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. 2003 Feb;163(2):485–494. doi: 10.1093/genetics/163.2.485

RecFOR function is required for DNA repair and recombination in a RecA loading-deficient recB mutant of Escherichia coli.

Ivana Ivancić-Baće 1, Petra Peharec 1, Suncana Moslavac 1, Nikolina Skrobot 1, Erika Salaj-Smic 1, Krunoslav Brcić-Kostić 1
PMCID: PMC1462458  PMID: 12618388

Abstract

The RecA loading activity of the RecBCD enzyme, together with its helicase and 5' --> 3' exonuclease activities, is essential for recombination in Escherichia coli. One particular mutant in the nuclease catalytic center of RecB, i.e., recB1080, produces an enzyme that does not have nuclease activity and is unable to load RecA protein onto single-stranded DNA. There are, however, previously published contradictory data on the recombination proficiency of this mutant. In a recF(-) background the recB1080 mutant is recombination deficient, whereas in a recF(+) genetic background it is recombination proficient. A possible explanation for these contrasting phenotypes may be that the RecFOR system promotes RecA-single-strand DNA filament formation and replaces the RecA loading defect of the RecB1080CD enzyme. We tested this hypothesis by using three in vivo assays. We compared the recombination proficiencies of recB1080, recO, recR, and recF single mutants and recB1080 recO, recB1080 recR, and recB1080 recF double mutants. We show that RecFOR functions rescue the repair and recombination deficiency of the recB1080 mutant and that RecA loading is independent of RecFOR in the recB1080 recD double mutant where this activity is provided by the RecB1080C(D(-)) enzyme. According to our results as well as previous data, three essential activities for the initiation of recombination in the recB1080 mutant are provided by different proteins, i.e., helicase activity by RecB1080CD, 5' --> 3' exonuclease by RecJ- and RecA-single-stranded DNA filament formation by RecFOR.

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Selected References

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  1. Al-Deib A. A., Mahdi A. A., Lloyd R. G. Modulation of recombination and DNA repair by the RecG and PriA helicases of Escherichia coli K-12. J Bacteriol. 1996 Dec;178(23):6782–6789. doi: 10.1128/jb.178.23.6782-6789.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Amundsen S. K., Neiman A. M., Thibodeaux S. M., Smith G. R. Genetic dissection of the biochemical activities of RecBCD enzyme. Genetics. 1990 Sep;126(1):25–40. doi: 10.1093/genetics/126.1.25. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. 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]
  4. Amundsen S. K., Taylor A. F., Smith G. R. The RecD subunit of the Escherichia coli RecBCD enzyme inhibits RecA loading, homologous recombination, and DNA repair. Proc Natl Acad Sci U S A. 2000 Jun 20;97(13):7399–7404. doi: 10.1073/pnas.130192397. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Anderson D. G., Churchill J. J., Kowalczykowski S. C. A single mutation, RecB(D1080A,) eliminates RecA protein loading but not Chi recognition by RecBCD enzyme. J Biol Chem. 1999 Sep 17;274(38):27139–27144. doi: 10.1074/jbc.274.38.27139. [DOI] [PubMed] [Google Scholar]
  6. Anderson D. G., Kowalczykowski S. C. The recombination hot spot chi is a regulatory element that switches the polarity of DNA degradation by the RecBCD enzyme. Genes Dev. 1997 Mar 1;11(5):571–581. doi: 10.1101/gad.11.5.571. [DOI] [PubMed] [Google Scholar]
  7. Anderson D. G., Kowalczykowski S. C. The translocating RecBCD enzyme stimulates recombination by directing RecA protein onto ssDNA in a chi-regulated manner. Cell. 1997 Jul 11;90(1):77–86. doi: 10.1016/s0092-8674(00)80315-3. [DOI] [PubMed] [Google Scholar]
  8. Arnold D. A., Kowalczykowski S. C. Facilitated loading of RecA protein is essential to recombination by RecBCD enzyme. J Biol Chem. 2000 Apr 21;275(16):12261–12265. doi: 10.1074/jbc.275.16.12261. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. Bork J. M., Cox M. M., Inman R. B. The RecOR proteins modulate RecA protein function at 5' ends of single-stranded DNA. EMBO J. 2001 Dec 17;20(24):7313–7322. doi: 10.1093/emboj/20.24.7313. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. 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]
  12. Churchill J. J., Anderson D. G., Kowalczykowski S. C. The RecBC enzyme loads RecA protein onto ssDNA asymmetrically and independently of chi, resulting in constitutive recombination activation. Genes Dev. 1999 Apr 1;13(7):901–911. doi: 10.1101/gad.13.7.901. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Clark A. J., Sandler S. J. Homologous genetic recombination: the pieces begin to fall into place. Crit Rev Microbiol. 1994;20(2):125–142. doi: 10.3109/10408419409113552. [DOI] [PubMed] [Google Scholar]
  14. Connelly J. C., de Leau E. S., Okely E. A., Leach D. R. Overexpression, purification, and characterization of the SbcCD protein from Escherichia coli. J Biol Chem. 1997 Aug 8;272(32):19819–19826. doi: 10.1074/jbc.272.32.19819. [DOI] [PubMed] [Google Scholar]
  15. Corrette-Bennett S. E., Lovett S. T. Enhancement of RecA strand-transfer activity by the RecJ exonuclease of Escherichia coli. J Biol Chem. 1995 Mar 24;270(12):6881–6885. doi: 10.1074/jbc.270.12.6881. [DOI] [PubMed] [Google Scholar]
  16. Cromie G. A., Connelly J. C., Leach D. R. Recombination at double-strand breaks and DNA ends: conserved mechanisms from phage to humans. Mol Cell. 2001 Dec;8(6):1163–1174. doi: 10.1016/s1097-2765(01)00419-1. [DOI] [PubMed] [Google Scholar]
  17. Cromie G. A., Leach D. R. Recombinational repair of chromosomal DNA double-strand breaks generated by a restriction endonuclease. Mol Microbiol. 2001 Aug;41(4):873–883. doi: 10.1046/j.1365-2958.2001.02553.x. [DOI] [PubMed] [Google Scholar]
  18. Ganesan A. K., Seawell P. C. The effect of lexA and recF mutations on post-replication repair and DNA synthesis in Escherichia coli K-12. Mol Gen Genet. 1975 Dec 1;141(3):189–205. doi: 10.1007/BF00341799. [DOI] [PubMed] [Google Scholar]
  19. Gibson F. P., Leach D. R., Lloyd R. G. Identification of sbcD mutations as cosuppressors of recBC that allow propagation of DNA palindromes in Escherichia coli K-12. J Bacteriol. 1992 Feb;174(4):1222–1228. doi: 10.1128/jb.174.4.1222-1228.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Harmon F. G., Kowalczykowski S. C. RecQ helicase, in concert with RecA and SSB proteins, initiates and disrupts DNA recombination. Genes Dev. 1998 Apr 15;12(8):1134–1144. doi: 10.1101/gad.12.8.1134. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. 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]
  22. Jockovich M. E., Myers R. S. Nuclease activity is essential for RecBCD recombination in Escherichia coli. Mol Microbiol. 2001 Aug;41(4):949–962. doi: 10.1046/j.1365-2958.2001.02573.x. [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. Recombinational repair of DNA damage in Escherichia coli and bacteriophage lambda. Microbiol Mol Biol Rev. 1999 Dec;63(4):751-813, table of contents. doi: 10.1128/mmbr.63.4.751-813.1999. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. LEHMAN I. R., NUSSBAUM A. L. THE DEOXYRIBONUCLEASES OF ESCHERICHIA COLI. V. ON THE SPECIFICITY OF EXONUCLEASE I (PHOSPHODIESTERASE). J Biol Chem. 1964 Aug;239:2628–2636. [PubMed] [Google Scholar]
  26. 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]
  27. Lloyd R. G., Porton M. C., Buckman C. Effect of recF, recJ, recN, recO and ruv mutations on ultraviolet survival and genetic recombination in a recD strain of Escherichia coli K12. Mol Gen Genet. 1988 May;212(2):317–324. doi: 10.1007/BF00334702. [DOI] [PubMed] [Google Scholar]
  28. Lovett S. T., Kolodner R. D. Identification and purification of a single-stranded-DNA-specific exonuclease encoded by the recJ gene of Escherichia coli. Proc Natl Acad Sci U S A. 1989 Apr;86(8):2627–2631. doi: 10.1073/pnas.86.8.2627. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Lovett S. T., Luisi-DeLuca C., Kolodner R. D. The genetic dependence of recombination in recD mutants of Escherichia coli. Genetics. 1988 Sep;120(1):37–45. doi: 10.1093/genetics/120.1.37. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Mahdi A. A., Lloyd R. G. Identification of the recR locus of Escherichia coli K-12 and analysis of its role in recombination and DNA repair. Mol Gen Genet. 1989 Apr;216(2-3):503–510. doi: 10.1007/BF00334397. [DOI] [PubMed] [Google Scholar]
  31. Marsić N., Roje S., Stojiljković I., Salaj-Smic E., Trgovcević Z. In vivo studies on the interaction of RecBCD enzyme and lambda Gam protein. J Bacteriol. 1993 Aug;175(15):4738–4743. doi: 10.1128/jb.175.15.4738-4743.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Mendonca V. M., Klepin H. D., Matson S. W. DNA helicases in recombination and repair: construction of a delta uvrD delta helD delta recQ mutant deficient in recombination and repair. J Bacteriol. 1995 Mar;177(5):1326–1335. doi: 10.1128/jb.177.5.1326-1335.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Muskavitch K. M., Linn S. A unified mechanism for the nuclease and unwinding activities of the recBC enzyme of Escherichia coli. J Biol Chem. 1982 Mar 10;257(5):2641–2648. [PubMed] [Google Scholar]
  34. Paskvan I., Salaj-Smic E., Ivancic-Baće I., Zahradka K., Trgovcević Z., Brcić-Kostić K. The genetic dependence of RecBCD-Gam mediated double strand end repair in Escherichia coli. FEMS Microbiol Lett. 2001 Dec 18;205(2):299–303. doi: 10.1111/j.1574-6968.2001.tb10964.x. [DOI] [PubMed] [Google Scholar]
  35. Rodenhuis Sjoerd, Bontenbal Marijke, Beex Louk V. A. M., Wagstaff John, Richel Dick J., Nooij Marianne A., Voest Emile E., Hupperets Pierre, van Tinteren Harm, Peterse Hans L. High-dose chemotherapy with hematopoietic stem-cell rescue for high-risk breast cancer. N Engl J Med. 2003 Jul 3;349(1):7–16. doi: 10.1056/NEJMoa022794. [DOI] [PubMed] [Google Scholar]
  36. Rosamond J., Telander K. M., Linn S. Modulation of the action of the recBC enzyme of Escherichia coli K-12 by Ca2+. J Biol Chem. 1979 Sep 10;254(17):8646–8652. [PubMed] [Google Scholar]
  37. Ryder L., Whitby M. C., Lloyd R. G. Mutation of recF, recJ, recO, recQ, or recR improves Hfr recombination in resolvase-deficient ruv recG strains of Escherichia coli. J Bacteriol. 1994 Mar;176(6):1570–1577. doi: 10.1128/jb.176.6.1570-1577.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. 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]
  39. Taylor A. F., Smith G. R. Regulation of homologous recombination: Chi inactivates RecBCD enzyme by disassembly of the three subunits. Genes Dev. 1999 Apr 1;13(7):890–900. doi: 10.1101/gad.13.7.890. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Umezu K., Kolodner R. D. Protein interactions in genetic recombination in Escherichia coli. Interactions involving RecO and RecR overcome the inhibition of RecA by single-stranded DNA-binding protein. J Biol Chem. 1994 Nov 25;269(47):30005–30013. [PubMed] [Google Scholar]
  41. Webb B. L., Cox M. M., Inman R. B. Recombinational DNA repair: the RecF and RecR proteins limit the extension of RecA filaments beyond single-strand DNA gaps. Cell. 1997 Oct 31;91(3):347–356. doi: 10.1016/s0092-8674(00)80418-3. [DOI] [PubMed] [Google Scholar]
  42. Yu M., Souaya J., Julin D. A. Identification of the nuclease active site in the multifunctional RecBCD enzyme by creation of a chimeric enzyme. J Mol Biol. 1998 Nov 6;283(4):797–808. doi: 10.1006/jmbi.1998.2127. [DOI] [PubMed] [Google Scholar]

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