1
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Alcón P, Kaczmarczyk AP, Ray KK, Liolios T, Guilbaud G, Sijacki T, Shen Y, McLaughlin SH, Sale JE, Knipscheer P, Rueda DS, Passmore LA. FANCD2-FANCI surveys DNA and recognizes double- to single-stranded junctions. Nature 2024; 632:1165-1173. [PMID: 39085614 PMCID: PMC11358013 DOI: 10.1038/s41586-024-07770-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 07/01/2024] [Indexed: 08/02/2024]
Abstract
DNA crosslinks block DNA replication and are repaired by the Fanconi anaemia pathway. The FANCD2-FANCI (D2-I) protein complex is central to this process as it initiates repair by coordinating DNA incisions around the lesion1. However, D2-I is also known to have a more general role in DNA repair and in protecting stalled replication forks from unscheduled degradation2-4. At present, it is unclear how DNA crosslinks are recognized and how D2-I functions in replication fork protection. Here, using single-molecule imaging, we show that D2-I is a sliding clamp that binds to and diffuses on double-stranded DNA. Notably, sliding D2-I stalls on encountering single-stranded-double-stranded (ss-ds) DNA junctions, structures that are generated when replication forks stall at DNA lesions5. Using cryogenic electron microscopy, we determined structures of D2-I on DNA that show that stalled D2-I makes specific interactions with the ss-dsDNA junction that are distinct from those made by sliding D2-I. Thus, D2-I surveys dsDNA and, when it reaches an ssDNA gap, it specifically clamps onto ss-dsDNA junctions. Because ss-dsDNA junctions are found at stalled replication forks, D2-I can identify sites of DNA damage. Therefore, our data provide a unified molecular mechanism that reconciles the roles of D2-I in the recognition and protection of stalled replication forks in several DNA repair pathways.
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Affiliation(s)
- Pablo Alcón
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Artur P Kaczmarczyk
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- MRC Laboratory of Medical Sciences, London, UK
| | - Korak Kumar Ray
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- MRC Laboratory of Medical Sciences, London, UK
| | - Themistoklis Liolios
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Yichao Shen
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute-KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - David S Rueda
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK.
- MRC Laboratory of Medical Sciences, London, UK.
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2
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Wang F, He Q, Yao NY, O'Donnell ME, Li H. The human ATAD5 has evolved unique structural elements to function exclusively as a PCNA unloader. Nat Struct Mol Biol 2024:10.1038/s41594-024-01332-4. [PMID: 38871854 DOI: 10.1038/s41594-024-01332-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 05/13/2024] [Indexed: 06/15/2024]
Abstract
Humans have three different proliferating cell nuclear antigen (PCNA) clamp-loading complexes: RFC and CTF18-RFC load PCNA onto DNA, but ATAD5-RFC can only unload PCNA from DNA. The underlying structural basis of ATAD5-RFC unloading is unknown. We show here that ATAD5 has two unique locking loops that appear to tie the complex into a rigid structure, and together with a domain that plugs the DNA-binding chamber, prevent conformation changes required for DNA binding, likely explaining why ATAD5-RFC is exclusively a PCNA unloader. These features are conserved in the yeast PCNA unloader Elg1-RFC. We observe intermediates in which PCNA bound to ATAD5-RFC exists as a closed planar ring, a cracked spiral or a gapped spiral. Surprisingly, ATAD5-RFC can open a PCNA gap between PCNA protomers 2 and 3, different from the PCNA protomers 1 and 3 gap observed in all previously characterized clamp loaders.
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Affiliation(s)
- Feng Wang
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Qing He
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Nina Y Yao
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Michael E O'Donnell
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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3
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He Q, Wang F, O’Donnell ME, Li H. Cryo-EM reveals a nearly complete PCNA loading process and unique features of the human alternative clamp loader CTF18-RFC. Proc Natl Acad Sci U S A 2024; 121:e2319727121. [PMID: 38669181 PMCID: PMC11067034 DOI: 10.1073/pnas.2319727121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/15/2024] [Indexed: 04/28/2024] Open
Abstract
The DNA sliding clamp PCNA is a multipurpose platform for DNA polymerases and many other proteins involved in DNA metabolism. The topologically closed PCNA ring needs to be cracked open and loaded onto DNA by a clamp loader, e.g., the well-studied pentameric ATPase complex RFC (RFC1-5). The CTF18-RFC complex is an alternative clamp loader found recently to bind the leading strand DNA polymerase ε and load PCNA onto leading strand DNA, but its structure and the loading mechanism have been unknown. By cryo-EM analysis of in vitro assembled human CTF18-RFC-DNA-PCNA complex, we have captured seven loading intermediates, revealing a detailed PCNA loading mechanism onto a 3'-ss/dsDNA junction by CTF18-RFC. Interestingly, the alternative loader has evolved a highly mobile CTF18 AAA+ module likely to lower the loading activity, perhaps to avoid competition with the RFC and to limit its role to leading strand clamp loading. To compensate for the lost stability due to the mobile AAA+ module, CTF18 has evolved a unique β-hairpin motif that reaches across RFC2 to interact with RFC5, thereby stabilizing the pentameric complex. Further, we found that CTF18 also contains a separation pin to locally melt DNA from the 3'-end of the primer; this ensures its ability to load PCNA to any 3'-ss/dsDNA junction, facilitated by the binding energy of the E-plug to the major groove. Our study reveals unique structural features of the human CTF18-RFC and contributes to a broader understanding of PCNA loading by the alternative clamp loaders.
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Affiliation(s)
- Qing He
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI49503
| | - Feng Wang
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI49503
| | - Michael E. O’Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, NY10065
- HHMI, The Rockefeller University, New York, NY10065
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI49503
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4
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Rankin BD, Rankin S. The MCM2-7 Complex: Roles beyond DNA Unwinding. BIOLOGY 2024; 13:258. [PMID: 38666870 PMCID: PMC11048021 DOI: 10.3390/biology13040258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024]
Abstract
The MCM2-7 complex is a hexameric protein complex that serves as a DNA helicase. It unwinds the DNA double helix during DNA replication, thereby providing the single-stranded replication template. In recent years, it has become clear that the MCM2-7 complex has additional functions that extend well beyond its role in DNA replication. Through physical and functional interactions with different pathways, it impacts other nuclear events and activities, including folding of the genome, histone inheritance, chromosome segregation, DNA damage sensing and repair, and gene transcription. Collectively, the diverse roles of the MCM2-7 complex suggest it plays a critical role in maintaining genome integrity by integrating the regulation of DNA replication with other pathways in the nucleus.
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Affiliation(s)
- Brooke D. Rankin
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
- Cell Biology Department, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Susannah Rankin
- Cell Cycle and Cancer Biology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA;
- Cell Biology Department, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
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5
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Tatsukawa K, Sakamoto R, Kawasoe Y, Kubota Y, Tsurimoto T, Takahashi T, Ohashi E. Resection of DNA double-strand breaks activates Mre11-Rad50-Nbs1- and Rad9-Hus1-Rad1-dependent mechanisms that redundantly promote ATR checkpoint activation and end processing in Xenopus egg extracts. Nucleic Acids Res 2024; 52:3146-3163. [PMID: 38349040 PMCID: PMC11014350 DOI: 10.1093/nar/gkae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 01/21/2024] [Accepted: 01/29/2024] [Indexed: 04/14/2024] Open
Abstract
Sensing and processing of DNA double-strand breaks (DSBs) are vital to genome stability. DSBs are primarily detected by the ATM checkpoint pathway, where the Mre11-Rad50-Nbs1 (MRN) complex serves as the DSB sensor. Subsequent DSB end resection activates the ATR checkpoint pathway, where replication protein A, MRN, and the Rad9-Hus1-Rad1 (9-1-1) clamp serve as the DNA structure sensors. ATR activation depends also on Topbp1, which is loaded onto DNA through multiple mechanisms. While different DNA structures elicit specific ATR-activation subpathways, the regulation and mechanisms of the ATR-activation subpathways are not fully understood. Using DNA substrates that mimic extensively resected DSBs, we show here that MRN and 9-1-1 redundantly stimulate Dna2-dependent long-range end resection and ATR activation in Xenopus egg extracts. MRN serves as the loading platform for ATM, which, in turn, stimulates Dna2- and Topbp1-loading. Nevertheless, MRN promotes Dna2-mediated end processing largely independently of ATM. 9-1-1 is dispensable for bulk Dna2 loading, and Topbp1 loading is interdependent with 9-1-1. ATR facilitates Mre11 phosphorylation and ATM dissociation. These data uncover that long-range end resection activates two redundant pathways that facilitate ATR checkpoint signaling and DNA processing in a vertebrate system.
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Affiliation(s)
- Kensuke Tatsukawa
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Reihi Sakamoto
- Graduate School of Systems Life Sciences, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshitaka Kawasoe
- Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yumiko Kubota
- Graduate School of Science, Osaka University, 1-1 Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Toshiki Tsurimoto
- Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Tatsuro S Takahashi
- Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Eiji Ohashi
- Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
- Nagahama Institute of Bio-Science and Technology, 1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
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6
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Landeck JT, Pajak J, Norman EK, Sedivy EL, Kelch BA. Differences between bacteria and eukaryotes in clamp loader mechanism, a conserved process underlying DNA replication. J Biol Chem 2024; 300:107166. [PMID: 38490435 PMCID: PMC11044049 DOI: 10.1016/j.jbc.2024.107166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/23/2024] [Accepted: 03/01/2024] [Indexed: 03/17/2024] Open
Abstract
Clamp loaders are pentameric ATPases that place circular sliding clamps onto DNA, where they function in DNA replication and genome integrity. The central activity of a clamp loader is the opening of the ring-shaped sliding clamp and the subsequent binding to primer-template (p/t)-junctions. The general architecture of clamp loaders is conserved across all life, suggesting that their mechanism is retained. Recent structural studies of the eukaryotic clamp loader replication factor C (RFC) revealed that it functions using a crab-claw mechanism, where clamp opening is coupled to a massive conformational change in the loader. Here we investigate the clamp loading mechanism of the Escherichia coli clamp loader at high resolution using cryo-electron microscopy. We find that the E. coli clamp loader opens the clamp using a crab-claw motion at a single pivot point, whereas the eukaryotic RFC loader uses motions distributed across the complex. Furthermore, we find clamp opening occurs in multiple steps, starting with a partly open state with a spiral conformation, and proceeding to a wide open clamp in a surprising planar geometry. Finally, our structures in the presence of p/t-junctions illustrate how the clamp closes around p/t-junctions and how the clamp loader initiates release from the loaded clamp. Our results reveal mechanistic distinctions in a macromolecular machine that is conserved across all domains of life.
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Affiliation(s)
- Jacob T Landeck
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Joshua Pajak
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Emily K Norman
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Emma L Sedivy
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Brian A Kelch
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA.
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7
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Nasheuer HP, Meaney AM. Starting DNA Synthesis: Initiation Processes during the Replication of Chromosomal DNA in Humans. Genes (Basel) 2024; 15:360. [PMID: 38540419 PMCID: PMC10969946 DOI: 10.3390/genes15030360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 06/14/2024] Open
Abstract
The initiation reactions of DNA synthesis are central processes during human chromosomal DNA replication. They are separated into two main processes: the initiation events at replication origins, the start of the leading strand synthesis for each replicon, and the numerous initiation events taking place during lagging strand DNA synthesis. In addition, a third mechanism is the re-initiation of DNA synthesis after replication fork stalling, which takes place when DNA lesions hinder the progression of DNA synthesis. The initiation of leading strand synthesis at replication origins is regulated at multiple levels, from the origin recognition to the assembly and activation of replicative helicase, the Cdc45-MCM2-7-GINS (CMG) complex. In addition, the multiple interactions of the CMG complex with the eukaryotic replicative DNA polymerases, DNA polymerase α-primase, DNA polymerase δ and ε, at replication forks play pivotal roles in the mechanism of the initiation reactions of leading and lagging strand DNA synthesis. These interactions are also important for the initiation of signalling at unperturbed and stalled replication forks, "replication stress" events, via ATR (ATM-Rad 3-related protein kinase). These processes are essential for the accurate transfer of the cells' genetic information to their daughters. Thus, failures and dysfunctions in these processes give rise to genome instability causing genetic diseases, including cancer. In their influential review "Hallmarks of Cancer: New Dimensions", Hanahan and Weinberg (2022) therefore call genome instability a fundamental function in the development process of cancer cells. In recent years, the understanding of the initiation processes and mechanisms of human DNA replication has made substantial progress at all levels, which will be discussed in the review.
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Affiliation(s)
- Heinz Peter Nasheuer
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, Biochemistry, University of Galway, H91 TK33 Galway, Ireland;
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8
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Hara K, Tatsukawa K, Nagata K, Iida N, Hishiki A, Ohashi E, Hashimoto H. Structural basis for intra- and intermolecular interactions on RAD9 subunit of 9-1-1 checkpoint clamp implies functional 9-1-1 regulation by RHINO. J Biol Chem 2024; 300:105751. [PMID: 38354779 PMCID: PMC10937111 DOI: 10.1016/j.jbc.2024.105751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
Eukaryotic DNA clamp is a trimeric protein featuring a toroidal ring structure that binds DNA on the inside of the ring and multiple proteins involved in DNA transactions on the outside. Eukaryotes have two types of DNA clamps: the replication clamp PCNA and the checkpoint clamp RAD9-RAD1-HUS1 (9-1-1). 9-1-1 activates the ATR-CHK1 pathway in DNA damage checkpoint, regulating cell cycle progression. Structure of 9-1-1 consists of two moieties: a hetero-trimeric ring formed by PCNA-like domains of three subunits and an intrinsically disordered C-terminal region of the RAD9 subunit, called RAD9 C-tail. The RAD9 C-tail interacts with the 9-1-1 ring and disrupts the interaction between 9-1-1 and DNA, suggesting a negative regulatory role for this intramolecular interaction. In contrast, RHINO, a 9-1-1 binding protein, interacts with both RAD1 and RAD9 subunits, positively regulating checkpoint activation by 9-1-1. This study presents a biochemical and structural analysis of intra- and inter-molecular interactions on the 9-1-1 ring. Biochemical analysis indicates that RAD9 C-tail binds to the hydrophobic pocket on the PCNA-like domain of RAD9, implying that the pocket is involved in multiple protein-protein interactions. The crystal structure of the 9-1-1 ring in complex with a RHINO peptide reveals that RHINO binds to the hydrophobic pocket of RAD9, shedding light on the RAD9-binding motif. Additionally, the study proposes a structural model of the 9-1-1-RHINO quaternary complex. Together, these findings provide functional insights into the intra- and inter-molecular interactions on the front side of RAD9, elucidating the roles of RAD9 C-tail and RHINO in checkpoint activation.
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Affiliation(s)
- Kodai Hara
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kensuke Tatsukawa
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Kiho Nagata
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Nao Iida
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Asami Hishiki
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Eiji Ohashi
- Faculty of Science, Department of Biology, Kyushu University, Fukuoka, Japan; Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, Japan
| | - Hiroshi Hashimoto
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.
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9
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Zheng F, Yao NY, Georgescu RE, Li H, O’Donnell ME. Structure of the PCNA unloader Elg1-RFC. SCIENCE ADVANCES 2024; 10:eadl1739. [PMID: 38427736 PMCID: PMC10906927 DOI: 10.1126/sciadv.adl1739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 01/26/2024] [Indexed: 03/03/2024]
Abstract
During DNA replication, the proliferating cell nuclear antigen (PCNA) clamps are loaded onto primed sites for each Okazaki fragment synthesis by the AAA+ heteropentamer replication factor C (RFC). PCNA encircling duplex DNA is quite stable and is removed from DNA by the dedicated clamp unloader Elg1-RFC. Here, we show the cryo-EM structure of Elg1-RFC in various states with PCNA. The structures reveal essential features of Elg1-RFC that explain how it is dedicated to PCNA unloading. Specifically, Elg1 contains two external loops that block opening of the Elg1-RFC complex for DNA binding, and an "Elg1 plug" domain that fills the central DNA binding chamber, thereby reinforcing the exclusive PCNA unloading activity of Elg1-RFC. Elg1-RFC was capable of unloading PCNA using non-hydrolyzable AMP-PNP. Both RFC and Elg1-RFC could remove PCNA from covalently closed circular DNA, indicating that PCNA unloading occurs by a mechanism that is distinct from PCNA loading. Implications for the PCNA unloading mechanism are discussed.
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Affiliation(s)
- Fengwei Zheng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Nina Y. Yao
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, NY, New York, USA
| | - Roxana E. Georgescu
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, NY, New York, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Michael E. O’Donnell
- DNA Replication Laboratory and Howard Hughes Medical Institute, The Rockefeller University, NY, New York, USA
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10
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Kawasoe Y, Shimokawa S, Gillespie PJ, Blow JJ, Tsurimoto T, Takahashi TS. The Atad5 RFC-like complex is the major unloader of proliferating cell nuclear antigen in Xenopus egg extracts. J Biol Chem 2024; 300:105588. [PMID: 38141767 PMCID: PMC10827553 DOI: 10.1016/j.jbc.2023.105588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/04/2023] [Accepted: 12/11/2023] [Indexed: 12/25/2023] Open
Abstract
Proliferating cell nuclear antigen (PCNA) is a homo-trimeric clamp complex that serves as the molecular hub for various DNA transactions, including DNA synthesis and post-replicative mismatch repair. Its timely loading and unloading are critical for genome stability. PCNA loading is catalyzed by Replication factor C (RFC) and the Ctf18 RFC-like complex (Ctf18-RLC), and its unloading is catalyzed by Atad5/Elg1-RLC. However, RFC, Ctf18-RLC, and even some subcomplexes of their shared subunits are capable of unloading PCNA in vitro, leaving an ambiguity in the division of labor in eukaryotic clamp dynamics. By using a system that specifically detects PCNA unloading, we show here that Atad5-RLC, which accounts for only approximately 3% of RFC/RLCs, nevertheless provides the major PCNA unloading activity in Xenopus egg extracts. RFC and Ctf18-RLC each account for approximately 40% of RFC/RLCs, while immunodepletion of neither Rfc1 nor Ctf18 detectably affects the rate of PCNA unloading in our system. PCNA unloading is dependent on the ATP-binding motif of Atad5, independent of nicks on DNA and chromatin assembly, and inhibited effectively by PCNA-interacting peptides. These results support a model in which Atad5-RLC preferentially unloads DNA-bound PCNA molecules that are free from their interactors.
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Affiliation(s)
| | - Sakiko Shimokawa
- Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Peter J Gillespie
- Division of Molecular, Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
| | - J Julian Blow
- Division of Molecular, Cell & Developmental Biology, School of Life Sciences, University of Dundee, Dundee, UK
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11
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Landeck JT, Pajak J, Norman EK, Sedivy EL, Kelch BA. Differences in clamp loader mechanism between bacteria and eukaryotes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569468. [PMID: 38076975 PMCID: PMC10705477 DOI: 10.1101/2023.11.30.569468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Clamp loaders are pentameric ATPases that place circular sliding clamps onto DNA, where they function in DNA replication and genome integrity. The central activity of a clamp loader is the opening of the ring-shaped sliding clamp, and the subsequent binding to primer-template (p/t)-junctions. The general architecture of clamp loaders is conserved across all life, suggesting that their mechanism is retained. Recent structural studies of the eukaryotic clamp loader Replication Factor C (RFC) revealed that it functions using a crab-claw mechanism, where clamp opening is coupled to a massive conformational change in the loader. Here we investigate the clamp loading mechanism of the E. coli clamp loader at high resolution using cryo-electron microscopy (cryo-EM). We find that the E. coli clamp loader opens the clamp using a crab-claw motion at a single pivot point, whereas the eukaryotic RFC loader uses motions distributed across the complex. Furthermore, we find clamp opening occurs in multiple steps, starting with a partly open state with a spiral conformation, and proceeding to a wide open clamp in a surprising planar geometry. Finally, our structures in the presence of p/t-junctions illustrate how clamp closes around p/t-junctions and how the clamp loader initiates release from the loaded clamp. Our results reveal mechanistic distinctions in a macromolecular machine that is conserved across all domains of life.
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Affiliation(s)
- Jacob T. Landeck
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester MA
| | - Joshua Pajak
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester MA
| | - Emily K. Norman
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester MA
| | - Emma L. Sedivy
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester MA
| | - Brian A. Kelch
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester MA
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12
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Fukumoto Y, Hoshino T, Nakayama Y, Ogra Y. The C-terminal tail of Rad17, iVERGE, binds the 9‒1‒1 complex independently of AAA+ ATPase domains to provide another clamp-loader interface. DNA Repair (Amst) 2023; 130:103567. [PMID: 37713925 DOI: 10.1016/j.dnarep.2023.103567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Revised: 08/17/2023] [Accepted: 09/03/2023] [Indexed: 09/17/2023]
Abstract
The ATR pathway plays a crucial role in maintaining genome integrity as the major DNA damage checkpoint. It also attracts attention as a therapeutic target in cancer treatment. The Rad17-RFC2-5 complex loads the Rad9-Hus1-Rad1 (9-1-1) DNA clamp complex onto damaged chromatin to activate the ATR pathway. We previously reported that phosphorylation of a polyanionic C-terminal tail of human Rad17, iVERGE, is essential for the interaction between Rad17 and the 9-1-1 complex. However, the molecular mechanism has remained unclear. Here, we show that iVERGE directly interacts with the Hus1 subunit of the 9-1-1 complex through Rad17-S667 phosphorylation independently of the AAA+ ATPase domains. An exogenous iVERGE peptide interacted with the 9-1-1 complex in vivo. The binding conformation of the iVERGE peptide was analyzed by de novo modeling with docking simulation, simulated annealing-molecular dynamics simulation, and the fragment molecular orbital method. The in silico analyses predicted the association of the iVERGE peptide with the hydrophobic and basic patches on the Hus1 protein, and the corresponding Hus1 mutants were deficient in the interaction with the iVERGE peptide in vivo. The iVERGE peptide occupied the same position as the C-terminus of Saccharomyces cerevisiae RAD24 on MEC3. The interaction energy calculation suggested that the Rad17 KYxxL motif and the iVERGE peptide are the primary and secondary interaction surfaces between the Rad17-RFC2-5 and 9-1-1 complexes. Our data reveal a novel molecular interface, iVERGE, between the Rad17-RFC2-5 and 9-1-1 complexes in vertebrates and implicate that Rad17 utilizes two distinct molecular interfaces to regulate the 9-1-1 complex.
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Affiliation(s)
- Yasunori Fukumoto
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan.
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
| | - Yuji Nakayama
- Department of Biochemistry & Molecular Biology, Kyoto Pharmaceutical University, Kyoto 607-8414, Japan
| | - Yasumitsu Ogra
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
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13
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Brambati A, Sacco O, Porcella S, Heyza J, Kareh M, Schmidt JC, Sfeir A. RHINO directs MMEJ to repair DNA breaks in mitosis. Science 2023; 381:653-660. [PMID: 37440612 PMCID: PMC10561558 DOI: 10.1126/science.adh3694] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023]
Abstract
Nonhomologous end-joining (NHEJ) and homologous recombination (HR) are the primary pathways for repairing DNA double-strand breaks (DSBs) during interphase, whereas microhomology-mediated end-joining (MMEJ) has been regarded as a backup mechanism. Through CRISPR-Cas9-based synthetic lethal screens in cancer cells, we identified subunits of the 9-1-1 complex (RAD9A-RAD1-HUS1) and its interacting partner, RHINO, as crucial MMEJ factors. We uncovered an unexpected function for RHINO in restricting MMEJ to mitosis. RHINO accumulates in M phase, undergoes Polo-like kinase 1 (PLK1) phosphorylation, and interacts with polymerase θ (Polθ), enabling its recruitment to DSBs for subsequent repair. Additionally, we provide evidence that MMEJ activity in mitosis repairs persistent DSBs that originate in S phase. Our findings offer insights into the synthetic lethal relationship between the genes POLQ and BRCA1 and BRAC2 and the synergistic effect of Polθ and poly(ADP-ribose) polymerase (PARP) inhibitors.
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Affiliation(s)
- Alessandra Brambati
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Olivia Sacco
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Sarina Porcella
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Joshua Heyza
- Institute for Quantitative Health Sciences and Engineering, Michigan State University; East Lansing, MI, USA
- Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University; East Lansing, MI, USA
| | - Mike Kareh
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY, USA
| | - Jens C. Schmidt
- Institute for Quantitative Health Sciences and Engineering, Michigan State University; East Lansing, MI, USA
- Department of Obstetrics, Gynecology, and Reproductive Biology, Michigan State University; East Lansing, MI, USA
| | - Agnel Sfeir
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center; New York, NY, USA
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14
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Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H. Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification on biology. Cell Rep 2023; 42:112694. [PMID: 37392384 PMCID: PMC10529453 DOI: 10.1016/j.celrep.2023.112694] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 05/01/2023] [Accepted: 06/09/2023] [Indexed: 07/03/2023] Open
Abstract
Rad24-RFC (replication factor C) loads the 9-1-1 checkpoint clamp onto the recessed 5' ends by binding a 5' DNA at an external surface site and threading the 3' single-stranded DNA (ssDNA) into 9-1-1. We find here that Rad24-RFC loads 9-1-1 onto DNA gaps in preference to a recessed 5' end, thus presumably leaving 9-1-1 on duplex 3' ss/double-stranded DNA (dsDNA) after Rad24-RFC ejects from DNA. We captured five Rad24-RFC-9-1-1 loading intermediates using a 10-nt gap DNA. We also determined the structure of Rad24-RFC-9-1-1 using a 5-nt gap DNA. The structures reveal that Rad24-RFC is unable to melt DNA ends and that a Rad24 loop limits the dsDNA length in the chamber. These observations explain Rad24-RFC's preference for a preexisting gap of over 5-nt ssDNA and suggest a direct role of the 9-1-1 in gap repair with various TLS (trans-lesion synthesis) polymerases in addition to signaling the ATR kinase.
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Affiliation(s)
- Fengwei Zheng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Roxana E Georgescu
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA
| | - Nina Y Yao
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA
| | - Michael E O'Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, NY, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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15
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Zheng F, Georgescu RE, Yao NY, O’Donnell ME, Li H. Structures of 9-1-1 DNA checkpoint clamp loading at gaps from start to finish and ramification to biology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539266. [PMID: 37205533 PMCID: PMC10187155 DOI: 10.1101/2023.05.03.539266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Recent structural studies show the Rad24-RFC loads the 9-1-1 checkpoint clamp onto a recessed 5' end by binding the 5' DNA on Rad24 at an external surface site and threading the 3' ssDNA into the well-established internal chamber and into 9-1-1. We find here that Rad24-RFC loads 9-1-1 onto DNA gaps in preference to a recessed 5' DNA end, thus presumably leaving 9-1-1 on a 3' ss/ds DNA after Rad24-RFC ejects from the 5' gap end and may explain reports of 9-1-1 directly functioning in DNA repair with various TLS polymerases, in addition to signaling the ATR kinase. To gain a deeper understanding of 9-1-1 loading at gaps we report high-resolution structures of Rad24-RFC during loading of 9-1-1 onto 10-nt and 5-nt gapped DNAs. At a 10-nt gap we captured five Rad24-RFC-9-1-1 loading intermediates in which the 9-1-1 DNA entry gate varies from fully open to fully closed around DNA using ATPγS, supporting the emerging view that ATP hydrolysis is not needed for clamp opening/closing, but instead for dissociation of the loader from the clamp encircling DNA. The structure of Rad24-RFC-9-1-1 at a 5-nt gap shows a 180° axially rotated 3'-dsDNA which orients the template strand to bridge the 3'- and 5'- junctions with a minimum 5-nt ssDNA. The structures reveal a unique loop on Rad24 that limits the length of dsDNA in the inner chamber, and inability to melt DNA ends unlike RFC, thereby explaining Rad24-RFC's preference for a preexisting ssDNA gap and suggesting a direct role in gap repair in addition to its checkpoint role.
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Affiliation(s)
- Fengwei Zheng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Roxana E. Georgescu
- DNA Replication Laboratory, The Rockefeller University, New York, New York, USA
| | - Nina Y. Yao
- DNA Replication Laboratory, The Rockefeller University, New York, New York, USA
| | - Michael E. O’Donnell
- DNA Replication Laboratory, The Rockefeller University, New York, New York, USA
- Howard Hughes Medical Institute, The Rockefeller University, New York, New York, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
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16
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Brambati A, Sacco O, Porcella S, Heyza J, Kareh M, Schmidt JC, Sfeir A. RHINO restricts MMEJ activity to mitosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.532763. [PMID: 36993461 PMCID: PMC10055031 DOI: 10.1101/2023.03.16.532763] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
DNA double-strand breaks (DSBs) are toxic lesions that can lead to genome instability if not properly repaired. Breaks incurred in G1 phase of the cell cycle are predominantly fixed by non-homologous end-joining (NHEJ), while homologous recombination (HR) is the primary repair pathway in S and G2. Microhomology-mediated end-joining (MMEJ) is intrinsically error-prone and considered a backup DSB repair pathway that becomes essential when HR and NHEJ are compromised. In this study, we uncover MMEJ as the major DSB repair pathway in M phase. Using CRISPR/Cas9-based synthetic lethal screens, we identify subunits of the 9-1-1 complex (RAD9A-HUS1-RAD1) and its interacting partner, RHINO, as critical MMEJ factors. Mechanistically, we show that the function of 9-1-1 and RHINO in MMEJ is inconsistent with their well-established role in ATR signaling. Instead, RHINO plays an unexpected and essential role in directing mutagenic repair to M phase by directly binding to Polymerase theta (Polθ) and promoting its recruitment to DSBs in mitosis. In addition, we provide evidence that mitotic MMEJ repairs persistent DNA damage that originates in S phase but is not repaired by HR. The latter findings could explain the synthetic lethal relationship between POLQ and BRCA1/2 and the synergistic effect of Polθ and PARP inhibitors. In summary, our study identifies MMEJ as the primary pathway for repairing DSBs during mitosis and highlights an unanticipated role for RHINO in directing mutagenic repair to M phase.
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17
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Hara K, Hishiki A, Hoshino T, Nagata K, Iida N, Sawada Y, Ohashi E, Hashimoto H. The 9-1-1 DNA clamp subunit RAD1 forms specific interactions with clamp loader RAD17, revealing functional implications for binding-protein RHINO. J Biol Chem 2023; 299:103061. [PMID: 36841485 PMCID: PMC10060742 DOI: 10.1016/j.jbc.2023.103061] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 02/18/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023] Open
Abstract
The RAD9-RAD1-HUS1 complex (9-1-1) is a eukaryotic DNA clamp with a crucial role at checkpoints for DNA damage. The ring-like structure of 9-1-1 is opened for loading onto 5' recessed DNA by the clamp loader RAD17 RFC-like complex (RAD17-RLC), in which the RAD17 subunit is responsible for specificity to 9-1-1. Loading of 9-1-1 is required for activation of the ATR-CHK1 checkpoint pathway and the activation is stimulated by a 9-1-1 interacting protein, RHINO, which interacts with 9-1-1 via a recently identified RAD1-binding motif. This discovery led to the hypothesis that other interacting proteins may contain a RAD1-binding motif as well. Here, we show that vertebrate RAD17 proteins also have a putative RAD1-binding motif in their N-terminal regions, and we report the crystal structure of human 9-1-1 bound to a human RAD17 peptide incorporating the motif at 2.1 Å resolution. Our structure confirms that the N-terminal region of RAD17 binds to the RAD1 subunit of 9-1-1 via specific interactions. Furthermore, we show that the RAD1-binding motif of RHINO disturbs the interaction of the N-terminal region of RAD17 with 9-1-1. Our results provide deeper understanding of how RAD17-RLC specifically recognizes 9-1-1 and imply that RHINO has a functional role in 9-1-1 loading/unloading and checkpoint activation.
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Affiliation(s)
- Kodai Hara
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Asami Hishiki
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Takako Hoshino
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kiho Nagata
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Nao Iida
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yukimasa Sawada
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Eiji Ohashi
- Department of Biology, Faculty of Science, Kyushu University, Fukuoka, Japan
| | - Hiroshi Hashimoto
- School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.
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18
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Day M, Oliver AW, Pearl LH. Structure of the human RAD17-RFC clamp loader and 9-1-1 checkpoint clamp bound to a dsDNA-ssDNA junction. Nucleic Acids Res 2022; 50:8279-8289. [PMID: 35819203 PMCID: PMC9371934 DOI: 10.1093/nar/gkac588] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 11/14/2022] Open
Abstract
The RAD9-RAD1-HUS1 (9-1-1) clamp forms one half of the DNA damage checkpoint system that signals the presence of substantial regions of single-stranded DNA arising from replication fork collapse or resection of DNA double strand breaks. Loaded at the 5'-recessed end of a dsDNA-ssDNA junction by the RAD17-RFC clamp loader complex, the phosphorylated C-terminal tail of the RAD9 subunit of 9-1-1 engages with the mediator scaffold TOPBP1 which in turn activates the ATR kinase, localised through the interaction of its constitutive partner ATRIP with RPA-coated ssDNA. Using cryogenic electron microscopy (cryoEM) we have determined the structure of a complex of the human RAD17-RFC clamp loader bound to human 9-1-1, engaged with a dsDNA-ssDNA junction. The structure answers the key questions of how RAD17 confers specificity for 9-1-1 over PCNA, and how the clamp loader specifically recognises the recessed 5' DNA end and fixes the orientation of 9-1-1 on the ssDNA.
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Affiliation(s)
- Matthew Day
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London SW1E 6BT, UK
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19
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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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20
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Zheng F, Georgescu RE, Yao NY, Li H, O'Donnell ME. Cryo-EM structures reveal that RFC recognizes both the 3'- and 5'-DNA ends to load PCNA onto gaps for DNA repair. eLife 2022; 11:77469. [PMID: 35829698 PMCID: PMC9293004 DOI: 10.7554/elife.77469] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/06/2022] [Indexed: 12/27/2022] Open
Abstract
RFC uses ATP to assemble PCNA onto primed sites for replicative DNA polymerases d and e. The RFC pentamer forms a central chamber that binds 3' ss/ds DNA junctions to load PCNA onto DNA during replication. We show here five structures that identify a 2nd DNA binding site in RFC that binds a 5' duplex. This 5' DNA site is located between the N-terminal BRCT domain and AAA+ module of the large Rfc1 subunit. Our structures reveal ideal binding to a 7-nt gap, which includes 2 bp unwound by the clamp loader. Biochemical studies show enhanced binding to 5 and 10 nt gaps, consistent with the structural results. Because both 3' and 5' ends are present at a ssDNA gap, we propose that the 5' site facilitates RFC's PCNA loading activity at a DNA damage-induced gap to recruit gap-filling polymerases. These findings are consistent with genetic studies showing that base excision repair of gaps greater than 1 base requires PCNA and involves the 5' DNA binding domain of Rfc1. We further observe that a 5' end facilitates PCNA loading at an RPA coated 30-nt gap, suggesting a potential role of the RFC 5'-DNA site in lagging strand DNA synthesis.
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Affiliation(s)
- Fengwei Zheng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, United States
| | - Roxana E Georgescu
- DNA Replication Laboratory, Rockefeller University, New York, United States
| | - Nina Y Yao
- DNA Replication Laboratory, Rockefeller University, New York, United States
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, United States
| | - Michael E O'Donnell
- Howard Hughes Medical Institute, Rockefeller University, New York, United States
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21
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Hashimoto H, Hara K, Hishiki A. Structural basis for molecular interactions on the eukaryotic DNA sliding clamps PCNA and RAD9-RAD1-HUS1. J Biochem 2022; 172:189-196. [PMID: 35731009 DOI: 10.1093/jb/mvac053] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/13/2022] [Indexed: 11/14/2022] Open
Abstract
DNA sliding clamps are widely conserved in all living organisms and play crucial roles in DNA replication and repair. Each DNA sliding clamp is a doughnut-shaped protein with a quaternary structure that encircles the DNA strand and recruits various factors involved in DNA replication and repair, thereby stimulating their biological functions. Eukaryotes have two types of DNA sliding clamp, proliferating cell nuclear antigen (PCNA) and RAD9-RAD1-HUS1 (9-1-1). The homo-trimer PCNA physically interacts with multiple proteins containing a PIP-box and/or APIM. The two motifs bind to PCNA by a similar mechanism; in addition, the bound PCNA structure is similar, implying a universality of PCNA interactions. In contrast to PCNA, 9-1-1 is a hetero-trimer composed of RAD9, RAD1, and HUS1 subunits. Although 9-1-1 forms a trimeric ring structure similar to PCNA, the C-terminal extension of the RAD9 is intrinsically unstructured. Based on the structural similarity between PCNA and 9-1-1, the mechanism underlying the interaction of 9-1-1 with its partners was thought to be analogous to that of PCNA. Unexpectedly, however, the recent structure of the 9-1-1 ring bound to a partner has revealed a novel interaction distinct from that of PCNA, potentially providing a new principle for molecular interactions on DNA sliding clamps.
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Affiliation(s)
- Hiroshi Hashimoto
- School of Pharmaceutical Science, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Kodai Hara
- School of Pharmaceutical Science, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
| | - Asami Hishiki
- School of Pharmaceutical Science, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka, Shizuoka 422-8002, Japan
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22
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The partner-swapping sliding clamp loader exposed. Nat Struct Mol Biol 2022; 29:283-286. [PMID: 35410371 DOI: 10.1038/s41594-022-00761-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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