nielsen, K. M., van Elsas, J. D. & Smalla, K. Transformation of Acinetobacter sp. strain BD413(pFG4 Delta nptII) with transgenic plant DNA in soil microcosms and effects of kanamycin on selection of transformants. Appl. Environ. Microbiol. 66, 1237–1242 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. 73

    Kay, E., Vogel, T. M., Bertolla, F., Nalin, R. & Simonet, P. In situ transfer of antibiotic resistance genes from transgenic (transplastomic) tobacco plants to bacteria. Appl. Environ. Microbiol. 68, 3345–3351 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  74. 74

    Funchain, P., Yeung, A., Stewart, J., Clendenin, W. M. & Miller, J. H. Amplification of mutator cells in a population as a result of horizontal transfer. J. Bacteriol. 183, 3737–3741 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  75. 75

    Feng, G., Tsui, H. C. T. & Winkler, M. E. Depletion of the cellular amounts of the MutS and MutH methyl-directed mismatch repair proteins in stationary-phase Escherichia coli K-12 cells. J. Bacteriol. 178, 2388–2396 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. 76

    LeClerc, J. E., Li, B. G., Payne, W. L. & Cebula, T. A. High mutation frequencies among Escherichia coli and Salmonella pathogens. Science 274, 1208–1211 (1996).

    CAS  PubMed  Google Scholar 

  77. 77

    Richardson, A. R., Yu, Z., Popovic, T. & Stojiljkovic, I. Mutator clones of Neisseria meningitidis in epidemic serogroup A disease. Proc. Natl Acad. Sci. USA 99, 6103–6107 (2002).

    CAS  PubMed  Google Scholar 

  78. 78

    Young, D. M. & Ornston, L. N. Functions of the mismatch repair gene mutS from Acinetobacter sp strain ADP1. J. Bacteriol. 183, 6822–6831 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. 79

    Burrus, V., Pavlovic, G., Decaris, B. & Guedon, G. Conjugative transposons: the tip of the iceberg. Mol. Microbiol. 46, 601–610 (2002).

    CAS  PubMed  Google Scholar 

  80. 80

    Flores, M. et al. Prediction, identification, and artificial selection of DNA rearrangements in Rhizobium: Toward a natural genomic design. Proc. Natl Acad. Sci. USA 97, 9138–9143 (2000).

    CAS  PubMed  Google Scholar 

  81. 81

    Mavingui, P. et al. Dynamics of genome architecture in Rhizobium sp strain NGR234. J. Bacteriol. 184, 171–176 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  82. 82

    Mahillon, J. & Chandler, M. Insertion sequences. Microbiol. Mol. Biol. Rev. 62, 725–774. (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  83. 83

    Reimmann, C. & Haas, D. Mode of replicon fusion mediated by the duplicated insertion-sequence IS21 in Escherichia coli. Genetics 115, 619–625 (1987).

    CAS  PubMed  PubMed Central  Google Scholar 

  84. 84

    Reimmann, C. et al. Genetic structure, function and regulation of the transposable element IS21. Mol. Gen. Genetics 215, 416–424 (1989).

    CAS  Google Scholar 

  85. 85

    Bao, T. H., Betermier, M., Polard, P. & Chandler, M. Assembly of a strong promoter following IS911 circularization and the role of circles in transposition. EMBO J. 16, 3357–3371 (1997).

    Google Scholar 

  86. 86

    Duval-Valentin, G., Marty-Cointin, B. & Chandler, M. Requirement of IS911 replication before integration defines a new bacterial transposition pathway. EMBO J. 23, 3897–3906 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  87. 87

    Duval-Valentin, G., Normand, C., Khemici, V., Marty, B. & Chandler, M. Transient promoter formation: a new feedback mechanism for regulation of IS911 transposition. EMBO J. 20, 5802–5811 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. 88

    McGrath, B. M. & Pembroke, J. T. Detailed analysis of the insertion site of the mobile elements R997, pMERPH, R392, R705 and R391 in E. coli K12. FEMS Microbiol. Lett. 237, 19–26 (2004).

    CAS  PubMed  Google Scholar 

  89. 89

    Mateos, L. M., Schafer, A., Kalinowski, J., Martin, J. F. & Puhler, A. Integration of narrow-host-range vectors from Escherichia coli into the genomes of amino acid-producing Corynebacteria after intergeneric conjugation. J. Bacteriol. 178, 5768–5775 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. 90

    Ikeda, H., Shimizu, H., Ukita, T. & Kumagai, M. A novel assay for illegitimate recombination in Escherichia coli — stimulation of λ-bio transducing phage formation by ultraviolet-light and its independence from RecA function. Adv. Biophys. 31, 197–208 (1995).

    CAS  PubMed  Google Scholar 

  91. 91

    Shiraishi, K., Hanada, K., Iwakura, Y. & Ikeda, H. Roles of recJ, RecO, and RecR in RecET-mediated illegitimate recombination in Escherichia coli. J. Bacteriol. 184, 4715–4721 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  92. 92

    Chiu, C.-M. & Thomas, C. M. Evidence for the past integration of IncP-1 plasmids into bacterial chromosomes. FEMS Lett. 241, 163–169 (2004).

    CAS  Google Scholar 

  93. 93

    Cascales, E. & Christie, P. J. The versatile bacterial type IV secretion systems. Nature Rev. Microbiol. 1, 137–149 (2003).

    CAS  Google Scholar 

  94. 94

    Anthony, K. G., Sherburne, C., Sherburne, R. & Frost, L. S. The role of the pilus in recipient cell recognition during bacterial conjugation mediated by F-like plasmids. Mol. Microbiol. 13, 939–953 (1994).

    CAS  PubMed  Google Scholar 

  95. 95

    Ishiwa, A. & Komano, T. PilV adhesins of plasmid R64 thin pili specifically bind to the lipopolysaccharides of recipient cells. J. Mol. Biol. 343, 615–625 (2004).

    CAS  PubMed  Google Scholar 

  96. 96

    Samuels, A. L., Lanka, E. & Davies, J. E. Conjugative junctions in RP4-mediated mating of Escherichia coli. J. Bacteriol. 182, 2709–2715 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  97. 97

    Kelly, B. A. & Kado, C. I. Agrobacterium-mediated T-DNA transfer and integration into the chromosome of Streptomyces lividans. Mol. Plant Pathol. 3, 125–134 (2002).

    CAS  PubMed  Google Scholar 

  98. 98

    Giebelhaus, L. A. et al. The Tra2 core of the IncP alpha plasmid RP4 is required for intergeneric mating between Escherichia coli and Streptomyces lividans. J. Bacteriol. 178, 6378–6381 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  99. 99

    Bingle, L. E. H., Zatyka, M., Manzoor, S. E. & Thomas, C. M. Co-operative interactions control conjugative transfer of broad host-range plasmid RK2: full effect of minor changes in TrbA operator depends on KorB. Mol. Microbiol. 49, 1095–1108 (2003).

    CAS  PubMed  Google Scholar 

  100. 100

    Grohmann, E., Muth, G. & Espinosa, M. Conjugative plasmid transfer in Gram-positive bacteria. Microbiol. Mol. Biol. Rev. 67, 277–301 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  101. 101

    Hirt, H., Schlievert, P. M. & Dunny, G. M. In vivo induction of virulence and antibiotic resistance transfer in Enterococcus faecalis mediated by the sex pheromone-sensing system of pCF10. Infect. Immun. 70, 716–723 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  102. 102

    Chandler, J. R. & Dunny, G. M. Enterococcal peptide sex pheromones: synthesis and control of biological activity. Peptides 25, 1377–1388 (2004).

    CAS  PubMed  Google Scholar 

  103. 103

    Waters, C. M. & Dunny, G. M. Analysis of functional domains of the Enterococcus faecalis pheromone-induced surface protein aggregation substance. J. Bacteriol. 183, 5659–5667 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  104. 104

    Flannagan, S. E. & Clewell, D. B. Identification and characterization of genes encoding sex pheromone cAM373 activity in Enterocccus faecalis and Staphylococcus aureus. Mol. Microbiol. 44, 803–817 (2002).

    CAS  PubMed  Google Scholar 

  105. 105

    Clewell, D. B., Francia, M. V., Flannagan, S. E. & An, F. Y. Enterococcal plasmid transfer: sex pheromones, transfer origins, relaxases, and the Staphylococcus aureus issue. Plasmid 48, 193–201 (2002).

    CAS  PubMed  Google Scholar 

  106. 106

    Kurenbach, B. R. et al. Intergeneric transfer of the Enterococcus faecalis plasmid pIP501 to Escherichia coli and Streptomyces lividans and sequence analysis of its tra region. Plasmid 50, 86–93 (2003).

    CAS  PubMed  Google Scholar 

  107. 107

    Maas, R. M., Gotz, J., Wohlleben, W. & Muth, G. The conjugative plasmid pSG5 from Streptomyces ghanaensis DSM 2932 differs in its transfer functions from other Streptomyces rolling-circle-type plasmids. Microbiology 144, 2809–2817 (1998).

    CAS  PubMed  Google Scholar 

  108. 108

    Pettis, G. S. & Cohen, S. N. Mutational analysis of the tra locus of the broad-host-range Streptomyces plasmid pIJ101. J. Bacteriol. 182, 4500–4504 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  109. 109

    Bentley, S. D. et al. SCP1, a 356,023 bp linear plasmid adapted to the ecology and developmental biology of its host, Streptomyces coelicolor A3(2). Mol. Microbiol. 51, 1615–1628 (2004).

    CAS  PubMed  Google Scholar 

  110. 110

    Haug, I. et al. Streptomyces coelicolor A3(2) plasmid SCP2*: deductions from the complete sequence. Microbiology 149, 505–513 (2003).

    CAS  PubMed  Google Scholar 

  111. 111

    Stecker, C., Johann, A., Herzberg, C., Averhoff, B. & Gottschalk, G. Complete nucleotide sequence and genetic organization of the 210-kilobase linear plasmid of Rhodococcus erythropolis BD2. J. Bacteriol. 185, 5269–5274 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  112. 112

    Cabezon, E., Sastre, J. I. & de la Cruz, F. Genetic evidence of a coupling role for the TraG protein family in bacterial conjugation. Mol. Gen. Genet. 254, 400–406 (1997).

    CAS  PubMed  Google Scholar 

  113. 113

    Llosa, M., Zunzunegui, S. & de la Cruz, F. Conjugative coupling proteins interact with cognate and heterologous VirB10-like proteins while exhibiting specificity for cognate relaxosomes. Proc. Natl Acad. Sci. USA 100, 10465–10470 (2003).

    CAS  PubMed  Google Scholar 

  114. 114

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

    CAS  PubMed  PubMed Central  Google Scholar 

  115. 115

    Haase, J., Kalkum, M. & Lanka, E. TrbK, a small cytoplasmic membrane lipoprotein, functions in entry exclusion of the IncP alpha plasmid RP4. J. Bacteriol. 178, 6720–6729 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  116. 116

    Hochhut, B., Beaber, J. W., Woodgate, R. & Waldor, M. K. Formation of chromosomal tandem arrays of the SXT element and R391, two conjugative chromosomally integrating elements that share an attachment site. J. Bacteriol. 183, 1124–1132 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  117. 117

    Pohlman, R. F., Genetti, H. D. & Winans, S. C. Entry exclusion of the IncN plasmid-pKM101 is mediated by a single hydrophilic protein containing a lipid attachment motif. Plasmid 31, 158–165 (1994).

    CAS  PubMed  Google Scholar 

  118. 118

    Possoz, C., Gagnat, J., Sezonov, G., Guerineau, M. & Pernodet, J. L. Conjugal immunity of Streptomyces strains carrying the integrative element pSAM2 is due to the pif gene (pSAM2 immunity factor). Mol. Microbiol. 47, 1385–1393 (2003).

    CAS  PubMed  Google Scholar 

  119. 119

    Boyd, E. F., Hill, C. W., Rich, S. M. & Hartl, D. L. Mosaic structure of plasmids from natural populations of Escherichia coli. Genetics 143, 1091–1100 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  120. 120

    Schluter, A. et al. The 64 508 bp IncP-1β antibiotic multiresistance plasmid pB10 isolated from a waste-water treatment plant provides evidence for recombination between members of different branches of the IncP-1β group. Microbiology 149, 3139–3153 (2003).

    CAS  PubMed  Google Scholar 

  121. 121

    Peters, J. E., Bartoszyk, I. M., Dheer, S. & Benson, S. A. Redundant homosexual F transfer facilitates selection-induced reversion of plasmid mutations. J. Bacteriol. 178, 3037–3043 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  122. 122

    Ghigo, J. M. Natural conjugative plasmids induce bacterial biofilm development. Nature 412, 442–445 (2001).

    CAS  PubMed  Google Scholar 

  123. 123

    Reisner, A., Haagensen, J. A. J., Schembri, M. A., Zechner, E. L. & Molin, S. Development and maturation of Escherichia coli K-12 biofilms. Mol. Microbiol. 48, 933–946 (2003).

    CAS  PubMed  Google Scholar 

  124. 124

    Sukulpovi, S. & O'Connor, C. D. TraT lipoprotein, a plasmid-specified mediator of interactions between Gram-negative bacteria and their environment. Microbiol. Rev. 54, 331–341 (1990).

    Google Scholar 

  125. 125

    Jeltsch, A. Maintenance of species identity and controlling speciation of bacteria: a new function for restriction/modification systems? Gene 317, 13–16 (2003).

    CAS  PubMed  Google Scholar 

  126. 126

    Lacks, S. A. & Springhorn, S. S. Transfer of recombinant plasmids containing the gene for DpnII DNA methylase into strains of Streptococcus pneumoniae that produce DpnI or DpnII restirction endonucleases. J. Bacteriol. 158, 905–909 (1984).

    CAS  PubMed  PubMed Central  Google Scholar 

  127. 127

    Moser, D. P., Zarka, D. & Kallas, T. Characterization of a restriction barrier and electrotransformation of the Cyanobacterium nostoc Pcc-7121. Arch. Microbiol. 160, 229–237 (1993).

    CAS  PubMed  Google Scholar 

  128. 128

    Purdy, D. et al. Conjugative transfer of clostridial shuttle vectors from Escherichia coli to Clostridium difficile through circumvention of the restriction barrier. Mol. Microbiol. 46, 439–452 (2002).

    CAS  PubMed  Google Scholar 

  129. 129

    Pinedo, C. A. & Smets, B. F. Conjugal TOL transfer from Pseudomonas putida to Pseudomonas aeruginosa: effects of restriction porificiency, toxicant exposure, cell density ratios, and conjugation detection method on observed transfer efficiencies. Appl. Environ. Microbiol. 71, 51–57 (2005).

    CAS  PubMed  Google Scholar 

  130. 130

    Wilkins, B. M., Chilley, P. M., Thomas, A. T. & Pocklington, M. J. Distribution of restriction enzyme recognition sequences on broad host range plasmid RP4: molecular and evolutionary implications. J. Mol. Biol. 258, 447–456 (1996).

    CAS  PubMed  Google Scholar 

  131. 131

    Bassett, C. L. & Janisiewicz, W. J. Electroporation and stable maintenance of plasmid DNAs in a biocontrol strain of Pseudomonas syringae. Biotechnol. Lett. 25, 199–203 (2003).

    CAS  PubMed  Google Scholar 

  132. 132

    Belogurov, A. A., Delver, E. P. & Rodzevich, O. V. IncN plasmid pKM101 and IncI1 plasmid ColIb-P9 encode homologous antirestriction proteins in their leading regions. J. Bacteriol. 174, 5079–5085 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  133. 133

    Belogurov, A. A., Delver, E. P. & Rodzevich, O. V. Plasmid pKM101 encodes 2 nonhomologous antirestriction proteins (ArdA and ArdB) whose expression is controlled by homologous regulatory sequences. J. Bacteriol. 175, 4843–4850 (1993).

    CAS  PubMed  PubMed Central  Google Scholar 

  134. 134

    Belogurov, A. A. et al. Antirestriction protein ard (TypeC) encoded by IncW plasmid pSa has a high similarity to the “protein transport” domain of the TraC1 primase of promiscous plasmid RP4. J. Mol. Biol. 296, 969–977 (2000).

    CAS  PubMed  Google Scholar 

  135. 135

    Chilley, P. M. & Wilkins, B. M. Distribution of the ArdA family of antirestriction gene on conjugative plasmids. Microbiology 141, 2157–2164 (1995).

    CAS  PubMed  Google Scholar 

  136. 136

    Larsen, M. H. & Figurski, D. H. Structure, expression, and regulation of the kilC operon of promiscuous IncP-α plasmids. J. Bacteriol. 176, 5022–5032 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  137. 137

    Thorsted, P.A et al. Complete sequence of the IncP β plasmid R751: implications for evolution and organisation of the IncP. backbone. J. Mol. Biol. 282, 969–990 (1998).

    CAS  PubMed  Google Scholar 

  138. 138

    Kobayashi, I. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res. 29, 3742–3756 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  139. 139

    Nakayama, Y. & Kobayashi, I. Restriction-modification gene complexes as selfish gene entities: roles of a regulatory system in their establishment, maintenance, and apoptotic mutual exclusion. Proc. Natl Acad. Sci. USA 95, 6442–6447 (1998).

    CAS  PubMed  Google Scholar 

  140. 140

    Adamczyk, M. & Jagura-Burdzy, G. Spread and survival of promiscuous IncP-1 plasmids. Acta Biochim. Pol. 50, 425–453 (2003).

    CAS  PubMed  Google Scholar 

  141. 141

    Rawlings, D. E. & Tietze, E. Comparative biology of IncQ and IncQ-like plasmids. Microbiol. Mol. Biol. Rev. 65, 481–496 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  142. 142

    Scherzinger, E., Haring, V., Lurz, R. & Otto, S. Plasmid RSF1010 DNA-replication in vitro promoted by purified RSF1010 RepA, RepB and RepC proteins. Nucleic Acids Res. 19, 1203–1211 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  143. 143

    Becker, E. C. & Meyer, R. J. Acquisition of resistance genes by the IncQ plasmid R1162 is limited by its high copy number and lack of a partitioning mechanism. J. Bacteriol. 179, 5947–5950 (1997).

    CAS  PubMed  PubMed Central  Google Scholar 

  144. 144

    Haines, A. S., Jones, K., Cheung, M. & Thomas, C. M. The IncP-6 plasmid Rms149 consists of a small mobilizable backbone with multiple large insertions. J. Bacteriol. 187, 4728–4738 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  145. 145

    Kramer, M. G., Espinosa, M., Misra, T. K. & Khan, S. A. Lagging strand replication of rolling-circle plasmids: specific recognition of the ssoA-type origins in different Gram-positive bacteria. Proc. Natl Acad. Sci. USA 95, 10505–10510 (1998).

    CAS  PubMed  Google Scholar 

  146. 146

    Anand, S. P., Mitra, P., Naqvi, A. & Khan, S. A. Bacillus anthracis and Bacillus cereus PcrA helicases can support DNA unwinding and in vitro rolling-circle replication of plasmid pT181 of Staphylococcus aureus. J. Bacteriol. 186, 2195–2199 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  147. 147

    Doran, K. S., Helinski, D. R. & Konieczny, I. Host-dependent requirement for specific DnaA boxes for plasmid RK2 replication. Mol. Microbiol. 33, 490–498 (1999).

    CAS  PubMed  Google Scholar 

  148. 148

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

    CAS  PubMed  PubMed Central  Google Scholar 

  149. 149

    Zhong, Z. P., Helinski, D. & Toukdarian, A. A specific region in the N terminus of a replication initiation protein of plasmid RK2 is required for recruitment of Pseudomonas aeruginosa DnaB helicase to the plasmid origin. J. Biol. Chem. 278, 45305–45310 (2003).

    CAS  PubMed  Google Scholar 

  150. 150

    Jiang, Y., Pacek, M., Helinski, D. R., Konieczny, I. & Toukdarian, A. A multifunctional plasmid-encoded replication initiation protein both recruits and positions an active helicase at the replication origin. Proc. Natl Acad. Sci. USA 100, 8692–8697 (2003).

    CAS  PubMed  Google Scholar 

  151. 151

    Bignell, C. R., Haines, A. S., Khare, D. & Thomas, C. M. Effect of growth rate and incC mutation on symmetric plasmid distribution by the IncP-1 partitioning apparatus. Mol. Microbiol. 34, 205–216 (1999).

    CAS  PubMed  Google Scholar 

  152. 152

    Siddique, A. & Figurski, D. H. The active partition gene incC of IncP plasmids is required for stable maintenance in a broad range of hosts. J. Bacteriol. 184, 1788–1793 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  153. 153

    Zhong, Z. P., Helinski, D. & Toukdarian, A. Plasmid host-range: restrictions to F replication in Pseudomonas. Plasmid 54, 48–56 (2005).

    CAS  PubMed  Google Scholar 

  154. 154

    Maestro, B. et al. Modulation of pPS10 host range by DnaA. Mol. Microbiol. 46, 223–234 (2002).

    CAS  PubMed  Google Scholar 

  155. 155

    Maestro, B., Sanz, J. M., Diaz-Orejas, R. & Fernandez-Tresguerres, E. Modulation of pPS10 host range by plasmid-encoded RepA initiator protein. J. Bacteriol. 185, 1367–1375 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  156. 156

    Greated, A., Titok, M., Krasowiak, R., Fairclough, R. J. & Thomas, C. M. The replication and stable-inheritance functions of IncP-9 plasmid pM3. Microbiology 146, 2249–2258 (2000).

    CAS  PubMed  Google Scholar 

  157. 157

    Sevastsyanovich, Y. R., Titok, M. A., Krasowiak, R., Bingle, L. E. H. & Thomas, C. M. Ability of IncP-9 plasmid pM3 to replicate in E. coli is dependent on both rep and par functions. Mol. Microbiol. 57, 819–833 (2005).

    CAS  PubMed  Google Scholar 

  158. 158

    Wu, L. T. & Tseng, Y. H. Characterization of the IncW cryptic plasmid pXV2 from Xanthomonas campestris pv. vesicatoria. Plasmid 44, 163–172 (2000).

    CAS  PubMed  Google Scholar 

  159. 159

    Nielsen, K. M. Barriers to horizontal gene transfer by natural transformation in soil bacteria. APMIS Suppl. 84, 77–84 (1998).

    CAS  PubMed  Google Scholar 

  160. 160

    Nielsen, K. M., Bones, A. M., Smalla, K. & van Elsas, J. D. Horizontal gene transfer from plants to terrestrial bacteria — a rare event? FEMS Microbiol. Rev. 22, 79–103 (1998).

    CAS  Google Scholar 

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Current work related to this review in the laboratory of C.M.T. is supported by The Wellcome Trust, INTAS, BBSRC and the Darwin Trust of Edinburgh. K.M.N. acknowledge support from The Research Council of Norway.

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The ability of bacteria to take up extracellular DNA.


The number of bacteria carrying the horizontally acquired DNA divided by the total number of bacteria exposed, per given time unit.


Recombination that depends on extensive segments of high sequence similarity between two DNA molecules.


A transposable DNA segment that normally only encodes the enzymes that mediate its own transposition and has no phenotypic marker.


The enzyme that promotes cutting the DNA at the ends of a transposable element and joining to the DNA molecule into which the element is to be inserted.


An abbreviation of bacteriophage — a virus that specifically infects bacteria.


A bacteriophage that integrates into a host-cell chromosome and then is excised again, bringing with it (as part of the phage genome) part of the host chromosome that can be transferred across to a new host.


The proteinaceous fibre made from multiple subunits of a protein called pilin that mediates contact between donor and recipient bacteria prior to conjugative transfer.


A diffusible small molecule that can act as a chemical signal.


The tube-like cellular growth associated with mycelial organisms.


The process of a non-self-transmissible element being allowed to tranfer by the presence of a self-transmissible element.


The protein–DNA complex at the transfer origin that results in nicking of the DNA when the proteins are denatured chemically or cleaved proteolytically.


The reduction of transfer frequency during conjugative transfer to recipients already carrying a related plasmid.


Homologous genes in the same organism that have evolved from a gene duplication and a subsequent divergence of function.


Homologues that are related to each other through a speciation event.


Enzyme that unwinds DNA duplexes.


Discontinuous synthesis on the strand running back from the replication fork, dependent on regular synthesis of primers by a primase and other primosome proteins.

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Thomas, C., Nielsen, K. Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria. Nat Rev Microbiol 3, 711–721 (2005).

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