Dial 9–1–1 for DNA damage: the Rad9–Hus1–Rad1 (9–1–1) clamp complex

Parrilla-Castellar, Edgardo R.; Arlander, Sonnet J.H.; Karnitz, Larry M.

doi:10.1016/j.dnarep.2004.03.032

Cited by 297 publications

(225 citation statements)

References 58 publications

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“…Rad24⅐RFC Damage Checkpoint Clamp Loader Unloads PCNAThe 911 heterotrimeric clamp is assembled onto DNA by the Rad⅐RFC clamp loader, in which Rfc1 is replaced by Rad24 protein (Rad17 in humans) (12). Although Rad⅐RFC is not known to load PCNA onto DNA, it has an intrinsic DNA-dependent ATPase activity that is stimulated by PCNA (37,43).…”

Section: Discussionmentioning

confidence: 99%

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Mechanism of Proliferating Cell Nuclear Antigen Clamp Opening by Replication Factor C

Yao

Johnson

Bowman

et al. 2006

Journal of Biological Chemistry

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The eukaryotic replication factor C (RFC) clamp loader is an AAA؉ spiral-shaped heteropentamer that opens and closes the circular proliferating cell nuclear antigen (PCNA) clamp processivity factor on DNA. In this study, we examined the roles of individual RFC subunits in opening the PCNA clamp. Interestingly, Rfc1, which occupies the position analogous to the ␦ clamp-opening subunit in the Escherichia coli clamp loader, is not required to open PCNA. The Rfc5 subunit is required to open PCNA. Consistent with this result, Rfc2⅐3⅐4⅐5 and Rfc2⅐5 subassemblies are capable of opening and unloading PCNA from circular DNA. Rfc5 is positioned opposite the PCNA interface from Rfc1, and therefore, its action with Rfc2 in opening PCNA indicates that PCNA is opened from the opposite side of the interface that the E. coli ␦ wrench acts upon. This marks a significant departure in the mechanism of eukaryotic and prokaryotic clamp loaders. Interestingly, the Rad⅐RFC DNA damage checkpoint clamp loader unloads PCNA clamps from DNA. We propose that Rad⅐RFC may clear PCNA from DNA to facilitate shutdown of replication in the face of DNA damage.The proliferating cell nuclear antigen (PCNA) 3 DNA sliding clamp is a ring-shaped homotrimer that is opened and closed around DNA by the replication factor C (RFC) clamp loader (1-4). The PCNA clamp then binds numerous different proteins, including the cellular replicases DNA polymerase ␦ and DNA polymerase ⑀ (5). The RFC clamp loader was initially identified as a factor required for SV40 DNA replication in vitro (2). Subsequent characterization of RFC showed it to consist of five different subunits in both yeast and human cells (6). The five subunits are homologous to one another and are members of the AAAϩ family of ATPases (7). The structures of yeast RFC and the Escherichia coli clamp loader ␥ complex reveal that the subunits are arranged in a similar spiral fashion (8, 9). To avoid confusion over the different nomenclatures used for the different systems, the positions of the various clamp loader subunits are designated A-E as listed in Table 1. The position of each subunit in the complex is indicated in parentheses with a letter when comparisons are made between systems.The yeast Rfc1(A) subunit (human p140(A)) is sometimes referred to as the large subunit, as it contains both N-and C-terminal extensions past its region of homology with the four small subunits. The other four RFC subunits, referred to as the small subunits, are in the 36 -40-kDa range: yeast Rfc2(D) (human p37), yeast Rfc3(C) (human p36), yeast Rfc4(B) (human p40), and yeast Rfc5(E) (human p38). The N-terminal region of Rfc1, up to the region of homology to the other RFC subunits, can be deleted in both yeast and human RFC without decreasing RFC clamp loader function with PCNA (10, 11). Alternative clamp loaders exist in which Rfc1 is replaced by another protein. An example of one such alternative clamp loader is the Rad⅐RFC DNA damage checkpoint clamp loader, in which Rad24(A) (Rad17 in humans) replaces Rfc1(A) and...

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Section: Discussionmentioning

confidence: 99%

“…Alternative clamp loaders exist in which Rfc1 is replaced by another protein. An example of one such alternative clamp loader is the Rad⅐RFC DNA damage checkpoint clamp loader, in which Rad24(A) (Rad17 in humans) replaces Rfc1(A) and loads the 911 heterotrimer clamp onto DNA (12).…”

mentioning

confidence: 99%

Mechanism of Proliferating Cell Nuclear Antigen Clamp Opening by Replication Factor C

Yao

Johnson

Bowman

et al. 2006

Journal of Biological Chemistry

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“…The activation of Mec1-Ddc2 (ATR-ATRIP in mammals) is regulated by a number of factors: First, Mec1 signaling is dependent on colocalization of the Mec1-Ddc2 with the PCNA-like 9-1-1 Ddc1-Rad17-Mec3 complex (RAD9-RAD1-HUS1, in mammals) (Parrilla-Castellar et al 2004;Bonilla et al 2008). Second, it has been reported that the yeast 9-1-1 complex can activate Mec1 directly in vitro (Majka et al 2006).…”

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confidence: 99%

Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex

et al. 2015

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ATP-dependent chromatin remodeling complexes alter chromatin structure through interactions with chromatin substrates such as DNA, histones, and nucleosomes. However, whether chromatin remodeling complexes have the ability to regulate nonchromatin substrates remains unclear. Saccharomyces cerevisiae checkpoint kinase Mec1 (ATR in mammals) is an essential master regulator of genomic integrity. Here we found that the SWI/SNF chromatin remodeling complex is capable of regulating Mec1 kinase activity. In vivo, Mec1 activity is reduced by the deletion of Snf2, the core ATPase subunit of the SWI/SNF complex. SWI/SNF interacts with Mec1, and cross-linking studies revealed that the Snf2 ATPase is the main interaction partner for Mec1. In vitro, SWI/SNF can activate Mec1 kinase activity in the absence of chromatin or known activators such as Dpb11. The subunit requirement of SWI/SNFmediated Mec1 regulation differs from that of SWI/SNF-mediated chromatin remodeling. Functionally, SWI/SNFmediated Mec1 regulation specifically occurs in S phase of the cell cycle. Together, these findings identify a novel regulator of Mec1 kinase activity and suggest that ATP-dependent chromatin remodeling complexes can regulate nonchromatin substrates such as a checkpoint kinase.

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“…This fact reflects the different protein partners the two clamps engage and the distinct roles these complexes play in coordinating DNA processing. In contrast to PCNA, the 9-1-1 complex is thought to serve as a recruitment platform to bring checkpoint effector kinases to sites of DNA damage, thus activating checkpoint control, and also functions to stabilize stalled replication forks that have encountered DNA lesions (21)(22)(23). It has also been demonstrated that 9-1-1 interacts with and stimulates enzymes involved in base excision repair (BER), such as NEIL1, MYH, TDG, FEN1, and DNA Ligase I, thus potentially linking BER activities to checkpoint coordination (24)(25)(26)(27).…”

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confidence: 99%

Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability

Querol-Audí

Cheng

et al. 2012

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

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Processivity clamps such as proliferating cell nuclear antigen (PCNA) and the checkpoint sliding clamp Rad9/Rad1/Hus1 (9-1-1) act as versatile scaffolds in the coordinated recruitment of proteins involved in DNA replication, cell-cycle control, and DNA repair. Association and handoff of DNA-editing enzymes, such as flap endonuclease 1 (FEN1), with sliding clamps are key processes in biology, which are incompletely understood from a mechanistic point of view. We have used an integrative computational and experimental approach to define the assemblies of FEN1 with double-flap DNA substrates and either proliferating cell nuclear antigen or the checkpoint sliding clamp 9-1-1. Fully atomistic models of these two ternary complexes were developed and refined through extensive molecular dynamics simulations to expose their conformational dynamics. Clustering analysis revealed the most dominant conformations accessible to the complexes. The cluster centroids were subsequently used in conjunction with single-particle electron microscopy data to obtain a 3D EM reconstruction of the human 9-1-1/FEN1/DNA assembly at 18-Å resolution. Comparing the structures of the complexes revealed key differences in the orientation and interactions of FEN1 and double-flap DNA with the two clamps that are consistent with their respective functions in providing inherent flexibility for lagging strand DNA replication or inherent stability for DNA repair.F lap endonuclease 1 (FEN1) belongs to a class of essential nucleases (the FEN1 5′ nuclease superfamily) present in all domains of life (1). FEN1 catalyzes the endonucleolytic cleavage of bifurcated DNA or RNA structures known as 5′ flaps. These 5′ flaps are generated during lagging strand DNA synthesis or during long-patch base excision repair. The FEN1 substrates are in fact double-flap DNA (dfDNA) with DNA on the opposite side of the 5′ flap, forming a single nucleotide 3′ flap when bound to the enzyme (2, 3). By removing the 5′ ssDNA or RNA flap from such substrates, FEN1 produces a single nicked product that could be sealed by the subsequent action of a DNA ligase (4). Consistent with its crucial role in DNA replication and repair, FEN1 is highly expressed in all proliferative tissues, and its activity is key for the maintenance of genomic integrity (5). FEN1 has been identified as a cancer susceptibility gene, and mutations in it have been linked to a number of genetic diseases, such as EM map myotonic dystrophy, Huntington disease, several ataxias, fragile X syndrome, and cancer (6-10).The nuclease activity of FEN1 can be stimulated by association with processivity clamps such as proliferating cell nuclear antigen (PCNA), which encircle DNA at sites of replication and repair (11)(12)(13). PCNA is a recognized master coordinator of cellular responses to DNA damage and interacts with numerous DNA repair and cell-cycle control proteins. In this capacity, PCNA serves not only as a mobile platform for the attachment of these proteins to DNA but, importantly, plays an active role in the recru...

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Dial 9–1–1 for DNA damage: the Rad9–Hus1–Rad1 (9–1–1) clamp complex

Cited by 297 publications

References 58 publications

Mechanism of Proliferating Cell Nuclear Antigen Clamp Opening by Replication Factor C

Mechanism of Proliferating Cell Nuclear Antigen Clamp Opening by Replication Factor C

Regulation of Mec1 kinase activity by the SWI/SNF chromatin remodeling complex

Repair complexes of FEN1 endonuclease, DNA, and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability

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