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Chapter 31 : Gene Transfer in Gram-Negative Bacteria

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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 . 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 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 . 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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Bacterial Proteins
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Bacterial Genetics
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Genetic Elements
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Chromosomal DNA
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Image of FIGURE 1
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.

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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Image of FIGURE 2
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.

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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Image of FIGURE 3
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.

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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Image of FIGURE 4
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 sites (FRT). (a) Primers are designed to amplify from a universal antibiotic-resistant cassette with 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 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 recombination sites removing the antibiotic resistance-conferring cassette. See the text for details.

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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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

Generic image for table
TABLE 1

Methods for transferring DNA in selected species within the phylum proteobacteria

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

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

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

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
Generic image for table
TABLE 2

strains.

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

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

The Δdeletion allele actually deletes ( ).

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
Generic image for table
TABLE 3

General classes of plasmids commonly used in gram-negative bacteria

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
Generic image for table
TABLE 4

Antibiotic concentrations for stock solutions and medium supplementation

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

Suspend in 100% ethanol.

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

Suspend in 100% methanol; store in the dark.

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

Suspend in DMSO.

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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