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. 1997 Feb;179(3):880–888. doi: 10.1128/jb.179.3.880-888.1997

Stability of linear DNA in recA mutant Escherichia coli cells reflects ongoing chromosomal DNA degradation.

A Kuzminov 1, F W Stahl 1
PMCID: PMC178773  PMID: 9006046

Abstract

To study the fate of linear DNA in Escherichia coli cells, we linearized plasmid DNA at a specific site in vivo and monitored its behavior in recA mutant cells deficient in recombinational repair. Earlier, we had found that in wild-type (WT) cells linearized DNA is degraded to completion by RecBCD nuclease. We had also found that in WT cells chi sites on linear DNA inhibit RecBCD degradation by turning off its nucleolytic activities. Now we report that chi sites do not work in the absence of the RecA protein, suggesting that RecA is required in vivo to turn off the degradative activities of the RecBCD enzyme. We also report that the degradation of linearized plasmid DNA, even devoid of chi sites, is never complete in recA cells. Investigation of this linear DNA stability indicates that a fraction of recA cells are recBC phenocopies due to ongoing chromosomal DNA degradation, which titrates RecBCD nuclease. A possible role for RecBCD-promoted DNA degradation in controlling chromosomal DNA replication in E. coli is discussed.

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Selected References

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  1. Amundsen S. K., Taylor A. F., Chaudhury A. M., Smith G. R. recD: the gene for an essential third subunit of exonuclease V. Proc Natl Acad Sci U S A. 1986 Aug;83(15):5558–5562. doi: 10.1073/pnas.83.15.5558. [DOI] [PMC free article] [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. Becker A., Murialdo H. Bacteriophage lambda DNA: the beginning of the end. J Bacteriol. 1990 Jun;172(6):2819–2824. doi: 10.1128/jb.172.6.2819-2824.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Birnboim H. C. A rapid alkaline extraction method for the isolation of plasmid DNA. Methods Enzymol. 1983;100:243–255. doi: 10.1016/0076-6879(83)00059-2. [DOI] [PubMed] [Google Scholar]
  5. Brcić-Kostić K., Salaj-Smic E., Marsić N., Kajić S., Stojiljković I., Trgovcević Z. Interaction of RecBCD enzyme with DNA damaged by gamma radiation. Mol Gen Genet. 1991 Aug;228(1-2):136–142. doi: 10.1007/BF00282458. [DOI] [PubMed] [Google Scholar]
  6. CLARK A. J., MARGULIES A. D. ISOLATION AND CHARACTERIZATION OF RECOMBINATION-DEFICIENT MUTANTS OF ESCHERICHIA COLI K12. Proc Natl Acad Sci U S A. 1965 Feb;53:451–459. doi: 10.1073/pnas.53.2.451. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Capaldo F. N., Barbour S. D. DNA content, synthesis and integrity in dividing and non-dividing cells of rec- strains of Escherichia coli K12. J Mol Biol. 1975 Jan 5;91(1):53–66. doi: 10.1016/0022-2836(75)90371-x. [DOI] [PubMed] [Google Scholar]
  8. Capaldo F. N., Ramsey G., Barbour S. D. Analysis of the growth of recombination-deficient strains of Escherichia coli K-12. J Bacteriol. 1974 Apr;118(1):242–249. doi: 10.1128/jb.118.1.242-249.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chambers S. P., Prior S. E., Barstow D. A., Minton N. P. The pMTL nic- cloning vectors. I. Improved pUC polylinker regions to facilitate the use of sonicated DNA for nucleotide sequencing. Gene. 1988 Aug 15;68(1):139–149. doi: 10.1016/0378-1119(88)90606-3. [DOI] [PubMed] [Google Scholar]
  10. Chaudhury A. M., Smith G. R. A new class of Escherichia coli recBC mutants: implications for the role of RecBC enzyme in homologous recombination. Proc Natl Acad Sci U S A. 1984 Dec;81(24):7850–7854. doi: 10.1073/pnas.81.24.7850. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Chow S., Daub E., Murialdo H. The overproduction of DNA terminase of coliphage lambda. Gene. 1987;60(2-3):277–289. doi: 10.1016/0378-1119(87)90236-8. [DOI] [PubMed] [Google Scholar]
  12. Churchward G., Belin D., Nagamine Y. A pSC101-derived plasmid which shows no sequence homology to other commonly used cloning vectors. Gene. 1984 Nov;31(1-3):165–171. doi: 10.1016/0378-1119(84)90207-5. [DOI] [PubMed] [Google Scholar]
  13. Clark A. J., Chamberlin M., Boyce R. P., Howard-Flanders P. Abnormal metabolic response to ultraviolet light of a recombination deficient mutant of Escherichia coli K12. J Mol Biol. 1966 Aug;19(2):442–454. doi: 10.1016/s0022-2836(66)80015-3. [DOI] [PubMed] [Google Scholar]
  14. 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]
  15. Csonka L. N., Clark A. J. Deletions generated by the transposon Tn10 in the srl recA region of the Escherichia coli K-12 chromosome. Genetics. 1979 Oct;93(2):321–343. doi: 10.1093/genetics/93.2.321. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Dabert P., Ehrlich S. D., Gruss A. Chi sequence protects against RecBCD degradation of DNA in vivo. Proc Natl Acad Sci U S A. 1992 Dec 15;89(24):12073–12077. doi: 10.1073/pnas.89.24.12073. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Dharmalingam K., Goldberg E. B. Mechanism localisation and control of restriction cleavage of phage T4 and lambda chromosomes in vivo. Nature. 1976 Apr 1;260(5550):406–410. doi: 10.1038/260406a0. [DOI] [PubMed] [Google Scholar]
  18. Dixon D. A., Churchill J. J., Kowalczykowski S. C. Reversible inactivation of the Escherichia coli RecBCD enzyme by the recombination hotspot chi in vitro: evidence for functional inactivation or loss of the RecD subunit. Proc Natl Acad Sci U S A. 1994 Apr 12;91(8):2980–2984. doi: 10.1073/pnas.91.8.2980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Dixon D. A., Kowalczykowski S. C. Role of the Escherichia coli recombination hotspot, chi, in RecABCD-dependent homologous pairing. J Biol Chem. 1995 Jul 7;270(27):16360–16370. doi: 10.1074/jbc.270.27.16360. [DOI] [PubMed] [Google Scholar]
  20. Dixon D. A., Kowalczykowski S. C. The recombination hotspot chi is a regulatory sequence that acts by attenuating the nuclease activity of the E. coli RecBCD enzyme. Cell. 1993 Apr 9;73(1):87–96. doi: 10.1016/0092-8674(93)90162-j. [DOI] [PubMed] [Google Scholar]
  21. Hickson I. D., Gordon R. L., Tomkinson A. E., Emmerson P. T. A temperature sensitive Reca protein of Escherichia coli. Mol Gen Genet. 1981;184(1):68–72. doi: 10.1007/BF00271197. [DOI] [PubMed] [Google Scholar]
  22. Kobayashi I., Stahl M. M., Stahl F. W. The mechanism of the chi-cos interaction in RecA-RecBC-mediated recombination in phage lambda. Cold Spring Harb Symp Quant Biol. 1984;49:497–506. doi: 10.1101/sqb.1984.049.01.056. [DOI] [PubMed] [Google Scholar]
  23. Kowalczykowski S. C., Dixon D. A., Eggleston A. K., Lauder S. D., Rehrauer W. M. Biochemistry of homologous recombination in Escherichia coli. Microbiol Rev. 1994 Sep;58(3):401–465. doi: 10.1128/mr.58.3.401-465.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Kuzminov A. Collapse and repair of replication forks in Escherichia coli. Mol Microbiol. 1995 May;16(3):373–384. doi: 10.1111/j.1365-2958.1995.tb02403.x. [DOI] [PubMed] [Google Scholar]
  25. Kuzminov A., Schabtach E., Stahl F. W. Chi sites in combination with RecA protein increase the survival of linear DNA in Escherichia coli by inactivating exoV activity of RecBCD nuclease. EMBO J. 1994 Jun 15;13(12):2764–2776. doi: 10.1002/j.1460-2075.1994.tb06570.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Köppen A., Krobitsch S., Thoms B., Wackernagel W. Interaction with the recombination hot spot chi in vivo converts the RecBCD enzyme of Escherichia coli into a chi-independent recombinase by inactivation of the RecD subunit. Proc Natl Acad Sci U S A. 1995 Jul 3;92(14):6249–6253. doi: 10.1073/pnas.92.14.6249. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Lindsley J. E., Cox M. M. Dissociation pathway for recA nucleoprotein filaments formed on linear duplex DNA. J Mol Biol. 1989 Feb 20;205(4):695–711. doi: 10.1016/0022-2836(89)90315-x. [DOI] [PubMed] [Google Scholar]
  28. Lloyd R. G., Buckman C., Benson F. E. Genetic analysis of conjugational recombination in Escherichia coli K12 strains deficient in RecBCD enzyme. J Gen Microbiol. 1987 Sep;133(9):2531–2538. doi: 10.1099/00221287-133-9-2531. [DOI] [PubMed] [Google Scholar]
  29. Myers R. S., Kuzminov A., Stahl F. W. The recombination hot spot chi activates RecBCD recombination by converting Escherichia coli to a recD mutant phenocopy. Proc Natl Acad Sci U S A. 1995 Jul 3;92(14):6244–6248. doi: 10.1073/pnas.92.14.6244. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Myers R. S., Stahl F. W. Chi and the RecBC D enzyme of Escherichia coli. Annu Rev Genet. 1994;28:49–70. doi: 10.1146/annurev.ge.28.120194.000405. [DOI] [PubMed] [Google Scholar]
  31. Myers R. S., Stahl M. M., Stahl F. W. Chi recombination activity in phage lambda decays as a function of genetic distance. Genetics. 1995 Nov;141(3):805–812. doi: 10.1093/genetics/141.3.805. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Oliver D. B., Goldberg E. B. Protection of parental T4 DNA from a restriction exonuclease by the product of gene 2. J Mol Biol. 1977 Nov;116(4):877–881. doi: 10.1016/0022-2836(77)90276-5. [DOI] [PubMed] [Google Scholar]
  33. Ponticelli A. S., Schultz D. W., Taylor A. F., Smith G. R. Chi-dependent DNA strand cleavage by RecBC enzyme. Cell. 1985 May;41(1):145–151. doi: 10.1016/0092-8674(85)90069-8. [DOI] [PubMed] [Google Scholar]
  34. Rinken R., Thomas B., Wackernagel W. Evidence that recBC-dependent degradation of duplex DNA in Escherichia coli recD mutants involves DNA unwinding. J Bacteriol. 1992 Aug;174(16):5424–5429. doi: 10.1128/jb.174.16.5424-5429.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Roman L. J., Eggleston A. K., Kowalczykowski S. C. Processivity of the DNA helicase activity of Escherichia coli recBCD enzyme. J Biol Chem. 1992 Feb 25;267(6):4207–4214. [PubMed] [Google Scholar]
  36. Roman L. J., Kowalczykowski S. C. Characterization of the helicase activity of the Escherichia coli RecBCD enzyme using a novel helicase assay. Biochemistry. 1989 Apr 4;28(7):2863–2873. doi: 10.1021/bi00433a018. [DOI] [PubMed] [Google Scholar]
  37. Sargentini N. J., Smith K. C. Quantitation of the involvement of the recA, recB, recC, recF, recJ, recN, lexA, radA, radB, uvrD, and umuC genes in the repair of X-ray-induced DNA double-strand breaks in Escherichia coli. Radiat Res. 1986 Jul;107(1):58–72. [PubMed] [Google Scholar]
  38. Silverstein J. L., Goldberg E. B. T4 DNA injection. I. Growth cycle of a gene 2 mutant. Virology. 1976 Jul 1;72(1):195–211. doi: 10.1016/0042-6822(76)90323-8. [DOI] [PubMed] [Google Scholar]
  39. Silverstein J. L., Goldberg E. B. T4 DNA injection. II. Protection of entering DNA from host exonuclease V. Virology. 1976 Jul 1;72(1):212–223. doi: 10.1016/0042-6822(76)90324-x. [DOI] [PubMed] [Google Scholar]
  40. Simmon V. F., Lederberg S. Degradation of bacteriophage lambda deoxyribonucleic acid after restriction by Escherichia coli K-12. J Bacteriol. 1972 Oct;112(1):161–169. doi: 10.1128/jb.112.1.161-169.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Skarstad K., Boye E. Degradation of individual chromosomes in recA mutants of Escherichia coli. J Bacteriol. 1993 Sep;175(17):5505–5509. doi: 10.1128/jb.175.17.5505-5509.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Stahl F. W., Thomason L. C., Siddiqi I., Stahl M. M. Further tests of a recombination model in which chi removes the RecD subunit from the RecBCD enzyme of Escherichia coli. Genetics. 1990 Nov;126(3):519–533. doi: 10.1093/genetics/126.3.519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Stoker N. G., Fairweather N. F., Spratt B. G. Versatile low-copy-number plasmid vectors for cloning in Escherichia coli. Gene. 1982 Jun;18(3):335–341. doi: 10.1016/0378-1119(82)90172-x. [DOI] [PubMed] [Google Scholar]
  44. Taylor A. F., Smith G. R. RecBCD enzyme is altered upon cutting DNA at a chi recombination hotspot. Proc Natl Acad Sci U S A. 1992 Jun 15;89(12):5226–5230. doi: 10.1073/pnas.89.12.5226. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Uhlin B. E., Clark A. J. Overproduction of the Escherichia coli recA protein without stimulation of its proteolytic activity. J Bacteriol. 1981 Oct;148(1):386–390. doi: 10.1128/jb.148.1.386-390.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Uzest M., Ehrlich S. D., Michel B. Lethality of rep recB and rep recC double mutants of Escherichia coli. Mol Microbiol. 1995 Sep;17(6):1177–1188. doi: 10.1111/j.1365-2958.1995.mmi_17061177.x. [DOI] [PubMed] [Google Scholar]
  47. West S. C., Cassuto E., Mursalim J., Howard-Flanders P. Recognition of duplex DNA containing single-stranded regions by recA protein. Proc Natl Acad Sci U S A. 1980 May;77(5):2569–2573. doi: 10.1073/pnas.77.5.2569. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Willetts N. S., Clark A. J. Characteristics of some multiply recombination-deficient strains of Escherichia coli. J Bacteriol. 1969 Oct;100(1):231–239. doi: 10.1128/jb.100.1.231-239.1969. [DOI] [PMC free article] [PubMed] [Google Scholar]

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