Synergistic action of the Saccharomyces cerevisiae homologous recombination factors Rad54 and Rad51 in chromatin remodeling

Kwon, Young Ho; Chi, Peter; Roh, Dong Hyun; Klein, Hannah L.; Sung, Patrick

doi:10.1016/j.dnarep.2007.04.012

Cited by 23 publications

(21 citation statements)

References 53 publications

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“…Owing to the presence of phased nucleosomes, the DNA in the substrate is rather resistant to the restriction enzyme HaeIII, and restructuring of the array by chromatin remodelers is conveniently revealed by an increased HaeIII accessibility ( Fig. 2A) (23,25). As shown in Fig.…”

Section: Rad51/rad52-dependent Dsb Recruitment Of Rdh54-chipmentioning

confidence: 95%

“…D-loop Formation on Naked and Chromatinized DNA Templates-D-loop reactions were performed essentially as described in our published work (19,25,31). Briefly, the Rad51 presynaptic filament was assembled by incubating a 32 P-labeled 90-mer oligonucleotide (2.4 M nucleotides) and Rad51 (0.8 M) in buffer D (35 mM Tris-HCl, pH 7.5, 1 mM dithiothreitol, 5 mM MgCl 2 , 60 mM KCl, 100 ng/l bovine serum albumin, 2 mM ATP, and an ATP-regenerating system comprising 20 g/ml creatine kinase and 20 mM creatine phosphate) for 5 min at 37°C.…”

Section: Methodsmentioning

confidence: 99%

“…Preparation of Chromatinized DNA-Nucleosomal arrays were assembled with pBluescript SK II DNA, and the histone octamer was purified from the nuclei of chicken erythrocytes (30) by the salt dialysis method, as described previously (24,25). For the construction of the mononucleosome substrates, a 314-bp DNA fragment derived from the RAD51 gene promoter was generated by PCR using plasmid pN124 as template (22).…”

Section: Methodsmentioning

confidence: 99%

“…Based on cytological and chromatin immunoprecipitation analyses, it has been suggested that Rdh54 and Rad54 also function to release the meiosis-specific recombinase Dmc1 from bulk chromatin (21). Importantly, and consistent with its relatedness to the Swi2/Snf2 family of chromatin remodelers, Rad54 protein has a chromatin-remodeling function that is fueled by its ATPase activity (22)(23)(24) and is greatly enhanced via its association with Rad51 (25). Rad54 also works with Rad51 to promote the formation of D-loops with a chromatinized template (23,24,26).…”

mentioning

confidence: 99%

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ATP-dependent Chromatin Remodeling by the Saccharomyces cerevisiae Homologous Recombination Factor Rdh54

Kwon

Seong

Chi

et al. 2008

Journal of Biological Chemistry

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Saccharomyces cerevisiae RDH54 is a key member of the evolutionarily conserved RAD52 epistasis group of genes needed for homologous recombination and DNA double strand break repair. The RDH54-encoded protein possesses a DNA translocase activity and functions together with the Rad51 recombinase in the D-loop reaction. By chromatin immunoprecipitation (ChIP), we show that Rdh54 is recruited, in a manner that is dependent on Rad51 and Rad52, to a site-specific DNA double strand break induced by the HO endonuclease. Because of its relatedness to Swi2/Snf2 chromatin remodelers, we have asked whether highly purified Rdh54 possesses chromatin-remodeling activity. Importantly, our results show that Rdh54 can mobilize a mononucleosome along DNA and render nucleosomal DNA accessible to a restriction enzyme, indicative of a chromatin-remodeling function. Moreover, Rdh54 co-operates with Rad51 in the utilization of naked or chromatinized DNA as template for D-loop formation. We also provide evidence for a strict dependence of the chromatin-remodeling attributes of Rdh54 on its ATPase activity and N-terminal domain. Interestingly, an N-terminal deletion mutant (rdh54⌬102) is unable to promote Rad51-mediated D-loop formation with a chromatinized template, while retaining substantial activity with naked DNA. These features of Rdh54 suggest a role of this protein factor in chromatin rearrangement during DNA recombination and repair.The genomic DNA in eukaryotic cells is organized into chromatin, which harbors repeated nucleosome units each comprising an octamer of four histone proteins, H2A, H2B, H3, and H4, and 147 bp of DNA (1, 2). The folding of DNA on the surface of histone proteins within the nucleosome inevitably poses an accessibility problem during various DNA transactions, including DNA replication, recombination, and repair.One mechanism to efficiently overcome this structural hindrance is by an ATP hydrolysis-dependent chromatin-remodeling process, such that remodeling proteins render DNA more accessible by weakening DNA:histone contacts, sliding nucleosomes along DNA, or removing H2A-H2B dimers from the nucleosome (3-5).We are interested in delineating the mechanism of homologous recombination (HR) 2 that is mediated by proteins of the RAD52 epistasis group, including how the HR machinery negotiates the constraints posed by chromatin structure. Regarding the latter, of special interest are two key members of the RAD52 epistasis group, Rad54 and Rdh54 proteins. These HR factors play multifaceted roles in HR (6 -8), and they belong to the Swi2/Snf2 protein superfamily, members of which are well known ATP hydrolysis-dependent chromatin remodelers (9, 10). Rad54 and Rdh54 both possess a DNA-dependent ATPase activity and a dsDNA translocase function that is fueled by ATP hydrolysis (8,(11)(12)(13)(14)(15). The DNA translocase activity of these Swi2/Snf2-like HR factors can modify DNA topology (11-13), enhance D-loop formation by the Rad51 recombinase (11, 16), accelerate the rate at which DNA strands are exchanged duri...

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Section: Rad51/rad52-dependent Dsb Recruitment Of Rdh54-chipmentioning

confidence: 95%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

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ATP-dependent Chromatin Remodeling by the Saccharomyces cerevisiae Homologous Recombination Factor Rdh54

Kwon

Seong

Chi

et al. 2008

Journal of Biological Chemistry

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“…By translocation on dsDNA they can induce local DNA distortion which contributes to nucleosome remodeling. Interestingly, the Swi2/Snf2-related Rdh54 and the Rad54 DNA branch migrating proteins exhibit not only nucleosome remodeling activity, but can displace Rad51 as well (48)(49)(50)(51). Also, from the Swi2/Snf2 family members Mot1 has been reported to have a nonnucleosomal protein remodeling activity.…”

Section: Discussionmentioning

confidence: 99%

Coordinated protein and DNA remodeling by human HLTF on stalled replication fork

Achar

Balogh

Haracska

2011

Proc. Natl. Acad. Sci. U.S.A.

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Human helicase-like transcription factor (HLTF) exhibits ubiquitin ligase activity for proliferating cell nuclear antigen (PCNA) polyubiquitylation as well as double-stranded DNA translocase activity for remodeling stalled replication fork by fork reversal, which can support damage bypass by template switching. However, a stalled replication fork is surrounded by various DNA-binding proteins which can inhibit the access of damage bypass players, and it is unknown how these proteins become displaced. Here we reveal that HLTF has an ATP hydrolysis-dependent protein remodeling activity, by which it can remove proteins bound to the replication fork. Moreover, we demonstrate that HLTF can displace a broad spectrum of proteins such as replication protein A (RPA), PCNA, and replication factor C (RFC), thereby providing the first example for a protein clearing activity at the stalled replication fork. Our findings clarify how remodeling of a stalled replication fork can occur if it is engaged in interactions with masses of proteins. U nrepaired DNA lesions are dangerous obstacles for the replication machinery because most of them cannot be accommodated into the active site of the replicative polymerases, thereby blocking the progression of the replication fork. Prolonged stalling might lead to DNA strand breaks, chromosomal rearrangements, or cell death (1-3). To minimize this danger cells have evolved various DNA damage bypass mechanisms that are initiated by exchanging protein components of the normal replication machinery for protein players which either carry out a direct damage bypass or manipulate the stalled fork to generate transitional DNA structures that facilitate damage bypass indirectly. In the first situation, specialized translesion synthesis polymerases that can accommodate even bulky lesions at their active sites take over the 3′ primer end from the accurate replicative polymerase and incorporate either a correct or an incorrect nucleotide opposite the lesion (4, 5). Alternatively, DNA remodeling might lead to the annealing of the stalled nascent strand to the newly synthesized strand of the undamaged sister duplex, resulting in template switch (6-9). Although the exact mechanism and factors of template switch have remained largely unknown, two proposed mechanisms have gained significant attention. One is named-based on the shape of the intermediate DNA structure-chicken foot model, which proposes pairing of the two newly synthesized strands of the sister chromatids by reversal of the stalled fork (9, 10). The other model also suggests pairing of the newly synthesized strands, but assumes that it occurs via a D-loop recombination intermediate (6,(11)(12)(13). It is possible that these mechanisms are not mutually exclusive and the choice can be regulated at the level of displacement and exchange of the protein components of the stalled replication machinery for various new players.It is generally accepted that in eukaryotic cells damage bypass is governed by Rad6 and Rad18, a ubiquitin conjugating and a ...

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Current awareness on yeast

2008

Yeast

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In order to keep subscribers up‐to‐date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly‐published material on yeasts. Each bibliography is divided into 10 sections. 1 Reviews; 2 General; 3 Biochemistry; 4 Biotechnology; 5 Cell Biology; 6 Gene Expression; 7 Genetics; 8 Physiology; 9 Medical Mycology; 10 Recombinant DNA Technology. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted. (4 weeks journals ‐ search completed 5th. Mar. 2008)

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Synergistic action of the Saccharomyces cerevisiae homologous recombination factors Rad54 and Rad51 in chromatin remodeling

Cited by 23 publications

References 53 publications

ATP-dependent Chromatin Remodeling by the Saccharomyces cerevisiae Homologous Recombination Factor Rdh54

ATP-dependent Chromatin Remodeling by the Saccharomyces cerevisiae Homologous Recombination Factor Rdh54

Coordinated protein and DNA remodeling by human HLTF on stalled replication fork

Current awareness on yeast

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