Gene Transfer in Gram-Negative Bacteria

Joseph E. Peters

doi:10.1128/9781555817497.ch31

Chapter 31 : Gene Transfer in Gram-Negative Bacteria

Author: Joseph E. Peters

Content Type: Reference

Publication Year: 2007

Category: Microbial Genetics and Molecular Biology

Book DOI: 10.1128/9781555817497

Chapter DOI: 10.1128/9781555817497.ch31

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Abstract:

One realization that has come from comparing multiple bacterial genome sequences, including multiple isolates from the same species, is that gene transfer is an important force in bacterial genome evolution. In the laboratory gene transfer is essential for the study of bacteria and for learning more about all living organisms. Three processes in bacteria can broadly define the transfer of DNA: transformation, transduction, and conjugation. This chapter focuses on the many genetic tools available to manipulate the genetic content of Escherichia coli. A DNA molecule that does not have its own origin of replication must integrate into either the host chromosome or another autonomously replicating element such as an endogenous plasmid. In E. coli a modified derivative of the bacteriophage T4 offers some advantages for transduction in that it packages twice as much DNA as P1 and also is less sensitive to capsules found on many pathogenic strains of E. coli. Transformation of bacteria by use of either naturally competent organisms, the process of electroporation, or chemical competency relies on the direct uptake of DNA by bacteria. Conjugation can be used as a tool to deliver plasmids that are capable of being stably maintained in the target host or as a tool to deliver “suicide vectors” that cannot replicate in the target host.

Citation: Peters J. 2007. Gene Transfer in Gram-Negative Bacteria, p 735-755. In Reddy C, Beveridge T, Breznak J, Marzluf G, Schmidt T, Snyder L (ed), Methods for General and Molecular Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817497.ch31

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Chromosomal DNA: 0.5170318

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Gene Transfer in Gram-Negative Bacteria

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FIGURE 1

Genetic information can be integrated into the chromosome of a bacterium using a single crossover from a circular DNA construct that cannot replicate in the host. (a) A single open reading frame (thick line) to be inactivated is shown with its promoter (solid arrow) and RNA transcript (dashed line with arrow). (b) A plasmid (circle) that cannot replicate in the strain can be maintained only by integrating into the chromosome using homology provided on the plasmid indicated with an “X.” Three arbitrary positions are indicated with numbers to show the orientation. (c) Integration of the circular DNA substrate disrupts and fuses the plasmid-borne genes behind the target gene promoter. Depending on the construct, the transcript may be terminated within the integrated DNA segment. Promoters within the plasmid could also activate adjacent genes in the chromosome.

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FIGURE 1

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FIGURE 2

Genetic information can be integrated into the chromosome of a bacterium using a double-crossover event from a circular DNA construct that cannot replicate in the host. (a) A single open reading frame (thick line) to be inactivated is shown with its promoter (solid arrow) and RNA transcript (dashed line with arrow). (b) A plasmid (oval) that cannot replicate in the strain can be maintained only by integrating into the chromosome using the homology provided on the plasmid indicated with “X's” (thick lines). Two crossover events ensure that only a portion of the circular DNA is integrated into the gene. Five arbitrary positions are indicated with numbers to show the DNA that is integrated and the orientation. A single crossover event likely occurs at a mid-step in the reaction and is not shown ( Fig. 1 ). (c) Integration of the circular DNA substrate removes all or a portion of the gene and fuses the encoded genes behind the target gene promoter. Depending on the construct, the transcript may be terminated within the integrated DNA segment. Promoters within the plasmid could activate adjacent genes in the chromosome.

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FIGURE 2

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FIGURE 3

Genetic information can be integrated into the chromosome of a bacterium using a double-crossover event from a linear DNA construct. (a) A single open reading frame (thick line) to be inactivated is shown with its promoter (solid arrow) and RNA transcript (dashed line with arrow). (b) Two crossover events must occur for the linear DNA to be integrated into the gene when selecting for gene products indicated by 1 or 2. Homology provided on the fragment is indicated with “X's.” (c) Integration of the DNA substrate removes all or a portion of the gene and fuses the genes carried behind the target gene promoter. Depending on the construct, the transcript may be terminated within the integrated DNA segment. Promoters within the integrated DNA segment could activate adjacent genes in the chromosome.

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FIGURE 3

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FIGURE 4

Recombination substrates can be made in vitro for use with λ Red recombination. The antibiotic resistance used to select for recombinants can subsequently be removed by expressing the Flp recombinase that will excise the region between the two frt sites (FRT). (a) Primers are designed to amplify from a universal antibiotic-resistant cassette with frt recombination sites using primer binding sites P1 and P2. The primers contain 5' “tails” that are complementary to the target gene at regions H1 and H2 for the subsequent crossover event. (b) The PCR-generated substrate is transformed into a cell expressing the Exo, Beta, and Gam proteins (substrate shown miniaturized). (c) Selecting for the antibiotic resistance marker crosses in the cassette with its flanking frt recombination sites using the homology at regions H1 and H2. (d) The Flp recombinase is transiently expressed and subsequently lost because replication from the pCP20 vector is temperature sensitive. The Flp recombinase efficiently catalyzes recombination between the frt recombination sites removing the antibiotic resistance-conferring cassette. See the text for details.

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FIGURE 4

References

/content/book/10.1128/9781555817497.chap31

1. Ausubel, F. M.,, R. Brent,, R. E. Kingston,, D. D. More,, J. G. Seidman,, J. A. Smith,, and K. Struhl. 1988. Current Protocols in Molecular Biology. Greene Publishing Associates Inc. and John Wiley & Sons, Inc., New York, NY.

2. Miller, J. H. 1991. A Short Course in Bacterial Genetics: A Laboratory Manual and Handbook for Escherichia coli and Related Bacteria. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

3. Miller, J. H. (ed.). 1991. Methods in Enzymology, vol. 204. Bacterial Genetic Systems. Academic Press, San Diego, CA.

4. Sambrook, J.,, and D. W. Russell. 2001. Molecular Cloning: A Laboratory Manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

5. Silhavy, T. J.,, M. L. Berman,, and L. Enquist. 1984. Experiments with Gene Fusions. Cold Spring Harbor Laboratory Press. Cold Spring Harbor, NY. 31.11.2. Specific References

6. Anderson, D. G.,, and S. C. Kowalczykowski. 1997. The translocating RecBCD enzyme stimulates recombination by directing RecA protein onto ssDNA in a chi-regulated manner. Cell 90: 77– 86.

7. Ausubel, F. M.,, R. Brent,, R. E. Kingston,, D. D. Moore,, J. G. Seidman,, J. A. Smith,, and K. Struhl. 1988. Current Protocols in Molecular Biology. Greene Publishing Associates Inc. and John Wiley & Sons, Inc., New York, NY.

8. Ayres, E. K.,, V. J. Thomson,, G. Merino,, D. Balderes,, and D. H. Figurski. 1993. Precise deletions in large bacterial genomes by vector-mediated excision (VEX). The trfA gene of promiscuous plasmid RK2 is essential for replication in several gram-negative hosts. J. Mol. Biol. 230: 174– 185.

9. Bachmann, B. J., 1996. Derivations and genotypes of some mutant derivatives of Escherichia coli K-12, p. 2460– 2488. In F. C. Neidhardt,, R. I. Curtiss,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed. American Society for Microbiology, Washington, DC.

10. Barbour, S. D.,, H. Nagaishi,, A. Templin,, and A. J. Clark. 1970. Biochemical and genetic studies of recombination proficiency in Escherichia coli. II. Rec+ revertants caused by indirect suppression of rec- mutations. Proc. Natl. Acad. Sci. USA 67: 128– 135.

11. Barcak, G. J.,, M. S. Chandler,, R. J. Redfield,, and J.-F. Tomb. 1991. Genetic systems in Haemophilus influenzae. Methods Enzymol. 204: 321– 342.

12. Baudin, A.,, O. Ozier-Kalogeropoulos,, A. Denouel,, F. Lacroute,, and C. Cullin. 1993. A simple and efficient method for direct gene deletion in Saccharomyces cerevisiae. Nucleic Acids Res. 21: 3329– 3330.

13. Bender, R. A. 1981. Improved generalized transducing bacteriophage for Caulobacter crescentus. J. Bacteriol. 148: 734– 735.

14. Berlyn, M. K.,, K. B. Low,, and K. E. Rudd,. 1996. Linkage map of Escherichia coli K-12. In F. C. Neidhardt,, R. I. Curtiss,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed. American Society for Microbiology, Washington, DC.

15. Blattner, F. R.,, G. Plunkett III,, C. A. Bloch,, N. T. Perna,, V. Burland,, M. Riley,, J. Collado-Vides,, J. D. Glasner,, C. K. Rode,, G. F. Mayhew,, J. Gregor,, N. W. Davis,, H. A. Kirkpatrick,, M. A. Goeden,, D. J. Rose,, B. Mau,, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277: 1453– 1474.

16. Blomfield, I. C.,, V. Vaughn,, R. F. Rest,, and B. I. Eisenstein. 1991. Allelic exchange in Escherichia coli using the Bacillus subtilis sacB gene and a temperature-sensitive pSC101 replicon. Mol. Microbiol. 5: 1447– 1457.

17. Bochner, B. R.,, H. C. Huang,, G. L. Schieven,, and B. N. Ames. 1980. Positive selection for loss of tetracycline resistance. J. Bacteriol. 143: 926– 933.

18. Bolivar, F.,, R. L. Rodriguez,, P. J. Greene,, M. C. Betlach,, H. L. Heyneker,, and H. W. Boyer. 1977. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene 2: 95– 113.

19. Boyd, D.,, D. S. Weiss,, J. C. Chen,, and J. Beckwith. 2000. Towards single-copy gene expression systems making gene cloning physiologically relevant: lambda InCh, a simple Escherichia coli plasmid-chromosome shuttle system. J. Bacteriol. 182: 842– 847.

20. Budzik, J. M.,, W. A. Rosche,, A. Rietsch,, and G. A. O’Toole. 2004. Isolation and characterization of a generalized transducing phage for Pseudomonas aeruginosa strains PAO1 and PA14. J. Bacteriol. 186: 3270– 3273.

21. Burrus, V.,, and M. K. Waldor. 2004. Shaping bacterial genomes with integrative and conjugative elements. Res. Microbiol. 155: 376– 386.

22. Cai, Y. P.,, and C. P. Wolk. 1990. Use of a conditionally lethal gene in Anabaena sp. strain PCC 7120 to select for double recombinants and to entrap insertion sequences. J. Bacteriol. 172: 3138– 3145.

23. Campos, J. M.,, J. Geisselsoder,, and D. R. Zusman. 1978. Isolation of bacteriophage MX4, a generalized transducing phage for Myxococcus xanthus. J. Mol. Biol. 119: 167– 178.

24. Cangelosi, G. A.,, E. A. Best,, G. Martinetti,, and E. W. Nester. 1991. Genetic analysis of Agrobacterium. Methods Enzymol. 204: 384– 397.

25. Casadaban, M. J. 1976. Transposition and fusion of the lac genes to selected promoters in Escherichia coli using bacteriophage lambda and Mu. J. Mol. Biol. 104: 541– 555.

26. Chang, A. C.,, and S. N. Cohen. 1978. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the p15A cryptic miniplasmid. J. Bacteriol. 134: 1141– 1156.

27. Cherepanov, P. P.,, and W. Wackernagel. 1995. Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibioticresistance determinant. Gene 158: 9– 14.

28. Chun, K. T.,, H. J. Edenberg,, M. R. Kelley,, and M. G. Goebl. 1997. Rapid amplification of uncharacterized transposon-tagged DNA sequences from genomic DNA. Yeast 13: 233– 400.

29. Claverys, J. P.,, and B. Martin. 2003. Bacterial “competence” genes: signatures of active transformation, or only remnants? Trends Microbiol. 11: 161– 165.

30. Close, T. J.,, D. Zaitlin,, and C. I. Kado. 1984. Design and development of amplifiable broad-host-range cloning vectors: analysis of the vir region of Agrobacterium tumefaciens plasmid pTiC58. Plasmid 12: 111– 118.

31. Cohen, M. F.,, J. C. Meeks,, Y. A. Cai,, and C. P. Wolk. 1998. Transposon mutagenesis of heterocyst-forming filamentous cyanobacteria. Methods Enzymol. 305: 3– 17.

32. Cohen, S. N.,, A. C. Chang,, and L. Hsu. 1972. Nonchromosomal antibiotic resistance in bacteria: genetic transformation of Escherichia coli by R-factor DNA. Proc. Natl. Acad. Sci. USA 69: 2110– 2114.

33. Conchas, R. F.,, and E. Carniel. 1990. A highly efficient electroporation system for transformation of Yersinia. Gene 87: 133– 137.

34. Copeland, N. G.,, N. A. Jenkins,, and D. L. Court. 2001. Recombineering: a powerful new tool for mouse functional genomics. Nat. Rev. Genet. 2: 769– 779.

35. Coppi, M. V.,, C. Leang,, S. J. Sandler,, and D. R. Lovley. 2001. Development of a genetic system for Geobacter sulfurreducens. Appl. Environ. Microbiol. 67: 3180– 3187.

36. Costantino, N.,, and D. L. Court. 2003. Enhanced levels of lambda Red-mediated recombinants in mismatch repair mutants. Proc. Natl. Acad. Sci. USA 100: 15748– 15753.

37. Court, D. L.,, J. A. Sawitzke,, and L. C. Thomason. 2002. Genetic engineering using homologous recombination. Annu. Rev. Genet. 36: 361– 388.

38. Court, D. L.,, S. Swaminathan,, D. Yu,, H. Wilson,, T. Baker,, M. Bubunenko,, J. Sawitzke,, and S. K. Sharan. 2003. Mini-lambda: a tractable system for chromosome and BAC engineering. Gene 315: 63– 69.

39. Datsenko, K. A.,, and B. L. Wanner. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97: 6640– 6645.

40. Davison, J.,, M. Heusterspreute,, N. Chevalier,, V. Ha-Thi,, and F. Brunel. 1987. Vectors with restriction site banks. V. pJRD215, a wide-host-range cosmid vector with multiple cloning sites. Gene 51: 275– 280.

41. de Lorenzo, V.,, M. Herrero,, J. M. Sanchez,, and K. N. Timmis. 1998. Mini-transposons in microbial ecology and environmental biotechnology. FEMS Microbiol. Ecol. 27: 211– 224.

42. Derbise, A.,, B. Lesic,, D. Dacheux,, J. M. Ghigo,, and E. Carniel. 2003. A rapid and simple method for inactivating chromosomal genes in Yersinia. FEMS Immunol. Med. Microbiol. 38: 113– 116.

43. DeWitt, S. K.,, and E. A. Adelberg. 1962. The occurrence of a genetic transposition in a strain of Escherichia coli. Genetics 47: 577– 585.

44. Donahue, J. P.,, D. A. Israel,, R. M. Peek,, M. J. Blaser,, and G. G. Miller. 2000. Overcoming the restriction barrier to plasmid transformation of Helicobacter pylori. Mol. Microbiol. 37: 1066– 1074.

45. Donohue, T. J.,, and S. Kaplan. 1991. Genetic techniques in Rhodospirillaceae. Methods Enzymol. 204: 459– 485.

46. Ely, B. 1991. Genetics of Caulobacter crescentus. Methods Enzymol. 204: 372– 384.

47. Finan, T. M.,, E. Hartweig,, K. LeMieux,, K. Bergman,, G. C. Walker,, and E. R. Signer. 1984. General transduction in Rhizobium meliloti. J. Bacteriol. 159: 120– 124.

48. Focareta, T.,, and P. A. Manning. 1991. Distinguishing between the extracellular DNases of Vibrio cholerae and development of a transformation system. Mol. Microbiol. 5: 2547– 2555.

49. Gay, P.,, D. Le Coq,, M. Steinmetz,, T. Berkelman,, and C. I. Kado. 1985. Positive selection procedure for entrapment of insertion sequence elements in gram-negative bacteria. J. Bacteriol. 164: 918– 921.

50. Glazebrook, J.,, and G. C. Walker. 1991. Genetic techniques in Rhizobium meliloti. Methods Enzymol. 204: 398– 418.

51. Gunn, J. S.,, and D. C. Stein. 1996. Use of a non-selective transformation technique to construct a multiply restriction/ modification-deficient mutant of Neisseria gonorrhoeae. Mol. Gen. Genet. 251: 509– 517.

52. Guzman, L.-M.,, D. Belin,, M. J. Carson,, and J. Beckwith. 1995. Tight regulation, modulation, and highlevel expression by vectors containing the arabinose PBAD promoter. J. Bacteriol. 177: 4121– 4130.

53. Haldimann, A.,, and B. L. Wanner. 2001. Conditionalreplication, integration, excision, and retrieval plasmidhost systems for gene structure-function studies of bacteria. J. Bacteriol. 183: 6384– 6393.

54. Hamilton, C. M.,, M. Aldea,, B. K. Washburn,, P. Babitzke,, and S. R. Kushner. 1989. New method for generating deletions and gene replacements in Escherichia coli. J. Bacteriol. 171: 4617– 4622.

55. Hanahan, D. 1983. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166: 557– 580.

56. Hanahan, D.,, J. Jessee,, and F. R. Bloom. 1991. Plasmid transformation of Escherichia coli and other bacteria. Methods Enzymol. 204: 63– 113.

57. Hava, D. L.,, and A. Camilli. 2001. Isolation and characterization of a temperature-sensitive generalized transducing bacteriophage for Vibrio cholerae. J. Microbiol. Methods 46: 217– 225.

58. Herring, C. D.,, J. D. Glasner,, and F. R. Blattner. 2003. Gene replacement without selection: regulated suppression of amber mutations in Escherichia coli. Gene 311: 153– 163.

59. Heuermann, D.,, and R. Haas. 1998. A stable shuttle vector system for efficient genetic complementation of Helicobacter pylori strains by transformation and conjugation. Mol. Gen. Genet. 257: 519– 528.

60. Hong, J. S.,, and B. N. Ames. 1971. Localized mutagenesis of any specific small region of the bacterial chromosome. Proc. Natl. Acad. Sci. USA 68: 3158– 3162.

61. Inoue, H.,, H. Nojima,, and H. Okayama. 1990. High efficiency transformation of Escherichia coli with plasmids. Gene 96: 23– 28.

62. Jacobs, M.,, S. Wnendt,, and U. Stahl. 1990. High-efficiency electro-transformation of Escherichia coli with DNA from ligation mixtures. Nucleic Acids Res. 18: 1653.

63. Jasin, M.,, and P. Schimmel. 1984. Deletion of an essential gene in Escherichia coli by site-specific recombination with linear DNA fragments. J. Bacteriol. 159: 783– 786.

64. Kaiser, D.,, and M. Dworkin. 1975. Gene transfer to Myxobacterium by Escherichia coli phage P1. Science 187: 653– 654.

65. Khlebnikov, A.,, K. A. Datsenko,, T. Skaug,, B. L. Wanner,, and J. D. Keasling. 2001. Homogeneous expression of the P(BAD) promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter. Microbiology 147: 3241– 3247.

66. Kinder, S. A.,, J. L. Badger,, G. O. Bryant,, J. C. Pepe,, and V. L. Miller. 1993. Cloning of the YenI restriction endonuclease and methyltransferase from Yersinia enterocolitica serotype O8 and construction of a transformable R-M+ mutant. Gene 136: 271– 275.

67. Koch, B.,, L. E. Jensen,, and O. Nybroe. 2001. A panel of Tn7-based vectors for insertion of the gfp marker gene or for delivery of cloned DNA into Gram-negative bacteria at a neutral chromosomal site. J. Microbiol. Methods 45: 187– 195.

68. Koksharova, O. A.,, and C. P. Wolk. 2002. Genetic tools for cyanobacteria. Appl. Microbiol. Biotechnol. 58: 123– 137.

69. Kolisnychenko, V.,, G. Plunkett III,, C. D. Herring,, T. Feher,, J. Posfai,, F. R. Blattner,, and G. Posfai. 2002. Engineering a reduced Escherichia coli genome. Genome Res. 12: 640– 647.

70. Kolter, R.,, M. Inuzuka,, and D. R. Helinski. 1978. Transcomplementation- dependent replication of a low molecular weight origin fragment from plasmid R6K. Cell 15: 1199– 1208.

71. Kovach, M. E.,, P. H. Elzer,, D. S. Hill,, G. T. Robertson,, M. A. Farris,, R. M. Roop II,, and K. M. Peterson. 1995. Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 166: 175– 176.

72. Kowalczykowski, S. C. 2000. Initiation of genetic recombination and recombination-dependent replication. Trends Biochem. Sci. 25: 156– 165.

73. Kowalczykowski, S. C.,, D. A. Dixon,, A. K. Eggleston,, S. D. Lauder,, and W. M. Rehrauer. 1994. Biochemistry of homologous recombination in Escherichia coli. Microbiol. Rev. 58: 401– 465.

74. Kuzminov, A. 1999. Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol. Mol. Biol. Rev. 63: 751– 813.

75. Lacks, S.,, and B. Greenberg. 1977. Complementary specificity of restriction endonucleases of Diplococcus pneumoniae with respect to DNA methylation. J. Mol. Biol. 114: 153– 168.

76. Lafontaine, D.,, and D. Tollervey. 1996. One-step PCR mediated strategy for the construction of conditionally expressed and epitope tagged yeast proteins. Nucleic Acids Res. 24: 3469– 3471.

77. Lederberg, J.,, and E. L. Tatum. 1946. Gene recombination in Escherichia coli. Nature 158: 558.

78. Lee, E. C.,, D. Yu,, J. Martinez de Velasco,, L. Tessarollo,, D. A. Swing,, D. L. Court,, N. A. Jenkins,, and N. G. Copeland. 2001. A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics 73: 56– 65.

79. Link, A. J.,, D. Phillips,, and G. M. Church. 1997. Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization. J. Bacteriol. 179: 6228– 6237.

80. Low, K. B. 1991. Conjugational methods for mapping with Hfr and F-prime strains. Methods Enzymol. 204: 43– 62.

81. Low, K. B.,, and D. D. Porter. 1978. Modes of gene transfer and recombination in bacteria. Annu. Rev. Genet. 12: 249– 287.

82. Mandel, M.,, and A. Higa. 1970. Calcium-dependent bacteriophage DNA infection. J. Mol. Biol. 53: 159– 162.

83. Margolin, P., 1987. Generalized transduction, p. 1154– 1168. In F. C. Neidhardt,, J. L. Ingraham,, K. B. Low,, B. Magasanik,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, vol. 2. American Society for Microbiology, Washington, DC.

84. Marra, A.,, and H. A. Shuman. 1989. Isolation of a Legionella pneumophila restriction mutant with increased ability to act as a recipient in heterospecific matings. J. Bacteriol. 171: 2238– 2240.

85. Marx, C. J.,, and M. E. Lidstrom. 2002. Broad-host-range cre- lox system for antibiotic marker recycling in gramnegative bacteria. BioTechniques 33: 1062– 1067.

86. Marx, C. J.,, and M. E. Lidstrom. 2001. Development of improved versatile broad-host-range vectors for use in methylotrophs and other Gram-negative bacteria. Microbiology 147: 2065– 2075.

87. Maxson, M. E.,, and A. J. Darwin. 2004. Identification of inducers of the Yersinia enterocolitica phage shock protein system and comparison to the regulation of the RpoE and Cpx extracytoplasmic stress responses. J. Bacteriol. 186: 4199– 4208.

88. Metcalf, W. W.,, W. Jiang,, L. L. Daniels,, S. K. Kim,, A. Haldimann,, and B. L. Wanner. 1996. Conditionally replicative and conjugative plasmids carrying lacZ alpha for cloning, mutagenesis, and allele replacement in bacteria. Plasmid 35: 1– 13.

89. Metcalf, W. W.,, W. Jiang,, and B. L. Wanner. 1994. Use of the rep technique for allele replacement to construct new Escherichia coli hosts for maintenance of R6K gamma origin plasmids at different copy numbers. Gene 138: 1– 7.

90. Miller, J. H. 1992. A Short Course in Bacterial Genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

91. Muramatsu, K.,, and H. Matsumoto. 1991. Two generalized transducing phages in Vibrio parahaemolyticus and Vibrio alginolyticus. Microbiol. Immunol. 35: 1073– 1084.

92. Nichols, B. P.,, O. Shafiq,, and V. Meiners. 1998. Sequence analysis of Tn 10 insertion sites in a collection of Escherichia coli strains used for genetic mapping and strain construction. J. Bacteriol. 180: 6408– 6411.

93. Nickoloff, J. 1995. Electroporation Protocols for Microorganisms, vol. 47. Humana Press, Totowa, NJ.

94. O’Connor, K. A.,, and D. R. Zusman. 1983. Coliphage P1-mediated transduction of cloned DNA from Escherichia coli to Myxococcus xanthus: use for complementation and recombinational analyses. J. Bacteriol. 155: 317– 329.

95. O’Connor, M.,, M. Peifer,, and W. Bender. 1989. Construction of large DNA segments in Escherichia coli. Science 244: 1307– 1312.

96. Oppenheim, A. B.,, A. J. Rattray,, M. Bubunenko,, L. C. Thomason,, and D. L. Court. 2004. In vivo recombineering of bacteriophage lambda by PCR fragments and single-strand oligonucleotides. Virology 319: 185– 189.

97. Orr-Weaver, T. L.,, J. W. Szostak,, and R. J. Rothstein. 1981. Yeast transformation: a model system for the study of recombination. Proc. Natl. Acad. Sci. USA 78: 6354– 6358.

98. Peters, J. E.,, and N. L. Craig. 2001. Tn7: smarter than we thought. Nat. Rev./Mol. Cell Biol. 2: 806– 814.

99. Peters, J. E.,, T. E. Thate,, and N. L. Craig. 2003. Definition of the Escherichia coli MC4100 genome by use of a DNA array. J. Bacteriol. 185: 2017– 2021.

100. Phillips, G. J. 1999. New cloning vectors with temperature- sensitive replication. Plasmid 41: 78– 81.

101. Posfai, G.,, V. Kolisnychenko,, Z. Bereczki,, and F. R. Blattner. 1999. Markerless gene replacement in Escherichia coli stimulated by a double-strand break in the chromosome. Nucleic Acids Res. 27: 4409– 4415.

102. Price-Carter, M.,, J. Tingey,, T. A. Bobik,, and J. R. Roth. 2001. The alternative electron acceptor tetrathionate supports B12-dependent anaerobic growth of Salmonella enterica serovar Typhimurium on ethanolamine or 1,2- propanediol. J. Bacteriol. 183: 2463– 2475.

103. Priefer, U. B.,, R. Simon,, and A. Puhler. 1985. Extension of the host range of Escherichia coli vectors by incorporation of RSF1010 replication and mobilization functions. J. Bacteriol. 163: 324– 330.

104. Raibaud, O.,, M. Mock,, and M. Schwartz. 1984. A technique for integrating any DNA fragment into the chromosome of Escherichia coli. Gene 29: 231– 241.

105. Rong, R.,, M. M. Slupska,, J. H. Chiang,, and J. H. Miller. 2004. Engineering large fragment insertions into the chromosome of Escherichia coli. Gene 336: 73– 80.

106. Rothmel, R. K.,, A. M. Chakrabarty,, A. Berry,, and A. Darzins. 1991. Genetic systems in Pseudomonas. Methods Enzymol. 204: 485– 514.

107. Russell, C. B.,, and F. W. Dahlquist. 1989. Exchange of chromosomal and plasmid alleles in Escherichia coli by selection for loss of a dominant antibiotic sensitivity marker. J. Bacteriol. 171: 2614– 2618.

108. Russell, C. B.,, D. S. Thaler,, and F. W. Dahlquist. 1989. Chromosomal transformation of Escherichia coli recD strains with linearized plasmids. J. Bacteriol. 171: 2609– 2613.

109. Sambrook, J.,, E. F. Fritsch,, and T. Maniatis. 1989. Molecular Cloning: a Laboratory Manual, 2nd ed. Cold Spring Harbor Press, Cold Spring Harbor, NY.

110. Sauer, B. 1998. Inducible gene targeting in mice using the Cre/ lox system. Methods 14: 381– 392.

111. Seifert, H. S.,, and M. So. 1991. Genetic systems in pathogenic Neisseriae. Methods Enzymol. 204: 342– 357.

112. Sexton, J. A.,, and J. P. Vogel. 2004. Regulation of hypercompetence in Legionella pneumophila. J. Bacteriol. 186: 3814– 3825.

113. Shi, Z. X.,, H. L. Wang,, K. Hu,, E. L. Feng,, X. Yao,, G. F. Su,, P. T. Huang,, and L. Y. Huang. 2003. Identification of alkA gene related to virulence of Shigella flexneri 2a by mutational analysis. World J. Gastroenterol. 9: 2720– 2725.

114. Shizuya, H.,, B. Birren,, U. J. Kim,, V. Mancino,, T. Slepak,, Y. Tachiiri,, and M. Simon. 1992. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc. Natl. Acad. Sci. USA 89: 8794– 8797.

115. Sik, T.,, J. Horvath,, and S. Chatterjee. 1980. Generalized transduction in Rhizobium meliloti. Mol. Gen. Genet. 178: 511– 516.

116. Silverman, M.,, R. Showalter,, and L. McCarter. 1991. Genetic analysis in Vibrio. Methods Enzymol. 204: 515– 536.

117. Simon, R.,, U. B. Priefer,, and A. Puhler. 1982. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram-negative bacteria. Biotechnology 1: 784– 791.

118. Singer, M.,, T. A. Baker,, G. Schnitzler,, S. M. Deischel,, M. Goel,, W. Dove,, K. J. Jaacks,, A. D. Grossman,, J. W. Erickson,, and C. A. Gross. 1989. A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol. Rev. 53: 1– 24.

119. Skorupski, K.,, and R. K. Taylor. 1996. Positive selection vectors for allelic exchange. Gene 169: 47– 52.

120. Slauch, J. M.,, and T. J. Silhavy. 1991. Genetic fusions as experimental tools. Methods Enzymol. 204: 213– 248.

121. Smeets, L. C.,, J. J. Bijlsma,, S. Y. Boomkens,, C. M. Vandenbroucke-Grauls,, and J. G. Kusters. 2000. comH, a novel gene essential for natural transformation of Helicobacter pylori. J. Bacteriol. 182: 3948– 3954.

122. Stalker, D. M.,, R. Kolter,, and D. R. Helinski. 1979. Nucleotide sequence of the region of an origin of replication of the antibiotic resistance plasmid R6K. Proc. Natl. Acad. Sci. USA 76: 1150– 1154.

123. Stein, D. C. 1991. Transformation of Neisseria gonorrhoeae: physical requirements of the transforming DNA. Can. J. Microbiol. 37: 345– 349.

124. Sternberg, N. L.,, and R. Maurer. 1991. Bacteriophagemediated generalized transduction in Escherichia coli and Salmonella typhimurium. Methods Enzymol. 204: 18– 43.

125. Stibitz, S.,, W. Black,, and S. Falkow. 1986. The construction of a cloning vector designed for gene replacement in Bordetella pertussis. Gene 50: 133– 140.

126. Szostak, J. W.,, T. Orr-Weaver,, R. J. Rothstein,, and F. W. Stahl. 1983. The double-strand-break repair model for recombination. Cell 33: 25– 35.

127. Trulzsch, K.,, T. Sporleder,, E. I. Igwe,, H. Russmann,, and J. Heesemann. 2004. Contribution of the major secreted Yops of Yersinia enterocolitica O:8 to pathogenicity in the mouse infection model. Infect. Immun. 72: 5227– 5234.

128. Uzzau, S.,, N. Figueroa-Bossi,, S. Rubino,, and L. Bossi. 2001. Epitope tagging of chromosomal genes in Salmonella. Proc. Natl. Acad. Sci. USA 98: 15264– 15269.

129. Visick, K. G.,, and E. G. Ruby. 1996. Construction and symbiotic competence of a luxA-deletion mutant of Vibrio fischeri. Gene 175: 89– 94.

130. Wang, Y.,, K. P. Roos,, and D. E. Taylor. 1993. Transformation of Helicobacter pylori by chromosomal metronidazole resistance and by a plasmid with a selectable chloramphenicol resistance marker. J. Gen. Microbiol. 139(Pt. 10): 2485– 2493.

131. Weiss, B. D.,, M. A. Capage,, M. Kessel,, and S. A. Benson. 1994. Isolation and characterization of a generalized transducing phage for Xanthomonas campestris pv. campestris. J. Bacteriol. 176: 3354– 3359.

132. Willson, T. A.,, and N. M. Gough. 1988. High voltage E. coli electro-transformation with DNA following ligation. Nucleic Acids Res. 16: 11820.

133. Winans, S. C.,, S. J. Elledge,, J. H. Krueger,, and G. C. Walker. 1985. Site-directed insertion and deletion mutagenesis with cloned fragments in Escherichia coli. J. Bacteriol. 161: 1219– 1221.

134. Woodcock, D. M.,, P. J. Crowther,, J. Doherty,, S. Jefferson,, E. DeCruz,, M. Noyer-Weidner,, S. S. Smith,, M. Z. Michael,, and M. W. Graham. 1989. Quantitative evaluation of Escherichia coli host strains for tolerance to cytosine methylation in plasmid and phage recombinants. Nucleic Acids Res. 17: 3469– 3478.

135. Yanisch-Perron, C.,, J. Vieira,, and J. Messing. 1985. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33: 103– 119.

136. Yu, D.,, H. M. Ellis,, E. C. Lee,, N. A. Jenkins,, N. G. Copeland,, and D. L. Court. 2000. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl. Acad. Sci. USA 97: 5978– 5983.

137. Yu, D.,, J. A. Sawitzke,, H. Ellis,, and D. L. Court. 2003. Recombineering with overlapping single-stranded DNA oligonucleotides: testing a recombination intermediate. Proc. Natl. Acad. Sci. USA 100: 7207– 7212.

138. Zabarovsky, E. R.,, and G. Winberg. 1990. High efficiency electroporation of ligated DNA into bacteria. Nucleic Acids Res. 18: 5912.

139. Zhang, Y.,, F. Buchholz,, J. P. Muyrers,, and A. F. Stewart. 1998. A new logic for DNA engineering using recombination in Escherichia coli. Nat. Genet. 20: 123– 128.

140. Zinder, N. D.,, and J. Lederberg. 1952. Genetic exchange in Salmonella. J. Bacteriol. 64: 679– 699.

Tables

Gene Transfer in Gram-Negative Bacteria

/content/10.1128/9781555817497.chap31.tab31-1

TABLE 1

Methods for transferring DNA in selected species within the phylum proteobacteria

a Mechanisms of introduction are abbreviated as follows (in order of preference): E, electroporation; M, mating via conjugation; N, natural competency; and C,chemical competency.

b Representatives from the narrow-host-range plasmids are reported to replicate in this species ( Table 3 ).

c Representatives from the broad-host-range plasmids are reported to replicate in this species ( Table 3 ).

10.1128/9781555817497/tab31-1_thmb.gif

10.1128/9781555817497/tab31-1.gif

TABLE 1

Methods for transferring DNA in selected species within the phylum proteobacteria

a Mechanisms of introduction are abbreviated as follows (in order of preference): E, electroporation; M, mating via conjugation; N, natural competency; and C,chemical competency.

b Representatives from the narrow-host-range plasmids are reported to replicate in this species ( Table 3 ).

c Representatives from the broad-host-range plasmids are reported to replicate in this species ( Table 3 ).

/content/10.1128/9781555817497.chap31.tab31-2

TABLE 2

E.coli strains.

a Unless indicated, all of the strains do not contain bacteriophage _ or the F plasmid.

b The catalog numbers for the American Type Culture Collection (ATCC) and the E. coli Genetic Stock Center (CGSC) are given when available.

c The Δ(argF-lac)169 deletion allele actually deletes ykfD-mhpD ( 99 ).

10.1128/9781555817497/tab31-2_thmb.gif

10.1128/9781555817497/tab31-2.gif

TABLE 2

E.coli strains.

a Unless indicated, all of the strains do not contain bacteriophage _ or the F plasmid.

b The catalog numbers for the American Type Culture Collection (ATCC) and the E. coli Genetic Stock Center (CGSC) are given when available.

c The Δ(argF-lac)169 deletion allele actually deletes ykfD-mhpD ( 99 ).

/content/10.1128/9781555817497.chap31.tab31-3

TABLE 3

General classes of plasmids commonly used in gram-negative bacteria

10.1128/9781555817497/tab31-3_thmb.gif

10.1128/9781555817497/tab31-3.gif

TABLE 3

General classes of plasmids commonly used in gram-negative bacteria

/content/10.1128/9781555817497.chap31.tab31-4

TABLE 4

Antibiotic concentrations for stock solutions and medium supplementation

a Filter sterilize the solution with a 0.2-μm-pore-size filter.

b Suspend in 100% ethanol.

c Suspend in 0.1 N NaOH, which converts the acid to the sodium salt.

d Suspend in 100% methanol; store in the dark.

e Tetracycline is reported to be incompatible with magnesium ions and therefore should be tested before being used in minimal media.

f Suspend in DMSO.

10.1128/9781555817497/tab31-4_thmb.gif

10.1128/9781555817497/tab31-4.gif

TABLE 4

Antibiotic concentrations for stock solutions and medium supplementation

a Filter sterilize the solution with a 0.2-μm-pore-size filter.

b Suspend in 100% ethanol.

c Suspend in 0.1 N NaOH, which converts the acid to the sodium salt.

d Suspend in 100% methanol; store in the dark.

e Tetracycline is reported to be incompatible with magnesium ions and therefore should be tested before being used in minimal media.

f Suspend in DMSO.