1
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Boavida A, Napolitano LM, Santos D, Cortone G, Jegadesan NK, Onesti S, Branzei D, Pisani FM. FANCJ DNA helicase is recruited to the replisome by AND-1 to ensure genome stability. EMBO Rep 2024; 25:876-901. [PMID: 38177925 PMCID: PMC10897178 DOI: 10.1038/s44319-023-00044-y] [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: 10/09/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024] Open
Abstract
FANCJ, a DNA helicase linked to Fanconi anemia and frequently mutated in cancers, counteracts replication stress by dismantling unconventional DNA secondary structures (such as G-quadruplexes) that occur at the DNA replication fork in certain sequence contexts. However, how FANCJ is recruited to the replisome is unknown. Here, we report that FANCJ directly binds to AND-1 (the vertebrate ortholog of budding yeast Ctf4), a homo-trimeric protein adaptor that connects the CDC45/MCM2-7/GINS replicative DNA helicase with DNA polymerase α and several other factors at DNA replication forks. The interaction between FANCJ and AND-1 requires the integrity of an evolutionarily conserved Ctf4-interacting protein (CIP) box located between the FANCJ helicase motifs IV and V. Disruption of the CIP box significantly reduces FANCJ association with the replisome, causing enhanced DNA damage, decreased replication fork recovery and fork asymmetry in cells unchallenged or treated with Pyridostatin, a G-quadruplex-binder, or Mitomycin C, a DNA inter-strand cross-linking agent. Cancer-relevant FANCJ CIP box variants display reduced AND-1-binding and enhanced DNA damage, a finding that suggests their potential role in cancer predisposition.
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Affiliation(s)
- Ana Boavida
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
- Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
| | | | - Diana Santos
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
- Università degli Studi della Campania "Luigi Vanvitelli", Caserta, Italy
| | - Giuseppe Cortone
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy
| | | | - Silvia Onesti
- Structural Biology Laboratory, Elettra-Sincrotrone Trieste, Trieste, Italy
| | - Dana Branzei
- IFOM ETS-The AIRC Institute of Molecular Oncology, Milan, Italy
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Pavia, Italy
| | - Francesca M Pisani
- Istituto di Biochimica e Biologia Cellulare, Consiglio Nazionale delle Ricerche, Naples, Italy.
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2
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Emond-Fraser V, Larouche M, Kubiniok P, Bonneil É, Li J, Bourouh M, Frizzi L, Thibault P, Archambault V. Identification of PP2A-B55 targets uncovers regulation of emerin during nuclear envelope reassembly in Drosophila. Open Biol 2023; 13:230104. [PMID: 37463656 PMCID: PMC10353892 DOI: 10.1098/rsob.230104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/21/2023] [Indexed: 07/20/2023] Open
Abstract
Mitotic exit requires the dephosphorylation of many proteins whose phosphorylation was needed for mitosis. Protein phosphatase 2A with its B55 regulatory subunit (PP2A-B55) promotes this transition. However, the events and substrates that it regulates are incompletely understood. We used proteomic approaches in Drosophila to identify proteins that interact with and are dephosphorylated by PP2A-B55. Among several candidates, we identified emerin (otefin in Drosophila). Emerin resides in the inner nuclear membrane and interacts with the DNA-binding protein barrier-to-autointegration factor (BAF) via a LEM domain. We found that the phosphorylation of emerin at Ser50 and Ser54 near its LEM domain negatively regulates its association with BAF, lamin and additional emerin in mitosis. We show that dephosphorylation of emerin at these sites by PP2A-B55 determines the timing of nuclear envelope reformation. Genetic experiments indicate that this regulation is required during embryonic development. Phosphoregulation of the emerin-BAF complex formation by PP2A-B55 appears as a key event of mitotic exit that is likely conserved across species.
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Affiliation(s)
- Virginie Emond-Fraser
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, H3T 1J4, Quebec, Canada
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, H3T 1J4, Quebec, Canada
| | - Myreille Larouche
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, H3T 1J4, Quebec, Canada
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, H3T 1J4, Quebec, Canada
| | - Peter Kubiniok
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, H3T 1J4, Quebec, Canada
| | - Éric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, H3T 1J4, Quebec, Canada
| | - Jingjing Li
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, H3T 1J4, Quebec, Canada
| | - Mohammed Bourouh
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, H3T 1J4, Quebec, Canada
| | - Laura Frizzi
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, H3T 1J4, Quebec, Canada
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, H3T 1J4, Quebec, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, H3T 1J4, Quebec, Canada
- Département de chimie, Université de Montréal, Montréal, H3T 1J4, Quebec, Canada
| | - Vincent Archambault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, H3T 1J4, Quebec, Canada
- Département de biochimie et médecine moléculaire, Université de Montréal, Montréal, H3T 1J4, Quebec, Canada
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3
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Yamaguchi M, Cotterill S. Association of Mutations in Replicative DNA Polymerase Genes with Human Disease: Possible Application of Drosophila Models for Studies. Int J Mol Sci 2023; 24:ijms24098078. [PMID: 37175782 PMCID: PMC10178534 DOI: 10.3390/ijms24098078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Replicative DNA polymerases, such as DNA polymerase α-primase, δ and ε, are multi-subunit complexes that are responsible for the bulk of nuclear DNA replication during the S phase. Over the last decade, extensive genome-wide association studies and expression profiling studies of the replicative DNA polymerase genes in human patients have revealed a link between the replicative DNA polymerase genes and various human diseases and disorders including cancer, intellectual disability, microcephalic primordial dwarfism and immunodeficiency. These studies suggest the importance of dissecting the mechanisms involved in the functioning of replicative DNA polymerases in understanding and treating a range of human diseases. Previous studies in Drosophila have established this organism as a useful model to understand a variety of human diseases. Here, we review the studies on Drosophila that explored the link between DNA polymerases and human disease. First, we summarize the recent studies linking replicative DNA polymerases to various human diseases and disorders. We then review studies on replicative DNA polymerases in Drosophila. Finally, we suggest the possible use of Drosophila models to study human diseases and disorders associated with replicative DNA polymerases.
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Affiliation(s)
| | - Sue Cotterill
- Molecular and Clinical Sciences Research Institute, St George's University of London, London SW17 0RE, UK
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4
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Li J, Zhang Y, Sun J, Chen L, Gou W, Chen C, Zhou Y, Li Z, Chan DW, Huang R, Pei H, Zheng W, Li Y, Xia M, Zhu W. Discovery and characterization of potent And-1 inhibitors for cancer treatment. Clin Transl Med 2021; 11:e627. [PMID: 34923765 PMCID: PMC8684776 DOI: 10.1002/ctm2.627] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 10/01/2021] [Accepted: 10/08/2021] [Indexed: 12/19/2022] Open
Abstract
Acidic nucleoplasmic DNA-binding protein 1 (And-1), an important factor for deoxyribonucleic acid (DNA) replication and repair, is overexpressed in many types of cancer but not in normal tissues. Although multiple independent studies have elucidated And-1 as a promising target gene for cancer therapy, an And-1 inhibitor has yet to be identified. Using an And-1 luciferase reporter assay to screen the Library of Pharmacologically Active Compounds (LOPAC) in a high throughput screening (HTS) platform, and then further screen the compound analog collection, we identified two potent And-1 inhibitors, bazedoxifene acetate (BZA) and an uncharacterized compound [(E)-5-(3,4-dichlorostyryl)benzo[c][1,2]oxaborol-1(3H)-ol] (CH3), which specifically inhibit And-1 by promoting its degradation. Specifically, through direct interaction with And-1 WD40 domain, CH3 interrupts the polymerization of And-1. Depolymerization of And-1 promotes its interaction with E3 ligase Cullin 4B (CUL4B), resulting in its ubiquitination and subsequent degradation. Furthermore, CH3 suppresses the growth of a broad range of cancers. Moreover, And-1 inhibitors re-sensitize platinum-resistant ovarian cancer cells to platinum drugs in vitro and in vivo. Since BZA is an FDA approved drug, we expect a clinical trial of BZA-mediated cancer therapy in the near future. Taken together, our findings suggest that targeting And-1 by its inhibitors is a potential broad-spectrum anti-cancer chemotherapy regimen.
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Affiliation(s)
- Jing Li
- Department of Biochemistry and Molecular MedicineThe George Washington University School of Medicine and Health SciencesWashingtonDistrict of ColumbiaUSA
- GW Cancer CenterThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
| | - Yi Zhang
- Department of Biochemistry and Molecular MedicineThe George Washington University School of Medicine and Health SciencesWashingtonDistrict of ColumbiaUSA
- GW Cancer CenterThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
| | - Jing Sun
- Department of Biochemistry and Molecular MedicineThe George Washington University School of Medicine and Health SciencesWashingtonDistrict of ColumbiaUSA
- GW Cancer CenterThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
| | - Leyuan Chen
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation MedicinePeking Union Medical College & Chinese Academy of Medical SciencesTianjinChina
| | - Wenfeng Gou
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation MedicinePeking Union Medical College & Chinese Academy of Medical SciencesTianjinChina
| | - Chi‐Wei Chen
- Department of Biochemistry and Molecular MedicineThe George Washington University School of Medicine and Health SciencesWashingtonDistrict of ColumbiaUSA
- GW Cancer CenterThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
| | - Yuan Zhou
- Department of Biochemistry and Molecular MedicineThe George Washington University School of Medicine and Health SciencesWashingtonDistrict of ColumbiaUSA
- GW Cancer CenterThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
| | - Zhuqing Li
- Department of Biochemistry and Molecular MedicineThe George Washington University School of Medicine and Health SciencesWashingtonDistrict of ColumbiaUSA
- GW Cancer CenterThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
| | - David W. Chan
- Department of Obstetrics and Gynecology, LKS Faculty of MedicineThe University of Hong KongHong, China
| | - Ruili Huang
- Division of Preclinical Innovation, National Center for Advancing Translational SciencesNational Institutes of HealthBethesdaMarylandUSA
| | - Huadong Pei
- Department of Biochemistry and Molecular MedicineThe George Washington University School of Medicine and Health SciencesWashingtonDistrict of ColumbiaUSA
- GW Cancer CenterThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
| | - Wei Zheng
- Division of Preclinical Innovation, National Center for Advancing Translational SciencesNational Institutes of HealthBethesdaMarylandUSA
| | - Yiliang Li
- Tianjin Key Laboratory of Radiation Medicine and Molecular Nuclear Medicine, Institute of Radiation MedicinePeking Union Medical College & Chinese Academy of Medical SciencesTianjinChina
| | - Menghang Xia
- Division of Preclinical Innovation, National Center for Advancing Translational SciencesNational Institutes of HealthBethesdaMarylandUSA
| | - Wenge Zhu
- Department of Biochemistry and Molecular MedicineThe George Washington University School of Medicine and Health SciencesWashingtonDistrict of ColumbiaUSA
- GW Cancer CenterThe George Washington UniversityWashingtonDistrict of ColumbiaUSA
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5
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Aricthota S, Haldar D. DDK/Hsk1 phosphorylates and targets fission yeast histone deacetylase Hst4 for degradation to stabilize stalled DNA replication forks. eLife 2021; 10:70787. [PMID: 34608864 PMCID: PMC8565929 DOI: 10.7554/elife.70787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/01/2021] [Indexed: 01/01/2023] Open
Abstract
In eukaryotes, paused replication forks are prone to collapse, which leads to genomic instability, a hallmark of cancer. Dbf4-dependent kinase (DDK)/Hsk1Cdc7 is a conserved replication initiator kinase with conflicting roles in replication stress response. Here, we show that fission yeast DDK/Hsk1 phosphorylates sirtuin, Hst4 upon replication stress at C-terminal serine residues. Phosphorylation of Hst4 by DDK marks it for degradation via the ubiquitin ligase SCFpof3. Phosphorylation-defective hst4 mutant (4SA-hst4) displays defective recovery from replication stress, faulty fork restart, slow S-phase progression and decreased viability. The highly conserved fork protection complex (FPC) stabilizes stalled replication forks. We found that the recruitment of FPC components, Swi1 and Mcl1 to the chromatin is compromised in the 4SA-hst4 mutant, although whole cell levels increased. These defects are dependent upon H3K56ac and independent of intra S-phase checkpoint activation. Finally, we show conservation of H3K56ac-dependent regulation of Timeless, Tipin, and And-1 in human cells. We propose that degradation of Hst4 via DDK increases H3K56ac, changing the chromatin state in the vicinity of stalled forks facilitating recruitment and function of FPC. Overall, this study identified a crucial role of DDK and FPC in the regulation of replication stress response with implications in cancer therapeutics.
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Affiliation(s)
- Shalini Aricthota
- Laboratory of Chromatin Biology and Epigenetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India.,Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Devyani Haldar
- Laboratory of Chromatin Biology and Epigenetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
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6
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Fumasoni M, Murray AW. The evolutionary plasticity of chromosome metabolism allows adaptation to constitutive DNA replication stress. eLife 2020; 9:e51963. [PMID: 32043971 PMCID: PMC7069727 DOI: 10.7554/elife.51963] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/11/2020] [Indexed: 01/22/2023] Open
Abstract
Many biological features are conserved and thus considered to be resistant to evolutionary change. While rapid genetic adaptation following the removal of conserved genes has been observed, we often lack a mechanistic understanding of how adaptation happens. We used the budding yeast, Saccharomyces cerevisiae, to investigate the evolutionary plasticity of chromosome metabolism, a network of evolutionary conserved modules. We experimentally evolved cells constitutively experiencing DNA replication stress caused by the absence of Ctf4, a protein that coordinates the enzymatic activities at replication forks. Parallel populations adapted to replication stress, over 1000 generations, by acquiring multiple, concerted mutations. These mutations altered conserved features of two chromosome metabolism modules, DNA replication and sister chromatid cohesion, and inactivated a third, the DNA damage checkpoint. The selected mutations define a functionally reproducible evolutionary trajectory. We suggest that the evolutionary plasticity of chromosome metabolism has implications for genome evolution in natural populations and cancer.
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Affiliation(s)
- Marco Fumasoni
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
| | - Andrew W Murray
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
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7
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AND-1 fork protection function prevents fork resection and is essential for proliferation. Nat Commun 2018; 9:3091. [PMID: 30082684 PMCID: PMC6079002 DOI: 10.1038/s41467-018-05586-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 07/13/2018] [Indexed: 12/31/2022] Open
Abstract
AND-1/Ctf4 bridges the CMG helicase and DNA polymerase alpha, facilitating replication. Using an inducible degron system in avian cells, we find that AND-1 depletion is incompatible with proliferation, owing to cells accumulating in G2 with activated DNA damage checkpoint. Replication without AND-1 causes fork speed slow-down and accumulation of long single-stranded DNA (ssDNA) gaps at the replication fork junction, with these regions being converted to DNA double strand breaks (DSBs) in G2. Strikingly, resected forks and DNA damage accumulation in G2, but not fork slow-down, are reverted by treatment with mirin, an MRE11 nuclease inhibitor. Domain analysis of AND-1 further revealed that the HMG box is important for fast replication but not for proliferation, whereas conversely, the WD40 domain prevents fork resection and subsequent DSB-associated lethality. Thus, our findings uncover a fork protection function of AND-1/Ctf4 manifested via the WD40 domain that is essential for proliferation and averts genome instability. AND-1, the vertebrate orthologue of Ctf4, is a critical player during DNA replication and for maintenance of genome integrity. Here the authors use a conditional AND-1 depletion system in avian DT40 cells to reveal the consequences of the lack of AND-1 on cell proliferation and DNA replication.
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8
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Kilkenny ML, Simon AC, Mainwaring J, Wirthensohn D, Holzer S, Pellegrini L. The human CTF4-orthologue AND-1 interacts with DNA polymerase α/primase via its unique C-terminal HMG box. Open Biol 2018; 7:rsob.170217. [PMID: 29167311 PMCID: PMC5717350 DOI: 10.1098/rsob.170217] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 10/30/2017] [Indexed: 11/12/2022] Open
Abstract
A dynamic multi-protein assembly known as the replisome is responsible for DNA synthesis in eukaryotic cells. In yeast, the hub protein Ctf4 bridges DNA helicase and DNA polymerase and recruits factors with roles in metabolic processes coupled to DNA replication. An important question in DNA replication is the extent to which the molecular architecture of the replisome is conserved between yeast and higher eukaryotes. Here, we describe the biochemical basis for the interaction of the human CTF4-orthologue AND-1 with DNA polymerase α (Pol α)/primase, the replicative polymerase that initiates DNA synthesis. AND-1 has maintained the trimeric structure of yeast Ctf4, driven by its conserved SepB domain. However, the primary interaction of AND-1 with Pol α/primase is mediated by its C-terminal HMG box, unique to mammalian AND-1, which binds the B subunit, at the same site targeted by the SV40 T-antigen for viral replication. In addition, we report a novel DNA-binding activity in AND-1, which might promote the correct positioning of Pol α/primase on the lagging-strand template at the replication fork. Our findings provide a biochemical basis for the specific interaction between two critical components of the human replisome, and indicate that important principles of replisome architecture have changed significantly in evolution.
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Affiliation(s)
- Mairi L Kilkenny
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Aline C Simon
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Jack Mainwaring
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - David Wirthensohn
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Sandro Holzer
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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9
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Rapid DNA Synthesis During Early Drosophila Embryogenesis Is Sensitive to Maternal Humpty Dumpty Protein Function. Genetics 2017; 207:935-947. [PMID: 28942426 DOI: 10.1534/genetics.117.300318] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/20/2017] [Indexed: 12/29/2022] Open
Abstract
Problems with DNA replication cause cancer and developmental malformations. It is not fully understood how DNA replication is coordinated with development and perturbed in disease. We had previously identified the Drosophila gene humpty dumpty (hd), and showed that null alleles cause incomplete DNA replication, tissue undergrowth, and lethality. Animals homozygous for the missense allele, hd272-9 , were viable, but adult females had impaired amplification of eggshell protein genes in the ovary, resulting in the maternal effects of thin eggshells and embryonic lethality. Here, we show that expression of an hd transgene in somatic cells of the ovary rescues amplification and eggshell synthesis but not embryo viability. The germline of these mothers remain mutant for the hd272-9 allele, resulting in reduced maternal Hd protein and embryonic arrest during mitosis of the first few S/M nuclear cleavage cycles with chromosome instability and chromosome bridges. Epistasis analysis of hd with the rereplication mutation plutonium indicates that the chromosome bridges of hd embryos are the result of a failed attempt to segregate incompletely replicated sister chromatids. This study reveals that maternally encoded Humpty dumpty protein is essential for DNA replication and genome integrity during the little-understood embryonic S/M cycles. Moreover, the two hd272-9 maternal-effect phenotypes suggest that ovarian gene amplification and embryonic cleavage are two time periods in development that are particularly sensitive to mild deficits in DNA replication function. This last observation has broader relevance for interpreting why mild mutations in the human ortholog of humpty dumpty and other DNA replication genes cause tissue-specific malformations of microcephalic dwarfisms.
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10
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Ctf4-related protein recruits LHP1-PRC2 to maintain H3K27me3 levels in dividing cells in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2017; 114:4833-4838. [PMID: 28428341 DOI: 10.1073/pnas.1620955114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Polycomb Repressive Complex (PRC) 2 catalyzes the H3K27me3 modification that warrants inheritance of a repressive chromatin structure during cell division, thereby assuring stable target gene repression in differentiated cells. It is still under investigation how H3K27me3 is passed on from maternal to filial strands during DNA replication; however, cell division can reinforce H3K27me3 coverage at target regions. To identify novel factors involved in the Polycomb pathway in plants, we performed a forward genetic screen for enhancers of the like heterochromatin protein 1 (lhp1) mutant, which shows relatively mild phenotypic alterations compared with other plant PRC mutants. We mapped enhancer of lhp1 (eol) 1 to a gene related to yeast Chromosome transmission fidelity 4 (Ctf4) based on phylogenetic analysis, structural similarities, physical interaction with the CMG helicase component SLD5, and an expression pattern confined to actively dividing cells. A combination of eol1 with the curly leaf (clf) allele, carrying a mutation in the catalytic core of PRC2, strongly enhanced the clf phenotype; furthermore, H3K27me3 coverage at target genes was strongly reduced in eol1 clf double mutants compared with clf single mutants. EOL1 physically interacted with CLF, its partially redundant paralog SWINGER (SWN), and LHP1. We propose that EOL1 interacts with LHP1-PRC2 complexes during replication and thereby participates in maintaining the H3K27me3 mark at target genes.
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11
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Guan C, Li J, Sun D, Liu Y, Liang H. The structure and polymerase-recognition mechanism of the crucial adaptor protein AND-1 in the human replisome. J Biol Chem 2017; 292:9627-9636. [PMID: 28381552 DOI: 10.1074/jbc.m116.758524] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 04/04/2017] [Indexed: 01/10/2023] Open
Abstract
DNA replication in eukaryotic cells is performed by a multiprotein complex called the replisome, which consists of helicases, polymerases, and adaptor molecules. Human acidic nucleoplasmic DNA-binding protein 1 (AND-1), also known as WD repeat and high mobility group (HMG)-box DNA-binding protein 1 (WDHD1), is an adaptor molecule crucial for DNA replication. Although structural information for the AND-1 yeast ortholog is available, the mechanistic details for how human AND-1 protein anchors the lagging-strand DNA polymerase α (pol α) to the DNA helicase complex (Cdc45-MCM2-7-GINS, CMG) await elucidation. Here, we report the structures of the N-terminal WD40 and SepB domains of human AND-1, as well as a biochemical analysis of the C-terminal HMG domain. We show that AND-1 exists as a homotrimer mediated by the SepB domain. Mutant study results suggested that a positively charged groove within the SepB domain provides binding sites for pol α. Different from its ortholog protein in budding yeast, human AND-1 is recruited to the CMG complex, mediated by unknown participants other than Go Ichi Ni San. In addition, we show that AND-1 binds to DNA in vitro, using its C-terminal HMG domain. In conclusion, our findings provide important insights into the mechanistic details of human AND-1 function, advancing our understanding of replisome formation during eukaryotic replication.
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Affiliation(s)
- Chengcheng Guan
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101 and.,the College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Li
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101 and.,the College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dapeng Sun
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101 and
| | - Yingfang Liu
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101 and
| | - Huanhuan Liang
- From the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101 and
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12
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Villa F, Simon AC, Ortiz Bazan MA, Kilkenny ML, Wirthensohn D, Wightman M, Matak-Vinkovíc D, Pellegrini L, Labib K. Ctf4 Is a Hub in the Eukaryotic Replisome that Links Multiple CIP-Box Proteins to the CMG Helicase. Mol Cell 2016; 63:385-96. [PMID: 27397685 PMCID: PMC4980431 DOI: 10.1016/j.molcel.2016.06.009] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/12/2016] [Accepted: 06/06/2016] [Indexed: 11/26/2022]
Abstract
Replisome assembly at eukaryotic replication forks connects the DNA helicase to DNA polymerases and many other factors. The helicase binds the leading-strand polymerase directly, but is connected to the Pol α lagging-strand polymerase by the trimeric adaptor Ctf4. Here, we identify new Ctf4 partners in addition to Pol α and helicase, all of which contain a “Ctf4-interacting-peptide” or CIP-box. Crystallographic analysis classifies CIP-boxes into two related groups that target different sites on Ctf4. Mutations in the CIP-box motifs of the Dna2 nuclease or the rDNA-associated protein Tof2 do not perturb DNA synthesis genome-wide, but instead lead to a dramatic shortening of chromosome 12 that contains the large array of rDNA repeats. Our data reveal unexpected complexity of Ctf4 function, as a hub that connects multiple accessory factors to the replisome. Most strikingly, Ctf4-dependent recruitment of CIP-box proteins couples other processes to DNA synthesis, including rDNA copy-number regulation. Ctf4 is a hub that links factors with diverse functions to the eukaryotic replisome Multiple Ctf4 partners bind via short sequences called “CIP-boxes” The CIP-boxes of Dna2 and Tof2 bind to distinct sites on Ctf4 Interaction of Dna2 and Tof2 with Ctf4 is important for rDNA copy number maintenance
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Affiliation(s)
- Fabrizio Villa
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Aline C Simon
- Department of Biochemistry, University of Cambridge, 80, Tennis Court Road, Cambridge CB2 1GA, UK
| | - Maria Angeles Ortiz Bazan
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Mairi L Kilkenny
- Department of Biochemistry, University of Cambridge, 80, Tennis Court Road, Cambridge CB2 1GA, UK
| | - David Wirthensohn
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Mel Wightman
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Dijana Matak-Vinkovíc
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, 80, Tennis Court Road, Cambridge CB2 1GA, UK.
| | - Karim Labib
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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13
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Replisome function during replicative stress is modulated by histone h3 lysine 56 acetylation through Ctf4. Genetics 2015; 199:1047-63. [PMID: 25697176 DOI: 10.1534/genetics.114.173856] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 02/06/2015] [Indexed: 11/18/2022] Open
Abstract
Histone H3 lysine 56 acetylation in Saccharomyces cerevisiae is required for the maintenance of genome stability under normal conditions and upon DNA replication stress. Here we show that in the absence of H3 lysine 56 acetylation replisome components become deleterious when replication forks collapse at natural replication block sites. This lethality is not a direct consequence of chromatin assembly defects during replication fork progression. Rather, our genetic analyses suggest that in the presence of replicative stress H3 lysine 56 acetylation uncouples the Cdc45-Mcm2-7-GINS DNA helicase complex and DNA polymerases through the replisome component Ctf4. In addition, we discovered that the N-terminal domain of Ctf4, necessary for the interaction of Ctf4 with Mms22, an adaptor protein of the Rtt101-Mms1 E3 ubiquitin ligase, is required for the function of the H3 lysine 56 acetylation pathway, suggesting that replicative stress promotes the interaction between Ctf4 and Mms22. Taken together, our results indicate that Ctf4 is an essential member of the H3 lysine 56 acetylation pathway and provide novel mechanistic insights into understanding the role of H3 lysine 56 acetylation in maintaining genome stability upon replication stress.
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14
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Simon AC, Zhou JC, Perera RL, van Deursen F, Evrin C, Ivanova ME, Kilkenny ML, Renault L, Kjaer S, Matak-Vinković D, Labib K, Costa A, Pellegrini L. A Ctf4 trimer couples the CMG helicase to DNA polymerase α in the eukaryotic replisome. Nature 2014; 510:293-297. [PMID: 24805245 PMCID: PMC4059944 DOI: 10.1038/nature13234] [Citation(s) in RCA: 158] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 03/06/2014] [Indexed: 11/30/2022]
Abstract
Efficient duplication of the genome requires the concerted action of helicase and DNA polymerases at replication forks to avoid stalling of the replication machinery and consequent genomic instability. In eukaryotes, the physical coupling between helicase and DNA polymerases remains poorly understood. Here we define the molecular mechanism by which the yeast Ctf4 protein links the Cdc45-MCM-GINS (CMG) DNA helicase to DNA polymerase α (Pol α) within the replisome. We use X-ray crystallography and electron microscopy to show that Ctf4 self-associates in a constitutive disk-shaped trimer. Trimerization depends on a β-propeller domain in the carboxy-terminal half of the protein, which is fused to a helical extension that protrudes from one face of the trimeric disk. Critically, Pol α and the CMG helicase share a common mechanism of interaction with Ctf4. We show that the amino-terminal tails of the catalytic subunit of Pol α and the Sld5 subunit of GINS contain a conserved Ctf4-binding motif that docks onto the exposed helical extension of a Ctf4 protomer within the trimer. Accordingly, we demonstrate that one Ctf4 trimer can support binding of up to three partner proteins, including the simultaneous association with both Pol α and GINS. Our findings indicate that Ctf4 can couple two molecules of Pol α to one CMG helicase within the replisome, providing a new model for lagging-strand synthesis in eukaryotes that resembles the emerging model for the simpler replisome of Escherichia coli. The ability of Ctf4 to act as a platform for multivalent interactions illustrates a mechanism for the concurrent recruitment of factors that act together at the fork.
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Affiliation(s)
- Aline C Simon
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Jin C Zhou
- Clare Hall Laboratories, Cancer Research U.K. London Research Institute, London EN6 3LD, UK
| | - Rajika L Perera
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Frederick van Deursen
- Cancer Research U.K. Manchester Institute, University of Manchester, Manchester M20 4BX, UK
| | - Cecile Evrin
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, UK
| | - Marina E Ivanova
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Mairi L Kilkenny
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Ludovic Renault
- Clare Hall Laboratories, Cancer Research U.K. London Research Institute, London EN6 3LD, UK
| | - Svend Kjaer
- Protein purification, Cancer Research U.K. London Research Institute, London WC2A 3LY, UK
| | | | - Karim Labib
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, UK
| | - Alessandro Costa
- Clare Hall Laboratories, Cancer Research U.K. London Research Institute, London EN6 3LD, UK
| | - Luca Pellegrini
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
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15
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Thu YM, Bielinsky AK. MCM10: one tool for all-Integrity, maintenance and damage control. Semin Cell Dev Biol 2014; 30:121-30. [PMID: 24662891 DOI: 10.1016/j.semcdb.2014.03.017] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/10/2014] [Indexed: 01/16/2023]
Abstract
Minichromsome maintenance protein 10 (Mcm10) is an essential replication factor that is required for the activation of the Cdc45:Mcm2-7:GINS helicase. Mcm10's ability to bind both ds and ssDNA appears vital for this function. In addition, Mcm10 interacts with multiple players at the replication fork, including DNA polymerase-α and proliferating cell nuclear antigen with which it cooperates during DNA elongation. Mcm10 lacks enzymatic function, but instead provides the replication apparatus with an oligomeric scaffold that likely acts in the coordination of DNA unwinding and DNA synthesis. Not surprisingly, loss of Mcm10 engages checkpoint, DNA repair and SUMO-dependent rescue pathways that collectively counteract replication stress and chromosome breakage. Here, we review Mcm10's structure and function and explain how it contributes to the maintenance of genome integrity.
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Affiliation(s)
- Yee Mon Thu
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, United States.
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16
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Interaction between human Ctf4 and the Cdc45/Mcm2-7/GINS (CMG) replicative helicase. Proc Natl Acad Sci U S A 2013; 110:19760-5. [PMID: 24255107 DOI: 10.1073/pnas.1320202110] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromosome transmission fidelity 4 (Ctf4) is a conserved protein required for DNA replication. In this report, interactions between human Ctf4 (hCtf4) and the replicative helicase containing the cell division cycle 45 (Cdc45)/minichromosome maintenance 2-7 (Mcm2-7)/Go, Ichi, Nii, and San (GINS) (CMG) proteins [human CMG (hCMG) complex] were examined. The hCtf4-CMG complex was isolated following in vitro interaction of purified proteins (hCtf4 plus the hCMG complex), coinfection of Spodoptera frugiperda (Sf9) insect cells with viruses expressing the hCMG complex and hCtf4, and from HeLa cell chromatin after benzonase and immunoprecipitation steps. The stability of the hCtf4-CMG complex depends upon interactions between hCtf4 and multiple components of the hCMG complex. The hCtf4-CMG complex, like the hCMG complex, contains DNA helicase activity that is more salt-resistant than the helicase activity of the hCMG complex. We demonstrate that the hCtf4-CMG complex contains a homodimeric hCtf4 and a monomeric hCMG complex and suggest that the homodimeric hCtf4 acts as a platform linking polymerase α to the hCMG complex. The role of the hCMG complex as the core of the replisome is also discussed.
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17
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Thu YM, Bielinsky AK. Enigmatic roles of Mcm10 in DNA replication. Trends Biochem Sci 2013; 38:184-94. [PMID: 23332289 DOI: 10.1016/j.tibs.2012.12.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 11/30/2012] [Accepted: 12/07/2012] [Indexed: 12/31/2022]
Abstract
Minichromosome maintenance protein 10 (Mcm10) is required for DNA replication in all eukaryotes. Although the exact contribution of Mcm10 to genome replication remains heavily debated, early reports suggested that it promotes DNA unwinding and origin firing. These ideas have been solidified by recent studies that propose a role for Mcm10 in helicase activation. Whereas the molecular underpinnings of this activation step have yet to be revealed, structural data on Mcm10 provide further insight into a possible mechanism of action. The essential role in DNA replication initiation is not mutually exclusive with additional functions that Mcm10 may have as part of the elongation machinery. Here, we review the recent findings regarding the role of Mcm10 in DNA replication and discuss existing controversies.
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Affiliation(s)
- Yee Mon Thu
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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18
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Shen Z, Prasanth SG. Emerging players in the initiation of eukaryotic DNA replication. Cell Div 2012; 7:22. [PMID: 23075259 PMCID: PMC3520825 DOI: 10.1186/1747-1028-7-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 10/12/2012] [Indexed: 12/23/2022] Open
Abstract
Faithful duplication of the genome in eukaryotes requires ordered assembly of a multi-protein complex called the pre-replicative complex (pre-RC) prior to S phase; transition to the pre-initiation complex (pre-IC) at the beginning of DNA replication; coordinated progression of the replisome during S phase; and well-controlled regulation of replication licensing to prevent re-replication. These events are achieved by the formation of distinct protein complexes that form in a cell cycle-dependent manner. Several components of the pre-RC and pre-IC are highly conserved across all examined eukaryotic species. Many of these proteins, in addition to their bona fide roles in DNA replication are also required for other cell cycle events including heterochromatin organization, chromosome segregation and centrosome biology. As the complexity of the genome increases dramatically from yeast to human, additional proteins have been identified in higher eukaryotes that dictate replication initiation, progression and licensing. In this review, we discuss the newly discovered components and their roles in cell cycle progression.
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Affiliation(s)
- Zhen Shen
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601 S, Goodwin Avenue, Urbana, IL 61801, USA.
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