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Rmi1 stimulates decatenation of double Holliday junctions during dissolution by Sgs1–Top3


A double Holliday junction (dHJ) is a central intermediate of homologous recombination that can be processed to yield crossover or non-crossover recombination products. To preserve genomic integrity, cells possess mechanisms to avoid crossing over. We show that Saccharomyces cerevisiae Sgs1 and Top3 proteins are sufficient to migrate and disentangle a dHJ to produce exclusively non-crossover recombination products, in a reaction termed “dissolution.” We show that Rmi1 stimulates dHJ dissolution at low Sgs1–Top3 protein concentrations, although it has no effect on the initial rate of Holliday junction (HJ) migration. Rmi1 serves to stimulate DNA decatenation, removing the last linkages between the repaired and template DNA molecules. Dissolution of a dHJ is a highly efficient and concerted alternative to nucleolytic resolution that prevents crossing over of chromosomes during recombinational DNA repair in mitotic cells and thereby contributes to genomic integrity.

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Figure 1: Sgs1 and Top3, stimulated by RPA, dissolve double Holliday junctions (dHJ) to yield non-crossover products.
Figure 2: Rmi1 stimulates a late step of dHJ dissolution catalyzed by Sgs1 and Top3.
Figure 3: Rmi1 greatly stimulates dissolution of DNA that contains dHJs separated by two topological links and that mimics a nearly dissolved dHJ.
Figure 4: Rmi1 promotes decatenation of kinetoplast DNA (kDNA) by Sgs1 and Top3.
Figure 5: Model for function of Sgs1–Top3–Rmi1 complex in the dissolution of double Holliday junctions (dHJs).


  1. Klein, H.L. & Symington, L.S. Breaking up just got easier to do. Cell 138, 20–22 (2009).

    Article  CAS  Google Scholar 

  2. Ira, G., Malkova, A., Liberi, G., Foiani, M. & Haber, J.E. Srs2 and Sgs1–Top3 suppress crossovers during double-strand break repair in yeast. Cell 115, 401–411 (2003).

    Article  CAS  Google Scholar 

  3. Heyer, W.D., Ehmsen, K.T. & Solinger, J.A. Holliday junctions in the eukaryotic nucleus: resolution in sight? Trends Biochem. Sci. 28, 548–557 (2003).

    Article  CAS  Google Scholar 

  4. Gangloff, S., McDonald, J.P., Bendixen, C., Arthur, L. & Rothstein, R. The yeast type I topoisomerase Top3 interacts with Sgs1, a DNA helicase homolog: a potential eukaryotic reverse gyrase. Mol. Cell. Biol. 14, 8391–8398 (1994).

    Article  CAS  Google Scholar 

  5. Wang, J.C. Cellular roles of DNA topoisomerases: a molecular perspective. Nat. Rev. Mol. Cell Biol. 3, 430–440 (2002).

    Article  CAS  Google Scholar 

  6. Wu, L. & Hickson, I.D. The Bloom's syndrome helicase suppresses crossing over during homologous recombination. Nature 426, 870–874 (2003).

    Article  CAS  Google Scholar 

  7. Chang, M. et al. RMI1/NCE4, a suppressor of genome instability, encodes a member of the RecQ helicase/Topo III complex. EMBO J. 24, 2024–2033 (2005).

    Article  CAS  Google Scholar 

  8. Mullen, J.R., Nallaseth, F.S., Lan, Y.Q., Slagle, C.E. & Brill, S.J. Yeast Rmi1/Nce4 controls genome stability as a subunit of the Sgs1–Top3 complex. Mol. Cell. Biol. 25, 4476–4487 (2005).

    Article  CAS  Google Scholar 

  9. Plank, J.L., Wu, J. & Hsieh, T.S. Topoisomerase IIIα and Bloom's helicase can resolve a mobile double Holliday junction substrate through convergent branch migration. Proc. Natl. Acad. Sci. USA 103, 11118–11123 (2006).

    Article  CAS  Google Scholar 

  10. Wu, L. et al. BLAP75/RMI1 promotes the BLM-dependent dissolution of homologous recombination intermediates. Proc. Natl. Acad. Sci. USA 103, 4068–4073 (2006).

    Article  CAS  Google Scholar 

  11. Bussen, W., Raynard, S., Busygina, V., Singh, A.K. & Sung, P. Holliday junction processing activity of the BLM–TopoIIIalpha–BLAP75 complex. J. Biol. Chem. 282, 31484–31492 (2007).

    Article  CAS  Google Scholar 

  12. Raynard, S., Bussen, W. & Sung, P. A double Holliday junction dissolvasome comprising BLM, topoisomerase IIIalpha, and BLAP75. J. Biol. Chem. 281, 13861–13864 (2006).

    Article  CAS  Google Scholar 

  13. Raynard, S. et al. Functional role of BLAP75 in BLM–topoisomerase IIIalpha-dependent Holliday junction processing. J. Biol. Chem. 283, 15701–15708 (2008).

    Article  CAS  Google Scholar 

  14. Cejka, P. & Kowalczykowski, S.C. The full-length Saccharomyces cerevisiae Sgs1 protein is a vigorous DNA helicase that preferentially unwinds Holliday junctions. J. Biol. Chem. 285, 8290–8301 (2010).

    Article  CAS  Google Scholar 

  15. Karow, J.K., Chakraverty, R.K. & Hickson, I.D. The Bloom's syndrome gene product is a 3′-5′ DNA helicase. J. Biol. Chem. 272, 30611–30614 (1997).

    Article  CAS  Google Scholar 

  16. Weinert, B.T. & Rio, D.C. DNA strand displacement, strand annealing and strand swapping by the Drosophila Bloom's syndrome helicase. Nucleic Acids Res (2007).

  17. Plank, J.L., Chu, S.H., Pohlhaus, J.R., Wilson-Sali, T. & Hsieh, T.S. Drosophila melanogaster topoisomerase IIIα preferentially relaxes a positively or negatively supercoiled bubble substrate and is essential during development. J. Biol. Chem. 280, 3564–3573 (2005).

    Article  CAS  Google Scholar 

  18. Hanai, R., Caron, P.R. & Wang, J.C. Human TOP3: a single-copy gene encoding DNA topoisomerase III. Proc. Natl. Acad. Sci. USA 93, 3653–3657 (1996).

    Article  CAS  Google Scholar 

  19. Fu, T.J., Tse-Dinh, Y.C. & Seeman, N.C. Holliday junction crossover topology. J. Mol. Biol. 236, 91–105 (1994).

    Article  CAS  Google Scholar 

  20. Plank, J.L. & Hsieh, T.S. A novel, topologically constrained DNA molecule containing a double Holliday junction: design, synthesis, and initial biochemical characterization. J. Biol. Chem. 281, 17510–17516 (2006).

    Article  CAS  Google Scholar 

  21. Plank, J. & Hsieh, T.S. Helicase-appended topoisomerases: new insight into the mechanism of directional strand transfer. J. Biol. Chem. 284, 30737–30741 (2009).

    Article  CAS  Google Scholar 

  22. Bell, L. & Byers, B. Separation of branched from linear DNA by two-dimensional gel electrophoresis. Anal. Biochem. 130, 527–535 (1983).

    Article  CAS  Google Scholar 

  23. Chen, C.F. & Brill, S.J. Binding and activation of DNA topoisomerase III by the Rmi1 subunit. J. Biol. Chem. 282, 28971–28979 (2007).

    Article  CAS  Google Scholar 

  24. Shapiro, T.A. & Englund, P.T. The structure and replication of kinetoplast DNA. Annu. Rev. Microbiol. 49, 117–143 (1995).

    Article  CAS  Google Scholar 

  25. Wang, J.C. DNA topoisomerases: Why so many? J. Biol. Chem. 266, 6659–6662 (1991).

    CAS  PubMed  Google Scholar 

  26. Bzymek, M., Thayer, N.H., Oh, S.D., Kleckner, N. & Hunter, N. Double Holliday junctions are intermediates of DNA break repair. Nature 464, 937–941 (2010).

    Article  CAS  Google Scholar 

  27. Chaganti, R.S., Schonberg, S. & German, J. A manyfold increase in sister chromatid exchanges in Bloom's syndrome lymphocytes. Proc. Natl. Acad. Sci. USA 71, 4508–4512 (1974).

    Article  CAS  Google Scholar 

  28. Bachrati, C.Z., Borts, R.H. & Hickson, I.D. Mobile D-loops are a preferred substrate for the Bloom's syndrome helicase. Nucleic Acids Res. 34, 2269–2279 (2006).

    Article  CAS  Google Scholar 

  29. German, J. Bloom syndrome: a mendelian prototype of somatic mutational disease. Medicine (Baltimore) 72, 393–406 (1993).

    Article  CAS  Google Scholar 

  30. Kantake, N., Sugiyama, T., Kolodner, R.D. & Kowalczykowski, S.C. The recombination-deficient mutant RPA (rfa1-t11) is displaced slowly from single-stranded DNA by Rad51 protein. J. Biol. Chem. 278, 23410–23417 (2003).

    Article  CAS  Google Scholar 

  31. Harmon, F.G., DiGate, R.J. & Kowalczykowski, S.C. RecQ helicase and topoisomerase III comprise a novel DNA strand passage function: a conserved mechanism for control of DNA recombination. Mol. Cell 3, 611–620 (1999).

    Article  CAS  Google Scholar 

  32. Harmon, F.G. & Kowalczykowski, S.C. RecQ helicase, in concert with RecA and SSB proteins, initiates and disrupts DNA recombination. Genes Dev. 12, 1134–1144 (1998).

    Article  CAS  Google Scholar 

  33. Gaillard, C. & Strauss, F. Ethanol precipitation of DNA with linear polyacrylamide as carrier. Nucl. Acids Res. 18, 378 (1990).

    Article  CAS  Google Scholar 

  34. Bachrati, C.Z. & Hickson, I.D. Dissolution of double Holliday junctions by the concerted action of BLM and topoisomerase IIIalpha. Methods Mol. Biol. 582, 91–102 (2009).

    Article  CAS  Google Scholar 

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We thank P. Janscak (University of Zurich), X. Veaute (Institute of Cellular and Molecular Radiation Biology, France), Tao-shih Hsieh (Duke University), B. Rad and A. Nimonkar (both University of California, Davis) for purified proteins and the members of the Kowalczykowski laboratory and W.D. Heyer (University of California, Davis) for their comments on the manuscript. This work was supported by the following grants: Swiss National Science Foundation Fellowship PA00A-115375 (P.C.), National Cancer Institute Award T32CA108459 (J.L.P.), Cancer Research UK (C.Z.B. and I.D.H.) and US National Institutes of Health grants GM-41347 and GM-62653 (S.C.K.).

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P.C., J.L.P. and S.C.K. conceived the general ideas for this study. All authors planned experiments and interpreted data; J.L.P. prepared DHJS; P.C. and C.Z.B. performed experiments. P.C., J.L.P. and S.C.K. wrote the manuscript; and all authors provided editorial input.

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Correspondence to Stephen C Kowalczykowski.

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Cejka, P., Plank, J., Bachrati, C. et al. Rmi1 stimulates decatenation of double Holliday junctions during dissolution by Sgs1–Top3. Nat Struct Mol Biol 17, 1377–1382 (2010).

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