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Googins MR, An P, Gauthier CH, Pipas JM. Polyomavirus large T antigens: Unraveling a complex interactome. Tumour Virus Res 2024; 19:200306. [PMID: 39675526 PMCID: PMC11720896 DOI: 10.1016/j.tvr.2024.200306] [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: 11/13/2024] [Revised: 12/12/2024] [Accepted: 12/12/2024] [Indexed: 12/17/2024] Open
Abstract
All members of the polyomavirus family encode a large T antigen (LT) protein that plays essential roles in viral DNA replication, regulation of viral gene expression, and the manipulation of numerous cellular pathways. Over 100 polyomaviruses have been discovered in hosts ranging from arthropods and fish to mammals, including fourteen that infect humans. LT is among the most studied viral proteins with thousands of articles describing its functions in viral productive infection and tumorigenesis. However, nearly all knowledge of LT activities is based on the studies of simian virus 40 (SV40) and a few other viruses. Comparative studies of LT proteins of different polyomaviruses have revealed a remarkable diversity in the mechanisms by which LT proteins function across different polyomavirus species. This review focuses on human polyomaviruses highlights the similarities and differences between polyomavirus LTs and highlights gaps in our understanding of this protein family. The concentration of knowledge around SV40 LT and the corresponding lack of mechanistic studies on LT proteins encoded by other human and animal polyomaviruses severely constrains our understanding of the biology of this important virus family.
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Affiliation(s)
- Matthew R Googins
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
| | - Ping An
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
| | - Christian H Gauthier
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
| | - James M Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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Wu Y, Fu W, Zang N, Zhou C. Structural characterization of human RPA70N association with DNA damage response proteins. eLife 2023; 12:e81639. [PMID: 37668474 PMCID: PMC10479964 DOI: 10.7554/elife.81639] [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: 07/05/2022] [Accepted: 08/09/2023] [Indexed: 09/06/2023] Open
Abstract
The heterotrimeric Replication protein A (RPA) is the ubiquitous eukaryotic single-stranded DNA (ssDNA) binding protein and participates in nearly all aspects of DNA metabolism, especially DNA damage response. The N-terminal OB domain of the RPA70 subunit (RPA70N) is a major protein-protein interaction element for RPA and binds to more than 20 partner proteins. Previous crystallography studies of RPA70N with p53, DNA2 and PrimPol fragments revealed that RPA70N binds to amphipathic peptides that mimic ssDNA. NMR chemical-shift studies also provided valuable information on the interaction of RPA70N residues with target sequences. However, it is still unclear how RPA70N recognizes and distinguishes such a diverse group of target proteins. Here, we present high-resolution crystal structures of RPA70N in complex with peptides from eight DNA damage response proteins. The structures show that, in addition to the ssDNA mimicry mode of interaction, RPA70N employs multiple ways to bind its partners. Our results advance the mechanistic understanding of RPA70N-mediated recruitment of DNA damage response proteins.
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Affiliation(s)
- Yeyao Wu
- School of Public Health & Sir Run Run Shaw Hospital, Zhejiang University School of MedicineZhejiangChina
| | - Wangmi Fu
- School of Public Health & Sir Run Run Shaw Hospital, Zhejiang University School of MedicineZhejiangChina
| | - Ning Zang
- School of Public Health & Sir Run Run Shaw Hospital, Zhejiang University School of MedicineZhejiangChina
| | - Chun Zhou
- School of Public Health & Sir Run Run Shaw Hospital, Zhejiang University School of MedicineZhejiangChina
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Nasheuer HP, Onwubiko NO. Lagging Strand Initiation Processes in DNA Replication of Eukaryotes-Strings of Highly Coordinated Reactions Governed by Multiprotein Complexes. Genes (Basel) 2023; 14:genes14051012. [PMID: 37239371 DOI: 10.3390/genes14051012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 04/27/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
In their influential reviews, Hanahan and Weinberg coined the term 'Hallmarks of Cancer' and described genome instability as a property of cells enabling cancer development. Accurate DNA replication of genomes is central to diminishing genome instability. Here, the understanding of the initiation of DNA synthesis in origins of DNA replication to start leading strand synthesis and the initiation of Okazaki fragment on the lagging strand are crucial to control genome instability. Recent findings have provided new insights into the mechanism of the remodelling of the prime initiation enzyme, DNA polymerase α-primase (Pol-prim), during primer synthesis, how the enzyme complex achieves lagging strand synthesis, and how it is linked to replication forks to achieve optimal initiation of Okazaki fragments. Moreover, the central roles of RNA primer synthesis by Pol-prim in multiple genome stability pathways such as replication fork restart and protection of DNA against degradation by exonucleases during double-strand break repair are discussed.
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Affiliation(s)
- Heinz Peter Nasheuer
- Centre for Chromosome Biology, Arts & Science Building, Main Concourse, School of Biological and Chemical Sciences, Biochemistry, University of Galway, Distillery Road, H91 TK33 Galway, Ireland
| | - Nichodemus O Onwubiko
- Centre for Chromosome Biology, Arts & Science Building, Main Concourse, School of Biological and Chemical Sciences, Biochemistry, University of Galway, Distillery Road, H91 TK33 Galway, Ireland
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Onwubiko NO, Borst A, Diaz SA, Passkowski K, Scheffel F, Tessmer I, Nasheuer HP. SV40 T antigen interactions with ssDNA and replication protein A: a regulatory role of T antigen monomers in lagging strand DNA replication. Nucleic Acids Res 2020; 48:3657-3677. [PMID: 32128579 PMCID: PMC7144908 DOI: 10.1093/nar/gkaa138] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/14/2020] [Accepted: 02/26/2020] [Indexed: 01/08/2023] Open
Abstract
DNA replication is a central process in all living organisms. Polyomavirus DNA replication serves as a model system for eukaryotic DNA replication and has considerably contributed to our understanding of basic replication mechanisms. However, the details of the involved processes are still unclear, in particular regarding lagging strand synthesis. To delineate the complex mechanism of coordination of various cellular proteins binding simultaneously or consecutively to DNA to initiate replication, we investigated single-stranded DNA (ssDNA) interactions by the SV40 large T antigen (Tag). Using single molecule imaging by atomic force microscopy (AFM) combined with biochemical and spectroscopic analyses we reveal independent activity of monomeric and oligomeric Tag in high affinity binding to ssDNA. Depending on ssDNA length, we obtain dissociation constants for Tag-ssDNA interactions (KD values of 10–30 nM) that are in the same order of magnitude as ssDNA binding by human replication protein A (RPA). Furthermore, we observe the formation of RPA-Tag-ssDNA complexes containing hexameric as well as monomeric Tag forms. Importantly, our data clearly show stimulation of primase function in lagging strand Okazaki fragment synthesis by monomeric Tag whereas hexameric Tag inhibits the reaction, redefining DNA replication initiation on the lagging strand.
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Affiliation(s)
- Nichodemus O Onwubiko
- Biochemistry, School of Natural Sciences, Center for Chromosome Biology, Biomedical SciencesBuilding, NUI Galway, New Castle Road, Galway, Ireland
| | - Angela Borst
- Rudolf Virchow Center for Experimental Biomedicine, University ofWürzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
| | - Suraya A Diaz
- Biochemistry, School of Natural Sciences, Center for Chromosome Biology, Biomedical SciencesBuilding, NUI Galway, New Castle Road, Galway, Ireland
| | - Katharina Passkowski
- Rudolf Virchow Center for Experimental Biomedicine, University ofWürzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
| | - Felicia Scheffel
- Rudolf Virchow Center for Experimental Biomedicine, University ofWürzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University ofWürzburg, Josef Schneider Strasse 2, 97080 Würzburg, Germany
| | - Heinz P Nasheuer
- Biochemistry, School of Natural Sciences, Center for Chromosome Biology, Biomedical SciencesBuilding, NUI Galway, New Castle Road, Galway, Ireland
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Yeom G, Kim J, Park CJ. Investigation of the core binding regions of human Werner syndrome and Fanconi anemia group J helicases on replication protein A. Sci Rep 2019; 9:14016. [PMID: 31570747 PMCID: PMC6768877 DOI: 10.1038/s41598-019-50502-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 09/12/2019] [Indexed: 12/24/2022] Open
Abstract
Werner syndrome protein (WRN) and Fanconi anemia group J protein (FANCJ) are human DNA helicases that contribute to genome maintenance. They interact with replication protein A (RPA), and these interactions dramatically enhance the unwinding activities of both helicases. Even though the interplay between these helicases and RPA is particularly important in the chemoresistance pathway of cancer cells, the precise binding regions, interfaces, and properties have not yet been characterized. Here we present systematic NMR analyses and fluorescence polarization anisotropy assays of both helicase-RPA interactions for defining core binding regions and binding affinities. Our results showed that two acidic repeats of human WRN bind to RPA70N and RPA70A. For FANCJ, the acidic-rich sequence in the C-terminal domain is the binding region for RPA70N. Our results suggest that each helicase interaction has unique features, although they both fit an acidic peptide into a basic cleft for RPA binding. Our findings shed light on the protein interactions involved in overcoming the DNA-damaging agents employed in the treatment of cancer and thus potentially provide insight into enhancing the efficacy of cancer therapy.
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Affiliation(s)
- Gyuho Yeom
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Jinwoo Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju, 61005, Republic of Korea.
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Kang D, Lee S, Ryu K, Cheong H, Kim E, Park C. Interaction of replication protein A with two acidic peptides from human Bloom syndrome protein. FEBS Lett 2018; 592:547-558. [DOI: 10.1002/1873-3468.12992] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 01/09/2018] [Accepted: 01/24/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Donguk Kang
- Department of Chemistry Gwangju Institute of Science and Technology Gwangju, Korea
| | - Sungjin Lee
- Department of Chemistry Gwangju Institute of Science and Technology Gwangju, Korea
| | | | | | - Eun‐Hee Kim
- Division of Magnetic Resonance KBSI Chungbuk Korea
| | - Chin‐Ju Park
- Department of Chemistry Gwangju Institute of Science and Technology Gwangju, Korea
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Bruck I, Dhingra N, Martinez MP, Kaplan DL. Dpb11 may function with RPA and DNA to initiate DNA replication. PLoS One 2017; 12:e0177147. [PMID: 28467467 PMCID: PMC5415106 DOI: 10.1371/journal.pone.0177147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/21/2017] [Indexed: 01/27/2023] Open
Abstract
Dpb11 is required for the initiation of DNA replication in budding yeast. We found that Dpb11 binds tightly to single-stranded DNA (ssDNA) or branched DNA structures, while its human homolog, TopBP1, binds tightly to branched-DNA structures. We also found that Dpb11 binds stably to CDK-phosphorylated RPA, the eukaryotic ssDNA binding protein, in the presence of branched DNA. A Dpb11 mutant specifically defective for DNA binding did not exhibit tight binding to RPA in the presence of DNA, suggesting that Dpb11-interaction with DNA may promote the recruitment of RPA to melted DNA. We then characterized a mutant of Dpb11 that is specifically defective in DNA binding in budding yeast cells. Expression of dpb11-m1,2,3,5,ΔC results in a substantial decrease in RPA recruitment to origins, suggesting that Dpb11 interaction with DNA may be required for RPA recruitment to origins. Expression of dpb11-m1,2,3,5,ΔC also results in diminished GINS interaction with Mcm2-7 during S phase, while Cdc45 interaction with Mcm2-7 is like wild-type. The reduced GINS interaction with Mcm2-7 may be an indirect consequence of diminished origin melting. We propose that the tight interaction between Dpb11, CDK-phosphorylated RPA, and branched-DNA may be required for the essential function of stabilizing melted origin DNA in vivo. We also propose an alternative model, wherein Dpb11-DNA interaction is required for some other function in DNA replication initiation, such as helicase activation.
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Affiliation(s)
- Irina Bruck
- Florida State University College of Medicine, Department of Biomedical Sciences, Tallahassee, Florida, United States of America
| | - Nalini Dhingra
- Florida State University College of Medicine, Department of Biomedical Sciences, Tallahassee, Florida, United States of America
| | - Matthew P. Martinez
- Florida State University College of Medicine, Department of Biomedical Sciences, Tallahassee, Florida, United States of America
| | - Daniel L. Kaplan
- Florida State University College of Medicine, Department of Biomedical Sciences, Tallahassee, Florida, United States of America
- * E-mail:
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