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Zheng F, Georgescu RE, Yao NY, O'Donnell ME, Li H. DNA is loaded through the 9-1-1 DNA checkpoint clamp in the opposite direction of the PCNA clamp. Nat Struct Mol Biol 2022; 29:376-385. [PMID: 35314830 PMCID: PMC9010301 DOI: 10.1038/s41594-022-00742-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 02/11/2022] [Indexed: 12/11/2022]
Abstract
The 9-1-1 DNA checkpoint clamp is loaded onto 5'-recessed DNA to activate the DNA damage checkpoint that arrests the cell cycle. The 9-1-1 clamp is a heterotrimeric ring that is loaded in Saccharomyces cerevisiae by Rad24-RFC (hRAD17-RFC), an alternate clamp loader in which Rad24 replaces Rfc1 in the RFC1-5 clamp loader of proliferating cell nuclear antigen (PCNA). The 9-1-1 clamp loading mechanism has been a mystery, because, unlike RFC, which loads PCNA onto a 3'-recessed junction, Rad24-RFC loads the 9-1-1 ring onto a 5'-recessed DNA junction. Here we report two cryo-EM structures of Rad24-RFC-DNA with a closed or 27-Å open 9-1-1 clamp. The structures reveal a completely unexpected mechanism by which a clamp can be loaded onto DNA. Unlike RFC, which encircles DNA, Rad24 binds 5'-DNA on its surface, not inside the loader, and threads the 3' ssDNA overhang into the 9-1-1 clamp from above the ring.
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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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2
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Zhang Z, Cai Z, Li K, Fang Y, An L, Hu Z, Wang S, Hang H. The Effect of Ionizing Radiation on mRNA Levels of the DNA Damage Response Genes Rad9, Rad1 and Hus1 in Various Mouse Tissues. Radiat Res 2015; 183:94-104. [DOI: 10.1667/rr13781.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Zhenya Zhang
- Department of General Surgery, the Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, 050011 China
| | - Zeyuan Cai
- Center for Peptide and Protein Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Kaiming Li
- Department of General Surgery, the Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, 050011 China
| | - Yu Fang
- Center for Peptide and Protein Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Lili An
- Center for Peptide and Protein Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhishang Hu
- Center for Peptide and Protein Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shihua Wang
- School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haiying Hang
- Center for Peptide and Protein Pharmaceuticals, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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3
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Lyndaker AM, Vasileva A, Wolgemuth DJ, Weiss RS, Lieberman HB. Clamping down on mammalian meiosis. Cell Cycle 2013; 12:3135-45. [PMID: 24013428 DOI: 10.4161/cc.26061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The RAD9A-RAD1-HUS1 (9-1-1) complex is a PCNA-like heterotrimeric clamp that binds damaged DNA to promote cell cycle checkpoint signaling and DNA repair. While various 9-1-1 functions in mammalian somatic cells have been established, mounting evidence from lower eukaryotes predicts critical roles in meiotic germ cells as well. This was investigated in 2 recent studies in which the 9-1-1 complex was disrupted specifically in the mouse male germline through conditional deletion of Rad9a or Hus1. Loss of these clamp subunits led to severely impaired fertility and meiotic defects, including faulty DNA double-strand break repair. While 9-1-1 is critical for ATR kinase activation in somatic cells, these studies did not reveal major defects in ATR checkpoint pathway signaling in meiotic cells. Intriguingly, this new work identified separable roles for 9-1-1 subunits, namely RAD9A- and HUS1-independent roles for RAD1. Based on these studies and the high-level expression of the paralogous proteins RAD9B and HUS1B in testis, we propose a model in which multiple alternative 9-1-1 clamps function during mammalian meiosis to ensure genome maintenance in the germline.
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Affiliation(s)
- Amy M Lyndaker
- Department of Biomedical Sciences; Cornell University; Ithaca, NY USA
| | - Ana Vasileva
- Center for Radiological Research; College of Physicians and Surgeons; Columbia University Medical Center; New York, NY USA
| | - Debra J Wolgemuth
- Genetics & Development and Obstetrics & Gynecology; The Institute of Human Nutrition; Herbert Irving Comprehensive Cancer Center; Columbia University Medical Center; New York, NY USA
| | - Robert S Weiss
- Department of Biomedical Sciences; Cornell University; Ithaca, NY USA
| | - Howard B Lieberman
- Department of Environmental Health Sciences; Mailman School of Public Health; Columbia University Medical Center; New York, NY USA
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4
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Sohn SY, Cho Y. Crystal structure of the human rad9-hus1-rad1 clamp. J Mol Biol 2009; 390:490-502. [PMID: 19464297 DOI: 10.1016/j.jmb.2009.05.028] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2009] [Revised: 05/13/2009] [Accepted: 05/15/2009] [Indexed: 11/17/2022]
Abstract
Three evolutionarily conserved proteins, Rad9, Hus1, and Rad1, form a heterotrimeric 9-1-1 complex that plays critical roles in cellular responses to DNA damage by activating checkpoints and by recruiting DNA repair enzymes to DNA lesions. We have determined the crystal structure of the human Rad9 (residues 1-272)-Hus1-Rad1 complex at 2.5 A resolution. The 9(1-272)-1-1 complex forms a closed ring, with each subunit having a similar structure. Despite its high level of similarity to proliferating cell nucleus antigen in terms of overall structure, the 9(1-272)-1-1 complex exhibits notable differences in local structures, including interdomain connecting loops, H2 and H3 helices, and loops in the vicinity of the helices of each subunit. These local structural variations provide several unique features to the 9-1-1 heterotrimeric complex-including structures of intermolecular interfaces and the inner surface around the central hole, and different electrostatic potentials at and near the interdomain connecting loops of each 9-1-1 subunit-compared to the proliferating cell nucleus antigen trimer. We propose that these structural features allow the 9-1-1 complex to bind to a damaged DNA during checkpoint control and to serve as a platform for base excision repair. We also show that the 9(1-272)-1-1 complex, but not the full-length 9-1-1 complex, forms a stable complex with the 5' recessed DNA, suggesting that the C-terminal tail of Rad9 is involved in the regulation of the 9-1-1 complex in DNA binding.
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Affiliation(s)
- Sun Young Sohn
- National Creative Research Center for Structural Biology and Department of Life Science, Pohang University of Science and Technology, Hyo-ja dong, Pohang, KyungBook, South Korea
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5
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Cabrera G, Cabrejos ME, Morassutti AL, Cabezón C, Orellana J, Hellman U, Zaha A, Galanti N. DNA damage, RAD9 and fertility/infertility of Echinococcus granulosus hydatid cysts. J Cell Physiol 2008; 216:498-506. [PMID: 18348165 DOI: 10.1002/jcp.21418] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hydatidosis, caused by the larval stage of the platyhelminth parasite Echinococcus granulosus, affects human and animal health. Hydatid fertile cysts are formed in intermediate hosts (human and herbivores) producing protoscoleces, the infective form to canines, at their germinal layers. Infertile cysts are also formed, but they are unable to produce protoscoleces. The molecular mechanisms involved in hydatid cysts fertility/infertility are unknown. Nevertheless, previous work from our laboratory has suggested that apoptosis is involved in hydatid cyst infertility and death. On the other hand, fertile hydatid cysts can resist oxidative damage due to reactive oxygen and nitrogen species. On these foundations, we have postulated that when oxidative damage of DNA in the germinal layers exceeds the capability of DNA repair mechanisms, apoptosis is triggered and hydatid cysts infertility occurs. We describe a much higher percentage of nuclei with oxidative DNA damage in dead protoscoleces and in the germinal layer of infertile cysts than in fertile cysts, suggesting that DNA repair mechanisms are active in fertile cysts. rad9, a conserved gene, plays a key role in cell cycle checkpoint modulation and DNA repair. We found that RAD9 of E. granulosus (EgRAD9) is expressed at the mRNA and protein levels. As it was found in other eukaryotes, EgRAD9 is hyperphosphorylated in response to DNA damage. Our results suggest that molecules involved in DNA repair in the germinal layer of fertile hydatid cysts and in protoscoleces, such as EgRAD9, may allow preserving the fertility of hydatid cysts in the presence of ROS and RNS.
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Affiliation(s)
- Gonzalo Cabrera
- Programa Disciplinario de Biología Celular y Molecular, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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6
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Lieberman HB. Rad9, an evolutionarily conserved gene with multiple functions for preserving genomic integrity. J Cell Biochem 2006; 97:690-7. [PMID: 16365875 DOI: 10.1002/jcb.20759] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The Rad9 gene is evolutionarily conserved. Analysis of the gene from yeast, mouse and human reveal roles in multiple, fundamental biological processes primarily but not exclusively important for regulating genomic integrity. The encoded mammalian proteins participate in promoting resistance to DNA damage, cell cycle checkpoint control, DNA repair, and apoptosis. Other functions include a role in embryogenesis, the transactivation of multiple target genes, co-repression of androgen-induced transcription activity of the androgen receptor, a 3'-5' exonuclease activity, and the regulation of ribonucleotide synthesis. Analyses of the functions of Rad9, and in particular its role in regulating and coordinating numerous fundamental biological activities, should not only provide information about the molecular mechanisms of several individual cellular processes, but might also lend insight into the more global control and coordination of what at least superficially present as independent pathways.
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Affiliation(s)
- Howard B Lieberman
- Center for Radiological Research, Columbia University, 630 W. 168th St., New York, New York 10032, USA.
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Travis LB, Rabkin CS, Brown LM, Allan JM, Alter BP, Ambrosone CB, Begg CB, Caporaso N, Chanock S, DeMichele A, Figg WD, Gospodarowicz MK, Hall EJ, Hisada M, Inskip P, Kleinerman R, Little JB, Malkin D, Ng AK, Offit K, Pui CH, Robison LL, Rothman N, Shields PG, Strong L, Taniguchi T, Tucker MA, Greene MH. Cancer Survivorship—Genetic Susceptibility and Second Primary Cancers: Research Strategies and Recommendations. ACTA ACUST UNITED AC 2006; 98:15-25. [PMID: 16391368 DOI: 10.1093/jnci/djj001] [Citation(s) in RCA: 216] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cancer survivors constitute 3.5% of the United States population, but second primary malignancies among this high-risk group now account for 16% of all cancer incidence. Although few data currently exist regarding the molecular mechanisms for second primary cancers and other late outcomes after cancer treatment, the careful measurement and documentation of potentially carcinogenic treatments (chemotherapy and radiotherapy) provide a unique platform for in vivo research on gene-environment interactions in human carcinogenesis. We review research priorities identified during a National Cancer Institute (NCI)-sponsored workshop entitled "Cancer Survivorship--Genetic Susceptibility and Second Primary Cancers." These priorities include 1) development of a national research infrastructure for studies of cancer survivorship; 2) creation of a coordinated system for biospecimen collection; 3) development of new technology, bioinformatics, and biomarkers; 4) design of new epidemiologic methods; and 5) development of evidence-based clinical practice guidelines. Many of the infrastructure resources and design strategies that would facilitate research in this area also provide a foundation for the study of other important nonneoplastic late effects of treatment and psychosocial concerns among cancer survivors. These research areas warrant high priority to promote NCI's goal of eliminating pain and suffering related to cancer.
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Affiliation(s)
- Lois B Travis
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20892, USA.
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8
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Zhu A, Zhou H, Leloup C, Marino SA, Geard CR, Hei TK, Lieberman HB. Differential impact of mouse Rad9 deletion on ionizing radiation-induced bystander effects. Radiat Res 2005; 164:655-61. [PMID: 16238443 PMCID: PMC4052439 DOI: 10.1667/rr3458.1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The cellular response to ionizing radiation is not limited to cells irradiated directly but can be demonstrated in neighboring "bystander" populations. The ability of mouse embryonic stem (ES) cells to express a bystander effect and the role of the radioresistance gene Rad9 were tested. Mouse ES cells differing in Rad9 status were exposed to broad-beam 125 keV/ microm 3He alpha particles. All populations, when confluent, demonstrated a dose-independent bystander effect with respect to cell killing, and the Rad9-/- genotype did not selectively alter that response or cell killing after direct exposure to this high-LET radiation. In contrast, relative to Rad9+/+ cells, the homozygous mutant was sensitive to direct exposure to alpha particles when in log phase, providing evidence of a role for Rad9 in repair of potentially lethal damage. Direct exposure to alpha particles induced an increase in the frequency of apoptosis and micronucleus formation, regardless of Rad9 status, although the null mutant showed high spontaneous levels of both end points. All populations demonstrated alpha-particle-induced bystander apoptosis, but that effect was most prominent in Rad9-/- cells. Minimal alpha-particle induction of micronuclei in bystander cells was observed, except for the Rad9-/- mutant, where a significant increase above background was detected. Therefore, the Rad9 null mutation selectively sensitizes mouse ES cells to spontaneous and high-LET radiation-induced bystander apoptosis and micronucleus formation, but it has much less impact on cell killing by direct or bystander alpha-particle exposure. Results are presented in the context of defining the function of Rad9 in the cellular response to radiation and its differential effects on individual bystander end points.
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Affiliation(s)
| | | | | | | | | | | | - Howard B. Lieberman
- Address for correspondence: Center for Radiological Research, Columbia University College of Physicians and Surgeons, 630 W. 168th St., New York, NY 10032;
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9
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Hopkins KM, Auerbach W, Wang XY, Hande MP, Hang H, Wolgemuth DJ, Joyner AL, Lieberman HB. Deletion of mouse rad9 causes abnormal cellular responses to DNA damage, genomic instability, and embryonic lethality. Mol Cell Biol 2004; 24:7235-48. [PMID: 15282322 PMCID: PMC479733 DOI: 10.1128/mcb.24.16.7235-7248.2004] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The fission yeast Schizosaccharomyces pombe rad9 gene promotes cell survival through activation of cell cycle checkpoints induced by DNA damage. Mouse embryonic stem cells with a targeted deletion of Mrad9, the mouse ortholog of this gene, were created to evaluate its function in mammals. Mrad9(-/-) cells demonstrated a marked increase in spontaneous chromosome aberrations and HPRT mutations, indicating a role in the maintenance of genomic integrity. These cells were also extremely sensitive to UV light, gamma rays, and hydroxyurea, and heterozygotes were somewhat sensitive to the last two agents relative to Mrad9(+/+) controls. Mrad9(-/-) cells could initiate but not maintain gamma-ray-induced G(2) delay and retained the ability to delay DNA synthesis rapidly after UV irradiation, suggesting that checkpoint abnormalities contribute little to the radiosensitivity observed. Ectopic expression of Mrad9 or human HRAD9 complemented Mrad9(-/-) cell defects, indicating that the gene has radioresponse and genomic maintenance functions that are evolutionarily conserved. Mrad9(+/-) mice were generated, but heterozygous intercrosses failed to yield Mrad9(-/-) pups, since embryos died at midgestation. Furthermore, Mrad9(-/-) mouse embryo fibroblasts were not viable. These investigations establish Mrad9 as a key mammalian genetic element of pathways that regulate the cellular response to DNA damage, maintenance of genomic integrity, and proper embryonic development.
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Affiliation(s)
- Kevin M Hopkins
- Center for Radiological Research, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
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10
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Affiliation(s)
- T Humphrey
- Radiation and Genome Stability Unit, Medical Research Council, Harwell, Oxfordshire OX11 ORD, Didcot, UK
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11
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Weiss RS, Kostrub CF, Enoch T, Leder P. Mouse Hus1, a homolog of the Schizosaccharomyces pombe hus1+ cell cycle checkpoint gene. Genomics 1999; 59:32-9. [PMID: 10395797 DOI: 10.1006/geno.1999.5865] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cell cycle checkpoints are regulatory mechanisms that arrest the cell cycle or initiate programmed cell death when critical events such as DNA replication fail to be completed or when DNA or spindle damage occurs. In fission yeast, cell cycle checkpoint responses to DNA replication blocks and DNA damage require the hus1+ gene. Mammalian homologs of hus1+ were recently identified, and here we report a detailed analysis of mouse Hus1. An approximately 4.2-kb full-length cDNA encoding the 32-kDa mouse Hus1 protein was isolated. The genomic structure and exon-intron boundary sequences of the gene were determined, and mouse Hus1 was found to consist of nine exons. Mouse Hus1 was mapped to the proximal end of chromosome 11 and is therefore a candidate gene for the mouse mutation germ cell deficient, which maps to the same genomic region. Finally, mouse Hus1 was found to be expressed in a variety of adult tissues and at several stages of embryonic development.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Blotting, Northern
- Cell Cycle/genetics
- Cell Cycle Proteins/genetics
- Chromosome Mapping
- Crosses, Genetic
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Fungal/chemistry
- DNA, Fungal/genetics
- Embryo, Mammalian/metabolism
- Embryonic and Fetal Development
- Female
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Fungal
- Genes, Fungal/genetics
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Inbred Strains
- Molecular Sequence Data
- Muridae
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Schizosaccharomyces/genetics
- Schizosaccharomyces pombe Proteins
- Sequence Analysis, DNA
- Tissue Distribution
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Affiliation(s)
- R S Weiss
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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