Yeast Rad54 Promotes Rad51-dependent Homologous DNA Pairing via ATP Hydrolysis-driven Change in DNA Double Helix Conformation

Abstract

Saccharomyces cerevisiae RAD54 gene functions in the formation of heteroduplex DNA, a key intermediate in recombination processes. Rad54 is monomeric in solution, but forms a dimer/oligomer on DNA. Rad54 dimer/oligomer alters the conformation of the DNA double helix in an ATP-dependent manner, as revealed by a change in the DNA linking number in a topoisomerase I-linked reaction. DNA conformational alteration does not occur in the presence of non-hydrolyzable ATP analogues, nor when mutant rad54 proteins defective in ATP hydrolysis replace Rad54. Accordingly, the Rad54 ATPase activity is shown to be required for biological functionin vivo and for promoting Rad51-mediated homologous DNA pairing in vitro. Taken together, the results are consistent with a model in which a Rad54 dimer/oligomer promotes nascent heteroduplex joint formation via a specific interaction with Rad51 protein and an ability to transiently unwind duplex DNA. Saccharomyces cerevisiae RAD54 gene functions in the formation of heteroduplex DNA, a key intermediate in recombination processes. Rad54 is monomeric in solution, but forms a dimer/oligomer on DNA. Rad54 dimer/oligomer alters the conformation of the DNA double helix in an ATP-dependent manner, as revealed by a change in the DNA linking number in a topoisomerase I-linked reaction. DNA conformational alteration does not occur in the presence of non-hydrolyzable ATP analogues, nor when mutant rad54 proteins defective in ATP hydrolysis replace Rad54. Accordingly, the Rad54 ATPase activity is shown to be required for biological functionin vivo and for promoting Rad51-mediated homologous DNA pairing in vitro. Taken together, the results are consistent with a model in which a Rad54 dimer/oligomer promotes nascent heteroduplex joint formation via a specific interaction with Rad51 protein and an ability to transiently unwind duplex DNA. Saccharomyces cerevisiae genes of the RAD52epistasis group, viz, RAD50, RAD51, RAD52, RAD54, RAD55, RAD57, RAD59, RDH54/TID1, MRE11, and XRS2, are required for genetic recombination and DNA double-strand break repair by recombination. Since genetic recombination is indispensable for the disjunction of homologous chromosomal pairs during meiosis I, mutational inactivation of the RAD52 group genes engenders severe meiotic defects, manifest as a failure to sporulate and spore inviability (1Bai Y. Symington L.S. Genes Dev. 1996; 10: 2025-2037Crossref PubMed Scopus (215) Google Scholar, 2Game J.C. Semin. Cancer Biol. 1993; 4: 73-83PubMed Google Scholar, 3Klein H. Genetics. 1997; 147: 1533-1543Crossref PubMed Google Scholar, 4Petes T.D. Malone R.E. Symington L.S. Broach J.R. Jones E.W. Pringle J.R. The Molecular and Cellular Biology of the Yeast Saccharomyces: Genome Dynamics, Protein Synthesis, and Energetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY1991: 407-521Google Scholar, 5Shinohara M. Shita-Yamaguchi E. Buerstedde J.M. Shinagawa H. Ogawa H. Shinohara A. Genetics. 1997; 147: 1545-1556Crossref PubMed Google Scholar). The results from recent cloning studies have revealed a remarkable degree of conservation of the RAD52group genes among eukaryotes, from yeast to humans. A conceptual model concerning the mechanism of homologous recombination has been formulated based on genetic studies in S. cerevisiae (6Szostak J.W. Orr-Weaver T.L. Rothstein R.J. Cell. 1983; 33: 25-35Abstract Full Text PDF PubMed Scopus (1748) Google Scholar). When S. cerevisiae cells enter meiosis, DNA double-strand breaks are formed at various chromosomal “hot spots” that exhibit a propensity to recombine. Subsequent to break formation, unidirectional nucleolytic end-processing of the break yields 3′ ssDNA 1The abbreviations used are:ssDNAsingle-stranded DNAdsDNAdouble-stranded DNAMMSmethyl methanesulfonateDTTdithiothreitolBSAbovine serum albuminMOPS4-morpholinepropanesulfonic acidATPγSadenosine 5′-O-(thiotriphosphate)BMHbis-maleimidohexane1The abbreviations used are:ssDNAsingle-stranded DNAdsDNAdouble-stranded DNAMMSmethyl methanesulfonateDTTdithiothreitolBSAbovine serum albuminMOPS4-morpholinepropanesulfonic acidATPγSadenosine 5′-O-(thiotriphosphate)BMHbis-maleimidohexane tails of a considerable length (7Cao L. Alani E. Kleckner N. Cell. 1990; 61: 1089-1101Abstract Full Text PDF PubMed Scopus (533) Google Scholar, 8Sun H. Treco D. Szostak J.W. Cell. 1991; 64: 1155-1161Abstract Full Text PDF PubMed Scopus (423) Google Scholar). It is believed that nucleation of various recombination factors onto the ssDNA tails gives rise to a nucleoprotein complex that has the ability to conduct a search to locate a DNA homolog and to invade the homolog to form heteroduplex DNA. Concurrent and subsequent events include DNA synthesis to replace the genetic information eliminated during double-strand break processing, resolution of the DNA intermediates, and DNA ligation to complete the recombination process. The repair of DNA double-strand breaks induced by ionizing radiation and radiomimetic chemicals very likely proceeds through the same mechanistic route, as the repair process shares the same requirement for the RAD52 epistasis group genes. single-stranded DNA double-stranded DNA methyl methanesulfonate dithiothreitol bovine serum albumin 4-morpholinepropanesulfonic acid adenosine 5′-O-(thiotriphosphate) bis-maleimidohexane single-stranded DNA double-stranded DNA methyl methanesulfonate dithiothreitol bovine serum albumin 4-morpholinepropanesulfonic acid adenosine 5′-O-(thiotriphosphate) bis-maleimidohexane Extensive genetic evidence has indicated that the nucleolytic end-processing of DNA double-strand breaks during recombination processes is on the RAD50, MRE11, genes. The protein from yeast M. Y. H. PubMed Scopus Google Scholar, S. J.R. Symington L.S. Cell. Biol. PubMed Scopus Google Scholar, H. Ogawa H. Ogawa Cell. Full Text Full Text PDF PubMed Scopus Google and M. Cell. Full Text Full Text PDF PubMed Scopus Google and a protein complex Biol. Full Text Full Text PDF PubMed Scopus Google of the and the of the gene in H. M. J.R. L. Cell. Full Text Full Text PDF PubMed Scopus Google Scholar, M. E. M. M. A. A. Cell. Full Text Full Text PDF PubMed Scopus Google have ssDNA and specific 3′ to It has been that the complex functions with a DNA to the 3′ ssDNA tails to form during recombination processes M. Y. H. PubMed Scopus Google Scholar, S. J.R. Symington L.S. Cell. Biol. PubMed Scopus Google Scholar, H. Ogawa H. Ogawa Cell. Full Text Full Text PDF PubMed Scopus Google Scholar, Biol. Full Text Full Text PDF PubMed Scopus Google Scholar). the 3′ is by the end-processing is believed that a number of recombination the ssDNA and onto ssDNA to form a nucleoprotein which a search to locate a DNA of the homolog by the nucleoprotein complex to the formation of heteroduplex DNA. 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