Chapter 28 : Plasmids as Genetic Tools for Study of Bacterial Gene Function

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Ebook: Choose a downloadable PDF or ePub file. Chapter is a downloadable PDF file. File must be downloaded within 48 hours of purchase

Buy this Chapter
Digital (?) $15.00

Preview this chapter:
Zoom in

Plasmids as Genetic Tools for Study of Bacterial Gene Function, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555817732/9781555812652_Chap28-1.gif /docserver/preview/fulltext/10.1128/9781555817732/9781555812652_Chap28-2.gif


This chapter provides a broad overview of many applications of plasmids for genetic analysis, primarily in bacteria. Ever since DNA sequencing became accessible to most research laboratories, reverse genetic analysis has become a standard experimental approach to study bacterial gene function. Similar suicide vectors have also been used for nontargeted insertional mutagenesis by cloning random chromosomal DNA fragments into the plasmid. The use of suicide vectors also allows for easy identification of the insertion mutations. Plasmids that utilize different combinations of double-counter selective markers have been used for diverse applications, including the search for extremely rare suppressor mutations of essential genes, and to improve the efficiency of allelic exchange on bacterial artificial chromosomes (BACs). Although temperature-sensitive vectors represent the majority of conditionally replicating plasmids, other plasmids that exhibit conditional replication have been described. Cloning by recombination was also achieved using the highly efficient DNA uptake and recombination systems in . Site-specific recombination machinery has also been incorporated into several expression vector systems to achieve very tight regulation of gene expression. Although antibiotic resistance is typically used to maintain selection for plasmids grown in culture, there are disadvantages to the use of antimicrobial agents for certain industrial, medical, and biotechnological applications.

Citation: Phillips G. 2004. Plasmids as Genetic Tools for Study of Bacterial Gene Function, p 567-588. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch28

Key Concept Ranking

Gene Expression and Regulation
Genetic Elements
Environmental Microbiology
Chromosomal DNA
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1
Figure 1

Allelic exchange mutagenesis using a temperature-sensitive replicon. The top portion of the figure shows the composition of a circular plasmid with a temperature-sensitive ( ). A mutant allele is created in vitro by insertion of an antibiotic-resistance gene into a gene targeted for mutagenesis (a continuous line with arrowhead indicates an intact gene and a broken line represents an interrupted gene; P and t represent promoter and terminator, respectively). The allele may be a simple insertion (as shown) or an insertion/deletion mutation. The temperature-sensitive vector also carries a distinct antibiotic-resistance marker and may also include a counterselection marker such B. Integration of the vector into the host chromosome occurs at the nonpermissive temperature by homologous recombination (crossover event at position A). The configuration of the integrated plasmid is shown in the middle, showing the duplication of the targeted sequences. Growth at the permissive temperature for plasmid replication selects for transformants that have undergone a second recombination event at position A or B. Only recombination at position B results in allelic exchange. Counterselection, such as growth on sucrose, may also be used to enhance the frequency at which recombinants that have undergone exchange at position B are recovered. The configuration of the chromosome after allelic exchange is shown at the bottom. The insertion mutation has been recombined onto the chromosome, and the wild-type allele is now carried by the vector and can complement the insertion mutation at the permissive temperature. If counterselection is used, however, the vector will be lost from the cell.

Citation: Phillips G. 2004. Plasmids as Genetic Tools for Study of Bacterial Gene Function, p 567-588. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch28
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

Knockout mutagenesis by use of an suicide vector. A suicide vector is constructed by inserting a DNA fragment representing an internal portion of the target gene (the region of homology between the target gene and region carried by the suicide vector is shown by diagonal crosshatching). The vector is introduced to the host by transformation or conjugation with selection for the antibiotic-resistance marker Recombination between homologous sequences results in disruption of the target gene, as shown by the bottom portion of the figure (a continuous line with arrowhead indicates an intact gene and a broken line represents an interrupted gene; and t, represent promoter and terminator, respectively).

Citation: Phillips G. 2004. Plasmids as Genetic Tools for Study of Bacterial Gene Function, p 567-588. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch28
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 3
Figure 3

Allelic exchange mutagenesis by using an suicide vector and counterselection. The top portion shows an R6K suicide vector carrying a DNA fragment representing an internal portion of the target gene (diagonal crosshatching) and disrupted with an antibiotic-resistance marker The vector also carries a counterselection marker, e.g., and a distinct antibiotic-resistance marker As described in the text, other counterselection markers may also be used. Recombination between homologous sequences (crossover event at position A) results in disruption of the target gene (a continuous line with arrowhead indicates an intact gene and a broken line represents an interrupted gene; P and t represent promoter and terminator, respectively) with duplication of the homologous sequences. Growth in the presence of appropriate antibiotic and sucrose (for selects for recombinants that have undergone a second recombination event at position B. The configuration of the chromosome after allelic exchange and loss of the suicide vector is shown at the bottom.

Citation: Phillips G. 2004. Plasmids as Genetic Tools for Study of Bacterial Gene Function, p 567-588. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch28
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 4
Figure 4

Construction of unmarked mutations by recombineering. Two strategies for engineering unmarked deletion/ insertion and point mutations into the bacteria chromosome or BACs using linear DNA recombination are shown. On the left, PCR is used to amplify an antibiotic resistance cassette using primers (short arrows) whose ends (gray extensions) are homologous to the gene targeted for mutagenesis (line with arrowhead flanked by P and t, representing promoter and terminator, respectively). The cassette is flanked by or site-specific recombinase recognition sites (arrowheads). The right portion of the figure shows similar primers used to amplify a cassette containing both a selectable marker and a counterselection gene The middle portion of the figure depicts the events after the linear DNA fragments are introduced by electroporation into an strain expressing bacteriophage recombinases (Red or RecET) with selection for antibiotic resistance. After replacement of the target gene, can be eliminated by expression of the appropriate site-specific recombinase, e.g., Flp, leaving only a short "scar" sequence (single arrowhead), as shown on the bottom, left. Alternatively, a second round of recombineering can be performed using a linear DNA fragment to which a desired point mutation or deletion (white box) has been introduced. Recombinants are recovered by selecting against the counterselection marker.

Citation: Phillips G. 2004. Plasmids as Genetic Tools for Study of Bacterial Gene Function, p 567-588. In Funnell B, Phillips G (ed), Plasmid Biology. ASM Press, Washington, DC. doi: 10.1128/9781555817732.ch28
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Abe, M.,, M. Tsuda,, M. Kimoto,, S. Inouye,, A. Nakazawa,, and T. Nakazawa. 1996. A genetic analysis system of Burkholderia cepacia: construction of mobilizable transposons and a cloning vector. Gene 174:191194.
2. Akerley, B. J.,, E. J. Rubin,, A. Camilli,, D. J. Lampe,, H. M. Robertson,, and J. J. Mekalanos. 1998. Systematic identification of essential genes by in vitro mariner mutagenesis. Proc. Natl. Acad. Sci. USA 95:89278932.
3. Albertini, A. M.,, M. P. Hofer,, M. P. Calos,, and J. H. Miller. 1982. On the formation of spontaneous deletions: the importance of short sequence homologies in the generation of large deletions. Cell 29:319328.
4. Alexeyev, M. F. 1995. Three kanamycin resistance gene cassettes with different polylinkcrs. BioTechniques 18:5256.
5. Alexeyev, M. F.,, and I. N. Shokolenko. 1995. Mini-Tn10 transposon derivatives for insertion mutagenesis and gene delivery into the chromosome of gram-negative bacteria. Gene 160:5962.
6. Alexeyev, M. F.,, I. N. Shokolenko,, and T. P. Croughan. 1995. Improved antibiotic-resistance gene cassettes and omega elements for Escherichia coli vector construction and in vitro deletion/insertion mutagenesis. Gene 160:6367.
7. Ambrosio, R. E. 1977. Influence of rec and pol genes on the maintenance of a Proteus plasmid (P-lac) in Escherichia coli. J . Bacteriol. 131:689692.
8. Atlung, T.,, A. Nielsen,, L. J. Rasmussen,, L. J. Nellemann,,and F. Holm. 1991. A versatile method for integration of genes and gene fusions into the λ attachment site of Escherichia coli. Gene 107:1117.
9. 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. 230:174185.
10. Balbas, P.,, M. Alexeyev,, I. Shokolenko,, F. Bolivar,, and F. Valle. 1996. A pBRINT family of plasmids for integration of cloned DNA into the Escherichia coli chromosome. Gene 172:6569.
11. Balbas, P.,, X. Alvarado,, F. Bolivar,, and F. Valle. 1993. Plasmid pBRINT: a vector for chromosomal insertion of cloned DNA. Gene 136:211213.
12. Balbas, P.,, and G. Gosset. 2001. Chromosomal editing in Escherichia coli. Mol. Biotechnol. 19:112.
13. Barany, F. 1988. Procedures for linker insertion mutagenesis and use of new kanamycin reisistance cassettes. DNA Protein Eng. Tech. 1:2944.
14. Beckwith, J.,, and E. R. Signer. 1966. Transposition of the Lac operon and transduction of Lac by ��80. J. Mol. Biol. 19:254265.
15. Biek, D. P.,, and S. N. Cohen. 1986. Identification and characterization of recD,a gene affecting plasmid maintenance and recombination in Escherichia coli. J. BacterioL 167:594603.
16. Biekcr, K. L.,, and T. J. Silhavy. 1990. PrlA (SecY) and PrlG (SecE) interact directly and function sequentially during protein translocation in E. coli. Cell 61:833842.
17. Blatny, J. M.,, T. Brautaset,, H. C. Winther-Larsen,, K. Haugan,, and S. Valla. 1997. Construction and use of a versatile set of broad-host-range cloning and expression vectors based on the RK2 replicon. Appl. Environ. Microbiol. 63:370379.
18. Blatny, J. M.,, T. Brautaset,, H. C Winther-Larsen,, P. Karunakaran,, and S. Valla. 1997. Improved broad-host-range RK2 vectors useful for high and low regulated gene expression levels in gram-negative bacteria. Plasmid 38:3551.
19. 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. 5:14471457.
20. Blondelet-Rouault, M. H.,, J. Weiser,, A. Lebrihi,, P. Branny,, and J. L. Pernodet. 1997. Antibiotic resistance gene cassettes derived from the omega interposon for use in E. coli and Streptomyces. Gene 190:315317.
21. Bolton, A. J.,, and D. E. Woods. 2000. Self-cloning mini-transposon phoA gene-fusion system promotes the rapid generic analysis of secreted proteins in gram-negative bacteria. BioTechniques 29:470474.
22. Boyd, A. C.,, and D. J. Sherratt. 1995. The pCLIP plasmids: versatile cloning vectors based on the bacteriophage λ origin of replication. Gene 153:5762.
23. Boyd, E.,, 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. 182:842847.
24. Brown, S.,, and M. J. Fournier. 1984. The 4.5S RNA gene of Escherichia coli is essential for cell growth. J Mol. Biol. 178:533550.
25. Brune, W. 2000. Forward with BACS: new tools for herpesvirus genomics. Trends Genet. 16:254259.
26. Bubeck, P.,, M. Winkler,, and W. Bautsch. 1993. Rapid cloning by homologous recombination in vivo. Nucleic Acids Res. 21:36013602.
27. Budd, M.,, and J. L. Campbell. 1987. Temperature-sensitive mutations in the yeast DNA polymerase I gene. Proc. Natl. Acad. Sci. USA 84:28382842.
28. Cairns, J.,, J . Overbaugh,, and S. Miller. 1988. The origin of mutants. Nature 335:142145.
29. Calos, M. P. 1978. DNA sequence for a low-level promoter of the lac repressor gene and an 'up' promoter mutation. Nature 274:762765.
30. Camilli, A.,, D. T. Beattie,, and J. J. Mekalanos. 1994. Use of genetic recombination as a reporter of gene expression. Proc. Natl. Acad. Sci. USA 91:26342638.
31. Camilli, A.,, and J. J. Mekalanos. 1995. Use of recombinase gene fusions to identify Vibrio cholerae genes induced during infection. Mol. Microbiol. 18:671683.
32. Camps, M.,, J. Naukkarinen,, B. P. Johnson,, and L. A. Loeb. 2003. Targeted gene evolution in Escherichia coli using a highly error-prone DNA polymerase I. Proc. Natl. Acad. Sci. USA 100:97279732.
33. Carter-Muenchau, P.,, and R. E. Wolfe. 1989. Growth-rate-dependent regulation of 6-phosphogluconatc dehydrogenase level mediated by an anti-Shine-Dalgarno sequence located within the Escherichia coli gnd structural gene. Proc. Natl. Acad. Sci. USA 86:11381142.
34. Casavant, N. C.,, G. A. Beattie,, G. J. Phillips,, and L. J, Halverson, 2002. Site-specific recombination-based genetic system for reporting transient or low-level gene expression. Appl. Environ. Microbiol. 68:35883596.
35. Chartier, C.,, E. Degryse,, M. Gantzer,, A. Dieterle,, A. Pavirani,, and M. Mehtali. 1996. Efficient generation of recombinant adenovirus vectors by homologous recombination in Escherichia coli.J. Virol. 70:48054810.
36. Chaveroche, M.-K.,, J.-M. Ghigo,, and C. d'Enfert. 2000. A rapid method for efficient gene replacement in the filamentous fungus. Aspergillus nidulans. Nucleic Acids Res. 28:e97.
37. 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 antibiotic-resistance determinant. Gene 158:914.
38. Chiang. S. L.,, J. J. Mekalanos,, and D. W. Holden. 1999. In vivo genetic analysis of bacterial virulence. Annu. Rev. Microbiol. 53:129154.
39. Chiang, S. L.,, and E. J. Rubin. 2002. Construction of a mariner-based transposon for epitope-tagging and genomic targeting. Gene 296:179185.
40. Chumley, F. G.,, R. Menzel,, and J. R. Roth. 1979. Hfr formation directed by Tn10. Genetics 91:639655.
41. Colleaux, L.,, L. d'Auriol,, M. Betermier,, G. Cottarel,, A. Jacquier,, F. Galibert,, and B. Dujon. 1986. Universal code equivalent of a yeast mitochondrial intron reading frame is expressed into E. coli as a specific double strand endonuclease. Cell 44:521533.
42. Copcland, N. G.,, N. A. Jenkins,, and D. L. Court. 2001. Recombineering: a powerful new tool for mouse functional genomics. Nat. Rev. Genet. 2:769779.
43. Coulondre, C.,, J. H. Miller,, P. J. Farabaugh,, and W. Gilbert. 1978. Molecular basis of base substitution hotspots in Escherichia coli. Nature 274:775780.
44. Court, D. L.,, J. A. Sawitzke,, and L. C. Thomason. 2002. Genetic engineering using homologous recombination. Annu. Rev. Genet. 36:361388.
45. Courvalin, P.,, S. Goussard,, and C. Grillot-Courvalin. 1995. Gene transfer from bacteria to mammalian cells. C. R. Acad. Sci. Ser. III 318:12071212.
46. Cranenburgh, R. M.,, J. A. Hanak,, S. G. Williams,, and D. J. Sherratt. 2001. Escherichia coli strains that allow antibiotic-free plasmid selection and maintenance by repressor titration. Nucleic Acids Res. 29:E26.
47. Crouzet, J.,, L. Naudin,, C. Orsini,, E. Vigne,, L. Ferrero,, A, Le Roux,, P, Benoit,, M, Latta,, C. Torrent,, D. Branellec,, P. Denefle,, J. F. Mayaux,, M. Perricaudet,, and P. Yeh. 1997. Recombinational construction in Escherichia coli of infectious adenoviral genomes. Proc. Natl. Acad. Sci. USA 94:14141419.
48. Cunningham, R. P.,, and B. Weiss. 1985. Endonuclease III (nth) mutations of Escherichia coli. Proc. Natl. Acad. Sci. USA 82:474478.
49. Darji, A.,, C. A. Guzman,, B. Gerstel,, P. Wachholz,, K. N. Timmis,, J. Wehland,, T. Chakraborty,, and S. Weiss. 1997. Oral somatic transgene vaccination using attenuated S. typhimurium. Cell 91:765775.
50. 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 97:66406645.
51. Davidson, J. 2002. Genetic tools for Pseudomonads, Rhizobia, and other gram-negative bacteria. BioTechniques 32:386401.
52. de Lorenzo, V.,, M. Herrero,, U. Jakubzik,, and K. N. Timmis. 1990. Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria. J. Bacteriol. 172:65686572.
53. Dennis, J. J.,, and G. J. Zylstra. 1998. Plasposons: modular self-cloning minitransposon derivatives for rapid genetic analysis of gram-negative bacterial genomes. Appl. Environ. Microbiol. 64:27102715.
54. Deonier, R. C.,, and N. Davidson. 1976. The sequence organization of the integrated F plasmid in two Hfr strains of Escherichia coli.J. Mol. Biol. 107:207222.
55. Diederich, L.,, L. J . Rasmussen,, and W. Messer. 1992. New cloning vectors for integration in the lambda attachment site attB of the Escherichia coli chromosome. Plasmid 28:1424.
56. Dietrich, G.,, A. Bubert,, I. Gentschev,, Z. Sokolovic,, A. Simm,, A. Catic,, S. H. Kaufmann,, J. Hess,, A. A. Szalay,, and W. Goebel. 1998. Delivery of antigen-encoding plasmid DNA into the cytosol of macrophages by attenuated suicide Listeria monocytogenes. Nat. Biotechnol. 16:181185.
57. Donnenberg, M, S.,, and J. B. Kaper. 1991. Construction of an eae deletion mutant of enteropathogenic Escherichia coti by using a positive-selection suicide vector. Infect. Immun. 59:43104317.
58. Dozois, C. M.,, M. Dho-Moulin,, A. Bree,, J. M. Fairbrothcr,, C. Desautels,, and R. Curtiss III. 2000. Relationship between the Tsh auto transporter and pathogenicity of avian Escherichia coli and localization and analysis of the tsh genetic region. Infect. Immun. 68:41454154.
59. Dunn, I. S. 1991. Pseudomonas aeruginosa plasmids as suicide vectors in Escherichia coli: resolution of genomic cointegrates through short regions of homology. Gene 108:109114.
60. Elledge, S. J.,, and R. W. Davis. 1988. A family of versatile centromeric vectors designed for use in the sector-shuffle mutagenesis assay in Saccharomyces cerevisiae. Gene 70:303312.
61. Ellermeier, C. D.,, A. Janakiraman,, and J. M. Slauch. 2002. Construction of targeted single copy lac fusions using lambda Red and FLP-mediated site-specific recombination in bacteria. Gene 290:153161.
62. Ellis, H. M.,, D. Yu,, T. DiTizio,, and D. L. Court. 2001. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc. Natl. Acad. Sci. USA 98:67426746.
63. Fabret, C.,, S. Poncet,, S. Danielsen,, T. V. Borchert,, S. D. Ehrlich,, and L. Janniere. 2000. Efficient gene targeted random mutagenesis in genetically stable Escherichia coli strains. Nucleic Acids Res. 28:E95.
64. Fairhead, C.,, B. Llorente,, F. Denis,, M. Soler,, and B. Dujon. 1996. New vectors for combinatorial deletions in yeast chromosomes and for gap-repair cloning using 'split-marker' recombination. Yeast 12:14391457.
65. Fairhead, C.,, A. Thierry,, F. Denis,, M. Eck,, and B. Dujon. 1998. 'Mass-murder' of ORFs from three regions of chromosome XI from Saccharomyces cerevisiae. Gene 223:3346.
66. Favre, D.,, and J.-F. Viret. 2000. Gene replacement in gram-negative bacteria: the pMAKSAC vectors. BioTechniques 28:198204.
67. Fellay, R.,, J. Frey,, and H. Krisch. 1987. Interposon mutagenesis of soil and water bacteria: a family of DNA fragments designed for in vitro insertional mutagenesis of gram-negative bacteria. Gene 52:147154.
68. Flinn, H.,, M. Burke,, C. J. Stirling,, and D. J. Sherratt. 1989. Use of gene replacement to construct Escherichia coli strains carrying mutations in two genes required for stability of multicopy plasmids. J. Bacteriol. 171:22412243.
69. Francois, V.,, A. Conter,, and J.-M. Louarn. 1990. Properties of new Escherichia coli Hfr strains constructed by integration of pSC 101 -derived conjugative plasmids. J. Bacteriol. 172:14361440.
70. Friedman, A. M.,, S. R. Long,, S. E. Brown,, W, J. Buikema,, and F. M. Ausubel. 1982. Construction of a broad host range cosmid cloning vector and its use in the genetic analysis of Rhizobium mutants. Gene 18:289296.
71. Froehlich, B. J.,, and J. R. Scott. 1991. A single-copy promoter- cloning vector for use in Escherichia coli. Gene 108:99101.
72. Fuqua, W. C. 1992. An improved chloramphenicol resistance gene cassette for site-directed marker replacement mutagenesis. BioTechniques 12:223225.
73. Gay, N. J. 1984. Construction and characterization of an Escherichia coli strain with a uncl mutation. J. Bacteriol. 158:820825.
74. Gay, P.,, D. Lecoq,, M. Steinmetz,, E. Ferrari,, and J. A. Hoch. 1983. Cloning structural gene sacB, which codes for exoenzyme levansucrase of Bacillus subtilis: expression of the gene in Escherichia coli.J. Bacteriol. 153:14241431.
75. German, M.,, and M. Syvanen. 1982. Incompatibility between bacteriophage lambda and the sex factor F. Plasmid 8:207210.
76. Gil, D.,, and J. P. Bouche. 1991. ColE1-type vectors with fully repressible replication. Gene 105:1722.
77. Goebel, W. 1974. Integrative suppression of temperature-sensitive mutants with a lesion in the initiation of DNA replication. Replication of autonomous plasmids in the suppressed state. Eur. J. Biochem. 43:125130.
78. Gryczan, T. J.,, J. Hahn,, S. Contente,, and D. Dubnau. 1982. Replication and incompatibility properties of plasmid pEl94 in Bacillus subtilis. J. Bacteriol. 152:722735.
79. Gueldener, U.,, J . Heinisch,, G. J. Koehler,, D. Voss,, and J. H Hegemann. 2002. A second set of loxP marker cassettes for Cre-mediated multiple gene knockouts in budding yeast. Nucleic Acids Res. 30:e23.
80. Gumbiner-Russo, L. M.,, M. J. Lombardo,, R. G. Ponder,, and S. M. Rosenberg. 2001. The TGV transgenic vectors for single-copy gene expression from the Escherichia coli chromosome. Gene 273:97104.
81. Guo, L.,, T. Katayama,, Y. Seyama,, K. Sekimizu,, and T. Miki. 1999. Isolation and characterization of novel cold-sensitive dnaA mutants of Escherichia coli. FEMS Microbiol. Lett. 176:357366.
82. Gutterson, N. L,, and J. Koshland, D. E. 1983. Replacement and amplification of bacterial genes with sequences altered in vivo. Proc. Natl. Acad. Sci. USA 80:48944898.
83. Hadley, R. G.,, and R. C. Deonier. 1979. Specificity in formation of type [] F' plasmids.J. Bacteriol. 139:961976.
84. Haldimann, A.,, I. I. Daniels,, and B L. Wanner. 1998. Use of new methods for construction of tightly regulated arabinose and rhamnose promoter fusions in studies of the Escherichia coli phosphate regulon. J. Bacteriol. 180:12771286.
85. Haldimann, A.,, M. K. Prahalad,, S. L. Fisher,, S.-K. Kim,, C. T. Walsh,, and B. L. Wanner. 1996. Altered recognition mutants of the response regulator PhoB: a new genetic strategy for studying protein-protein interactions. Proc. Natl. Acad. Sci. USA 93:1436114366.
86. Haldimann, A.,, and B. L. Wanner. 2001. Conditional-replication, integration, excision, and retrieval plasmid-host systems for gene structure-function studies of bacteria. J. Bacteriol. 183:63846393.
87. 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. 171:46174622.
88. Hare, R. S.,, S. S. Walker,, T. E. Dorman,, J. R. Greene,, L. M. Guzman,, T. J. Kenney,, M. C. Sulavik,, K. Baradaran,, C. Houseweart,, H. Yu,, Z. Foldes,, A. Motzer,, M. Walbridge,, G. H. ShimerJr.,, and K. J. Shaw. 2001. Genetic footprinting in bacteria.J. Bacteriol. 183:16941706.
89. Hasan, N.,, M. Koob,, and W. Szybalski. 1994. Escherichia coli genome targeting, I. Cre-lox-mediated in vitro generation of ori plasmids and their in vivo chromosomal integration and retrieval. Gene 150:5156.
90. Hasan, N.,, and W. Szybalski. 1987. Control of cloned gene expression by promoter inversion in vivo: construction of improved vectors with a multiple cloning site and the Plac promoter. Gene 56:145151.
91. Hashimoto, T.,, and M. Sekiguchi. 1976. Isolation of temperature- sensitive mutants of R plasmid by in vitro mutagenesis with hydroxylamine.J. Bacteriol. 127:15611563.
92. Hashimoto-Gotoh, T.,, F. C. Franklin,, A. Nordheim,, and K. N. Timmis. 1981. Specific-purpose plasmid cloning vectors. I. Low copy number, temperature-sensitive, mobilization-defective pSC101-derived containment vectors. Gene 16:227235.
93. Hashimoto-Gotoh, T.,, M. Yamaguchi,, K. Yasojima,, A. Tsujimura,, Y. Wakabayashi,, and Y. Watanabe. 2000. A set of temperature sensitive-replication/-segregation and temperature resistant plasmid vectors with different copy numbers and in an isogenic background (chloramphenicol, kanamycin, lacZ, repAy par, polA). Gene 241:185191.
94. He, T. C.,, S. Zhou,, L. T. da Costa,, J. Yu,, K. W. Kinzler,, and B. Vogelstein. 1998. A simplified system for generating recombinant adenoviruses. Proc. Natl. Acad. Sci. USA 95:25092514.
95. Hoang, T. T.,, R. R. Karkhoff-Schweizer,, A. J. Kutchma,, and H. D. Schweizer. 1998. A broad-host-range Flp-FRT recombination system for site-specific excision of chromosomally-located DNA sequences: application for isolation of unmarked Pseudomonas aeruginosa mutants. Gene 212:7786.
96. Hoang, T.T.,, A. J. Kutchma,, A. Becher,, and H. D. Schweizer. 2000. Integration proficient plasmids for Pseudomonas aeruginosa: site-specific integration and use for engineering of reporter and expression strains. Plasmid 43:5972.
97. Hoch, J. A. 1991. Genetic analysis in Bacillus subtilis. Methods Enzymol. 204:305320.
98. Hosted, T. J.,, and R. H. Baltz. 1997. Use of rpsL for dominance selection and gene replacement in Streptomyces roseosporus.J. Bacteriol. 179:180186.
99. Itaya, M.,, and T. Tanaka. 1997. Experimental surgery to create subgenomes of Bacillus subtilis 168. Proc. Natl. Acad. Sci. USA 94:53785382.
100. Jacob, F.,, and E.-L. Wollman. 1958. Genetic and physical determinations of chromosomal segments in E. coli. Symp. Soc. Exp. Biol. 12:7592.
101. Jacob, F.,, and E.-L. Wollman. 1961. Sexuality and the Genetics of Bacteria. Academic Press, New York, N.Y..
102. Jacobs, W. R. J.,, M. Tuckman,, and B. R. Bloom. 1987. Introduction of foreign DNA into mycobacteria using a shuttle phasmid. Nature 327:532535.
103. Julio, S. M.,, C. P. Conner,, D. M. Heithoff,, and M.J. Mahan. 1998. Directed formation of chromosomal deletions in Salmonella typhimurium: targeting of specific genes induced during infection. Mol. Gen. Genet. 258:178181.
104. Kalogeraki, V. S.,, and S. C. Winans. 1997. Suicide plasmids containing promoterless reporter genes can simultaneously disrupt and create fusions to target genes of diverse bacteria. Gene 188:6975.
105. Kameyama, L.,, L. Fernandez,, D. L. Court,, and G. Guarneros. 1991. RNase III activation of bacteriophage lambda N synthesis. Mol. Microbiol. 5:29532963.
106. Kang, H. Y.,, C. M. Dozois,, S. A. Tinge,, T. H. Lee,, and R. Curtiss III. 2002. Transduction-mediated transfer of unmarked deletion and point mutations through use of counterselectable suicide vectors.J. Bacteriol. 184:307312.
107. Karunakaran, P.,, D. T. Endresen,, H. Ertesvag,, J. M. Blatny,, and S. Valla. 1999. A small derivative of the broad-host-range plasmid RK2 which can be switched from a replicating to a non-replicating state as a response to an externally added inducer. FEMS Microbiol. Lett. 180:221227.
108. Kato, J.,, and H. Ikeda. 1996. Construction of mini-F plamid vectors for plasmid shuffling in Escherichia coli. Gene 170:141142.
109. Keen, N. T.,, S. Tamaki,, D. Kobayashi,, and D. Trollinger. 1988. Improved broad-host-range plasmids for DNA cloning in gram-negative bacteria. Gene 70:191197.
110. Kiel, J. A. K. W.,, J. P. M. J. Vosscn,, and G. Venema. 1987. A general method for the construction of Escherichia coli mutants by homologous recombination and plasmid segregation. Mol. Gen. Genet. 207:294301.
111. Kieser, T.,, and D. A. Hopwood. 1991. Genetic manipulation of Streptomyces: integrating vectors and gene replacement. Methods Enzymol. 204:430458.
112. Kofoid, E.,, U. Bergthorsson,, E. S. Slechta,, and J. R, Roth. 2003. Formation of an F' plasmid by recombination between imperfectly repeated chromosomal Rep sequences: a closer look at an old friend (F'128 pro lac).J. Bacteriol. 185:660663.
113. Kolisnyehenko, V.,, G. Plunkett 3rd,, C. D. Herring,, T. Feher,, J. Posfai,, F. R. Blattner,, and G. Posfai. 2002. Engineering a reduced Escherichia coli genome. Genome Res. 12:640647.
114. Kolter, R.,, M. Inuzuka,, and D. R. Helinski. 1978. Transcomplementation- dependent replication of a low molecular weight origin fragment from plasmid R6K. Cell 15:11991208.
115. Koop, A. H.,, M. E. Hartley,, and S. Bourgeois, 1987. A low-copy- number vector utilizing β-galactosidase for the analysis of gene control elements. Gene 52:245256.
116. Kovach, M. E.,, P. H. Elzer,, D. S. Hill,, G. T. Robertson,, M. A. Farris,, R. M. Roop2nd,, and K. M. Peterson. 1995. Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 166:175176.
117. Kovach, M. E.,, R. W. Phillips,, P. H. Elzer,, R. M. Roop 2nd,, and K. M. Peterson. 1994. pBBR1MCS: a broad-host-range cloning vector.BioTechniques 16:800802.
118. Kristensen, C. S.,, L. Eberl,, J. M. Sanchez-Romero,, M. Givskov,, S. Molin,, and V. de Lorenzo. 1995. Site-specific deletions of chromosomally located DNA segments with the multimer resolution system of broad-host-range plasmid RP4.J. Bacteriol. 177:5258.
119. Kumar, A.,, and M. Snyder. 2001. Emerging technologies in yeast genomes. Nat. Genetics 2:302312.
120. Kushner, S. R.,, H. Nagaishi,, and A. J. Clark. 1972. Indirect suppression of recB and recC mutations by exonuclease I deficiency. Proc. Natl. Acad. Sci. USA 69:13661370.
121. Larsen, R. A.,, M. M. Wilson,, A. M. Guss,, and W. W. Metcalf. 2002. Genetic analysis of pigment biosynthesis in Xanthobacter autotrophics Py2 using a new, highly efficient transposon mutagenesis system that is functional in a wide variety of bacteria. Arch. Microbiol. 178:193201.
122. Law, J.,, G. Buist,, A. Haandrikman,, J. Kok,, G. Venema,, and K. Leenhouts. 1995. A system to generate chromosomal mutations in Lactococcus lactis which allows fast analysis of targeted genes.J. Bacteriol. 177:70117018.
123. Le Borgne, S.,, B. Palmeros,, F. Bolivar,, and G. Gosset. 2001. Improvement of the pBRINT-Ts plasmid family to obtain marker-free chromosomal insertion of cloned DNA in E. coli. BioTechniques 30:252256.
124. Le Borgne, S.,, B. Palmeros,, F. Valle,, F. Bolivar,, and G. Gosset. 1998. pBRINT-Ts: a plasmid family with a temperature-sensitive replicon, designed for chromosomal integration into the lacZ gene of Escherichia coli. Gene 223:213219.
125. Lederberg, J.,, L. L. Cavalli,, and E. M. Lederberg. 1952. Sex compatibility in E. coli. Genetics 37:720730.
126. Lederberg, J.,, and E. L. Tatum. 1946. Gene recombination in E. coli. Nature 158:558.
127. Leenhouts, K.,, J. Kok,, and G. Venema. 1991. Repacement recombination in Lactococcus lactis. J. Bacteriol. 17:47944798.
128. Leenhouts, K. J.,, J. Kok,, and G. Vencma. 1989. Campbelllike integration of heterologous plasmid DNA into the chromsome of Lactococcus lactis subsp. lactis. J. Bacteriol. 55:394400.
129. Lerner, C. G.,, P. S. Gulati,, and M. Inouye. 1995. Cold-sensitive conditional mutation in Era, an essential Escherichia coli GTPase, isolated by localized random polymerase chain reaction mutagenesis. FEMS Microbiol. Lett. 126:291298.
130. 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. 179:62286237.
131. Linn, T.,, and R. St. Pierre, 1990. Improved vector system for constructing transcriptional fusons that ensures independent translation of lacZ.J. Bacteriol. 172:10771084.
132. Liu, Q.,, M. Z. Li,, D. Leibham,, D. Cortcz,, and S. J. Elledge. 1998. The univector plasmid-fusion system, a method for rapid construction of recombinant DNA without restriction enzymes. Curr. Biol 8:13001309.
133. Liu, Q.,, M. Z. Li,, D. Liu,, and S.J. Elledge. 2000. Rapid construction of recombinant DNA by the univector plasmid-fusion system. Methods Enzymol. 328:530549.
134. Long, S.,, S. McCune,, and G. C. Walker. 1988. Symbiotic loci of Rhizobium meliloti identified by random TnphoA mutagenesis.J. Bacteriol. 170:42574265.
135. Lutz, C. T.,, W. C. Hollifield,, B. Seed,, J. M. Davie,, and H. V. Huang. 1987. Syrinx 2A: an improved lambda phage vector designed for screening DNA libraries by recombination in vivo. Proc. Natl. Acad. Sci. USA 84:43794383.
136. Maguin, E.,, P. Duwat,, T. Hege,, D. Ehrlich,, and A. Gruss. 1992. New thermosensittve plasmid for gram-positive bacteria.J. Bacteriol. 174:56335638.
137. Mahan, M.J.,, and J. R. Roth. 1988. Reciprocality of recombination events that rearrange the chromosome. Genetics 120:2335.
138. Mahan, M. J.,, J. M. Slauch,, and J. J. Mekalanos. 1993. Bacteriophage P22 transduction of integrated plasmids: single-step cloning of Salmonella typhimurium gene fusions. J. Bacteriol. 175:70867091.
139. Mahan, M. J.,, J. M. Slauch,, and J. J. Mekalanos. 1993. Selection of bacterial virulence genes that are specifically induced in host tissues. Science 259:686688.
140. Mahillon, J.,, and N. Kleckner, 1992. New IS10 transposition vectors based on a gram-positive replication origin. Gene 116:6974.
141. Mann, C.,, J.-M. Buhler,, I. Treich,, and A. Sentenac. 1987. PRC40, a unique gene for a subunit shared between yeast RNA polymerase A and C. Cell 48:627637.
142. Marsch-Moreno, R.,, G. Hernandez-Guzman,, and A. Alvarez-Morales. 1998. pTn5cat: a Tn5-derived genetic clement to facilitate insertion mutagenesis, promoter probing, physical mapping, cloning, and marker exchange in phytopathogenic and other gram-negative bacteria. Plasmid 39:205214.
143. Martinez-Morales, F.,, A. C. Borges,, A. Martinez,, K. T. Shanmugam,, and L. O. Ingram. 1999. Chromosomal integration of heterologous DNA in Escherichia coli with precise removal of markers and replicons used during construction, J. Bacteriol. 181:71437148.
144. 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 147:20652075.
145. McVey, D.,, M. Zuber,, D. Ettyreddy,, D. E. Brough,, and I. Kovesdi. 2002. Rapid construction of adenoviral vectors by lambda phage genetics.J. Virol. 76:36703677.
146. Melnikov, A.,, and P. J. Youngman. 1999. Random mutagenesis by recombinational capture of PCR products in Bacillus subtilis and Acinetobacter calcoaceticus. Nucleic Acids Res. 27:10561062.
147. Merlin, C.,, S. McAteer,, and M. Masters. 2002. Tools for characterization of Escherichia coli genes of unknown function.J. Bacteriol. 184:45734581.
148. Merriman, T. R.,, and L. L. Lamont. 1993. Construction and use of a self-cloning promoter probe vector for gram-negative bacteria. Gene 126:1723.
149. Messerle, M.,, I. Crnkovic,, W. Hammerschmidt,, H. Ziegler,, and U. H. Koszinowski. 1997. Cloning and mutagenesis of a herpesvirus genome as an infectious bacterial artificial chromosome. Proc. Natl. Acad Sci. USA 94:1475914763.
150. 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? for cloning, mutagenesis, and allele replacement in bacteria. Plasmid 35:113.
151. 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 138:17.
152. Miller, J. H.,, and K. B. Low, 1984. Specificity of mutagenesis resulting from the induction of the SOS system in the absence of mutagenic treatment. Cell 37:675682.
153. Mitchell, D. H.,, W. S. Reznikoff,, and J . Beckwith. 1975. Genetic fusions defining trp and lac operon regulatory elements,J. Mol. Biol. 93:331350.
154. Miwa, K.,, S. Nakamori,, K. Sano,, and H. Momose. 1984. Novel host-vector system for selection and maintenance of plasmid-bearing, streptomycin-dependent Escherichia coli cells in antibiotic-free media. Gene 31:275277.
155. Mongkolsuk, S.,, P. Vattanaviboon,, S. Rabibhadana,, and P. Kiatpapan. 1993. Versatile gene cassette plasmids to facilitate the construction of generalized and specialized cloning vectors. Gene 124:131132.
156. Monteilhet, C.,, A. Perrin,, A. Thierry,, L. Colleaux,, and B. Dujon. 1990. Purification and characterization of the in vitro activity of I-Sce 1, a novel and highly specific endonuclease encoded by a group I intron. Nucleic Acids Res. 18:14071413.
157. Morales, V. M.,, and L. Sequeira. 1985. Suicide vector for transposon mutagenesis in Pseudomonas solanacearum. J. Bacteriol. 163:12631264.
158. Motamedi, H.,, A. Shafiec,, and S. J. Cai. 1995. Integrative vectors for heterologous gene expression in Streptomyces spp. Gene 160:2531.
159. Muro-Pastor, A. M., and S. Maloy. 1995. Direct cloning of mutant alleles from the bacterial chromosome into plasmid vectors in vivo. BioTechniques 18:386390.
160. Murphy, C. K.,, E. J. Stewart,, and J. Beckwith. 1995. A double counter-selection system for the study of null alleles of essential genes in Escherichia coli. Gene 155:17.
161. Musso, R. E.,, and T. Hodam. 1989. Construction and characterization of versatile kanamycin-resistance cassettes derived from the Tn5 transposon. Gene 85:205207.
162. Muyrers, J. P.,, Y. Zhang,, V. Benes,, G. Testa,, W. Ansorge,, and A. F. Stewart. 2000. Point mutation of bacterial artificial chromosomes by ET recombination. EMBO Rep. 1:239243.
163. Muyrers, J. P. P.,, Y. Zhang,, and E. J . Stewart. 2001. Techniques: recombinogeneic engineering—new options for cloning and manipulating DNA. Trends Biochem. Sci. 26:325331.
164. Newman, J. R.,, and C. Fuqua. 1999. Broad-host-range expression vectors that carry the L-arabinose-inducible Escherichia coli araBAD promoter and the araC regulator. Gene 227:197203.
165. Oden, K. L.,, L. C. DeVeaux,, C. R. T . Vibat,, J. Cronan,, J. E., and R. B. Gennis. 1990. Genomic replacement in Escherichia coli K-12 using covalently closed circular plasmid DNA. Gene 96:2936.
166. Oke, V.,, and S. R. Long. 1999. Bacterial genes induced within the nodule during the Rhizohium-legume symbiosis. Mol. Microbiol. 32:837849.
167. Oliner, J. D.,, K. W. Kinzler,, and B. Vogelstein. 1993. In vivo cloning of PCR products in E. coli. Nucleic Acids Res. 21:51925197.
168. Osbourn, A. E.,, C. E. Barber,, and M. J. Daniels. 1987. Identification of plant-induced genes of the bacterial pathogen Xanthomonas campestris pathovar campestris using a promoter-probe plasmid. EMBO J. 6:2328.
169. Ouimet, M.-C,, and G. T. Marezynski. 2000. Transcription reporters that shuttle cloned DNA between high-copy Escherichia coli plasmids and low-copy-broad-host-range-plasmids. Plasmid 44:152162.
170. Palmeros, B.,, J. Wild,, W. Szybalski,, S. Le Borgne,, G. Hernandez-Chavez,, G. Gosset,, F. Valle,, and F. Bolivar. 2000. A family of removable cassettes designed to obtain antibiotic-resistance-free genomic modifications of Escherichia coli and other bacteria. Gene 247:255264.
171. Park, C.,, and G. L. Hazelbauer. 1986. Transfer of chromosomal mutations to plasmids via Hfr-mediated conduction. J. Bacteriol. 165:312314.
172. Park, S. K.,, F. Jiang,, R. E. Dalbey,, and G. J . Phillips. 2002. Functional analysis of the signal recognition particle in Escherichia coli by characterization of a temperature-sensitive ffh mutant.J. Bacteriol. 184:26422653.
173. Pelicic, V.,, M. Jackson,, J.-M. Reyrat,, W. R. JacobsJr.,, B. Gicquel,, and C. Guilhot. 1997. Efficient allelic exchange and transposon mutageneis in Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. USA 94:1095510960.
174. Phillips, G. J. 1999. Alteration of open reading frames by use of new gene cassettes. Anal. Biochem. 269:207210.
175. Phillips, G. J. 1999. New cloning vectors with temperature-sensitive replication. Plasmid 41:7881.
176. Phillips, G. J.,, and T. J. Silhavy. 1992. The E. coli ffh gene is necessary for viability and efficient protein export. Nature 359:744746.
177. Pierce, J. C.,, B. Sauer,, and N. Sternberg. 1992. A positive selection vector for cloning high molecular weight DNA by the bacteriophage PI system: improved cloning efficacy. Prof. Natl Acad. Sci. USA 89:20562060.
178. Platt, R.,, C. Drescher,, S. K. Park,, and G. J. Phillips. 2000. Genetic system for reversible integration of DNA constructs and lacZ gene fusions into the Escherichia coli chromosome. Plasmid 43:1223.
179. Platt, R.,, D. L. Reynolds,, and G. J. Phillips. 2003. Development of a novel method of lytic phage delivery by use of a bacteriophage P22 site-specific recombination system. FEMS Microbiol. Lett. 223:259265.
180. Podhajska, A. J.,, N. Hasan,, and W. Szybalski. 1985. Control of cloned gene expression by promoter inversion in vivo: construction of the heat-pulse-activated att-nutL-p-att-N module. Gene 40:163168.
181. Poncelet, M.,, C. Cassier-Chauvat,, X. Leschelle,, H. Bottin,, and F. Chauvat. 1998. Targeted deletion and mutational analysis of the essential (2Fe-2S) plant-like ferredoxin in Syneehocystis PCC6803 by plasmid shuffling. Mol. Microbiol. 28:813821.
182. 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. 27:44094415.
183. Posfai, G.,, M. Koob,, Z. Hradeena,, N. Hasan,, M. Filutowiez,, and W. Szybalski. 1994. In vivo excision and amplification of large segments of the Escherichia coli genome. Nucleic Acids Res. 22:23922398.
184. Posfai, G.,, M. D. Koob,, H. A. Kirkpatrick,, and F. R. Blattner. 1997. Versatile insertion plasmids for targeted genome manipulations in bacteria: isolation, deletion, and rescue of the pathogenicity island LEE of the Escherichia coli O157:H7genome.J. Bacteriol. 179:44264428.
185. Quandt, J.,, and M. F. Hyncs. 1993. Versatile suicide vectors which allow direct selection for gene replacement in gram-negative bacteria. Gene 127:1521.
186. Raibaud, O.,, M. Mock,, and M. Schwartz. 1984. A technique for integrating any DNA fragment into the chromosome of Escherichia coli. Gene 29:231241.
187. Rainey, P. B.,, D. M. Heithoff,, and M. J. Mahan. 1997. Single-step conjugative cloning of bacterial gene fusions involved in microbe-host interactions. Mol. Gen. Genet. 256:8487.
188. Reece, K. S.,, and G. J. Phillips. 1995. New plasmids carrying antibiotic-resistance cassettes. Gene 165:141142.
189. Resnik, E.,, and D. C. LaPort. 1991. Introduction of single-copy sequences into the chromosome of Escherichia coli: application to gene and operon fusions. Gene 107:1925.
190. Reyrat, J.-M.,, V. Pelicic,, B. Giequel,, and R. Rappuoli. 1998. Counterselectable markers: untapped tools for bacterial genetics and pathogenesis. Infect. Immun. 66:40114017.
191. Rondon, M. R.,, S. J. Raffel,, R. M. Goodman,, and J. Handeslman. 1999. Toward functional genomics in bacteria: analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of Bacillus cereus. Proc. Natl. Acad. Sci. USA 96:64516455.
192. Rossignol, M.,, A. Basset,, O. Espeli,, and F. Boccard. 2001. NKBOR, a mini-Tn10-based transposon for random insertion in the chromosome of gram-negative bacteria and the rapid recovery of sequences flanking the insertion sites in Escherichia coli. Res. Microbiol. 152:481485.
193. Ross-Macdonald, P.,, P. S. Coelho,, T. Roemer,, S. Agarwal,, A. Kumar,, R. Jansen,, K. H. Cheung,, A. Sheehan,, D. Symoniatis,, L. Umansky,, M. Heidtman,, F. K. Nelson,, H. Iwasaki,, K. Hager,, M. Gerstein,, P. Miller,, G. S. Roeder,, and M. Snyder. 1999. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402:413418.
194. 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. 171:26142618.
195. Ruvkun, G. B.,, and F. M. Ausubel. 1981. A general method for site-directed mutagenesis in prokaryotes. Nature 289:8588.
196. Sander, P.,, A. Meier,, and E. C. Bottger. 1995. rpsL+; a dominant selectable marker for gene replacement in mycobacteria. Mol. Microbiol. 16:9911000.
197. Santos, P. M.,, I. Di Bartolo,, J. M. Blatny,, E. Zennaro,, and S. Valla. 2001. New broad-host-range promoter probe vectors based on the plasmid RK2 replicon. FEMS Microbiol. Lett. 195:9196.
198. Schmidhauser, T. J.,, G. Ditta,, and D. R. Helinski. 1988. Broad-host-range plasmid cloning vectors for gram-negative bacteria. BioTechnology 10:287332.
199. Schmoll, T.,, M. Ott,, B. Oudega,, and J. Hacker. 1990. Use of a wild-type gene fusion to determine the influence of environmental conditions on expression of the S fimbrial adhesin in an Escherichia coli pathogen.J. Bacteriol. 172:51035111.
200. Schweizer, H. D. 1993. Small broad-host-range gentamycin resistance gene cassettes for site-specific insertion and deletion mutagenesis. BioTechniques 15:831834.
201. Schweizer, H. D. 2001. Vectors to express foreign genes and techniques to monitor gene expression in Pseudomonas. Curr. Opin. Biotechnol. 12:439445.
202. Schweizer, H. D.,, and A. Becher. 2000. Integration-proficient Pseudomonas aeruginosa vectors for isolation of single copy chromosomal lacZ and lux gene fusions. BioTechniques 29:948954.
203. Seed, B. 1983. Purification of genomic sequences from bacteriophage libraries by recombination and selection in vivo. Nucleic Acids Res. 11:24272445.
204. Seifert, H. S.,, E. Y. Chen,, M. So,, and F. Heffron. 1986. Shuttle mutagenesis: a method of transposon mutagenesis for Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 83:735739.
205. Sektas, M.,, N. Hasan,, and W. Szybalski, 2001. Expression plasmid with a very tight two-step control: Int/att-mediated gene inversion with respect to the stationary promoter. Gene 267:213220.
206. Shi, J.,, and D. P. Biek. 1995. A versatile low-copy-number cloning vector derived from plasmid F. Gene 164:5558.
207. Shizuya, H.,, B. Birren,, U. -J- Kim,, V. Mancino,, T. Slepak,, Y. Tachiiri,, and M. Simon. 1992. Cloning and stable maintenance of 300-kilobasc-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc. Natl. Acad. Sci. USA 89:87948797.
208. Sikorski, R. S.,, and J. D. Boeke. 1991. In vitro mutagenesis and plasmid shuffling: from cloned gene to mutant yeast. Methods Enzymol. 194:302318.
209. Silhavy, T. J.,, M. L. Berman,, and L. W. Enquist. 1984. Experiments with gene fusions. Cold Spring Harbor Press, Cold Spring Harbor, N.Y.
210. Simon, R.,, U. Priefer,, and A. Puhler, 1983. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gram negative bacteria. BioTechnology 1:784791.
211. Simons, R. W.,, F. Houman,, and N. Kleckner. 1987. Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene 53:8596.
212. Sizemore, D. R.,, A. A. Branstrom,, and J. C. Sadoff. 1995. Attenuated Shigella as a DNA delivery vehicle for DNA-mediated immunization. Science 270:299302.
213. Skogman, S. G.,, and J. Nilsson. 1984. Temperature-dependent retention of a tryptophan-operon-bearing plasmid in Escherichia coli. Gene 31:117122.
214. Skorupski, K.,, and R. K. Taylor. 1996. Positive selection vectors for allelic exchange. Gene 169:4752.
215. Slauch, J. M.,, and A. Camilli. 2000. IVET and RIVET: use of gene fusions to identify bacterial virulence factors specifically induced in host tissues. Methods Enzymol. 326:7396.
216. Slauch, J. M.,, M. J. Mahan,, and J. J. Mekalanos. 1994. In vivo expression technology for selection of bacterial genes specifically induced in host tissues. Methods Enzymol. 235:481492.
217. Smith, V.,, K. N. Chou,, D. Lashkari,, D. Botstein,, and P. O. Brown. 1996. Functional analysis of the genes of yeast chromosome V by generic footprinting. Science 274:20692074.
218. Smith-White, B. 1999. Site-directed insertion and insertion-deletion mutations in the Escherichia coli chromosome simplified. Genet. Anal. 15:239244.
219. Snapper, S. B.,, L. Lugosi,, A. Jekkel,, R. E. Melton,, T. Kieser,, B. R. Bloom,, and W. R.J. Jacobs. 1988. Lysogeny and transformation in mycobacteria: stable expression of foreign genes. Proc. Natl. Acad. Sci. USA 85:69876991.
220. Stavropoulos, T. A., and C. A. Strathdee. 2001. Synergy between tetA and rpsL provides high-stringency positive and negative selection in bacterial artificial chromosome vectors. Genomics 72:99104.
221. Steensma, H. Y.,, and J. J. Ter Linde. 2001. Plasmids with the Cre-recombinase and the dominant nat marker, suitable for use in prototrophic strains of Saccharomyces cerevisiae and Khuyveromyces lactis. Yeast 18:469472.
222. Stibitz, S.,, W. Black,, and S. Falkow. 1986. The construction of a cloning vector designed for gene replacement in Bordetella pertussis. Gene 50:133140.
223. Stojiljkovic, I.,, J . Bozja,, and E. Salaj-Smic. 1994. Molecular cloning of bacterial DNA in vivo using a transposable R6K ori and a P1vir phage. J. Bacteriol. 176:11881191.
224. St. Pierre, R.,, and T. Linn. 1996. A refined vector system for the in vitro construction of single-copy transcriptional or translational fusions to lacZ. Gene 169:6568.
225. Swaminathan, S.,, H. M. Ellis,, L. S. Waters,, D. Yu,, E. C. Lee,, D. L. Court,, and S. K. Sharan. 2001. Rapid engineering of bacterial artificial chromosomes using oligonucleotides. Genesis 29:1421.
226. Tatum, E. L.,, and J. Lederberg. 1947. Gene recombination in the bacterium Escherichia coli. J. Bacteriol. 53:673684.
227. Tlsty, T. D.,, A. M. Albertini,, and J. H. Miller. 1984. Gene amplification in the lac region of E. coli. Cell 37:217224.
228. Toder, D. S. 1994. Gene replacement in Pseudomonas aeruginosa. Methods Enzymol. 235:466474.
229. Tresguerres, E. F.,, H. G. Nandadasa,, and R. H. Pritchard. 1975. Suppression of initiation-negative strains of Escherichia coli by integration of the sex factor F. J. Bacteriol. 121:554561.
230. Trun, N. J.,, and T. J. Silhavy. 1987. Characterization and in vivo cloning of prlC9 a suppressor of signal sequence mutations in Escherichia coli K-12. Genetics 116:513521.
231. Tsang, T.,, V. Copeland,, and G. T. Bowden. 1991. A set of cassette cloning vectors for rapid and versatile adaptation of restriction fragments. BioTechniques 10:330.
232. Tsuda, M. 1998. Use of transposon-encoded site-specific resolution system for construction of large and defined deletion mutations in bacterial chromosome. Gene 207:3341.
233. Wang, G.,, R. W. Blakesley,, D. E. Berg, and C M. Berg. 1993. pDUAL: a transposon-based cosmid cloning vector for generating nested deletions and DNA sequencing templates in vivo. Proc. Natl. Acad. Sci. USA 90:78747878.
234. Wang, J.,, A. Mushegian,, S. Lory,, and S. Jin. 1996. Large- scale isolation of candidate virulence genes of Pseudomonas aeruginosa by in vivo selection. Proc. Natl. Acad. Sci. USA 93:1043410439.
235. Whoriskey, S.,, K. V. H. Nghiem,, P. M. Leong,, J. M. Masson,, and J. H. Miller. 1987. Genetic rearrangements and gene amplification in Escherichia coli: DNA sequences at the junctures of amplified gene fusions. Genes Dev. 1:227237.
236. Wielbo, J.,, and A. Skorupska. 2001. Construction of improved vectors and cassettes containing gusA and antibiotic resistance genes for studies of transcriptional activity and bacterial localization.J. Microbiol. Methods. 45:197205.
237. Wild, J.,, Z. Hradecna,, G. Posfai,, and W. Szybalski. 1996. A broad-host-range in vivo pop-out and amplification system for generating large quantities of 50- to 100-kb genomic fragments for direct DNA sequencing. Gene 179:181188.
238. Wild, J.,, Z. Hradecna,, and W. Szybalski. 2002. Conditionally amplifiable BACs: switching from single-copy to high-copy vectors and genomic clones. Genome Res. 12: 14341444.
239. Wild, J.,, M. Sektas,, Z. Hradecna,, and W. Szybalski. 1998. Targeting and retrofitting pre-existing libraries of transposon insertions with FRTand oriV elements for in-vivo generation of large quantities of any genomic fragment. Gene 223:5566.
240. Windgassen, M.,, A. Urban,, and K.-E. Jaeger. 2000. Rapid gene inactivation in Pseudomonas aeruginosa. FEMS Microbiol. Lett. 193:201205.
241. Wollman, E.-L.,, F. Jacob,, and W. Hayes. 1956. Conjugation and genetic recombination in Escherichia coli K-12. Cold Spring Harbor Symp. Quant. Biol. 21:141162.
242. Wong, S. M.,, and J. J. Mekalanos. 2000. Genetic footprinting with mariner-based transposition in Pseudomonas aeruginosa. Proc. Natl. Acad. Sci. USA 97:1019110196.
243. Yokochi, T.,, J . Kato, and H, Ikeda. 1996. Construction of β-lactamase-encoding ApRgene cassettes for rapid identification of cloned genes. Gene 170:143144.
244. Yoon, Y. G.,, G. Posfai,, W. Szybalski,, and S. C. Kim. 1998. Cre/loxP-mediated in vivo excision of large segments from yeast genome and their amplification based on the 2��m plasmid- derived system. Gene 223:6776.
245. Yu, D.,, and D. L. Court. 1988. A new system to place copies of genes, sites and lacZ fusions on the Escherichia coli chromosome. Gene 223:7781.
246. 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 97:59785983.
247. Zhang, P.,, M. Z. Li,, and S. J. Elledge. 2002. Towards genetic genome projects: genomic library screening and gene-targeting vector construction in a single step. Nat. Genet. 30:3139.
248. Zhang, P.,, J. P. P. Muyrers,, G. Testa,, and A. F. Stewart. 2000. DNA cloning by homologous recombination in Escherichia coli. Nat. Biotechnol. 18:13141317.
249. Zhang, Y.,, F. Buchholz,, J. P. P. Muyrers,, and A. F. Stewart.1998. A new logic for DNA engineering using recombination in Escherichia coli. Nat. Genet. 20:123128.