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Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1990 Apr;87(8):3166–3169. doi: 10.1073/pnas.87.8.3166

Improved genetic selection for screening bacteriophage libraries by homologous recombination in vivo.

D M Kurnit 1, B Seed 1
PMCID: PMC53855  PMID: 2183225

Abstract

Three major difficulties have hindered the general application of in vivo recombination techniques to library screening: (i) the original selection could not be applied to libraries prepared in phage vectors lacking amber mutations, (ii) nonirradiated packaging extracts gave high backgrounds even when amber mutated vectors were used, and (iii) most red- vectors lacked rap, a recently discovered phage gene promoting phage-plasmid recombination. Here we describe a selection scheme for phage bearing suppressor tRNA plasmids, which relies upon an Escherichia coli host bearing an amber mutation in the dnaB gene. The selection is tight enough to allow library screening by recombination, is applicable to almost every phage vector in common use, and overcomes the background associated with nonirradiated packaging extracts. We also describe an ancillary plasmid that supplies the rap gene function in trans, permitting the recombination level to be raised fruitfully in phage libraries lacking endogenous rap. Finally, we demonstrate simple procedures for preparing and detecting phages that have lost integrated suppressor tRNA plasmids by homologous recombination.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bachmann B. J. Linkage map of Escherichia coli K-12, edition 7. Microbiol Rev. 1983 Jun;47(2):180–230. doi: 10.1128/mr.47.2.180-230.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Blattner F. R., Williams B. G., Blechl A. E., Denniston-Thompson K., Faber H. E., Furlong L., Grunwald D. J., Kiefer D. O., Moore D. D., Schumm J. W. Charon phages: safer derivatives of bacteriophage lambda for DNA cloning. Science. 1977 Apr 8;196(4286):161–169. doi: 10.1126/science.847462. [DOI] [PubMed] [Google Scholar]
  3. Bochner B. R., Huang H. C., Schieven G. L., Ames B. N. Positive selection for loss of tetracycline resistance. J Bacteriol. 1980 Aug;143(2):926–933. doi: 10.1128/jb.143.2.926-933.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bolivar F., Rodriguez R. L., Greene P. J., Betlach M. C., Heyneker H. L., Boyer H. W., Crosa J. H., Falkow S. Construction and characterization of new cloning vehicles. II. A multipurpose cloning system. Gene. 1977;2(2):95–113. [PubMed] [Google Scholar]
  5. Chang A. C., Cohen S. N. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J Bacteriol. 1978 Jun;134(3):1141–1156. doi: 10.1128/jb.134.3.1141-1156.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Coulson A., Sulston J., Brenner S., Karn J. Toward a physical map of the genome of the nematode Caenorhabditis elegans. Proc Natl Acad Sci U S A. 1986 Oct;83(20):7821–7825. doi: 10.1073/pnas.83.20.7821. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Court D., Sato K. Studies of novel transducing variants of lambda: dispensability of genes N and Q. Virology. 1969 Oct;39(2):348–352. doi: 10.1016/0042-6822(69)90060-9. [DOI] [PubMed] [Google Scholar]
  8. D'Ari R., Jaffé-Brachet A., Touati-Schwartz D., Yarmolinsky M. B. A dnaB analog specified by bacteriophage P1. J Mol Biol. 1975 May 25;94(3):341–366. doi: 10.1016/0022-2836(75)90207-7. [DOI] [PubMed] [Google Scholar]
  9. Friedman D. I., Plantefaber L. C., Olson E. J., Carver D., O'Dea M. H., Gellert M. Mutations in the DNA gyrB gene that are temperature sensitive for lambda site-specific recombination, Mu growth, and plasmid maintenance. J Bacteriol. 1984 Feb;157(2):490–497. doi: 10.1128/jb.157.2.490-497.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Frischauf A. M., Lehrach H., Poustka A., Murray N. Lambda replacement vectors carrying polylinker sequences. J Mol Biol. 1983 Nov 15;170(4):827–842. doi: 10.1016/s0022-2836(83)80190-9. [DOI] [PubMed] [Google Scholar]
  11. Guarente L., Lauer G., Roberts T. M., Ptashne M. Improved methods for maximizing expression of a cloned gene: a bacterium that synthesizes rabbit beta-globin. Cell. 1980 Jun;20(2):543–553. doi: 10.1016/0092-8674(80)90640-6. [DOI] [PubMed] [Google Scholar]
  12. Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol. 1983 Jun 5;166(4):557–580. doi: 10.1016/s0022-2836(83)80284-8. [DOI] [PubMed] [Google Scholar]
  13. Ikeda H., Aoki K., Naito A. Illegitimate recombination mediated in vitro by DNA gyrase of Escherichia coli: structure of recombinant DNA molecules. Proc Natl Acad Sci U S A. 1982 Jun;79(12):3724–3728. doi: 10.1073/pnas.79.12.3724. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Kurachi S., Baldori N., Kurnit D. M. Sumo15A: a lambda phasmid that permits easy selection for and against cloned inserts. Gene. 1989 Dec 21;85(1):35–43. doi: 10.1016/0378-1119(89)90461-7. [DOI] [PubMed] [Google Scholar]
  15. Kurnit D. M., Roy S., Stewart G. D., Schwedock J., Neve R. L., Bruns G. A., Van Keuren M. L., Patterson D. The 724 family of DNA sequences is interspersed about the pericentromeric regions of human acrocentric chromosomes. Cytogenet Cell Genet. 1986;43(1-2):109–116. doi: 10.1159/000132305. [DOI] [PubMed] [Google Scholar]
  16. Lacatena R. M., Cesareni G. Base pairing of RNA I with its complementary sequence in the primer precursor inhibits ColE1 replication. Nature. 1981 Dec 17;294(5842):623–626. doi: 10.1038/294623a0. [DOI] [PubMed] [Google Scholar]
  17. Lacatena R. M., Cesareni G. Interaction between RNA1 and the primer precursor in the regulation of Co1E1 replication. J Mol Biol. 1983 Nov 5;170(3):635–650. doi: 10.1016/s0022-2836(83)80125-9. [DOI] [PubMed] [Google Scholar]
  18. Lawn R. M., Fritsch E. F., Parker R. C., Blake G., Maniatis T. The isolation and characterization of linked delta- and beta-globin genes from a cloned library of human DNA. Cell. 1978 Dec;15(4):1157–1174. doi: 10.1016/0092-8674(78)90043-0. [DOI] [PubMed] [Google Scholar]
  19. Lutz C. T., Hollifield W. C., Seed B., Davie J. M., Huang H. V. Syrinx 2A: an improved lambda phage vector designed for screening DNA libraries by recombination in vivo. Proc Natl Acad Sci U S A. 1987 Jul;84(13):4379–4383. doi: 10.1073/pnas.84.13.4379. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Maloy S. R., Nunn W. D. Selection for loss of tetracycline resistance by Escherichia coli. J Bacteriol. 1981 Feb;145(2):1110–1111. doi: 10.1128/jb.145.2.1110-1111.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Marvo S. L., King S. R., Jaskunas S. R. Role of short regions of homology in intermolecular illegitimate recombination events. Proc Natl Acad Sci U S A. 1983 May;80(9):2452–2456. doi: 10.1073/pnas.80.9.2452. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Neve R. L., Bruns G. A., Dryja T. P., Kurnit D. M. Retrieval of human DNA from rodent-human genomic libraries by a recombination process. Gene. 1983 Sep;23(3):343–354. doi: 10.1016/0378-1119(83)90023-9. [DOI] [PubMed] [Google Scholar]
  23. Neve R. L., Kurnit D. M. Comparison of sequence repetitiveness of human cDNA and genomic DNA using the miniplasmid vector, piVX. Gene. 1983 Sep;23(3):355–367. doi: 10.1016/0378-1119(83)90024-0. [DOI] [PubMed] [Google Scholar]
  24. Neve R. L., Stewart G. D., Newcomb P., Van Keuren M. L., Patterson D., Drabkin H. A., Kurnit D. M. Human chromosome 21-encoded cDNA clones. Gene. 1986;49(3):361–369. doi: 10.1016/0378-1119(86)90372-0. [DOI] [PubMed] [Google Scholar]
  25. Ogawa T. Analysis of dnaB function of Escherichia coli K12 and the dnaB-like function of P1 prophage. J Mol Biol. 1975 May 25;94(3):327–340. doi: 10.1016/0022-2836(75)90206-5. [DOI] [PubMed] [Google Scholar]
  26. Olson M. V., Dutchik J. E., Graham M. Y., Brodeur G. M., Helms C., Frank M., MacCollin M., Scheinman R., Frank T. Random-clone strategy for genomic restriction mapping in yeast. Proc Natl Acad Sci U S A. 1986 Oct;83(20):7826–7830. doi: 10.1073/pnas.83.20.7826. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Perry M. D., Moran L. A. Isolation of a mouse heat-shock gene (hsp68) by recombinational screening. Gene. 1987;51(2-3):227–236. doi: 10.1016/0378-1119(87)90311-8. [DOI] [PubMed] [Google Scholar]
  28. Phadnis S. H., Huang H. V., Berg D. E. Tn5supF, a 264-base-pair transposon derived from Tn5 for insertion mutagenesis and sequencing DNAs cloned in phage lambda. Proc Natl Acad Sci U S A. 1989 Aug;86(15):5908–5912. doi: 10.1073/pnas.86.15.5908. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Poustka A., Rackwitz H. R., Frischauf A. M., Hohn B., Lehrach H. Selective isolation of cosmid clones by homologous recombination in Escherichia coli. Proc Natl Acad Sci U S A. 1984 Jul;81(13):4129–4133. doi: 10.1073/pnas.81.13.4129. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Seed B. Purification of genomic sequences from bacteriophage libraries by recombination and selection in vivo. Nucleic Acids Res. 1983 Apr 25;11(8):2427–2445. doi: 10.1093/nar/11.8.2427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Shulman M. J., Hallick L. M., Echols H., Signer E. R. Properties of recombination-deficient mutants of bacteriophage lambda. J Mol Biol. 1970 Sep 28;52(3):501–520. doi: 10.1016/0022-2836(70)90416-x. [DOI] [PubMed] [Google Scholar]
  32. Wyman A. R., Wolfe L. B., Botstein D. Propagation of some human DNA sequences in bacteriophage lambda vectors requires mutant Escherichia coli hosts. Proc Natl Acad Sci U S A. 1985 May;82(9):2880–2884. doi: 10.1073/pnas.82.9.2880. [DOI] [PMC free article] [PubMed] [Google Scholar]

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