Skip to main content
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
. 1984 May;81(9):2757–2761. doi: 10.1073/pnas.81.9.2757

Mechanism of the concerted action of recA protein and helix-destabilizing proteins in homologous recombination.

K Muniyappa, S L Shaner, S S Tsang, C M Radding
PMCID: PMC345149  PMID: 6326142

Abstract

Secondary structure in single-stranded DNA impedes the presynaptic association of recA protein and consequently blocks the formation of joint molecules as evidenced by effects of temperature, nucleotide sequence, and ionic conditions. Escherichia coli single-strand-binding protein eliminates sequence-specific "cold spots" by removing folds even from sites of strong secondary structure. Thus, destabilization of secondary structure in single-stranded DNA is critical for the action of recA protein, whereas specific interactions directly between helix-destabilizing proteins and recA protein are unimportant.

Full text

PDF
2757

Images in this article

Selected References

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

  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. Beattie K. L., Wiegand R. C., Radding C. M. Uptake of homologous single-stranded fragments by superhelical DNA. II. Characterization of the reaction. J Mol Biol. 1977 Nov;116(4):783–803. doi: 10.1016/0022-2836(77)90271-6. [DOI] [PubMed] [Google Scholar]
  3. Bianchi M., DasGupta C., Radding C. M. Synapsis and the formation of paranemic joints by E. coli RecA protein. Cell. 1983 Oct;34(3):931–939. doi: 10.1016/0092-8674(83)90550-0. [DOI] [PubMed] [Google Scholar]
  4. Blakesley R. W., Dodgson J. B., Nes I. F., Wells R. D. Duplex regions in "single-stranded" phiX174 DNA are cleaved by a restriction endonuclease from Haemophilus aegyptius. J Biol Chem. 1977 Oct 25;252(20):7300–7306. [PubMed] [Google Scholar]
  5. 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]
  6. Chrysogelos S., Griffith J. Escherichia coli single-strand binding protein organizes single-stranded DNA in nucleosome-like units. Proc Natl Acad Sci U S A. 1982 Oct;79(19):5803–5807. doi: 10.1073/pnas.79.19.5803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Cox M. M., Lehman I. R. Directionality and polarity in recA protein-promoted branch migration. Proc Natl Acad Sci U S A. 1981 Oct;78(10):6018–6022. doi: 10.1073/pnas.78.10.6018. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Cox M. M., Lehman I. R. recA protein-promoted DNA strand exchange. Stable complexes of recA protein and single-stranded DNA formed in the presence of ATP and single-stranded DNA binding protein. J Biol Chem. 1982 Jul 25;257(14):8523–8532. [PubMed] [Google Scholar]
  9. Craig N. L., Roberts J. W. E. coli recA protein-directed cleavage of phage lambda repressor requires polynucleotide. Nature. 1980 Jan 3;283(5742):26–30. doi: 10.1038/283026a0. [DOI] [PubMed] [Google Scholar]
  10. Cunningham R. P., DasGupta C., Shibata T., Radding C. M. Homologous pairing in genetic recombination: recA protein makes joint molecules of gapped circular DNA and closed circular DNA. Cell. 1980 May;20(1):223–235. doi: 10.1016/0092-8674(80)90250-0. [DOI] [PubMed] [Google Scholar]
  11. Dunn K., Chrysogelos S., Griffith J. Electron microscopic visualization of recA-DNA filaments: evidence for a cyclic extension of duplex DNA. Cell. 1982 Apr;28(4):757–765. doi: 10.1016/0092-8674(82)90055-1. [DOI] [PubMed] [Google Scholar]
  12. Flory J., Radding C. M. Visualization of recA protein and its association with DNA: a priming effect of single-strand-binding protein. Cell. 1982 Apr;28(4):747–756. doi: 10.1016/0092-8674(82)90054-x. [DOI] [PubMed] [Google Scholar]
  13. Glassberg J., Meyer R. R., Kornberg A. Mutant single-strand binding protein of Escherichia coli: genetic and physiological characterization. J Bacteriol. 1979 Oct;140(1):14–19. doi: 10.1128/jb.140.1.14-19.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Golub E. I., Low K. B. Indirect stimulation of genetic recombination. Proc Natl Acad Sci U S A. 1983 Mar;80(5):1401–1405. doi: 10.1073/pnas.80.5.1401. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gonda D. K., Radding C. M. By searching processively RecA protein pairs DNA molecules that share a limited stretch of homology. Cell. 1983 Sep;34(2):647–654. doi: 10.1016/0092-8674(83)90397-5. [DOI] [PubMed] [Google Scholar]
  16. Kahn R., Cunningham R. P., DasGupta C., Radding C. M. Polarity of heteroduplex formation promoted by Escherichia coli recA protein. Proc Natl Acad Sci U S A. 1981 Aug;78(8):4786–4790. doi: 10.1073/pnas.78.8.4786. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Kuhnlein U., Penhoet E. E., Linn S. An altered apurinic DNA endonuclease activity in group A and group D xeroderma pigmentosum fibroblasts. Proc Natl Acad Sci U S A. 1976 Apr;73(4):1169–1173. doi: 10.1073/pnas.73.4.1169. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Lieberman H. B., Witkin E. M. DNA degradation, UV sensitivity and SOS-mediated mutagenesis in strains of Escherichia coli deficient in single-strand DNA binding protein: effects of mutations and treatments that alter levels of Exonuclease V or recA protein. Mol Gen Genet. 1983;190(1):92–100. doi: 10.1007/BF00330329. [DOI] [PubMed] [Google Scholar]
  19. Low R. L., Shlomai J., Kornberg A. Protein n, a primosomal DNA replication protein of Escherichia coli. Purification and characterization. J Biol Chem. 1982 Jun 10;257(11):6242–6250. [PubMed] [Google Scholar]
  20. 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]
  21. Radding C. M., Flory J., Wu A., Kahn R., DasGupta C., Gonda D., Bianchi M., Tsang S. S. Three phases in homologous pairing: polymerization of recA protein on single-stranded DNA, synapsis, and polar strand exchange. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 2):821–828. doi: 10.1101/sqb.1983.047.01.094. [DOI] [PubMed] [Google Scholar]
  22. Radding C. M. Homologous pairing and strand exchange in genetic recombination. Annu Rev Genet. 1982;16:405–437. doi: 10.1146/annurev.ge.16.120182.002201. [DOI] [PubMed] [Google Scholar]
  23. Resnick J., Sussman R. Escherichia coli single-strand DNA binding protein from wild type and lexC113 mutant affects in vitro proteolytic cleavage of phage lambda repressor. Proc Natl Acad Sci U S A. 1982 May;79(9):2832–2835. doi: 10.1073/pnas.79.9.2832. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Shibata T., Cunningham R. P., Radding C. M. Homologous pairing in genetic recombination. Purification and characterization of Escherichia coli recA protein. J Biol Chem. 1981 Jul 25;256(14):7557–7564. [PubMed] [Google Scholar]
  25. 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]
  26. Shibata T., DasGupta C., Cunningham R. P., Williams J. G., Osber L., Radding C. M. Homologous pairing in genetic recombination. The pairing reaction catalyzed by Escherichia coli recA protein. J Biol Chem. 1981 Jul 25;256(14):7565–7572. [PubMed] [Google Scholar]
  27. Soltis D. A., Lehman I. R. recA protein promoted DNA strand exchange. J Biol Chem. 1983 May 25;258(10):6073–6077. [PubMed] [Google Scholar]
  28. Studier F. W. Conformational changes of single-stranded DNA. J Mol Biol. 1969 Apr;41(2):189–197. doi: 10.1016/0022-2836(69)90384-2. [DOI] [PubMed] [Google Scholar]
  29. West S. C., Cassuto E., Howard-Flanders P. Heteroduplex formation by recA protein: polarity of strand exchanges. Proc Natl Acad Sci U S A. 1981 Oct;78(10):6149–6153. doi: 10.1073/pnas.78.10.6149. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. West S. C., Cassuto E., Howard-Flanders P. Role of SSB protein in RecA promoted branch migration reactions. Mol Gen Genet. 1982;186(3):333–338. doi: 10.1007/BF00729451. [DOI] [PubMed] [Google Scholar]
  31. Whittier R. F., Chase J. W. DNA repair properties of Escherichia coli tif-1, recAo281 and lexA1 strains deficient in single-strand DNA binding protein. Mol Gen Genet. 1983;190(1):101–111. doi: 10.1007/BF00330330. [DOI] [PubMed] [Google Scholar]
  32. Wu A. M., Bianchi M., DasGupta C., Radding C. M. Unwinding associated with synapsis of DNA molecules by recA protein. Proc Natl Acad Sci U S A. 1983 Mar;80(5):1256–1260. doi: 10.1073/pnas.80.5.1256. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. van Wezenbeek P. M., Hulsebos T. J., Schoenmakers J. G. Nucleotide sequence of the filamentous bacteriophage M13 DNA genome: comparison with phage fd. Gene. 1980 Oct;11(1-2):129–148. doi: 10.1016/0378-1119(80)90093-1. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES