Gene replacement with linear DNA fragments in wild-type Escherichia coli: Enhancement by Chi sites

Genetics

Volumn 145, Issue 4, 1997, Pages 877-889

  Dabert, Patrick ^a,b   Smith, Gerald R ^a  

^a Fred Hutchinson Cancer Research Center   (United States)

^b LABORATOIRE DE BIOTECHNOLOGIE DE L ENVIRONNEMENT   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; DOUBLE STRANDED DNA;

ALLELISM; ANIMAL CELL; ARTICLE; CONJUGATION; DNA BINDING; ENZYME ACTIVITY; GENE STRUCTURE; GENE TARGETING; GENETIC ANALYSIS; GENETIC TRANSDUCTION; NONHUMAN; PRIORITY JOURNAL;

BACTERIAL PROTEINS; DNA, BACTERIAL; DNA, RECOMBINANT; DNA, SINGLE-STRANDED; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; EXODEOXYRIBONUCLEASE V; EXODEOXYRIBONUCLEASES; GENES, BACTERIAL; REC A RECOMBINASES; RECOMBINATION, GENETIC; REGULATORY SEQUENCES, NUCLEIC ACID; SPECIES SPECIFICITY; TRANSDUCTION, GENETIC; TRANSFORMATION, BACTERIAL;

ANIMALIA; BACTERIOPHAGE LAMBDA; ESCHERICHIA COLI;

EID: 0030930989     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (60)

1. AMUNDSEN, S. K., A. F. TAYLOR, A. M. CHAUDHURY and G. R. SMITH, 1986 recD: The gene for an essential third subunit of exonuclease V. Proc. Natl. Acad. Sci. USA 83: 5558-5562.
2. BACHMANN, B. J., 1987 Derivations and genotypes of some mutant derivatives of Escherichia coli K-12, pp. 1190-1219 in: Escherichia coli and Salmonella typhimurium Cellular and Molecular Biology, edited by F. C. NEIDHARDT. American Society for Microbiology, Washington, DC.
3. BISWAS, I., E. MAGUIN, S. D. EHRLICH and A. GRUSS, 1995 A 7-basepair sequence protects DNA from exonucleolytic degradation in Lactococcus lactis. Proc. Natl. Acad. Sci. USA 92: 2244-2248.
4. BOLIVAR, F., R. L. RODRIGUEZ, P. J. GREENE, M. C. BETLACH, H. L. HEYNEKER et al., 1977 Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene 2: 95-113.
5. CARLOMAGNO, M. S., L. CHIARIOTTI, P. ALIFANO, A. G. NAPPO and C. B. BRUNI, 1988 Structure and function of the Salmonella typhimurium and Escherichia coli K-12 histidine operons. J. Mol. Biol. 203: 585-606.
6. CHANG, A. C. Y. and S. N. COHEN, 1978 Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from p15A, the cryptic miniplasmid. J. Bacteriol. 134: 1141-1156.
7. CHAUDHURY, A. M. and G. R. SMIIH, 1984 A new class of Escherichia coli recBC mutants: Implications for the role of RecBC enzyme in homologous recombination. Proc. Natl. Acad. Sci. USA 81: 7850-7854.
8. CHENG, K. C. and G. R. SMITH, 1984 Recombinational hotspot activity of Chi-like sequences. J. Mol. Biol. 180: 371-377.
9. CHENG, K. C. and G. R. SMITH, 1987 Cutting of Chi-like sequences by the RecBCD enzyme of Escherichia coli. J. Mol. Biol. 194: 747-750.
10. CHENG, K. C. and G. R. SMITH, 1989 Distribution of Chi-stimulated recombinational exchanges and heteroduplex endpoints in phage lambda. Genetics 123: 5-17.
11. DABERT, P., S. D. EHRLICH and A. GRUSS, 1992 χ sequence protects against RecBCD degradation of DNA in vivo. Proc. Natl. Acad. Sci. USA 89: 12073-12077.
12. DIXON, D. A. and S. C. KOWALCZYKOWSKI, 1991 Homologous pairing in vitro stimulated by the recombination hotspot, Chi. Cell 66: 361-371.
13. DIXON, D. A. and S. C. KOWALCZYKOWSKI, 1993 The recombination hotspot χ is a regulatory sequence that acts by attenuating the nuclease activity of the E. coli RecBCD enzyme. Cell 73: 87-96.
14. DOWER, N. A. and F. W. STAHL, 1981 Chi activity during transduction-associated recombination. Proc. Natl. Acad. Sci. USA 78: 7033-7037.
15. FAULDS, D., N. DOWER, M. M. STAHL and F. W. STVHL, 1979 Orientation-dependent recombination hotspot activity in bacteriophage lambda. J. Mol. Biol. 131: 681-695.
16. GRUSS, A. and S. D. EHRLICH, 1988 Insertion of foreign DNA into plasmids from gram-positive bacteria induces formation of high-molecular-weight plasmid multimers. J. Bacteriol. 170: 1183-1190.
17. GUTTERSON, N. I. and D. E. KOSHLAND, 1983 Replacement and amplification of bacterial genes with sequences altered in vitro. Proc. Natl. Acad. Sci. USA 80: 4894-4898.
18. 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.
19. HANAHAN, D., 1983 Studies of transformation of Escherichia coli with plasmids. J. Mol. Biol. 166: 557-580.
20. 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.
21. JOVANOVIC, G., T. KOSTIC, M. JANKOVIC and D. J. SAVIC, 1994 Nucleotide sequence of the Escherichia coli K12 histidine operon revisited. J. MoL. Biol. 239: 433-435.
22. JOYCE, C. M. and N. D. F. GRINDLEY, 1984 Method for determining whether a gene of Escherichia coli is essential: application to the polA gene. J. Bacteriol. 158: 636-643.
23. KOBAYASHI, I., H. MURIALDO, J. M. CRASEMANN, M. M. STAHL and F. W. STAHL, 1982 Orientation of cohesive end site cas determines the active orientation of chi sequence in stimulating recA-recBC mediated recombination in phage lambda lytic infections. Proc. Natl. Acad. Sci. USA 79: 5981-5985.
24. KÖPPEN, A., S. KROBITSCH, B. THOMS and W. WACKERNAGEL, 1995 Interaction with the recombination hot spot χ in vivo converts the RecBCD enzyme of Escherichia coli into a χ-independent recombinase by inactivation of the RecD subunit. Proc. Natl. Acad. Sci. USA 92: 6249-6253.
25. 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.
26. KULAKAUSKAS, S., P. M. WIKSTROM and D.E. BEKG, 1991 Efficient introduction of cloned mutant alleles into the Escherichia coli chromosome. J. Bacteriol. 173: 2633-2638.
27. LAM, S. T., M. M. STAIIL, K. D. MCMILIN and F. W. STAHL, 1974 Recmediatcd recombinational hotspot activity in bacteriophage lambda. II. A mutation which causes hotspot activity. Genetics 77: 425-433.
28. MCFARIANE, R. J. and J. R. SAUNDERS, 1996 Molecular mechanisms of intramolecular recombination-dependent recircularization of linearized plasmid DNA in Escherichia coli: requirements for the ruvA, ruvB, recG, recF and recR gene products. Gene 177: 209-216.
29. MCKITTRICK, N. H. and G. R. SMITH, 1989 Activation of Chi recombinational hotspots by RecBCD-like enzymes from enteric bacteria. J. Mol. Biol. 210: 485-495.
30. MYERS, R. S., A. KUZMINOV and F. W. STAHL, 1995a The recombination hot spot χ activates RecBCD recombination by converting Escherichia coli to a recD mutant phenocopy. Proc. Natl. Acad. Sci. USA 92: 6244-6248.
31. MYERS, R. S. and F. W. STAHL, 1994 χ and the RecBCD enzyme of Escherichia coli. Annu. Rev. Genet. 28: 49-70.
32. MYERS, R. S., M. M. STAHL and F. W. STAHL, 1995b χ recombination activity in phage λ decays as a function of genetic distance. Genetics 141: 805-812.
33. NEWMAN, A. K., R. A. RUBIN, S.-H. KIM and P. MODRICH, 1981 DNA sequences of structural genes for EcoRI DNA restriction and modification enzymes. J. Biol. Chem. 256: 2131-2139.
34. NUSSBAUM, A., M. SHALIT and A. COHEN, 1992 Restriction-stimulated homologous recombination of plasmids by the RecE pathway of Escherichia coli. Genetics 130: 37-49.
35. PARKER, B. and M. G. MARINUS, 1988 A simple and rapid method to obtain substitution mutations in Escherichia coli: isolation of a dam deletion/insertion mutation. Gene 73: 531-535.
36. PONTICELLI, A. S., D. W. SCHULTZ, A. F. TAYLOR and G. R. SMITH, 1985 Chi-dependent DNA strand cleavage by RecBC enzyme. Cell 41: 145-151.
37. RINKEN, R., J. DE VRIES, D. WEICHENHAN and W. WACKERNAGEL, 1991 The recA-recBCD dependent recombination pathways of Serratia marcescens and Proteus mirabilis in Escherichia coli: functions of hybrid enzymes and hybrid pathways. Biochimie 73: 375-384.
38. 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.
39. SAMBROOK, J., E. F. FRITSCH and T. MANIATIS, 1989 Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
40. SCHULTZ, D. W. and G. R. SMITH, 1986 Conservation of Chi cutting activity in terrestrial and marine enteric bacteria. J. Mol. Biol. 189: 585-595.
41. SCHULTZ, D. W., J. SWINDLE and G. R. SMITH, 1981 Clustering of mutations inactivating a Chi recombinational hotspot. J. Mol. Biol. 146: 275-286.
42. SCHULTZ, D. W., A. F. TAYLOR and G. R. SMITH, 1983 Escherichia coli RecBC pseudorevertants lacking Chi recombinational hotspot activity. J. Bacteriol. 155: 664-680.
43. SHEVELL, D. E., A. M. ABOU-ZAMZAM, B. DEMPLE and G. C. WALKER, 1988 Construction of an Escherichia coli K-12 ada deletion by gene replacement in a recD strain reveals a second methyltransferase that repairs alkylated DNA. J. Bacteriol. 170: 3294-3296.
44. SMITH, G. R., 1989 Homologous recombination in E. coli: multiple pathways for multiple reasons. Cell 58: 807-809.
45. SMITH, G. R., 1991 Conjugational recombination in E. coli: myths and mechanisms. Cell 64: 19-27.
46. SMITH, G. R., 1994 Hotspots of homologous recombination. Experientia 50: 234-241.
47. SMITH, G. R., S. M. KUNES, D. W. SCHULTZ, A. TAYLOR and K. L. TRIMAN, 1981 Structure of Chi hotspots of generalized recombination. Cell 24: 429-436.
48. SMITH, G. R., C. M. ROBERTS and D. W. SCHULTZ, 1986 Activity of Chi recombinational hotspots in Salmonella typhimurium. Genetics 112: 429-439.
49. SOUTHERN, E. M., 1975 Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98: 503-517.
50. SPRAGUE, K. U., D. H. FAULDS and G. R. SMITH, 1978 A single base-change creates a Chi recombinational hotspot in bacteriophage lambda. Proc. Natl. Acad. Sci. USA 75: 6182-6186.
51. STAHL, F. W. and M. M. STAHL, 1975 Rec-mediated recombinational hot spot activity in bacteriophage lambda. IV. Effect of heterology on Chi-stimulated crossing over. Mol. Gen. Genet. 140: 29-37.
52. STAHL, F. W., M. M. STAHL, R. E. MALONE and J. M. CRASEMANN, 1980 Directionality and nonreciprocality of Chi-stimulated recombination in phage lambda. Genetics 94: 235-248.
53. STAHL, F. W., L. C. THOMASON, I. SIDDIQI and M. M. STAHL, 1990 Further tests of a recombination model in which Chi removes the RecD subunit from the RecBCD enzyme of Escherichia coli. Genetics 126: 519-533.
54. TAYLOR, A. F. and G. R. SMITH, 1992 RecBCD enzyme is altered upon cutting DNA at a Chi recombination hotspot. Proc. Natl. Acad. Sci. USA 89: 5226-5230.
55. TAYLOR, A. F., D. W. SCHULTZ, A. S. PONTICELLI and G. R. SMITH, 1985 RecBC enzyme nicking at Chi sites during DNA unwinding: location and orientation dependence of the cutting. Cell 41: 153-163.
56. VIÈIRA, J. and J. MESSING, 1982 The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene 19: 259-268.
57. WEICHENHAN, D. and W. WACKERNAGEL, 1989 Functional analyses of Proteus mirabilis wild-type and mutant RecBCD enzymes in Escherichia coli reveal a new mutant phenotype. Mol. Microb. 3: 1777-1784.
58. 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.
59. YANISCH-PERRON, C., J. VIÈIRA and J. MESSING, 1985 Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33: 103-119.
60. YOUNG, R. A. and R. W. DAVIS, 1983 Efficient isolation of genes by using antibody probes. Proc. Natl. Acad. Sci. USA 80: 1194-1198.