DNA recognition properties of the N-terminal DNA binding domain within the large subunit of replication factor C

Allen, Beth; Uhlmann, Frank; Gaur, Lalit Kumar; Mulder, Brent A.; Posey, Karen L.; Jones, Leslie B.; Hardin, Susan H.

doi:10.1093/nar/26.17.3877

Cited by 29 publications

(45 citation statements)

References 27 publications

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“…7B, lanes 2 to 4). This is consistent with the specific affinity of this RF-C subunit for both 3Ј-hydroxyl and 5Ј-phosphoryl termini within duplex DNA (2,88). We note that the substitution of ATP by ATP␥S increased the amount of RF-C p140 bound to DNA (compare lanes 1 and 5).…”

Section: Resultssupporting

confidence: 86%

“…Among the known PCNA-interacting proteins, RF-C is able to load PCNA onto DNA containing singlestrand breaks (66), and the largest RF-C subunit (p140) pos- sesses specific DNA binding domains for both 3Ј-hydroxyl and 5Ј-phosphoryl termini within duplex DNA (2,88). The RF-C complex is thought to facilitate the opening of the PCNA ring structure in the presence of ATP, while closure of the PCNA ring structure around a DNA molecule and dissociation of RF-C is stimulated by ATP hydrolysis.…”

Section: Discussionmentioning

confidence: 99%

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A CAF-1–PCNA-Mediated Chromatin Assembly Pathway Triggered by Sensing DNA Damage

Moggs

Grandi

Quivy

et al. 2000

Molecular and Cellular Biology

307

259

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Sensing DNA damage is crucial for the maintenance of genomic integrity and cell cycle progression. The participation of chromatin in these events is becoming of increasing interest. We show that the presence of single-strand breaks and gaps, formed either directly or during DNA damage processing, can trigger the propagation of nucleosomal arrays. This nucleosome assembly pathway involves the histone chaperone chromatin assembly factor 1 (CAF-1). The largest subunit (p150) of this factor interacts directly with proliferating cell nuclear antigen (PCNA), and critical regions for this interaction on both proteins have been mapped. To isolate proteins specifically recruited during DNA repair, damaged DNA linked to magnetic beads was used. The binding of both PCNA and CAF-1 to this damaged DNA was dependent on the number of DNA lesions and required ATP. Chromatin assembly linked to the repair of single-strand breaks was disrupted by depletion of PCNA from a cell-free system. This defect was rescued by complementation with recombinant PCNA, arguing for role of PCNA in mediating chromatin assembly linked to DNA repair. We discuss the importance of the PCNA-CAF-1 interaction in the context of DNA damage processing and checkpoint control.Sensing and signaling the presence of DNA damage to the cell cycle checkpoint machinery is crucial for the maintenance of genomic integrity and the regulation of cell cycle progression (12,25,61,97). Checkpoints respond to DNA damage by halting cell cycle progression, providing time for DNA repair. This strategy avoids the replication and segregation of damaged chromosomes which could otherwise lead to genomic instability. DNA damage is caused by physical and chemical agents as well as normal cellular processes including DNA replication and oxidative stress. A variety of distinct DNA repair mechanisms involving lesion-specific DNA damage recognition proteins have been characterized in eukaryotic cells (reviewed in reference 15). The DNA damage checkpoint machinery may recognize structural perturbations in DNA and/or components of the DNA damage processing machinery during specific phases of the cell cycle. Yeast model systems have proven powerful in identifying components of mitotic DNA damage checkpoint pathways (5,37,43,71,97) which, by analogy with signal transduction pathways, consist of sensor, transducer, and effector molecules. Several checkpoint proteins have been proposed to be directly involved in DNA damage recognition based on their similarity to proteins involved in DNA metabolism, including a structural relative of a 3Ј-5Ј exonuclease (Saccharomyces cerevisiae Rad17 [Rad17 sc ]) and a replication factor C (RF-C)-like protein (Rad24 sc ). Protein kinases such as Mec1 sc and Rad53 sc appear to transduce signals from DNA damage sensors to the cell cycle machinery. Significant progress has been made in delineating the proteinprotein interactions and phosphorylation events occurring among some of these factors and their potential interfaces with DNA repair (96). However, the mol...

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Section: Resultssupporting

confidence: 86%

Section: Discussionmentioning

confidence: 99%

A CAF-1–PCNA-Mediated Chromatin Assembly Pathway Triggered by Sensing DNA Damage

Moggs

Grandi

Quivy

et al. 2000

Molecular and Cellular Biology

307

259

View full text Add to dashboard Cite

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“…The DNA lengths were chosen to be in excess of the reported RFC footprint of 12 bases on the 5Ј single-stranded overhang and 8 -15 bases on the duplex region of a primer-template DNA (33). During assay development, we noted that RFC has high affinity for a 5Ј-phosphate residue on any DNA structure (single-stranded, double-stranded, or primer-template); a similar property of human and D. melanogaster RFC1 amino-terminal domains for recognizing 5Ј-phosphate on duplex DNA has been reported recently (35). In order to eliminate possible misinterpretation of 5Ј-phosphate recognition as interaction between RFC and DNAs other than the primertemplate, the DNA substrates used in this study were 32 Plabeled by incorporation of [␣- 32 P]dATP at the 3Ј-end by phage T7 DNA polymerase.…”

Section: S Cerevisiae Rfc Purified From E Coli Assembles Pcna Clampsupporting

confidence: 66%

“…cerevisiae RFC binding to double-stranded DNA (29 -32), primer-template DNA with either a 3Ј primertemplate junction (33,34) or a 5Ј phosphorylated primer-template junction (35), and single-stranded DNA (33,36,37). These results suggest a relatively low specificity of RFC binding to primer-template DNA, and since the concentration of primed sites is expected to be much lower than that of singleand double-stranded regions in replicating DNA, how does the clamp loader rapidly recognize a primed DNA site for clamp assembly?…”

mentioning

confidence: 99%

On the Specificity of Interaction between the Saccharomyces cerevisiae Clamp Loader Replication Factor C and Primed DNA Templates during DNA Replication

Hingorani

Coman

2002

Journal of Biological Chemistry

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Replication factor C (RFC) catalyzes assembly of circular proliferating cell nuclear antigen clamps around primed DNA, enabling processive synthesis by DNA polymerase during DNA replication and repair. In order to perform this function efficiently, RFC must rapidly recognize primed DNA as the substrate for clamp assembly, particularly during lagging strand synthesis. Earlier reports as well as quantitative DNA binding experiments from this study indicate, however, that RFC interacts with primer-template as well as single-and doublestranded DNA (ssDNA and dsDNA, respectively) with similar high affinity (apparent K d Ϸ 10 nM). How then can RFC distinguish primed DNA sites from excess ssDNA and dsDNA at the replication fork? Further analysis reveals that despite its high affinity for various DNA structures, RFC selects primer-template DNA even in the presence of a 50-fold excess of ssDNA and dsDNA. The interaction between ssDNA or dsDNA and RFC is far less stable than between primed DNA and RFC (k off > 0.2 s ؊1 versus 0.025 s ؊1 , respectively). We propose that the ability to rapidly bind and release single-and double-stranded DNA coupled with selective, stable binding to primer-template DNA allows RFC to scan DNA efficiently for primed sites where it can pause to initiate clamp assembly.Replicative DNA polymerases synthesize DNA with high processivity in collaboration with two key accessory proteins: a circular clamp and a clamp loader complex (see Fig. 1; reviewed in Refs. 1 and 2). These accessory proteins are conserved in structure and function among a variety of organisms including bacteriophage (e.g. T4 gp45 clamp and gp44/62 clamp loader), bacteria (e.g. Escherichia coli ␤ clamp and ␥ complex clamp loader), archaebacteria (e.g. Pyrococcus furiosus proliferating cell nuclear antigen (PCNA) 1 clamp and replication factor C (RFC) clamp loader), and eukaryotes such as Saccharomyces cerevisiae and humans (PCNA and RFC) as well (see Ref.3 for a review of recent crystal structures). Clamps are ring-shaped multisubunit proteins with an inner diameter of ϳ35 Å that is large enough to encircle duplex DNA (e.g. homotrimeric PCNA) (4). When bound to polymerase and DNA, the clamp forms a sliding tether that stabilizes polymerase on the primer-template and facilitates processive DNA replication (5). A polymerase-clamp complex, such as S. cerevisiae Pol ␦⅐PCNA, can extend DNA with a processivity of hundreds of nucleotides per template binding event, a substantial increase from the 6 -12-nucleotide processivity of Pol ␦ alone (6, 7).The circular clamp is opened and assembled around primertemplate DNA by the clamp loader, a multiprotein machine whose action is fueled by ATP binding and hydrolysis. Clamps must be present at primed DNA sites for polymerase to bind them and initiate processive DNA synthesis (7,8). Efficient clamp assembly is particularly important during lagging DNA synthesis when a clamp is required at the initiation of every Okazaki fragment (Fig. 1). Given an estimated Okazaki fragment size of 100 -200 nucl...

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“…DmRfc1 and DmRfc4 had been previously reported) (1,15). By analysis of the sequenced Drosophila genome, we were able to identify by homology all five subunits of the RFC complex and also the homologue of SpRad17 and ScRad24 (an Rfc1-related gene) (13,24).…”

Section: Vol 21 2001 Loss Of Checkpoint Control In Dmrfc4 Mutantssupporting

confidence: 52%

Loss of Cell Cycle Checkpoint Control in Drosophila Rfc4 Mutants

Krause

Loupart

Vass

et al. 2001

Molecular and Cellular Biology

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Two alleles of the Drosophila melanogaster Rfc4 (DmRfc4) gene, which encodes subunit 4 of the replication factor C (RFC) complex, cause striking defects in mitotic chromosome cohesion and condensation. These mutations produce larval phenotypes consistent with a role in DNA replication but also result in mitotic chromosomal defects appearing either as premature chromosome condensation-like or precocious sister chromatid separation figures. Though the DmRFC4 protein localizes to all replicating nuclei, it is dispersed from chromatin in mitosis. Thus the mitotic defects appear not to be the result of a direct role for RFC4 in chromosome structure. We also show that the mitotic defects in these two DmRfc4 alleles are the result of aberrant checkpoint control in response to DNA replication inhibition or damage to chromosomes. Not all surveillance function is compromised in these mutants, as the kinetochore attachment checkpoint is operative. Intriguingly, metaphase delay is frequently observed with the more severe of the two alleles, indicating that subsequent chromosome segregation may be inhibited. This is the first demonstration that subunit 4 of RFC functions in checkpoint control in any organism, and our findings additionally emphasize the conserved nature of RFC's involvement in checkpoint control in multicellular eukaryotes.Control of cell cycle progression is critical for ensuring the precise duplication and distribution of the genome during cell division. One convenient way to envisage the cell cycle is as distinct phases, in which gap phases intervene before and between DNA replication and mitosis. However, a more accurate picture of the cell cycle emerges when the cell's ability to faithfully monitor crucial events is taken into account. Not only must the genome be completely and correctly replicated, but any remaining lesions in the sister chromatids must also be repaired prior to the entry into mitosis. Critically, the symmetric attachment of sister kinetochores to microtubules, achieving biorientation on the mitotic spindle, must occur prior to sister chromatid separation at the metaphase-to-anaphase transition. The concept of cell cycle checkpoints was initially proposed more than a decade ago with the characterization of the rad9 (for radiation sensitive) mutant in budding yeast (16). Since then, an explosion of studies of many diverse systems has served to illuminate three important checkpoints that normal cells progress through on the way to the completion of cell division: the DNA replication and DNA damage checkpoints (which may jointly be considered as DNA structure checkpoints) and the kinetochore attachment checkpoint. Precise molecular components have been identified in different model systems, primarily through genetic analysis of each of these checkpoints (6). Mutation of checkpoint components has been observed in many human cancers (9, 31).Though much of the original identification and analysis of cell cycle checkpoints was achieved with budding and fission yeast, studies with Drosophila me...

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DNA recognition properties of the N-terminal DNA binding domain within the large subunit of replication factor C

Cited by 29 publications

References 27 publications

A CAF-1–PCNA-Mediated Chromatin Assembly Pathway Triggered by Sensing DNA Damage

A CAF-1–PCNA-Mediated Chromatin Assembly Pathway Triggered by Sensing DNA Damage

On the Specificity of Interaction between the Saccharomyces cerevisiae Clamp Loader Replication Factor C and Primed DNA Templates during DNA Replication

Loss of Cell Cycle Checkpoint Control in Drosophila Rfc4 Mutants

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