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Rad54 protein promotes branch migration of Holliday junctions

Nature volume 442, pages 590–593 (2006)Cite this article

Abstract

Homologous recombination has a crucial function in the repair of DNA double-strand breaks and in faithful chromosome segregation1,2,3. The mechanism of homologous recombination involves the search for homology and invasion of the ends of a broken DNA molecule into homologous duplex DNA to form a cross-stranded structure, a Holliday junction (HJ)4,5,6,7. A HJ is able to undergo branch migration along DNA, generating increasing or decreasing lengths of heteroduplex. In both prokaryotes and eukaryotes, the physical evidence for HJs, the key intermediate in homologous recombination, was provided by electron microscopy8. In bacteria there are specialized enzymes that promote branch migration of HJs7. However, in eukaryotes the identity of homologous recombination branch-migration protein(s) has remained elusive. Here we show that Rad54, a Swi2/Snf2 protein9, binds HJ-like structures with high specificity and promotes their bidirectional branch migration in an ATPase-dependent manner. The activity seemed to be conserved in human and yeast Rad54 orthologues. In vitro, Rad54 has been shown to stimulate DNA pairing of Rad51, a key homologous recombination protein10,11,12. However, genetic data indicate that Rad54 protein might also act at later stages of homologous recombination, after Rad51 (ref. 13). Novel DNA branch-migration activity is fully consistent with this late homologous recombination function of Rad54 protein.

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Figure 1: hRad54 protein binds preferentially to branched DNA molecules.
Figure 2: Rad54 promotes an ATPase-dependent BM of synthetic PX junction DNA.
Figure 3: Rad54 promotes BM of synthetic four-way HJs (X junctions).
Figure 4: hRad54 protein catalyses BM of joint molecules (α-structures) generated by hRad51 in four-stranded DNA exchange.

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References

  1. Krogh, B. O. & Symington, L. S. Recombination proteins in yeast. Annu. Rev. Genet. 38, 233–271 (2004)

    Article  CAS  Google Scholar 

  2. Pα̂ques, F. & Haber, J. E. Multiple pathways of recombination induced by double-strand breaks in Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 63, 349–404 (1999)

    Google Scholar 

  3. Wyman, C., Ristic, D. & Kanaar, R. Homologous recombination-mediated double-strand break repair. DNA Repair (Amst.) 3, 827–833 (2004)

    Article  CAS  Google Scholar 

  4. Holliday, R. A mechanism for gene conversion in fungi. Genet. Res. 5, 282–304 (1964)

    Article  Google Scholar 

  5. Sung, P., Krejci, L., Van Komen, S. & Sehorn, M. G. Rad51 recombinase and recombination mediators. J. Biol. Chem. 278, 42729–42732 (2003)

    Article  CAS  Google Scholar 

  6. Bianco, P. R., Tracy, R. B. & Kowalczykowski, S. C. DNA strand exchange proteins: a biochemical and physical comparison. Front. Biosci. 3, D570–D603 (1998)

    Article  CAS  Google Scholar 

  7. Liu, Y. & West, S. C. Happy Hollidays: 40th anniversary of the Holliday junction. Nature Rev. Mol. Cell Biol. 5, 937–944 (2004)

    Article  CAS  Google Scholar 

  8. Dressler, D. & Potter, H. Molecular mechanisms in genetic recombination. Annu. Rev. Biochem. 51, 727–761 (1982)

    Article  CAS  Google Scholar 

  9. Thoma, N. H. et al. Structure of the SWI2/SNF2 chromatin-remodeling domain of eukaryotic Rad54. Nature Struct. Mol. Biol. 12, 350–356 (2005)

    Article  Google Scholar 

  10. Petukhova, G., Stratton, S. & Sung, P. Catalysis of homologous DNA pairing by yeast Rad51 and Rad54 proteins. Nature 393, 91–94 (1998)

    Article  ADS  CAS  Google Scholar 

  11. Mazin, A. V., Bornarth, C. J., Solinger, J. A., Heyer, W. D. & Kowalczykowski, S. C. Rad54 protein is targeted to pairing loci by the Rad51 nucleoprotein filament. Mol. Cell 6, 583–592 (2000)

    Article  CAS  Google Scholar 

  12. Mazina, O. M. & Mazin, A. V. Human Rad54 protein stimulates DNA strand exchange activity of hRad51 protein in the presence of Ca2+. J. Biol. Chem. 279, 52042–52051 (2004)

    Article  CAS  Google Scholar 

  13. Kim, P. M., Paffett, K. S., Solinger, J. A., Heyer, W. D. & Nickoloff, J. A. Spontaneous and double-strand break-induced recombination, and gene conversion tract lengths, are differentially affected by overexpression of wild-type or ATPase-defective yeast Rad54. Nucleic Acids Res. 30, 2727–2735 (2002)

    Article  CAS  Google Scholar 

  14. Essers, J. et al. Disruption of mouse RAD54 reduces ionizing radiation resistance and homologous recombination. Cell 89, 195–204 (1997)

    Article  CAS  Google Scholar 

  15. Suslova, N. G. & Zakharov, I. A. Genetic control of radiosensitivity in yeast, VII. Identification of the genes determining the sensitivity to X-rays. Genetika 6, 158–169 (1970)

    Google Scholar 

  16. Ristic, D., Wyman, C., Paulusma, C. & Kanaar, R. The architecture of the human Rad54–DNA complex provides evidence for protein translocation along DNA. Proc. Natl Acad. Sci. USA 98, 8454–8460 (2001)

    Article  ADS  CAS  Google Scholar 

  17. Jaskelioff, M., Van Komen, S., Krebs, J. E., Sung, P. & Peterson, C. L. Rad54p is a chromatin remodeling enzyme required for heteroduplex DNA joint formation with chromatin. J. Biol. Chem. 278, 9212–9218 (2003)

    Article  CAS  Google Scholar 

  18. Parsons, C. A., Tsaneva, I., Lloyd, R. G. & West, S. C. Interaction of Escherichia coli RuvA and RuvB proteins with synthetic Holliday junctions. Proc. Natl Acad. Sci. USA 89, 5452–5456 (1992)

    Article  ADS  CAS  Google Scholar 

  19. Swagemakers, S. M., Essers, J., de Wit, J., Hoeijmakers, J. H. & Kanaar, R. The human RAD54 recombinational DNA repair protein is a double-stranded DNA-dependent ATPase. J. Biol. Chem. 273, 28292–28297 (1998)

    Article  CAS  Google Scholar 

  20. Panyutin, I. G. & Hsieh, P. Formation of a single base mismatch impedes spontaneous DNA branch migration. J. Mol. Biol. 230, 413–424 (1993)

    Article  CAS  Google Scholar 

  21. Tsaneva, I. R., Muller, B. & West, S. C. ATP-dependent branch migration of Holliday junctions promoted by the RuvA and RuvB proteins of E. coli. Cell 69, 1171–1180 (1992)

    Article  CAS  Google Scholar 

  22. West, S. C. Processing of recombination intermediates by the RuvABC proteins. Annu. Rev. Genet. 31, 213–244 (1997)

    Article  CAS  Google Scholar 

  23. Eggleston, A. K., Mitchell, A. H. & West, S. C. In vitro reconstitution of the late steps of genetic recombination in E. coli. Cell 89, 607–617 (1997)

    Article  CAS  Google Scholar 

  24. Lusser, A. & Kadonaga, J. T. Chromatin remodeling by ATP-dependent molecular machines. Bioessays 25, 1192–1200 (2003)

    Article  CAS  Google Scholar 

  25. van Brabant, A. J. et al. Binding and melting of D-loops by the Bloom syndrome helicase. Biochemistry 39, 14617–14625 (2000)

    Article  CAS  Google Scholar 

  26. Constantinou, A., Davies, A. A. & West, S. C. Branch migration and Holliday junction resolution catalyzed by activities from mammalian cells. Cell 104, 259–268 (2001)

    Article  CAS  Google Scholar 

  27. Liu, Y., Masson, J. Y., Shah, R., O'Regan, P. & West, S. C. RAD51C is required for Holliday junction processing in mammalian cells. Science 303, 243–246 (2004)

    Article  ADS  CAS  Google Scholar 

  28. Interthal, H. & Heyer, W. D. MUS81 encodes a novel helix–hairpin–helix protein involved in the response to UV- and methylation-induced DNA damage in Saccharomyces cerevisiae. Mol. Gen. Genet. 263, 812–827 (2000)

    Article  CAS  Google Scholar 

  29. Shinohara, M. et al. Characterization of the roles of the Saccharomyces cerevisiae RAD54 gene and a homologue of RAD54, RDH54/TID1, in mitosis and meiosis. Genetics 147, 1545–1556 (1997)

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Bugreev, D. V. & Mazin, A. V. Ca2+ activates human homologous recombination protein Rad51 by modulating its ATPase activity. Proc. Natl Acad. Sci. USA 101, 9988–9993 (2004)

    Article  ADS  CAS  Google Scholar 

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Acknowledgements

We thank P. Sung and M. Wold for hRad51 and hRPA expression vectors; S. Kowalczykowski, M. Spies and A. Alexeev for RecA, yRad51 and yRad54; J. Kadonaga for ISWI; G. Schnitzler and N. Ulyanova for hSWI/SNF; M. Bouchard and A. Kuzminov for comments and discussion. This work was supported by an NIH grant to A.V.M.

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Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Pennsylvania, 19102-1192, Philadelphia, USA

    Dmitry V. Bugreev, Olga M. Mazina & Alexander V. Mazin

  2. Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Science, 630090, Novosibirsk, Russia

    Dmitry V. Bugreev

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Correspondence to Alexander V. Mazin.

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Bugreev, D., Mazina, O. & Mazin, A. Rad54 protein promotes branch migration of Holliday junctions. Nature 442, 590–593 (2006). https://doi.org/10.1038/nature04889

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