Skip to main content
NCBI home page
Journal of Virology logoLink to Journal of Virology
. 1983 Mar;45(3):971–976. doi: 10.1128/jvi.45.3.971-976.1983

Role of R loops in recA-independent homologous recombination of bacteriophage lambda.

T Matsumoto, H Ikeda
PMCID: PMC256503  PMID: 6220161

Abstract

We have previously shown that the DNA-dependent RNA polymerase of Escherichia coli can promote homologous recombination of bacteriophage lambda independently of the recA function. To detect this recombination, we jointly infected the cells with a pair of lambda phages in the presence of chloramphenicol, extracted intracellular lambda DNA molecules, packaged them in vitro, and measured the number of resulting recombinant phage particles. We showed that the recombination of DNA molecules takes place in vitro after extraction of DNA from the cells. We fractionated recombinogenic forms of intracellular lambda DNA and showed that they carry RNA. These and other results suggest that the R (RNA) loop structures, generated by transcription within the cells, promote homologous recombination in vitro. We discuss possible mechanisms of this recombination and compare those with the other forms of general recombination.

Full text

PDF
971

Selected References

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

  1. Baas P. D., Keegstra W., Teertstra W. R., Jansz H. S. R-loops in bacteriophage phiX174 RF DNA. J Mol Biol. 1978 Oct 25;125(2):187–205. doi: 10.1016/0022-2836(78)90344-3. [DOI] [PubMed] [Google Scholar]
  2. Bick M. D., Lee C. S., Thomas C. A., Jr Local destabilization of DNA during transcription. J Mol Biol. 1972 Oct 28;71(1):1–9. doi: 10.1016/0022-2836(72)90395-6. [DOI] [PubMed] [Google Scholar]
  3. Chattoraj D. K., Stahl F. W. Evidence of RNA in D loops of intracellular lambda DNA. Proc Natl Acad Sci U S A. 1980 Apr;77(4):2153–2157. doi: 10.1073/pnas.77.4.2153. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Cunningham R. P., Shibata T., DasGupta C., Radding C. M. Single strands induce recA protein to unwind duplex DNA for homologous pairing. Nature. 1979 Sep 20;281(5728):191–195. doi: 10.1038/281191a0. [DOI] [PubMed] [Google Scholar]
  5. DasGupta C., Shibata T., Cunningham R. P., Radding C. M. The topology of homologous pairing promoted by RecA protein. Cell. 1980 Nov;22(2 Pt 2):437–446. doi: 10.1016/0092-8674(80)90354-2. [DOI] [PubMed] [Google Scholar]
  6. Echolas H., Gingery R. Mutants of bacteriophage lambda defective in vegetative genetic recombination. J Mol Biol. 1968 Jul 14;34(2):239–249. doi: 10.1016/0022-2836(68)90249-0. [DOI] [PubMed] [Google Scholar]
  7. Echols H., Gingery R., Moore L. Integrative recombination function of bacteriophage lambda: evidence for a site-specific recombination enzyme. J Mol Biol. 1968 Jul 14;34(2):251–260. doi: 10.1016/0022-2836(68)90250-7. [DOI] [PubMed] [Google Scholar]
  8. Hsieh T., Wang J. C. Physiochemical studies on interactions between DNA and RNA polymerase. Ultraviolet absorption measurements. Nucleic Acids Res. 1978 Sep;5(9):3337–3345. doi: 10.1093/nar/5.9.3337. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Ikeda H., Kobayashi I. Involvement of DNA-dependent RNA polymerase in a recA-independent pathway of genetic recombination in Escheria coli. Proc Natl Acad Sci U S A. 1977 Sep;74(9):3932–3936. doi: 10.1073/pnas.74.9.3932. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Ikeda H., Matsumoto T. Transcription promotes recA-independent recombination mediated by DNA-dependent RNA polymerase in Escherichia coli. Proc Natl Acad Sci U S A. 1979 Sep;76(9):4571–4575. doi: 10.1073/pnas.76.9.4571. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Ikeda H., Tomizawa J. I. Transducing fragments in generalized transduction by phage P1. I. Molecular origin of the fragments. J Mol Biol. 1965 Nov;14(1):85–109. doi: 10.1016/s0022-2836(65)80232-7. [DOI] [PubMed] [Google Scholar]
  12. Kobayashi I., Ikeda H. Formation of recombinant DNA of bacteriophage lambda by recA function of Escherichia coli without duplication, transcription, translation, and maturation. Mol Gen Genet. 1977 Jun 24;153(3):237–245. doi: 10.1007/BF00431589. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. Melnikova A. F., Beabealashvilli R., Mirzabekov A. D. A study of unwinding of DNA and shielding of the DNA grooves by RNA polymerase by using methylation with dimethylsulphate. Eur J Biochem. 1978 Mar;84(1):301–309. doi: 10.1111/j.1432-1033.1978.tb12169.x. [DOI] [PubMed] [Google Scholar]
  15. Shibata T., Cunningham R. P., DasGupta C., Radding C. M. Homologous pairing in genetic recombination: complexes of recA protein and DNA. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5100–5104. doi: 10.1073/pnas.76.10.5100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Siebenlist U. RNA polymerase unwinds an 11-base pair segment of a phage T7 promoter. Nature. 1979 Jun 14;279(5714):651–652. doi: 10.1038/279651a0. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. Sternberg N., Tiemeier D., Enquist L. In vitro packaging of a lambda Dam vector containing EcoRI DNA fragments of Escherichia coli and phage P1. Gene. 1977 May;1(3-4):255–280. doi: 10.1016/0378-1119(77)90049-x. [DOI] [PubMed] [Google Scholar]
  19. Weil J., Signer E. R. Recombination in bacteriophage lambda. II. Site-specific recombination promoted by the integration system. J Mol Biol. 1968 Jul 14;34(2):273–279. doi: 10.1016/0022-2836(68)90252-0. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Virology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES