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Schrecker M, Castaneda JC, Devbhandari S, Kumar C, Remus D, Hite RK. Multistep loading of a DNA sliding clamp onto DNA by replication factor C. eLife 2022; 11:e78253. [PMID: 35939393 PMCID: PMC9359705 DOI: 10.7554/elife.78253] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/07/2022] [Indexed: 11/13/2022] Open
Abstract
The DNA sliding clamp proliferating cell nuclear antigen (PCNA) is an essential co-factor for many eukaryotic DNA metabolic enzymes. PCNA is loaded around DNA by the ATP-dependent clamp loader replication factor C (RFC), which acts at single-stranded (ss)/double-stranded DNA (dsDNA) junctions harboring a recessed 3' end (3' ss/dsDNA junctions) and at DNA nicks. To illuminate the loading mechanism we have investigated the structure of RFC:PCNA bound to ATPγS and 3' ss/dsDNA junctions or nicked DNA using cryogenic electron microscopy. Unexpectedly, we observe open and closed PCNA conformations in the RFC:PCNA:DNA complex, revealing that PCNA can adopt an open, planar conformation that allows direct insertion of dsDNA, and raising the question of whether PCNA ring closure is mechanistically coupled to ATP hydrolysis. By resolving multiple DNA-bound states of RFC:PCNA we observe that partial melting facilitates lateral insertion into the central channel formed by RFC:PCNA. We also resolve the Rfc1 N-terminal domain and demonstrate that its single BRCT domain participates in coordinating DNA prior to insertion into the central RFC channel, which promotes PCNA loading on the lagging strand of replication forks in vitro. Combined, our data suggest a comprehensive and fundamentally revised model for the RFC-catalyzed loading of PCNA onto DNA.
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Affiliation(s)
- Marina Schrecker
- Structural Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Juan C Castaneda
- Weill Cornell Medicine Graduate School, Weill Cornell MedicineNew YorkUnited States
- Molecular Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Sujan Devbhandari
- Molecular Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Charanya Kumar
- Molecular Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Dirk Remus
- Molecular Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
| | - Richard K Hite
- Structural Biology Program, Memorial Sloan Kettering Cancer CenterNew YorkUnited States
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Subramanian S, Gorday K, Marcus K, Orellana MR, Ren P, Luo XR, O'Donnell ME, Kuriyan J. Allosteric communication in DNA polymerase clamp loaders relies on a critical hydrogen-bonded junction. eLife 2021; 10:e66181. [PMID: 33847559 PMCID: PMC8121543 DOI: 10.7554/elife.66181] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/03/2021] [Indexed: 02/06/2023] Open
Abstract
Clamp loaders are AAA+ ATPases that load sliding clamps onto DNA. We mapped the mutational sensitivity of the T4 bacteriophage sliding clamp and clamp loader by deep mutagenesis, and found that residues not involved in catalysis or binding display remarkable tolerance to mutation. An exception is a glutamine residue in the AAA+ module (Gln 118) that is not located at a catalytic or interfacial site. Gln 118 forms a hydrogen-bonded junction in a helical unit that we term the central coupler, because it connects the catalytic centers to DNA and the sliding clamp. A suppressor mutation indicates that hydrogen bonding in the junction is important, and molecular dynamics simulations reveal that it maintains rigidity in the central coupler. The glutamine-mediated junction is preserved in diverse AAA+ ATPases, suggesting that a connected network of hydrogen bonds that links ATP molecules is an essential aspect of allosteric communication in these proteins.
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Affiliation(s)
- Subu Subramanian
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Kent Gorday
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Biophysics Graduate Group, University of California, BerkeleyBerkeleyUnited States
| | - Kendra Marcus
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
| | - Matthew R Orellana
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
| | - Peter Ren
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
| | - Xiao Ran Luo
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
| | - Michael E O'Donnell
- Howard Hughes Medical Institute, Rockefeller UniversityNew YorkUnited States
| | - John Kuriyan
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
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Liu J, Zhou Y, Hingorani MM. Linchpin DNA-binding residues serve as go/no-go controls in the replication factor C-catalyzed clamp-loading mechanism. J Biol Chem 2017; 292:15892-15906. [PMID: 28808059 DOI: 10.1074/jbc.m117.798702] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/02/2017] [Indexed: 11/06/2022] Open
Abstract
DNA polymerases depend on circular sliding clamps for processive replication. Clamps must be loaded onto primer-template DNA (ptDNA) by clamp loaders that open and close clamps around ptDNA in an ATP-fueled reaction. All clamp loaders share a core structure in which five subunits form a spiral chamber that binds the clamp at its base in a twisted open form and encloses ptDNA within, while binding and hydrolyzing ATP to topologically link the clamp and ptDNA. To understand how clamp loaders perform this complex task, here we focused on conserved arginines that might play a central coordinating role in the mechanism because they can alternately contact ptDNA or Walker B glutamate in the ATPase site and lie close to the clamp loader-clamp-binding interface. We mutated Arg-84, Arg-88, and Arg-101 in the ATPase-active B, C, and D subunits of Saccharomyces cerevisiae replication factor C (RFC) clamp loader, respectively, and assessed the impact on multiple transient events in the reaction: proliferating cell nuclear antigen (PCNA) clamp binding/opening/closure/release, ptDNA binding/release, and ATP hydrolysis/product release. The results show that these arginines relay critical information between the PCNA-binding, DNA-binding, and ATPase sites at all steps of the reaction, particularly at a checkpoint before RFC commits to ATP hydrolysis. Moreover, their actions are subunit-specific with RFC-C Arg-88 serving as an accelerator that enables rapid ATP hydrolysis upon contact with ptDNA and RFC-D Arg-101 serving as a brake that confers specificity for ptDNA as the correct substrate for loading PCNA.
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Affiliation(s)
- Juan Liu
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Yayan Zhou
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
| | - Manju M Hingorani
- From the Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, Connecticut 06459
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Kobayashi H, Matsuda Y, Hitomi T, Okuda H, Shioi H, Matsuda T, Imai H, Sone M, Taura D, Harada KH, Habu T, Takagi Y, Miyamoto S, Koizumi A. Biochemical and Functional Characterization of RNF213 (Mysterin) R4810K, a Susceptibility Mutation of Moyamoya Disease, in Angiogenesis In Vitro and In Vivo. J Am Heart Assoc 2015; 4:JAHA.115.002146. [PMID: 26126547 PMCID: PMC4608092 DOI: 10.1161/jaha.115.002146] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Background P.R4810K of RNF213 (mysterin: rs112735431), which is an AAA+ ATPase, is the susceptibility polymorphism for moyamoya disease (MMD) in East Asians. However, the role of RNF213 R4810K in the etiology of MMD is unknown. Methods and Results To clarify the role of RNF213 in known angiogenic pathways, RNF213 expression was analyzed in endothelial cells (ECs) treated with several angiogenic and antiangiogenic factors, including interferons (IFNs). RNF213 was upregulated by IFN-β through signal transducer and activator of transcription x in the promoter and mediated antiangiogenic activity of IFN-β. RNF213 wild-type (WT) overexpression could not lower angiogenesis without IFN-β, but RNF213 R4810K overexpression could. To correlate biochemical function as ATPase and the role of RNF213 oligomer formation with antiangiogenic activity, we investigated the effects of mutations in the AAA+ module. A mutation of the Walker B motif (WEQ), which stabilizes oligomerization, inhibited angiogenesis, but AAA+ module deletion, which cannot initiate oligomerization, did not. Intriguingly, R4810K, similar to WEQ, decreased ATPase activity, suggesting its antiangiogenic activity through stabilizing oligomers. To confirm the antiangiogenic effect of RNF213 upregulation in vivo, vascular EC- or smooth muscle cell-specific Rnf213 R4757K (R4810K ortholog) or WT transgenic (Tg) mice were exposed to hypoxia. Cerebral angiogenesis by hypoxia was suppressed in EC-specific Rnf213 R4757K Tg mice, whereas it was not suppressed in other mice. Conclusions This study suggests the importance of inflammatory signals as environmental factors and R4810K carriers for susceptibility to cerebral hypoxia. A specific inhibitor of ATP binding to the first AAA+ could be a promising therapeutic candidate for MMD.
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Affiliation(s)
- Hatasu Kobayashi
- Department of Health and Environmental Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan (H.K., T.H., H.O., H.S., K.H.H., A.K.)
| | - Yoshiko Matsuda
- Department of Neurosurgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan (Y.M., Y.T., S.M.)
| | - Toshiaki Hitomi
- Department of Health and Environmental Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan (H.K., T.H., H.O., H.S., K.H.H., A.K.) Department of Preventive Medicine, St Marianna University School of Medicine, Kawasaki, Japan (T.H.)
| | - Hiroko Okuda
- Department of Health and Environmental Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan (H.K., T.H., H.O., H.S., K.H.H., A.K.)
| | - Hirotomo Shioi
- Department of Health and Environmental Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan (H.K., T.H., H.O., H.S., K.H.H., A.K.)
| | - Tetsuya Matsuda
- Department of Systems Science, Graduate School of Informatics, Kyoto University, Kyoto, Japan (T.M., H.I.)
| | - Hirohiko Imai
- Department of Systems Science, Graduate School of Informatics, Kyoto University, Kyoto, Japan (T.M., H.I.)
| | - Masakatsu Sone
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan (M.S., D.T.)
| | - Daisuke Taura
- Department of Diabetes, Endocrinology and Nutrition, Graduate School of Medicine, Kyoto University, Kyoto, Japan (M.S., D.T.)
| | - Kouji H Harada
- Department of Health and Environmental Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan (H.K., T.H., H.O., H.S., K.H.H., A.K.)
| | - Toshiyuki Habu
- Radiation Biology Center, Kyoto University, Kyoto, Japan (T.H.)
| | - Yasushi Takagi
- Department of Neurosurgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan (Y.M., Y.T., S.M.)
| | - Susumu Miyamoto
- Department of Neurosurgery, Graduate School of Medicine, Kyoto University, Kyoto, Japan (Y.M., Y.T., S.M.)
| | - Akio Koizumi
- Department of Health and Environmental Sciences, Graduate School of Medicine, Kyoto University, Kyoto, Japan (H.K., T.H., H.O., H.S., K.H.H., A.K.)
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Chang HY, Liao CY, Su GC, Lin SW, Wang HW, Chi P. Functional Relationship of ATP Hydrolysis, Presynaptic Filament Stability, and Homologous DNA Pairing Activity of the Human Meiotic Recombinase DMC1. J Biol Chem 2015; 290:19863-73. [PMID: 26088134 DOI: 10.1074/jbc.m115.666289] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Indexed: 11/06/2022] Open
Abstract
DMC1 and RAD51 are conserved recombinases that catalyze homologous recombination. DMC1 and RAD51 share similar properties in DNA binding, DNA-stimulated ATP hydrolysis, and catalysis of homologous DNA strand exchange. A large body of evidence indicates that attenuation of ATP hydrolysis leads to stabilization of the RAD51-ssDNA presynaptic filament and enhancement of DNA strand exchange. However, the functional relationship of ATPase activity, presynaptic filament stability, and DMC1-mediated homologous DNA strand exchange has remained largely unexplored. To address this important question, we have constructed several mutant variants of human DMC1 and characterized them biochemically to gain mechanistic insights. Two mutations, K132R and D223N, that change key residues in the Walker A and B nucleotide-binding motifs ablate ATP binding and render DMC1 inactive. On the other hand, the nucleotide-binding cap D317K mutant binds ATP normally but shows significantly attenuated ATPase activity and, accordingly, forms a highly stable presynaptic filament. Surprisingly, unlike RAD51, presynaptic filament stabilization achieved via ATP hydrolysis attenuation does not lead to any enhancement of DMC1-catalyzed homologous DNA pairing and strand exchange. This conclusion is further supported by examining wild-type DMC1 with non-hydrolyzable ATP analogues. Thus, our results reveal an important mechanistic difference between RAD51 and DMC1.
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Affiliation(s)
- Hao-Yen Chang
- From the Institute of Biochemical Sciences, National Taiwan University, Number 1, Section 4, Roosevelt Road, Taipei 10617 Taiwan
| | - Chia-Yu Liao
- From the Institute of Biochemical Sciences, National Taiwan University, Number 1, Section 4, Roosevelt Road, Taipei 10617 Taiwan
| | - Guan-Chin Su
- From the Institute of Biochemical Sciences, National Taiwan University, Number 1, Section 4, Roosevelt Road, Taipei 10617 Taiwan
| | - Sheng-Wei Lin
- the Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan, and
| | - Hong-Wei Wang
- the Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Joint Center for Life Sciences, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Peter Chi
- From the Institute of Biochemical Sciences, National Taiwan University, Number 1, Section 4, Roosevelt Road, Taipei 10617 Taiwan, the Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan, and
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Marzahn MR, Hayner JN, Finkelstein J, O'Donnell M, Bloom LB. The ATP sites of AAA+ clamp loaders work together as a switch to assemble clamps on DNA. J Biol Chem 2014; 289:5537-48. [PMID: 24436332 DOI: 10.1074/jbc.m113.541466] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Clamp loaders belong to a family of proteins known as ATPases associated with various cellular activities (AAA+). These proteins utilize the energy from ATP binding and hydrolysis to perform cellular functions. The clamp loader is required to load the clamp onto DNA for use by DNA polymerases to increase processivity. ATP binding and hydrolysis are coordinated by several key residues, including a conserved Lys located within the Walker A motif (or P-loop). This residue is required for each subunit to bind ATP. The specific function of each ATP molecule bound to the Saccharomyces cerevisiae clamp loader is unknown. A series of point mutants, each lacking a single Walker A Lys residue, was generated to study the effects of abolishing ATP binding in individual clamp loader subunits. A variety of biochemical assays were used to analyze the function of ATP binding during discrete steps of the clamp loading reaction. All mutants reduced clamp binding/opening to different degrees. Decreased clamp binding activity was generally correlated with decreases in the population of open clamps, suggesting that differences in the binding affinities of Walker A mutants stem from differences in stabilization of proliferating cell nuclear antigen in an open conformation. Walker A mutations had a smaller effect on DNA binding than clamp binding/opening. Our data do not support a model in which each ATP site functions independently to regulate a different step in the clamp loading cycle to coordinate these steps. Instead, the ATP sites work in unison to promote conformational changes in the clamp loader that drive clamp loading.
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Affiliation(s)
- Melissa R Marzahn
- From the Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida 32610 and
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