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. 1989 Jun;171(6):3523–3529. doi: 10.1128/jb.171.6.3523-3529.1989

Suppression of recA deficiency in plasmid recombination by bacteriophage lambda beta protein in RecBCD- ExoI- Escherichia coli cells.

I Berger 1, A Cohen 1
PMCID: PMC210080  PMID: 2542228

Abstract

Plasmid recombination, like other homologous recombination in Escherichia coli, requires RecA protein in most conditions. We have found that the plasmid recombination defect in a recA mutant can be efficiently suppressed by the beta protein of bacteriophage lambda. beta protein is required for homologous recombination of lambda chromosomes during lytic phage growth in a recA host and is known to have a strand-annealing activity resembling that of RecA protein. The bioluminescence recombination assay was used for genetic analysis of beta-protein-mediated plasmid recombination. Efficient suppression of the recA mutation by beta protein required the absence of the E. coli nucleases exonuclease I and RecBCD nuclease. These nucleases inhibit a RecA-mediated plasmid recombination pathway that is more efficient than the pathway functioning in wild-type cells. Like RecA-mediated plasmid recombination in RecBCD- ExoI- cells, beta-protein-mediated plasmid recombination depended on concurrent DNA replication and on the activity of the recQ gene. However, unlike RecA-mediated plasmid recombination, beta-protein-mediated recombination in RecBCD- ExoI- cells was independent of recF and recJ activities. We propose that inactivation of exonuclease I and RecBCD nuclease stabilizes a recombination intermediate that is involved in RecA- and beta-protein-catalyzed homologous pairing reactions. We suggest that the intermediate may be linear plasmid DNA with a protruding 3' end, since these nucleases are known to interfere with the synthesis of such linear forms. The different recF and recJ requirements for beta-protein-dependent and RecA-dependent recombinations imply that the mechanisms of formation or processing of the putative intermediate differ in the two cases.

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Selected References

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  1. Alberts B. M., Frey L. T4 bacteriophage gene 32: a structural protein in the replication and recombination of DNA. Nature. 1970 Sep 26;227(5265):1313–1318. doi: 10.1038/2271313a0. [DOI] [PubMed] [Google Scholar]
  2. Bachmann B. J. Pedigrees of some mutant strains of Escherichia coli K-12. Bacteriol Rev. 1972 Dec;36(4):525–557. doi: 10.1128/br.36.4.525-557.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Birge E. A., Low K. B. Detection of transcribable recombination products following conjugation in rec+, reCB- and recC-strains of Escherichia coli K12. J Mol Biol. 1974 Mar 15;83(4):447–457. doi: 10.1016/0022-2836(74)90506-3. [DOI] [PubMed] [Google Scholar]
  4. 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]
  5. 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]
  6. Bryant F. R., Lehman I. R. On the mechanism of renaturation of complementary DNA strands by the recA protein of Escherichia coli. Proc Natl Acad Sci U S A. 1985 Jan;82(2):297–301. doi: 10.1073/pnas.82.2.297. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. 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]
  8. Christiansen C., Baldwin R. L. Catalysis of DNA reassociation by the Escherichia coli DNA binding protein: A polyamine-dependent reaction. J Mol Biol. 1977 Sep 25;115(3):441–454. doi: 10.1016/0022-2836(77)90164-4. [DOI] [PubMed] [Google Scholar]
  9. Clark A. J. Recombination deficient mutants of E. coli and other bacteria. Annu Rev Genet. 1973;7:67–86. doi: 10.1146/annurev.ge.07.120173.000435. [DOI] [PubMed] [Google Scholar]
  10. Cohen A., Clark A. J. Synthesis of linear plasmid multimers in Escherichia coli K-12. J Bacteriol. 1986 Jul;167(1):327–335. doi: 10.1128/jb.167.1.327-335.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Cohen A., Laban A. Plasmidic recombination in Escherichia coli K-12: the role of recF gene function. Mol Gen Genet. 1983;189(3):471–474. doi: 10.1007/BF00325911. [DOI] [PubMed] [Google Scholar]
  12. Fishel R. A., James A. A., Kolodner R. recA-independent general genetic recombination of plasmids. Nature. 1981 Nov 12;294(5837):184–186. doi: 10.1038/294184a0. [DOI] [PubMed] [Google Scholar]
  13. Friedman S. A., Hays J. B. Selective inhibition of Escherichia coli recBC activities by plasmid-encoded GamS function of phage lambda. Gene. 1986;43(3):255–263. doi: 10.1016/0378-1119(86)90214-3. [DOI] [PubMed] [Google Scholar]
  14. Horii Z., Clark A. J. Genetic analysis of the recF pathway to genetic recombination in Escherichia coli K12: isolation and characterization of mutants. J Mol Biol. 1973 Oct 25;80(2):327–344. doi: 10.1016/0022-2836(73)90176-9. [DOI] [PubMed] [Google Scholar]
  15. James A. A., Morrison P. T., Kolodner R. Genetic recombination of bacterial plasmid DNA. Analysis of the effect of recombination-deficient mutations on plasmid recombination. J Mol Biol. 1982 Sep 25;160(3):411–430. doi: 10.1016/0022-2836(82)90305-9. [DOI] [PubMed] [Google Scholar]
  16. Kmiec E., Holloman W. K. Beta protein of bacteriophage lambda promotes renaturation of DNA. J Biol Chem. 1981 Dec 25;256(24):12636–12639. [PubMed] [Google Scholar]
  17. Kobayashi I., Ikeda H. On the role of recA gene product in genetic recombination: an analysis by in vitro packaging of recombinant DNA molecules formed in the absence of protein synthesis. Mol Gen Genet. 1978 Oct 25;166(1):25–29. doi: 10.1007/BF00379725. [DOI] [PubMed] [Google Scholar]
  18. Kolodner R., Fishel R. A., Howard M. Genetic recombination of bacterial plasmid DNA: effect of RecF pathway mutations on plasmid recombination in Escherichia coli. J Bacteriol. 1985 Sep;163(3):1060–1066. doi: 10.1128/jb.163.3.1060-1066.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Kushner S. R., Nagaishi H., Clark A. J. Indirect suppression of recB and recC mutations by exonuclease I deficiency. Proc Natl Acad Sci U S A. 1972 Jun;69(6):1366–1370. doi: 10.1073/pnas.69.6.1366. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Kushner S. R., Nagaishi H., Templin A., Clark A. J. Genetic recombination in Escherichia coli: the role of exonuclease I. Proc Natl Acad Sci U S A. 1971 Apr;68(4):824–827. doi: 10.1073/pnas.68.4.824. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. LURIA S. E., BURROUS J. W. Hybridization between Escherichia coli and Shigella. J Bacteriol. 1957 Oct;74(4):461–476. doi: 10.1128/jb.74.4.461-476.1957. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Laban A., Cohen A. Interplasmidic and intraplasmidic recombination in Escherichia coli K-12. Mol Gen Genet. 1981;184(2):200–207. doi: 10.1007/BF00272905. [DOI] [PubMed] [Google Scholar]
  23. Lloyd R. G., Benson F. E., Shurvinton C. E. Effect of ruv mutations on recombination and DNA repair in Escherichia coli K12. Mol Gen Genet. 1984;194(1-2):303–309. doi: 10.1007/BF00383532. [DOI] [PubMed] [Google Scholar]
  24. Lloyd R. G., Buckman C. Identification and genetic analysis of sbcC mutations in commonly used recBC sbcB strains of Escherichia coli K-12. J Bacteriol. 1985 Nov;164(2):836–844. doi: 10.1128/jb.164.2.836-844.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Lloyd R. G., Picksley S. M., Prescott C. Inducible expression of a gene specific to the RecF pathway for recombination in Escherichia coli K12. Mol Gen Genet. 1983;190(1):162–167. doi: 10.1007/BF00330340. [DOI] [PubMed] [Google Scholar]
  26. Madiraju M. V., Templin A., Clark A. J. Properties of a mutant recA-encoded protein reveal a possible role for Escherichia coli recF-encoded protein in genetic recombination. Proc Natl Acad Sci U S A. 1988 Sep;85(18):6592–6596. doi: 10.1073/pnas.85.18.6592. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. McEntee K., Weinstock G. M., Lehman I. R. Initiation of general recombination catalyzed in vitro by the recA protein of Escherichia coli. Proc Natl Acad Sci U S A. 1979 Jun;76(6):2615–2619. doi: 10.1073/pnas.76.6.2615. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. McEntee K., Weinstock G. M., Lehman I. R. recA protein-catalyzed strand assimilation: stimulation by Escherichia coli single-stranded DNA-binding protein. Proc Natl Acad Sci U S A. 1980 Feb;77(2):857–861. doi: 10.1073/pnas.77.2.857. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Muniyappa K., Radding C. M. The homologous recombination system of phage lambda. Pairing activities of beta protein. J Biol Chem. 1986 Jun 5;261(16):7472–7478. [PubMed] [Google Scholar]
  30. Muniyappa K., Shaner S. L., Tsang S. S., Radding C. M. Mechanism of the concerted action of recA protein and helix-destabilizing proteins in homologous recombination. Proc Natl Acad Sci U S A. 1984 May;81(9):2757–2761. doi: 10.1073/pnas.81.9.2757. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Nakayama H., Nakayama K., Nakayama R., Irino N., Nakayama Y., Hanawalt P. C. Isolation and genetic characterization of a thymineless death-resistant mutant of Escherichia coli K12: identification of a new mutation (recQ1) that blocks the RecF recombination pathway. Mol Gen Genet. 1984;195(3):474–480. doi: 10.1007/BF00341449. [DOI] [PubMed] [Google Scholar]
  32. Nussbaum A., Cohen A. Use of a bioluminescence gene reporter for the investigation of red-dependent and gam-dependent plasmid recombination in Escherichia coli K12. J Mol Biol. 1988 Sep 20;203(2):391–402. doi: 10.1016/0022-2836(88)90007-1. [DOI] [PubMed] [Google Scholar]
  33. Radding C. M. Genetic recombination: strand transfer and mismatch repair. Annu Rev Biochem. 1978;47:847–880. doi: 10.1146/annurev.bi.47.070178.004215. [DOI] [PubMed] [Google Scholar]
  34. Radding C. M. Regulation of lambda exonuclease. I. Properties of lambda exonuclease purified from lysogens of lambda T11 and wild type. J Mol Biol. 1966 Jul;18(2):235–250. doi: 10.1016/s0022-2836(66)80243-7. [DOI] [PubMed] [Google Scholar]
  35. Shibata T., DasGupta C., Cunningham R. P., Radding C. M. Homologous pairing in genetic recombination: formation of D loops by combined action of recA protein and a helix-destabilizing protein. Proc Natl Acad Sci U S A. 1980 May;77(5):2606–2610. doi: 10.1073/pnas.77.5.2606. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Shibata T., DasGupta C., Cunningham R. P., Radding C. M. Purified Escherichia coli recA protein catalyzes homologous pairing of superhelical DNA and single-stranded fragments. Proc Natl Acad Sci U S A. 1979 Apr;76(4):1638–1642. doi: 10.1073/pnas.76.4.1638. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Signer E. R., Weil J. Recombination in bacteriophage lambda. I. Mutants deficient in general recombination. J Mol Biol. 1968 Jul 14;34(2):261–271. doi: 10.1016/0022-2836(68)90251-9. [DOI] [PubMed] [Google Scholar]
  38. Silberstein Z., Cohen A. Synthesis of linear multimers of OriC and pBR322 derivatives in Escherichia coli K-12: role of recombination and replication functions. J Bacteriol. 1987 Jul;169(7):3131–3137. doi: 10.1128/jb.169.7.3131-3137.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Stahl F. W., Kobayashi I., Stahl M. M. In phage lambda, cos is a recombinator in the red pathway. J Mol Biol. 1985 Jan 20;181(2):199–209. doi: 10.1016/0022-2836(85)90085-3. [DOI] [PubMed] [Google Scholar]
  40. Stahl F. W. Roles of double-strand breaks in generalized genetic recombination. Prog Nucleic Acid Res Mol Biol. 1986;33:169–194. doi: 10.1016/s0079-6603(08)60023-9. [DOI] [PubMed] [Google Scholar]
  41. Symington L. S., Morrison P., Kolodner R. Intramolecular recombination of linear DNA catalyzed by the Escherichia coli RecE recombination system. J Mol Biol. 1985 Dec 5;186(3):515–525. doi: 10.1016/0022-2836(85)90126-3. [DOI] [PubMed] [Google Scholar]
  42. Thaler D. S., Stahl M. M., Stahl F. W. Double-chain-cut sites are recombination hotspots in the Red pathway of phage lambda. J Mol Biol. 1987 May 5;195(1):75–87. doi: 10.1016/0022-2836(87)90328-7. [DOI] [PubMed] [Google Scholar]
  43. Thaler D. S., Stahl M. M., Stahl F. W. Evidence that the normal route of replication-allowed Red-mediated recombination involves double-chain ends. EMBO J. 1987 Oct;6(10):3171–3176. doi: 10.1002/j.1460-2075.1987.tb02628.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Thaler D. S., Stahl M. M., Stahl F. W. Tests of the double-strand-break repair model for red-mediated recombination of phage lambda and plasmid lambda dv. Genetics. 1987 Aug;116(4):501–511. doi: 10.1093/genetics/116.4.501. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Vapnek D., Alton N. K., Bassett C. L., Kushner S. R. Amplification in Escherichia coli of enzymes involved in genetic recombination: construction of hybrid ColE1 plasmids carrying the structural gene for exonuclease I. Proc Natl Acad Sci U S A. 1976 Oct;73(10):3492–3496. doi: 10.1073/pnas.73.10.3492. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Volkert M. R., Hartke M. A. Suppression of Escherichia coli recF mutations by recA-linked srfA mutations. J Bacteriol. 1984 Feb;157(2):498–506. doi: 10.1128/jb.157.2.498-506.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Weinstock G. M., McEntee K., Lehman I. R. ATP-dependent renaturation of DNA catalyzed by the recA protein of Escherichia coli. Proc Natl Acad Sci U S A. 1979 Jan;76(1):126–130. doi: 10.1073/pnas.76.1.126. [DOI] [PMC free article] [PubMed] [Google Scholar]

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