1
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Pangeni S, Biswas G, Kaushik V, Kuppa S, Yang O, Lin CT, Mishra G, Levy Y, Antony E, Ha T. Rapid Long-distance Migration of RPA on Single Stranded DNA Occurs Through Intersegmental Transfer Utilizing Multivalent Interactions. J Mol Biol 2024; 436:168491. [PMID: 38360091 PMCID: PMC10949852 DOI: 10.1016/j.jmb.2024.168491] [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: 12/28/2023] [Revised: 02/04/2024] [Accepted: 02/08/2024] [Indexed: 02/17/2024]
Abstract
Replication Protein A (RPA) is asingle strandedDNA(ssDNA)binding protein that coordinates diverse DNA metabolic processes including DNA replication, repair, and recombination. RPA is a heterotrimeric protein with six functional oligosaccharide/oligonucleotide (OB) domains and flexible linkers. Flexibility enables RPA to adopt multiple configurations andis thought to modulate its function. Here, usingsingle moleculeconfocal fluorescencemicroscopy combinedwith optical tweezers and coarse-grained molecular dynamics simulations, we investigated the diffusional migration of single RPA molecules on ssDNA undertension.The diffusioncoefficientDis the highest (20,000nucleotides2/s) at 3pNtension and in 100 mMKCl and markedly decreases whentensionor salt concentrationincreases. We attribute the tension effect to intersegmental transfer which is hindered by DNA stretching and the salt effect to an increase in binding site size and interaction energy of RPA-ssDNA. Our integrative study allowed us to estimate the size and frequency of intersegmental transfer events that occur through transient bridging of distant sites on DNA by multiple binding sites on RPA. Interestingly, deletion of RPA trimeric core still allowed significant ssDNA binding although the reduced contact area made RPA 15-fold more mobile. Finally, we characterized the effect of RPA crowding on RPA migration. These findings reveal how the high affinity RPA-ssDNA interactions are remodeled to yield access, a key step in several DNA metabolic processes.
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Affiliation(s)
- Sushil Pangeni
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Gargi Biswas
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO, USA
| | - Sahiti Kuppa
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO, USA
| | - Olivia Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chang-Ting Lin
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Garima Mishra
- Department of Physics, Ashoka University, Sonepet, Haryana, India
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, St. Louis, MO, USA.
| | - Taekjip Ha
- TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA; Department of Pediatrics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA.
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2
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Fousek-Schuller VJ, Borgstahl GEO. The Intriguing Mystery of RPA Phosphorylation in DNA Double-Strand Break Repair. Genes (Basel) 2024; 15:167. [PMID: 38397158 PMCID: PMC10888239 DOI: 10.3390/genes15020167] [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: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Human Replication Protein A (RPA) was historically discovered as one of the six components needed to reconstitute simian virus 40 DNA replication from purified components. RPA is now known to be involved in all DNA metabolism pathways that involve single-stranded DNA (ssDNA). Heterotrimeric RPA comprises several domains connected by flexible linkers and is heavily regulated by post-translational modifications (PTMs). The structure of RPA has been challenging to obtain. Various structural methods have been applied, but a complete understanding of RPA's flexible structure, its function, and how it is regulated by PTMs has yet to be obtained. This review will summarize recent literature concerning how RPA is phosphorylated in the cell cycle, the structural analysis of RPA, DNA and protein interactions involving RPA, and how PTMs regulate RPA activity and complex formation in double-strand break repair. There are many holes in our understanding of this research area. We will conclude with perspectives for future research on how RPA PTMs control double-strand break repair in the cell cycle.
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Affiliation(s)
| | - Gloria E. O. Borgstahl
- Eppley Institute for Research in Cancer & Allied Diseases, UNMC, Omaha, NE 68198-6805, USA
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3
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Pike AM, Friend CM, Bell SP. Distinct RPA functions promote eukaryotic DNA replication initiation and elongation. Nucleic Acids Res 2023; 51:10506-10518. [PMID: 37739410 PMCID: PMC10602884 DOI: 10.1093/nar/gkad765] [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: 11/17/2022] [Revised: 08/14/2023] [Accepted: 09/10/2023] [Indexed: 09/24/2023] Open
Abstract
Replication protein A (RPA) binds single-stranded DNA (ssDNA) and serves critical functions in eukaryotic DNA replication, the DNA damage response, and DNA repair. During DNA replication, RPA is required for extended origin DNA unwinding and DNA synthesis. To determine the requirements for RPA during these processes, we tested ssDNA-binding proteins (SSBs) from different domains of life in reconstituted Saccharomyces cerevisiae origin unwinding and DNA replication reactions. Interestingly, Escherichia coli SSB, but not T4 bacteriophage Gp32, fully substitutes for RPA in promoting origin DNA unwinding. Using RPA mutants, we demonstrated that specific ssDNA-binding properties of RPA are required for origin unwinding but that its protein-interaction domains are dispensable. In contrast, we found that each of these auxiliary RPA domains have distinct functions at the eukaryotic replication fork. The Rfa1 OB-F domain negatively regulates lagging-strand synthesis, while the Rfa2 winged-helix domain stimulates nascent strand initiation. Together, our findings reveal a requirement for specific modes of ssDNA binding in the transition to extensive origin DNA unwinding and identify RPA domains that differentially impact replication fork function.
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Affiliation(s)
- Alexandra M Pike
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Department of Biology, Cambridge, MA 02139, USA
| | - Caitlin M Friend
- Massachusetts Institute of Technology, Department of Biology, Cambridge, MA 02139, USA
| | - Stephen P Bell
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Department of Biology, Cambridge, MA 02139, USA
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4
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Onwubiko NO, Scheffel F, Tessmer I, Nasheuer HP. SV40 T antigen helicase domain regions responsible for oligomerisation regulate Okazaki fragment synthesis initiation. FEBS Open Bio 2022; 12:649-663. [PMID: 35073603 PMCID: PMC8886539 DOI: 10.1002/2211-5463.13373] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/21/2021] [Accepted: 01/21/2022] [Indexed: 11/11/2022] Open
Affiliation(s)
- Nichodemus O Onwubiko
- Biochemistry School of Biological and Chemical Sciences Biomedical Sciences Building NUI Galway, New Castle Road, Galway, H91 W2TY Ireland
| | - Felicia Scheffel
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef Schneider Strasse 2, D‐97080 Würzburg Germany
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, Josef Schneider Strasse 2, D‐97080 Würzburg Germany
| | - Heinz Peter Nasheuer
- Biochemistry School of Biological and Chemical Sciences Biomedical Sciences Building NUI Galway, New Castle Road, Galway, H91 W2TY Ireland
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5
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Tokorodani M, Ichikawa H, Yuasa K, Takahashi T, Hijikata T. SV40 microRNA miR-S1-3p Downregulates the Expression of T Antigens to Control Viral DNA Replication, and TNFα and IL-17F Expression. Biol Pharm Bull 2020; 43:1715-1728. [PMID: 33132317 DOI: 10.1248/bpb.b20-00415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
SV40-encoded microRNA (miRNA), miR-S1, downregulates the large and small T antigens (LTag and STag), which promote viral replication and cellular transformation, thereby presumably impairing LTag and STag functions essential for the viral life cycle. To explore the functional significance of miR-S1-mediated downregulation of LTag and STag as well as the functional roles of miR-S1, we evaluated viral DNA replication and proinflammatory cytokine induction in cells transfected with simian virus 40 (SV40) genome plasmid and its mutated form lacking miR-S1 expression. The SV40 genome encodes two mature miR-S1s, miR-S1-3p and miR-S1-5p, of which miR-S1-3p is the predominantly expressed form. MiR-S1-3p exerted strong repressive effects on a reporter containing full-length sequence complementarity, but only marginal effect on one harboring a sequence complementary to its seed sequence. Consistently, miR-S1-3p downregulated LTag and STag transcripts with complete sequence complementarity through miR-S1-3p-Ago2-mediated mRNA decay. Transfection of SV40 plasmid induced higher DNA replication and lower LTag and STag transcripts in most of the examined cells compared to that miR-S1-deficient SV40 plasmid. However, miR-S1 itself did not affect DNA replication without the downregulation of LTag transcripts. Both LTag and STag induced the expression of tumor necrosis factor α (TNFα) and interleukin (IL)-17F, which was slightly reduced by miR-S1 due to miR-S1-mediated downregulation of LTag and STag. Forced miR-S1 expression did not affect TNFα expression, but increased IL-17F expression. Overall, our findings suggest that miR-S1-3p is a latent modifier of LTag and STag functions, ensuring efficient viral replication and attenuating cytokine expression detrimental to the viral life cycle.
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Affiliation(s)
- Misa Tokorodani
- Department of Anatomy and Cell Biology, Research Institute of Pharmaceutical Science, Faculty of Pharmacy, Musashino University
| | - Hirona Ichikawa
- Department of Anatomy and Cell Biology, Research Institute of Pharmaceutical Science, Faculty of Pharmacy, Musashino University
| | - Katsutoshi Yuasa
- Department of Anatomy and Cell Biology, Research Institute of Pharmaceutical Science, Faculty of Pharmacy, Musashino University
| | - Tetsuyuki Takahashi
- Department of Anatomy and Cell Biology, Research Institute of Pharmaceutical Science, Faculty of Pharmacy, Musashino University
| | - Takao Hijikata
- Department of Anatomy and Cell Biology, Research Institute of Pharmaceutical Science, Faculty of Pharmacy, Musashino University
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6
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Peters DK, Erickson KD, Garcea RL. Live Cell Microscopy of Murine Polyomavirus Subnuclear Replication Centers. Viruses 2020; 12:v12101123. [PMID: 33023278 PMCID: PMC7650712 DOI: 10.3390/v12101123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/22/2020] [Accepted: 09/30/2020] [Indexed: 01/24/2023] Open
Abstract
During polyomavirus (PyV) infection, host proteins localize to subnuclear domains, termed viral replication centers (VRCs), to mediate viral genome replication. Although the protein composition and spatial organization of VRCs have been described using high-resolution immunofluorescence microscopy, little is known about the temporal dynamics of VRC formation over the course of infection. We used live cell fluorescence microscopy to analyze VRC formation during murine PyV (MuPyV) infection of a mouse fibroblast cell line that constitutively expresses a GFP-tagged replication protein A complex subunit (GFP-RPA32). The RPA complex forms a heterotrimer (RPA70/32/14) that regulates cellular DNA replication and repair and is a known VRC component. We validated previous observations that GFP-RPA32 relocalized to sites of cellular DNA damage in uninfected cells and to VRCs in MuPyV-infected cells. We then used GFP-RPA32 as a marker of VRC formation and expansion during live cell microscopy of infected cells. VRC formation occurred at variable times post-infection, but the rate of VRC expansion was similar between cells. Additionally, we found that the early viral protein, small TAg (ST), was required for VRC expansion but not VRC formation, consistent with the role of ST in promoting efficient vDNA replication. These results demonstrate the dynamic nature of VRCs over the course of infection and establish an approach for analyzing viral replication in live cells.
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Affiliation(s)
- Douglas K. Peters
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80309, USA; (D.K.P.); (K.D.E.)
| | - Kimberly D. Erickson
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80309, USA; (D.K.P.); (K.D.E.)
| | - Robert L. Garcea
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80309, USA; (D.K.P.); (K.D.E.)
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- Correspondence:
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7
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Caldwell CC, Spies M. Dynamic elements of replication protein A at the crossroads of DNA replication, recombination, and repair. Crit Rev Biochem Mol Biol 2020; 55:482-507. [PMID: 32856505 PMCID: PMC7821911 DOI: 10.1080/10409238.2020.1813070] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 01/19/2023]
Abstract
The heterotrimeric eukaryotic Replication protein A (RPA) is a master regulator of numerous DNA metabolic processes. For a long time, it has been viewed as an inert protector of ssDNA and a platform for assembly of various genome maintenance and signaling machines. Later, the modular organization of the RPA DNA binding domains suggested a possibility for dynamic interaction with ssDNA. This modular organization has inspired several models for the RPA-ssDNA interaction that aimed to explain how RPA, the high-affinity ssDNA binding protein, is replaced by the downstream players in DNA replication, recombination, and repair that bind ssDNA with much lower affinity. Recent studies, and in particular single-molecule observations of RPA-ssDNA interactions, led to the development of a new model for the ssDNA handoff from RPA to a specific downstream factor where not only stability and structural rearrangements but also RPA conformational dynamics guide the ssDNA handoff. Here we will review the current knowledge of the RPA structure, its dynamic interaction with ssDNA, and how RPA conformational dynamics may be influenced by posttranslational modification and proteins that interact with RPA, as well as how RPA dynamics may be harnessed in cellular decision making.
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Affiliation(s)
- Colleen C. Caldwell
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242
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8
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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: 2.3] [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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9
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Peters DK, Garcea RL. Murine polyomavirus DNA transitions through spatially distinct nuclear replication subdomains during infection. PLoS Pathog 2020; 16:e1008403. [PMID: 32203554 PMCID: PMC7117779 DOI: 10.1371/journal.ppat.1008403] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 04/02/2020] [Accepted: 02/13/2020] [Indexed: 12/16/2022] Open
Abstract
The replication of small DNA viruses requires both host DNA replication and repair factors that are often recruited to subnuclear domains termed viral replication centers (VRCs). Aside from serving as a spatial focus for viral replication, little is known about these dynamic areas in the nucleus. We investigated the organization and function of VRCs during murine polyomavirus (MuPyV) infection using 3D structured illumination microscopy (3D-SIM). We localized MuPyV replication center components, such as the viral large T-antigen (LT) and the cellular replication protein A (RPA), to spatially distinct subdomains within VRCs. We found that viral DNA (vDNA) trafficked sequentially through these subdomains post-synthesis, suggesting their distinct functional roles in vDNA processing. Additionally, we observed disruption of VRC organization and vDNA trafficking during mutant MuPyV infections or inhibition of DNA synthesis. These results reveal a dynamic organization of VRC components that coordinates virus replication.
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Affiliation(s)
- Douglas K. Peters
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Robert L. Garcea
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, Colorado, United States of America
- BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, United States of America
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10
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Grubman SA, Shin J, Phelan PJ, Gong A, Can H, Dilworth R, Kini SK, Gagnon D, Archambault J, Meinke G, Bohm A, Jefferson DM, Bullock PA. Isolation of a monoclonal antibody that recognizes the origin binding domain of JCV, but not SV40, large T-antigen. Virology 2016; 497:92-101. [PMID: 27433780 DOI: 10.1016/j.virol.2016.07.006] [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: 05/16/2016] [Revised: 06/27/2016] [Accepted: 07/05/2016] [Indexed: 11/26/2022]
Abstract
Within immunocompromised populations, the JC polyomavirus is the cause of the often-fatal disease Progressive Multifocal Leukoencephalopathy (PML). JC virus encodes a protein, termed T-antigen (T-ag), which is essential for its replication and pathogenicity. Previous studies of JCV T-ag have, in general, used antibodies raised against SV40 T-ag. Unfortunately, SV40 T-ag is also detected in humans and therefore there have been concerns about cross-reactivity. To address this issue, we have isolated a monoclonal antibody that binds to the JCV, but not the SV40, T-ag origin-binding domain (OBD). Furthermore, the region on the surface of the JCV T-ag OBD that is recognized by the "anti-JCV OBD mAb" has been mapped. We also demonstrate that the "anti-JCV OBD mAb" will be a useful reagent for standard techniques (e.g., Westerns blots and ELISAs). Finally, we note that additional monoclonal Abs that are specific for the T-ags encoded by the other human polyomaviruses could be generated by adopting the approach described herein.
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Affiliation(s)
- Shelley A Grubman
- Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, 02111 MA, USA; Cell Essentials Inc., 75 Kneeland Street, Boston, MA 02111, USA
| | - Jong Shin
- Sackler Institute of Graduate Biomedical Medicine, New York University School of Medicine, 550 First Avenue, New York, NY 10016-6481, USA
| | - Paul J Phelan
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, 02111 MA, USA
| | - Aaron Gong
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, 02111 MA, USA
| | - Hande Can
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, 02111 MA, USA
| | - Ryan Dilworth
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, 02111 MA, USA
| | - Sandeep Kuntadi Kini
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, 02111 MA, USA
| | - David Gagnon
- Institut de Recherches Cliniques de Montreal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7; Department of Biochemistry and Molecular Medicine Universite de Montreal Montreal, Quebec, Canada
| | - Jacques Archambault
- Institut de Recherches Cliniques de Montreal (IRCM), 110 Pine Avenue West, Montreal, Quebec, Canada H2W 1R7; Department of Biochemistry and Molecular Medicine Universite de Montreal Montreal, Quebec, Canada
| | - Gretchen Meinke
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, 02111 MA, USA
| | - Andrew Bohm
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, 02111 MA, USA
| | - Douglas M Jefferson
- Department of Integrative Physiology and Pathobiology, Tufts University School of Medicine, Boston, 02111 MA, USA
| | - Peter A Bullock
- Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine, Boston, 02111 MA, USA.
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11
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Liu T, Huang J. Replication protein A and more: single-stranded DNA-binding proteins in eukaryotic cells. Acta Biochim Biophys Sin (Shanghai) 2016; 48:665-70. [PMID: 27151292 DOI: 10.1093/abbs/gmw041] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/07/2016] [Indexed: 01/30/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) play essential roles in DNA replication, recombinational repair, and maintenance of genome stability. In human, the major SSB, replication protein A (RPA), is a stable heterotrimer composed of subunits of RPA1, RPA2, and RPA3, each of which is conserved not only in mammals but also in all other eukaryotic species. In addition to RPA, other SSBs have also been identified in the human genome, including sensor of single-stranded DNA complexes 1 and 2 (SOSS1/2). In this review, we summarize our current understanding of how these SSBs contribute to the maintenance of genome stability.
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Affiliation(s)
- Ting Liu
- Department of Cell Biology and Program in Molecular Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Jun Huang
- Life Sciences Institute and Innovation Center for Cell Signaling Network, Zhejiang University, Hangzhou 310058, China
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12
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Abstract
Geminiviruses are a family of plant viruses that cause economically important plant diseases worldwide. These viruses have circular single-stranded DNA genomes and four to eight genes that are expressed from both strands of the double-stranded DNA replicative intermediate. The transcription of these genes occurs under the control of two bidirectional promoters and one monodirectional promoter. The viral proteins function to facilitate virus replication, virus movement, the assembly of virus-specific nucleoprotein particles, vector transmission and to counteract plant host defence responses. Recent research findings have provided new insights into the structure and function of these proteins and have identified numerous host interacting partners. Most of the viral proteins have been shown to be multifunctional, participating in multiple events during the infection cycle and have, indeed, evolved coordinated interactions with host proteins to ensure a successful infection. Here, an up-to-date review of viral protein structure and function is presented, and some areas requiring further research are identified.
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Affiliation(s)
- Vincent N Fondong
- Department of Biological Sciences, Delaware State University, 1200 North DuPont Highway, Dover, DE 19901, USA.
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13
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Simmons DT. Modeling of the SV40 DNA Replication Machine. Genes (Basel) 2012; 3:742-58. [PMID: 24705083 PMCID: PMC3902795 DOI: 10.3390/genes3040742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2012] [Revised: 10/24/2012] [Accepted: 11/04/2012] [Indexed: 12/04/2022] Open
Abstract
The mechanism of SV40 DNA replication is certainly not completely understood. The proteins that are necessary for replication have been known for quite some time, but how they work together to form a nanomachine capable of faithfully replicating the virus DNA is only partially understood. Some of the proteins involved have been crystallized and their 3D structures determined, and several EM reconstructions of SV40 T antigen have been generated. In addition, there is a fair amount of biochemical data that pinpoints the sites of interaction between various proteins. With this information, various models were assembled that show how the SV40 DNA replication nanomachine could be structured in three dimensional space. This process was aided by the use of a 3D docking program as well as fitting of structures. The advantage of the availability of these models is that they are experimentally testable and they provide an insight into how the replication machine could work. Another advantage is that it is possible to quickly compare newly published structures to the models in order to come up with improved models.
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Affiliation(s)
- Daniel T Simmons
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA.
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14
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Prakash A, Borgstahl GEO. The structure and function of replication protein A in DNA replication. Subcell Biochem 2012; 62:171-96. [PMID: 22918586 DOI: 10.1007/978-94-007-4572-8_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In all organisms from bacteria and archaea to eukarya, single-stranded DNA binding proteins play an essential role in most, if not all, nuclear metabolism involving single-stranded DNA (ssDNA). Replication protein A (RPA), the major eukaryotic ssDNA binding protein, has two important roles in DNA metabolism: (1) in binding ssDNA to protect it and to keep it unfolded, and (2) in coordinating the assembly and disassembly of numerous proteins and protein complexes during processes such as DNA replication. Since its discovery as a vital player in the process of replication, RPAs roles in recombination and DNA repair quickly became evident. This chapter summarizes the current understanding of RPA's roles in replication by reviewing the available structural data, DNA-binding properties, interactions with various replication proteins, and interactions with DNA repair proteins when DNA replication is stalled.
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Affiliation(s)
- Aishwarya Prakash
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, University of Vermont, Given Medical Building, 89 Beaumont Avenue, Burlington, VT, 05405, USA
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15
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Structure-based analysis of the interaction between the simian virus 40 T-antigen origin binding domain and single-stranded DNA. J Virol 2010; 85:818-27. [PMID: 20980496 DOI: 10.1128/jvi.01738-10] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The origin-binding domain (OBD) of simian virus 40 (SV40) large T-antigen (T-Ag) is essential for many of T-Ag's interactions with DNA. Nevertheless, many important issues related to DNA binding, for example, how single-stranded DNA (ssDNA) transits along the T-Ag OBD, have yet to be established. Therefore, X-ray crystallography was used to determine the costructure of the T-Ag OBD bound to DNA substrates such as the single-stranded region of a forked oligonucleotide. A second structure of the T-Ag OBD crystallized in the presence of poly(dT)(12) is also reported. To test the conclusions derived from these structures, residues identified as being involved in binding to ssDNA by crystallography or by an earlier nuclear magnetic resonance study were mutated, and their binding to DNA was characterized via fluorescence anisotropy. In addition, these mutations were introduced into full-length T-Ag, and these mutants were tested for their ability to support replication. When considered in terms of additional homology-based sequence alignments, our studies refine our understanding of how the T-Ag OBDs encoded by the polyomavirus family interact with ssDNA, a critical step during the initiation of DNA replication.
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16
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Huang H, Zhao K, Arnett DR, Fanning E. A specific docking site for DNA polymerase {alpha}-primase on the SV40 helicase is required for viral primosome activity, but helicase activity is dispensable. J Biol Chem 2010; 285:33475-33484. [PMID: 20685648 PMCID: PMC2963361 DOI: 10.1074/jbc.m110.156240] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 07/31/2010] [Indexed: 11/06/2022] Open
Abstract
Replication of simian virus 40 (SV40) DNA, a model for eukaryotic chromosomal replication, can be reconstituted in vitro using the viral helicase (large tumor antigen, or Tag) and purified human proteins. Tag interacts physically with two cellular proteins, replication protein A and DNA polymerase α-primase (pol-prim), constituting the viral primosome. Like the well characterized primosomes of phages T7 and T4, this trio of proteins coordinates parental DNA unwinding with primer synthesis to initiate the leading strand at the viral origin and each Okazaki fragment on the lagging strand template. We recently determined the structure of a previously unrecognized pol-prim domain (p68N) that docks on Tag, identified the p68N surface that contacts Tag, and demonstrated its vital role in primosome function. Here, we identify the p68N-docking site on Tag by using structure-guided mutagenesis of the Tag helicase surface. A charge reverse substitution in Tag disrupted both p68N-binding and primosome activity but did not affect docking with other pol-prim subunits. Unexpectedly, the substitution also disrupted Tag ATPase and helicase activity, suggesting a potential link between p68N docking and ATPase activity. To assess this possibility, we examined the primosome activity of Tag with a single residue substitution in the Walker B motif. Although this substitution abolished ATPase and helicase activity as expected, it did not reduce pol-prim docking on Tag or primosome activity on single-stranded DNA, indicating that Tag ATPase is dispensable for primosome activity in vitro.
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Affiliation(s)
- Hao Huang
- From the Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235-1634
| | - Kun Zhao
- From the Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235-1634
| | - Diana R Arnett
- From the Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235-1634
| | - Ellen Fanning
- From the Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235-1634.
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17
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Surovaya AN, Grokhovsky SL, Gursky YG, Andronova VL, Arkhipova VS, Bazhulina NP, Galegov GA, Gursky GV. Complex of the herpes simplex virus initiator protein UL9 with DNA as a platform for the design of a new type of antiviral drugs. Biophysics (Nagoya-shi) 2010. [DOI: 10.1134/s0006350910020077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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18
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Mason AC, Roy R, Simmons DT, Wold MS. Functions of alternative replication protein A in initiation and elongation. Biochemistry 2010; 49:5919-28. [PMID: 20545304 DOI: 10.1021/bi100380n] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Replication protein A (RPA) is a single-stranded DNA-binding complex that is essential for DNA replication, repair, and recombination in eukaryotic cells. In addition to this canonical complex, we have recently characterized an alternative replication protein A complex (aRPA) that is unique to primates. aRPA is composed of three subunits: RPA1 and RPA3, also present in canonical RPA, and a primate-specific subunit RPA4, homologous to canonical RPA2. aRPA has biochemical properties similar to those of the canonical RPA complex but does not support DNA replication. We describe studies that aimed to identify what properties of aRPA prevent it from functioning in DNA replication. We show aRPA has weakened interaction with DNA polymerase alpha (pol alpha) and that aRPA is not able to efficiently stimulate DNA synthesis by pol alpha on aRPA-coated DNA. Additionally, we show that aRPA is unable to support de novo priming by pol alpha. Because pol alpha activity is essential for both initiation and Okazaki strand synthesis, we conclude that the inability of aRPA to support pol alpha loading causes aRPA to be defective in DNA replication. We also show that aRPA stimulates synthesis by DNA polymerase alpha in the presence of PCNA and RFC. This indicates that aRPA can support extension of DNA strands by DNA polymerase partial differential. This finding along with the previous observation that aRPA supports early steps of nucleotide excision repair and recombination indicates that aRPA can support DNA repair synthesis that requires polymerase delta, PCNA, and RFC and support a role for aRPA in DNA repair.
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Affiliation(s)
- Aaron C Mason
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242, USA
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19
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Insights into eukaryotic DNA priming from the structure and functional interactions of the 4Fe-4S cluster domain of human DNA primase. Proc Natl Acad Sci U S A 2010; 107:13684-9. [PMID: 20643958 DOI: 10.1073/pnas.1002009107] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
DNA replication requires priming of DNA templates by enzymes known as primases. Although DNA primase structures are available from archaea and bacteria, the mechanism of DNA priming in higher eukaryotes remains poorly understood in large part due to the absence of the structure of the unique, highly conserved C-terminal regulatory domain of the large subunit (p58C). Here, we present the structure of this domain determined to 1.7-A resolution by X-ray crystallography. The p58C structure reveals a novel arrangement of an evolutionarily conserved 4Fe-4S cluster buried deeply within the protein core and is not similar to any known protein structure. Analysis of the binding of DNA to p58C by fluorescence anisotropy measurements revealed a strong preference for ss/dsDNA junction substrates. This approach was combined with site-directed mutagenesis to confirm that the binding of DNA occurs to a distinctively basic surface on p58C. A specific interaction of p58C with the C-terminal domain of the intermediate subunit of replication protein A (RPA32C) was identified and characterized by isothermal titration calorimetry and NMR. Restraints from NMR experiments were used to drive computational docking of the two domains and generate a model of the p58C-RPA32C complex. Together, our results explain functional defects in human DNA primase mutants and provide insights into primosome loading on RPA-coated ssDNA and regulation of primase activity.
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20
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A structure-guided mutational analysis of simian virus 40 large T antigen: identification of surface residues required for viral replication and transformation. J Virol 2009; 83:8781-8. [PMID: 19553311 DOI: 10.1128/jvi.00621-09] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Simian virus 40 large T antigen (TAg) transforms cells in culture and induces tumors in rodents. Genetic studies suggest that TAg interaction with the chaperone hsp70 and tumor suppressors pRb and p53 may not be sufficient to elicit complete transformation of cells. In order to identify additional cellular factors important for transformation, we designed mutations on the solvent-exposed surface of TAg. We hypothesized that surface residues would interact directly with cellular targets and that the mutation of these residues might disrupt this interaction without perturbing TAg's global structure. Using structural data, we identified 61 amino acids on the surface of TAg. Each surface amino acid was changed to an alanine. Furthermore, five patches containing clusters of charged amino acids on the surface of TAg were identified. Within these patches, we selectively mutated three to four charged amino acids and thus generated five mutants (patch mutants 1 to 5). We observed that while patch mutants 3 and 4 induced foci in REF52 cells, patch mutants 1 and 2 were deficient in focus formation. We determined that the patch 1 mutant is defective in p53 binding, thus explaining its defect in transformation. The patch 2 mutant can interact with the Rb family members and p53 like wild-type TAg but is unable to transform cells, suggesting that it is defective for action on an unknown cellular target essential for transformation. Our results suggest that the histone acetyltransferase CBP/p300 is one of the potential targets affected by the mutations in patch 2.
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21
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Pestryakov PE, Lavrik OI. Mechanisms of single-stranded DNA-binding protein functioning in cellular DNA metabolism. BIOCHEMISTRY (MOSCOW) 2009; 73:1388-404. [PMID: 19216707 DOI: 10.1134/s0006297908130026] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
This review deals with analysis of mechanisms involved in coordination of DNA replication and repair by SSB proteins; characteristics of eukaryotic, prokaryotic, and archaeal SSB proteins are considered, which made it possible to distinguish general mechanisms specific for functioning of proteins from organisms of different life domains. Mechanisms of SSB protein interactions with DNA during metabolism of the latter are studied; structural organization of the SSB protein complexes with DNA, as well as structural and functional peculiarities of different SSB proteins are analyzed.
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Affiliation(s)
- P E Pestryakov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
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22
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Khopde S, Roy R, Simmons DT. The binding of topoisomerase I to T antigen enhances the synthesis of RNA-DNA primers during simian virus 40 DNA replication. Biochemistry 2008; 47:9653-60. [PMID: 18702506 DOI: 10.1021/bi800825r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Topoisomerase I (topo I) is required for the proper initiation of simian virus 40 (SV40) DNA replication. This enzyme binds to SV40 large T antigen at two places, close to the N-terminal end and near the C-terminal end of the helicase domain. We have recently demonstrated that the binding of topo I to the C-terminal site is necessary for the stimulation of DNA synthesis by topo I and for the formation of normal amounts of completed daughter molecules. In this study, we investigated the mechanism by which this stimulation occurs. Contrary to our expectation that the binding of topo I to this region of T antigen provides the proper unwound DNA substrate for initiation to occur, we demonstrate that binding of topo I stimulates polymerase alpha/primase (pol/prim) to synthesize larger amounts of primers consisting of short RNA and about 30 nucleotides of DNA. Topo I binding also stimulates the production of large molecular weight DNA by pol/prim. Mutant T antigens that fail to bind topo I normally do not participate in the synthesis of expected amounts of primers or large molecular weight DNAs indicating that the association of topo I with the C-terminal binding site on T antigen is required for these activities. It is also shown that topo I has the ability to bind to human RPA directly, suggesting that the stimulation of pol/prim activity may be mediated in part through RPA in the DNA synthesis initiation complex.
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Affiliation(s)
- Sujata Khopde
- Department of Biological Sciences, University of Delaware, Newark, Delaware 19716-2590, USA
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23
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Taneja P, Nasheuer HP, Hartmann H, Grosse F, Fanning E, Weisshart K. Timed interactions between viral and cellular replication factors during the initiation of SV40 in vitro DNA replication. Biochem J 2008; 407:313-20. [PMID: 17666013 PMCID: PMC2049014 DOI: 10.1042/bj20070794] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The initiation of SV40 (simian virus 40) DNA replication requires the co-operative interactions between the viral Tag (large T-antigen), RPA (replication protein A) and Pol (DNA polymerase alpha-primase) on the template DNA. Binding interfaces mapped on these enzymes and expressed as peptides competed with the mutual interactions of the native proteins. Prevention of the genuine interactions was accomplished only prior to the primer synthesis step and blocked the assembly of a productive initiation complex. Once the complex was engaged in the synthesis of an RNA primer and its extension, the interfering effects of the peptides ceased, suggesting a stable association of the replication factors during the initiation phase. Specific antibodies were still able to disrupt preformed interactions and inhibited primer synthesis and extension activities, underlining the crucial role of specific protein-protein contacts during the entire initiation process.
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Affiliation(s)
- Poonam Taneja
- *Department of Biological Sciences, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37235, U.S.A
| | - Heinz-Peter Nasheuer
- †Department of Biochemistry, National University of Ireland, Galway, University Road, Galway, Ireland
| | - Hella Hartmann
- ‡Leibniz Institute for Age Research, Fritz Lipmann Institute (formerly Institute for Molecular Biotechnology), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Frank Grosse
- ‡Leibniz Institute for Age Research, Fritz Lipmann Institute (formerly Institute for Molecular Biotechnology), Beutenbergstrasse 11, 07745 Jena, Germany
| | - Ellen Fanning
- *Department of Biological Sciences, Vanderbilt University, 465 21st Avenue South, Nashville, TN 37235, U.S.A
| | - Klaus Weisshart
- ‡Leibniz Institute for Age Research, Fritz Lipmann Institute (formerly Institute for Molecular Biotechnology), Beutenbergstrasse 11, 07745 Jena, Germany
- To whom correspondence should be sent. Present address: Carl Zeiss MicroImaging GmbH, Carl-Zeiss-Promenade 10, 07745 Jena, Germany (email )
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24
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Simian virus 40 DNA replication is dependent on an interaction between topoisomerase I and the C-terminal end of T antigen. J Virol 2007; 82:1136-45. [PMID: 18003733 DOI: 10.1128/jvi.01314-07] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Topoisomerase I (topo I) is needed for efficient initiation of simian virus 40 (SV40) DNA replication and for the formation of completed DNA molecules. Two distinct binding sites for topo I have been previously mapped to the N-terminal (residues 83 to 160) and C-terminal (residues 602 to 708) regions of T antigen. By mutational analysis, we identified a cluster of six residues on the surface of the helicase domain at the C-terminal binding site that are necessary for efficient binding to topo I in enzyme-linked immunosorbent assay and far-Western blot assays. Mutant T antigens with single substitutions of these residues were unable to participate normally in SV40 DNA replication. Some mutants were completely defective in supporting DNA replication, and replication was not enhanced in the presence of added topo I. The same mutants were the ones that were severely compromised in binding topo I. Other mutants demonstrated intermediate levels of activity in the DNA replication assay and were correspondingly only partially defective in binding topo I. Mutations of nearby residues outside this cluster had no effect on DNA replication or on the ability to bind topo I. These results strongly indicate that the association of topo I with these six residues in T antigen is essential for DNA replication. These residues are located on the back edges of the T-antigen double hexamer. We propose that topo I binds to one site on each hexamer to permit the initiation of SV40 DNA replication.
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25
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Jiang X, Klimovich V, Arunkumar AI, Hysinger EB, Wang Y, Ott RD, Guler GD, Weiner B, Chazin WJ, Fanning E. Structural mechanism of RPA loading on DNA during activation of a simple pre-replication complex. EMBO J 2006; 25:5516-26. [PMID: 17110927 PMCID: PMC1679769 DOI: 10.1038/sj.emboj.7601432] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2006] [Accepted: 10/19/2006] [Indexed: 11/09/2022] Open
Abstract
We report that during activation of the simian virus 40 (SV40) pre-replication complex, SV40 T antigen (Tag) helicase actively loads replication protein A (RPA) on emerging single-stranded DNA (ssDNA). This novel loading process requires physical interaction of Tag origin DNA-binding domain (OBD) with the RPA high-affinity ssDNA-binding domains (RPA70AB). Heteronuclear NMR chemical shift mapping revealed that Tag-OBD binds to RPA70AB at a site distal from the ssDNA-binding sites and that RPA70AB, Tag-OBD, and an 8-nucleotide ssDNA form a stable ternary complex. Intact RPA and Tag also interact stably in the presence of an 8-mer, but Tag dissociates from the complex when RPA binds to longer oligonucleotides. Together, our results imply that an allosteric change in RPA quaternary structure completes the loading reaction. A mechanistic model is proposed in which the ternary complex is a key intermediate that directly couples origin DNA unwinding to RPA loading on emerging ssDNA.
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Affiliation(s)
- Xiaohua Jiang
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Vitaly Klimovich
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Alphonse I Arunkumar
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Erik B Hysinger
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Yingda Wang
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Robert D Ott
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Gulfem D Guler
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Brian Weiner
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Walter J Chazin
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Departments of Biochemistry and Chemistry and Center for Structural Biology, 5140 BIOSCI/MRBIII, Vanderbilt University, Nashville, TN 37232-8725, USA. E-mail:
| | - Ellen Fanning
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
- Department of Biological Sciences, Vanderbilt University, 2325 Stevenson Ctr., 1161 21st Avenue South, Nashville, TN 37232-8725, USA. Tel.: +1 615 343 5677; Fax: +1 615 343 6707; E-mail:
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26
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Lilyestrom W, Klein MG, Zhang R, Joachimiak A, Chen XS. Crystal structure of SV40 large T-antigen bound to p53: interplay between a viral oncoprotein and a cellular tumor suppressor. Genes Dev 2006; 20:2373-82. [PMID: 16951253 PMCID: PMC1560412 DOI: 10.1101/gad.1456306] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The transformation potential of Simian Virus 40 depends on the activities of large T-antigen (LTag), which interacts with several cellular tumor suppressors including the important "guardian" of the genome, p53. Inhibition of p53 function by LTag is necessary for both efficient viral replication and cellular transformation. We determined the crystal structure of LTag in complex with p53. The structure reveals an unexpected hexameric complex of LTag binding six p53 monomers. Structure-guided mutagenesis of LTag and p53 residues supported the p53-LTag interface defined by the complex structure. The structure also shows that LTag binding induces dramatic conformational changes at the DNA-binding area of p53, which is achieved partially through an unusual "methionine switch" within p53. In the complex structure, LTag occupies the whole p53 DNA-binding surface and likely interferes with formation of a functional p53 tetramer. In addition, we showed that p53 inhibited LTag helicase function through direct complex formation.
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Affiliation(s)
- Wayne Lilyestrom
- Molecular and Computational Biology, University of Southern California at Los Angeles, Los Angeles, California 90089, USA
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27
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Reese DK, Meinke G, Kumar A, Moine S, Chen K, Sudmeier JL, Bachovchin W, Bohm A, Bullock PA. Analyses of the interaction between the origin binding domain from simian virus 40 T antigen and single-stranded DNA provide insights into DNA unwinding and initiation of DNA replication. J Virol 2006; 80:12248-59. [PMID: 17005644 PMCID: PMC1676264 DOI: 10.1128/jvi.01201-06] [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: 11/20/2022] Open
Abstract
DNA helicases are essential for DNA metabolism; however, at the molecular level little is known about how they assemble or function. Therefore, as a model for a eukaryotic helicase, we are analyzing T antigen (T-ag) the helicase encoded by simian virus 40. In this study, nuclear magnetic resonance (NMR) methods were used to investigate the transit of single-stranded DNA (ssDNA) through the T-ag origin-binding domain (T-ag OBD). When the residues that interact with ssDNA are viewed in terms of the structure of a hexamer of the T-ag OBD, comprised of residues 131 to 260, they indicate that ssDNA passes over one face of the T-ag OBD and then transits through a gap in the open ring structure. The NMR-based conclusions are supported by an analysis of previously described mutations that disrupt critical steps during the initiation of DNA replication. These and related observations are discussed in terms of the threading of DNA through T-ag hexamers and the initiation of viral DNA replication.
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Affiliation(s)
- Danielle K Reese
- Department of Biochemistry A703, Tufts University School of Medicine, 136 Harrison Ave., Boston, MA 02111, USA
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28
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Fanning E, Klimovich V, Nager AR. A dynamic model for replication protein A (RPA) function in DNA processing pathways. Nucleic Acids Res 2006; 34:4126-37. [PMID: 16935876 PMCID: PMC1616954 DOI: 10.1093/nar/gkl550] [Citation(s) in RCA: 433] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Processing of DNA in replication, repair and recombination pathways in cells of all organisms requires the participation of at least one major single-stranded DNA (ssDNA)-binding protein. This protein protects ssDNA from nucleolytic damage, prevents hairpin formation and blocks DNA reannealing until the processing pathway is successfully completed. Many ssDNA-binding proteins interact physically and functionally with a variety of other DNA processing proteins. These interactions are thought to temporally order and guide the parade of proteins that 'trade places' on the ssDNA, a model known as 'hand-off', as the processing pathway progresses. How this hand-off mechanism works remains poorly understood. Recent studies of the conserved eukaryotic ssDNA-binding protein replication protein A (RPA) suggest a novel mechanism by which proteins may trade places on ssDNA by binding to RPA and mediating conformation changes that alter the ssDNA-binding properties of RPA. This article reviews the structure and function of RPA, summarizes recent studies of RPA in DNA replication and other DNA processing pathways, and proposes a general model for the role of RPA in protein-mediated hand-off.
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Affiliation(s)
- Ellen Fanning
- Department of Biological Sciences, Vanderbilt University, VU Station B 351634, Nashville, TN 37235-1634, USA.
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29
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Park CJ, Lee JH, Choi BS. Solution structure of the DNA-binding domain of RPA from Saccharomyces cerevisiae and its interaction with single-stranded DNA and SV40 T antigen. Nucleic Acids Res 2005; 33:4172-81. [PMID: 16043636 PMCID: PMC1180672 DOI: 10.1093/nar/gki736] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Replication protein A (RPA) is a three-subunit complex with multiple roles in DNA metabolism. DNA-binding domain A in the large subunit of human RPA (hRPA70A) binds to single-stranded DNA (ssDNA) and is responsible for the species-specific RPA–T antigen (T-ag) interaction required for Simian virus 40 replication. Although Saccharomyces cerevisiae RPA70A (scRPA70A) shares high sequence homology with hRPA70A, the two are not functionally equivalent. To elucidate the similarities and differences between these two homologous proteins, we determined the solution structure of scRPA70A, which closely resembled the structure of hRPA70A. The structure of ssDNA-bound scRPA70A, as simulated by residual dipolar coupling-based homology modeling, suggested that the positioning of the ssDNA is the same for scRPA70A and hRPA70A, although the conformational changes that occur in the two proteins upon ssDNA binding are not identical. NMR titrations of hRPA70A with T-ag showed that the T-ag binding surface is separate from the ssDNA-binding region and is more neutral than the corresponding part of scRPA70A. These differences might account for the species-specific nature of the hRPA70A–T-ag interaction. Our results provide insight into how these two homologous RPA proteins can exhibit functional differences, but still both retain their ability to bind ssDNA.
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Affiliation(s)
| | | | - Byong-Seok Choi
- To whom correspondence should be addressed at Department of Chemistry, Center for Repair System of Damaged DNA, Korea Advanced Institute of Science and Technology, 373-1, Guseong-dong, Yuseong-gu, Daejon 305-701 Korea. Tel: +82 42 869 2828; Fax: +82 42 869 2810;
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30
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Arunkumar AI, Klimovich V, Jiang X, Ott RD, Mizoue L, Fanning E, Chazin WJ. Insights into hRPA32 C-terminal domain--mediated assembly of the simian virus 40 replisome. Nat Struct Mol Biol 2005; 12:332-9. [PMID: 15793585 PMCID: PMC2600586 DOI: 10.1038/nsmb916] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2004] [Accepted: 03/04/2005] [Indexed: 11/09/2022]
Abstract
Simian virus 40 (SV40) provides a model system for the study of eukaryotic DNA replication, in which the viral protein, large T antigen (Tag), marshals human proteins to replicate the viral minichromosome. SV40 replication requires interaction of Tag with the host single-stranded DNA-binding protein, replication protein A (hRPA). The C-terminal domain of the hRPA32 subunit (RPA32C) facilitates initiation of replication, but whether it interacts with Tag is not known. Affinity chromatography and NMR revealed physical interaction between hRPA32C and the Tag origin DNA-binding domain, and a structural model of the complex was determined. Point mutations were then designed to reverse charges in the binding sites, resulting in substantially reduced binding affinity. Corresponding mutations introduced into intact hRPA impaired initiation of replication and primosome activity, implying that this interaction has a critical role in assembly and progression of the SV40 replisome.
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Affiliation(s)
- Alphonse I Arunkumar
- Department of Biochemistry, Vanderbilt University, Nashville Tennessee 37232-8725 USA
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31
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Weisshart K, Friedl S, Taneja P, Nasheuer HP, Schlott B, Grosse F, Fanning E. Partial proteolysis of simian virus 40 T antigen reveals intramolecular contacts between domains and conformation changes upon hexamer assembly. J Biol Chem 2004; 279:38943-51. [PMID: 15247253 DOI: 10.1074/jbc.m406159200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Simian virus 40 large tumor antigen (Tag) is a multi-functional viral protein that binds specifically to SV40 origin DNA, serves as the replicative DNA helicase, and orchestrates the assembly and operation of the viral replisome. Tag associated with Mg-ATP forms hexamers and, in the presence of SV40 origin DNA, double hexamers. Limited tryptic digestion of monomeric Tag revealed three major stable structural domains. The N-terminal domain spans amino acids 1-130, the central domain comprises amino acids 131-476, and the C-terminal domain extends from amino acid 513 to amino acid 698. Co-immunoprecipitation of digestion products of monomeric Tag suggests that the N-terminal domain associates stably with sequences located in the central region of the same Tag molecule. Hexamer formation protected the tryptic cleavage sites in the exposed region between the central and C-terminal domains. Upon hexamerization, this exposed region also became less accessible to a monoclonal antibody whose epitope maps in that region. The tryptic digestion products of the soluble hexamer and the DNA-bound double hexamer were indistinguishable. A low-resolution model of the intramolecular and intermolecular interactions among Tag domains in the double hexamer is proposed.
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Affiliation(s)
- Klaus Weisshart
- Institute for Molecular Biotechnology, Beutenbergstrasse 11, 07745 Jena, Federal Republic of Germany
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32
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Weisshart K, Pestryakov P, Smith RWP, Hartmann H, Kremmer E, Lavrik O, Nasheuer HP. Coordinated regulation of replication protein A activities by its subunits p14 and p32. J Biol Chem 2004; 279:35368-76. [PMID: 15205463 DOI: 10.1074/jbc.m403825200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The heterotrimeric replication protein A (RPA) has multiple essential activities in eukaryotic DNA metabolism and in signaling pathways. Despite extensive analyses, the functions of the smallest RPA subunit p14 are still unknown. To solve this issue we produced and characterized a dimeric RPA complex lacking p14, RPADeltap14, consisting of p70 and p32. RPADeltap14 was able to bind single-stranded DNA, but its binding mode and affinity differed from those of the heterotrimeric complex. Moreover, in the RPADeltap14 complex p32 only minimally recognized the 3'-end of a primer in a primer-template junction. Partial proteolytic digests revealed that p14 and p32 together stabilize the C terminus of p70 against degradation. Although RPADeltap14 efficiently supported bidirectional unwinding of double-stranded DNA and interacted with both the simian virus 40 (SV40) large T antigen and cellular DNA polymerase alpha-primase, it did not support cell-free SV40 DNA replication. This inability manifested itself in a failure to support both the primer synthesis and primer elongation reactions. These data reveal that efficient binding and correct positioning of the RPA complex on single-stranded DNA requires all three subunits to support DNA replication.
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Affiliation(s)
- Klaus Weisshart
- Institute of Molecular Biotechnology, Beutenbergstrasse 11, Jena 07745, Germany
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33
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Loo YM, Melendy T. Recruitment of replication protein A by the papillomavirus E1 protein and modulation by single-stranded DNA. J Virol 2004; 78:1605-15. [PMID: 14747526 PMCID: PMC369418 DOI: 10.1128/jvi.78.4.1605-1615.2004] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
With the exception of viral proteins E1 and E2, papillomaviruses depend heavily on host replication machinery for replication of their viral genome. E1 and E2 are known to recruit many of the necessary cellular replication factors to the viral origin of replication. Previously, we reported a physical interaction between E1 and the major human single-stranded DNA (ssDNA)-binding protein, replication protein A (RPA). E1 was determined to bind to the 70-kDa subunit of RPA, RPA70. In this study, using E1-affinity coprecipitation and enzyme-linked immunosorbent assay-based interaction assays, we show that E1 interacts with the major ssDNA-binding domain of RPA. Consistent with our previous report, no measurable interaction between E1 and the two smaller subunits of RPA was detected. The interaction of E1 with RPA was substantially inhibited by ssDNA. The extent of this inhibition was dependent on the length of the DNA. A 31-nucleotide (nt) oligonucleotide strongly inhibited the E1-RPA interaction, while a 16-nt oligonucleotide showed an intermediate level of inhibition. In contrast, a 10-nt oligonucleotide showed no observable effect on the E1-RPA interaction. This inhibition was not dependent on the sequence of the DNA. Furthermore, ssDNA also inhibited the interaction of RPA with papillomavirus E2, simian virus 40 T antigen, human polymerase alpha-primase, and p53. Taken together, our results suggest a potential role for ssDNA in modulating RPA-protein interactions, in particular, the RPA-E1 interactions during papillomavirus DNA replication. A model for recruitment of RPA by E1 during papillomavirus DNA replication is proposed.
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Affiliation(s)
- Yueh-Ming Loo
- Department of Microbiology, and Witebsky Center for Microbial Pathogenesis and Immunology, School of Medicine and Biomedical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, USA
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34
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Simmons DT, Gai D, Parsons R, Debes A, Roy R. Assembly of the replication initiation complex on SV40 origin DNA. Nucleic Acids Res 2004; 32:1103-12. [PMID: 14960720 PMCID: PMC373383 DOI: 10.1093/nar/gkh236] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The assembly of the complex that forms over the simian virus 40 origin to initiate DNA replication is not well understood. This complex is composed of the virus-coded T antigen and three cellular proteins, replication protein A (RPA), DNA polymerase alpha/primase (pol/prim) and topoisomerase I (topo I) in association with the origin. The order in which these various proteins bind to the DNA was investigated by performing binding assays using biotinylated origin DNA. We demonstrate that in the presence of all four proteins, pol/prim was essential to stabilize the initiation complex from the disruptive effects of topo I. At the optimal concentration of pol/prim, topo I and RPA bound efficiently to the complex, although pol/prim itself was not detected in significant amounts. At higher concentrations less topo I was recruited, suggesting that DNA polymerase is an important modulator of the binding of topo I. Topo I, in turn, appeared to be involved in recruiting RPA. RPA, in contrast, seemed to have little or no effect on the recruitment of the other proteins to the origin. These and other data suggested that pol/prim is the first cellular protein to interact with the double-hexameric T antigen bound to the origin. This is likely followed by topo I and then RPA, or perhaps by a complex of topo I and RPA. Stoichiometric analysis of the topo I and T antigen present in the complex suggested that two molecules of topo I are recruited per double hexamer. Finally, we demonstrate that DNA has a role in recruiting topo I to the origin.
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Affiliation(s)
- Daniel T Simmons
- Department of Biological Sciences, University of Delaware, Newark, DE 19716-2590, USA.
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35
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Stracker TH, Cassell GD, Ward P, Loo YM, van Breukelen B, Carrington-Lawrence SD, Hamatake RK, van der Vliet PC, Weller SK, Melendy T, Weitzman MD. The Rep protein of adeno-associated virus type 2 interacts with single-stranded DNA-binding proteins that enhance viral replication. J Virol 2004; 78:441-53. [PMID: 14671124 PMCID: PMC303412 DOI: 10.1128/jvi.78.1.441-453.2004] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Adeno-associated virus (AAV) type 2 is a human parvovirus whose replication is dependent upon cellular proteins as well as functions supplied by helper viruses. The minimal herpes simplex virus type 1 (HSV-1) proteins that support AAV replication in cell culture are the helicase-primase complex of UL5, UL8, and UL52, together with the UL29 gene product ICP8. We show that AAV and HSV-1 replication proteins colocalize at discrete intranuclear sites. Transfections with mutant genes demonstrate that enzymatic functions of the helicase-primase are not essential. The ICP8 protein alone enhances AAV replication in an in vitro assay. We also show localization of the cellular replication protein A (RPA) at AAV centers under a variety of conditions that support replication. In vitro assays demonstrate that the AAV Rep68 and Rep78 proteins interact with the single-stranded DNA-binding proteins (ssDBPs) of Ad (Ad-DBP), HSV-1 (ICP8), and the cell (RPA) and that these proteins enhance binding and nicking of Rep proteins at the origin. These results highlight the importance of intranuclear localization and suggest that Rep interaction with multiple ssDBPs allows AAV to replicate under a diverse set of conditions.
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Affiliation(s)
- Travis H Stracker
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA
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36
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Adamec T, Palková Z, Forstová J. Mouse polyomavirus large T antigen inhibits cell growth and alters cell and colony morphology in Saccharomyces cerevisiae. FEBS Lett 2004; 555:268-73. [PMID: 14644426 DOI: 10.1016/s0014-5793(03)01246-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The gene for mouse polyomavirus large tumor (LT) antigen, a potent oncoprotein, was expressed in Saccharomyces cerevisiae from the inducible GAL1 promoter. Substantial cell growth inhibition as well as colony and cell morphology changes dependent on cyclic adenosine monophosphate (cAMP) were observed. In contrast to cell and colony morphology alterations, the growth inhibition appeared to be transient, thus indicating the existence of an active adaptation of yeast cells to the LT antigen presence.
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Affiliation(s)
- T Adamec
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Vinicná 5, 128 44, Prague 2, Czech Republic
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37
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Roy R, Trowbridge P, Yang Z, Champoux JJ, Simmons DT. The cap region of topoisomerase I binds to sites near both ends of simian virus 40 T antigen. J Virol 2003; 77:9809-16. [PMID: 12941889 PMCID: PMC224608 DOI: 10.1128/jvi.77.18.9809-9816.2003] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Two independent binding sites on simian virus 40 (SV40) T antigen for topoisomerase I (topo I) were identified. One was mapped to the N-terminal domain (residues 83 to 160) by a combination of enzyme-linked immunosorbent assays (ELISAs) and glutathione S-transferase (GST) pull-down assays performed with various T antigen deletion mutants. The second was mapped to the C-terminal domain (residues 602 to 708). The region in human topo I that binds to both sites in T antigen was identified by ELISAs, GST pull-down assays, and double-hexamer binding assays with topo I deletion mutants. This region corresponds to a distinct domain on topo I known as the cap region that maps from residues 175 to 433. By combining these data with information about the structure of T-antigen double hexamers associated with origin DNA, we propose that the cap region of topo I associates specifically with both ends of the double hexamer bound to the SV40 origin to initiate DNA replication.
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Affiliation(s)
- Rupa Roy
- Department of Biological Sciences, University of Delaware, Newark, DE 19716-2590, USA
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38
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Taneja P, Gu J, Peng R, Carrick R, Uchiumi F, Ott RD, Gustafson E, Podust VN, Fanning E. A dominant-negative mutant of human DNA helicase B blocks the onset of chromosomal DNA replication. J Biol Chem 2002; 277:40853-61. [PMID: 12181327 DOI: 10.1074/jbc.m208067200] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A cDNA encoding a human ortholog of mouse DNA helicase B, which may play a role in DNA replication, has been cloned and expressed as a recombinant protein. The predicted human DNA helicase B (HDHB) protein contains conserved helicase motifs (superfamily 1) that are strikingly similar to those of bacterial recD and T4 dda proteins. The HDHB gene is expressed at low levels in liver, spleen, kidney, and brain and at higher levels in testis and thymus. Purified recombinant HDHB hydrolyzed ATP and dATP in the presence of single-stranded DNA, displayed robust 5'-3' DNA helicase activity, and interacted physically and functionally with DNA polymerase alpha-primase. HDHB proteins with mutations in the Walker A or B motif lacked ATPase and helicase activity but retained the ability to interact with DNA polymerase alpha-primase, suggesting that the mutants might be dominant over endogenous HDHB in human cells. When purified HDHB protein was microinjected into the nucleus of cells in early G(1), the mutant proteins inhibited DNA synthesis, whereas the wild type protein had no effect. Injection of wild type or mutant protein into cells at G(1)/S did not prevent DNA synthesis. The results suggest that HDHB function is required for S phase entry.
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Affiliation(s)
- Poonam Taneja
- Department of Biological Sciences and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN 37232, USA
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39
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Ott RD, Rehfuess C, Podust VN, Clark JE, Fanning E. Role of the p68 subunit of human DNA polymerase alpha-primase in simian virus 40 DNA replication. Mol Cell Biol 2002; 22:5669-78. [PMID: 12138179 PMCID: PMC133971 DOI: 10.1128/mcb.22.16.5669-5678.2002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA polymerase alpha-primase (pol-prim) is a heterotetramer with DNA polymerase and primase activities. The polymerase (p180) and primase (p48 and p58) subunits synthesize primers and extend them, but the function of the remaining subunit (p68) is poorly understood. Genetic studies in yeast suggested an essential role for the p68 ortholog in early S phase prior to the hydroxyurea-sensitive step, possibly a regulatory role in initiation of DNA replication, but found no evidence for an essential function of p68 later in S phase. To investigate whether the human p68 subunit has an essential role in DNA replication, we examined the ability of a purified trimeric human pol-prim lacking p68 to initiate simian virus 40 DNA replication in vitro and to synthesize and elongate primers on single-stranded DNA in the presence of T antigen and replication protein A (RPA). Both activities of trimeric pol-prim were defective, but activity was recovered upon addition of separately purified p68. Phosphorylation of p68 by cyclin A-dependent protein kinase also inhibited both activities of pol-prim. The data strongly suggest that the p68 subunit is required for priming activity of pol-prim in the presence of RPA and T antigen, both during initiation at the origin and during lagging strand replication.
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Affiliation(s)
- Robert D Ott
- Department of Biological Sciences and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, USA
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40
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Uhlmann-Schiffler H, Seinsoth S, Stahl H. Preformed hexamers of SV40 T antigen are active in RNA and origin-DNA unwinding. Nucleic Acids Res 2002; 30:3192-201. [PMID: 12136101 PMCID: PMC135737 DOI: 10.1093/nar/gkf416] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Preformed hexamers of simian virus 40 (SV40) large tumor antigen (T antigen) constitute the bulk of T antigen in infected cells and are stable under physiological conditions. In spite of this they could not be assigned a function in virus replication or transformation. We report that preformed hexamers represent the active T antigen RNA helicase. Monomers and smaller oligomeric forms of T antigen were inactive due to the lack of hexamer formation under RNA unwinding conditions. In contrast to the immunologically related cellular DEAD-box protein p68, the T antigen RNA helicase is found to act in a much more processive way and it does not catalyze rearrangements of structured RNAs. Thereby, it rather seems to resemble other virus-encoded RNA helicases, like vaccinia virus NPH-II. Surprisingly, in our hands preformed hexamers also strikingly bound to and unwound the SV40 replication origin, pointing to a possible role of preformed hexamers in the initiation step of viral DNA replication. Furthermore, we have detected an extra hexamer-specific, high-affinity T antigen ATP binding site with a very slow exchange rate constant, the function of which is discussed.
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MESH Headings
- Adenosine Triphosphate/metabolism
- Animals
- Antigens, Polyomavirus Transforming/chemistry
- Antigens, Polyomavirus Transforming/metabolism
- Antigens, Polyomavirus Transforming/ultrastructure
- Binding, Competitive
- Cell Line
- DNA, Viral/chemistry
- DNA, Viral/metabolism
- DNA, Viral/ultrastructure
- Dimerization
- Microscopy, Electron
- Nucleic Acid Conformation
- Protein Binding
- RNA Helicases/metabolism
- RNA, Viral/chemistry
- RNA, Viral/metabolism
- Replication Origin/genetics
- Simian virus 40/genetics
- Simian virus 40/immunology
- Virus Replication
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Affiliation(s)
- Heike Uhlmann-Schiffler
- Medizinische Biochemie und Molekularbiologie, Universität des Saarlandes, Gebäude 44/45, D-66421 Homburg, SAAR, Germany
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41
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Wilson VG, West M, Woytek K, Rangasamy D. Papillomavirus E1 proteins: form, function, and features. Virus Genes 2002; 24:275-90. [PMID: 12086149 DOI: 10.1023/a:1015336817836] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The E1 proteins are the essential origin recognition proteins for papillomavirus (PV) replication. E1 proteins bind to specific DNA elements in the viral origin of replication and assemble into hexameric helicases with the aid of a second viral protein, E2. The resultant helicase complex initiates origin DNA unwinding to provide the template for subsequent syntheses of progeny DNA. In addition to ATP-dependent helicase activity, E1 proteins interact with and recruit several host cell replication proteins to viral origin, including DNA polymerase alpha and RPA. This review will compare the basic structures and features of the human (HPV) and bovine (BPV1) papillomaviruses with an emphasis on mechanisms of replication function.
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Affiliation(s)
- Van G Wilson
- Department of Medical Microbiology and Immunology, College of Medicine, Texas A & M University System Health Science Center, College Station 77843-1114, USA.
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42
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Ott RD, Wang Y, Fanning E. Mutational analysis of simian virus 40 T-antigen primosome activities in viral DNA replication. J Virol 2002; 76:5121-30. [PMID: 11967327 PMCID: PMC136129 DOI: 10.1128/jvi.76.10.5121-5130.2002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The recruitment of DNA polymerase alpha-primase (pol-prim) is a crucial step in the establishment of a functional replication complex in eukaryotic cells, but the mechanism of pol-prim loading and the composition of the eukaryotic primosome are poorly understood. In the model system for simian virus 40 (SV40) DNA replication in vitro, synthesis of RNA primers at the origin of replication requires only the viral tumor (T) antigen, replication protein A (RPA), pol-prim, and topoisomerase I. On RPA-coated single-stranded DNA (ssDNA), T antigen alone mediates priming by pol-prim, constituting a relatively simple primosome. T-antigen activities proposed to participate in its primosome function include DNA helicase and protein-protein interactions with RPA and pol-prim. To test the role of these activities of T antigen in mediating priming by pol-prim, three replication-defective T antigens with mutations in the ATPase or helicase domain have been characterized. All three mutant proteins interacted physically and functionally with RPA and pol-prim and bound ssDNA, and two of them displayed some helicase activity. However, only one of these, 5030, mediated primer synthesis and elongation by pol-prim on RPA-coated ssDNA. The results suggest that a novel activity, present in 5030 T antigen and absent in the other two mutants, is required for T-antigen primosome function.
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Affiliation(s)
- Robert D Ott
- Department of Biological Sciences and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37232, USA
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43
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Eom CY, Lehman IR. The human DnaJ protein, hTid-1, enhances binding of a multimer of the herpes simplex virus type 1 UL9 protein to oris, an origin of viral DNA replication. Proc Natl Acad Sci U S A 2002; 99:1894-8. [PMID: 11854491 PMCID: PMC122290 DOI: 10.1073/pnas.042689499] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have identified cellular proteins that interact with the herpes simplex virus type 1 (HSV-1) origin-binding protein (UL9 protein) by screening a HeLa cell complementary DNA library by using the yeast two-hybrid system. Approximately 7 x 10(5) colonies were screened. Five of the 48 positive clones contained cDNAs that encoded the p150(Glued) component of the dynactin complex, three contained cDNAs for the neural F Box 42-kDa protein (NFB42), which is highly enriched in neural tissue, and three contained hTid-1, a human homologue of the bacterial DnaJ protein. We have focused in this report on the interaction of the viral UL9 protein with the cellular hTid-1. In vitro immunoprecipitation experiments confirmed that hTid-1 interacts with the UL9 protein. Electrophoretic mobility-shift assays indicated that the hTid-1 enhances the binding of UL9 protein to an HSV-1 origin, ori(s), and facilitates formation of the multimer from the dimeric UL9 protein. hTid-1 had no effect on the DNA-dependent ATPase or helicase activities associated with the UL9 protein. These findings implicate hTid-1 in HSV-1 DNA replication, and suggest that this cellular protein may provide a chaperone function analogous to the DnaJ protein in Escherichia coli DNA replication.
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Affiliation(s)
- Chi-Yong Eom
- Department of Biochemistry, Beckman Center, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
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44
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Kautz AR, Weisshart K, Schneider A, Grosse F, Nasheuer HP. Amino acids 257 to 288 of mouse p48 control the cooperation of polyomavirus large T antigen, replication protein A, and DNA polymerase alpha-primase to synthesize DNA in vitro. J Virol 2001; 75:8569-78. [PMID: 11507202 PMCID: PMC115102 DOI: 10.1128/jvi.75.18.8569-8578.2001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although p48 is the most conserved subunit of mammalian DNA polymerase alpha-primase (pol-prim), the polypeptide is the major species-specific factor for mouse polyomavirus (PyV) DNA replication. Human and murine p48 contain two regions (A and B) that show significantly lower homology than the rest of the protein. Chimerical human-murine p48 was prepared and coexpressed with three wild-type subunits of pol-prim, and four subunit protein complexes were purified. All enzyme complexes synthesized DNA on single-stranded (ss) DNA and replicated simian virus 40 DNA. Although the recombinant protein complexes physically interacted with PyV T antigen (Tag), we determined that the murine region A mediates the species specificity of PyV DNA replication in vitro. More precisely, the nonconserved phenylalanine 262 of mouse p48 is crucial for this activity, and pol-prim with mutant p48, h-S262F, supports PyV DNA replication in vitro. DNA synthesis on RPA-bound ssDNA revealed that amino acid (aa) 262, aa 266, and aa 273 to 288 are involved in the functional cooperation of RPA, pol-prim, and PyV Tag.
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Affiliation(s)
- A R Kautz
- Abteilung Biochemie, Institut für Molekulare Biotechnologie e.V., D-07745 Jena, Germany
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45
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Maga G, Frouin I, Spadari S, Hubscher U. Replication protein A as a "fidelity clamp" for DNA polymerase alpha. J Biol Chem 2001; 276:18235-42. [PMID: 11278525 DOI: 10.1074/jbc.m009599200] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The current view of DNA replication in eukaryotes predicts that DNA polymerase alpha (pol alpha)-primase synthesizes the first 10-ribonucleotide-long RNA primer on the leading strand and at the beginning of each Okazaki fragment on the lagging strand. Subsequently, pol alpha elongates such an RNA primer by incorporating about 20 deoxynucleotides. pol alpha displays a low processivity and, because of the lack of an intrinsic or associated 3'--> 5' exonuclease activity, it is more error-prone than other replicative pols. Synthesis of the RNA/DNA primer catalyzed by pol alpha-primase is a critical step in the initiation of DNA synthesis, but little is known about the role of the DNA replication accessory proteins in its regulation. In this paper we provide evidences that the single-stranded DNA-binding protein, replication protein A (RP-A), acts as an auxiliary factor for pol alpha playing a dual role: (i) it stabilizes the pol alpha/primer complex, thus acting as a pol clamp; and (ii) it significantly reduces the misincorporation efficiency by pol alpha. Based on these results, we propose a hypothetical model in which RP-A is involved in the regulation of the early events of DNA synthesis by acting as a "fidelity clamp" for pol alpha.
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Affiliation(s)
- G Maga
- Istituto di Genetica Biochimica ed Evoluzionistica-Consiglio Nazionale delle Ricerche, I-27100 Pavia, Italy
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46
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Affiliation(s)
- D T Simmons
- Department of Biological Sciences, University of Delaware, Newark 19716, USA
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47
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Kautz AR, Schneider A, Weisshart K, Geiger C, Nasheuer HP. Different regions of primase subunit p48 control mouse polyomavirus and simian virus 40 DNA replication in vitro. J Virol 2001; 75:1751-60. [PMID: 11160673 PMCID: PMC114084 DOI: 10.1128/jvi.75.4.1751-1760.2001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
DNA polymerase alpha-primase (pol-prim), a complex consisting of four subunits, is the major species-specific factor for mouse polyomavirus (PyV) and simian virus 40 (SV40) DNA replication. Although p48 is the most conserved subunit of pol-prim, it is required for in vitro PyV DNA replication but can inhibit cell-free SV40 DNA replication. Production of chimeric human-mouse p48 revealed that different regions of p48 are involved in supporting PyV DNA replication and inhibiting SV40 DNA replication. The N and C-terminal parts of p48 do not have species-specific functions in cell-free PyV DNA replication, but the central part (amino acids [aa] 129 to 320) controls PyV DNA replication in vitro. However, PyV T antigen physically binds to mouse, human, and chimeric pol-prim complexes independently, whether they support PyV DNA replication or not. In contrast to the PyV system, the inhibitory effects of mouse p48 on SV40 DNA replication are mediated by N- and C-terminal regions of p48. Thus, a chimeric p48 containing human aa 1 to 128, mouse aa 129 to 320, and human aa 321 to 418 is active in both PyV and SV40 DNA replication in vitro.
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Affiliation(s)
- A R Kautz
- Abteilung Biochemie, Institut für Molekulare Biotechnologie e.V., D-07745 Jena, Germany
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48
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Van Craenenbroeck K, Vanhoenacker P, Haegeman G. Episomal vectors for gene expression in mammalian cells. EUROPEAN JOURNAL OF BIOCHEMISTRY 2000; 267:5665-78. [PMID: 10971576 DOI: 10.1046/j.1432-1327.2000.01645.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An important reason for preferring mammalian cells for heterologous gene expression is their ability to make authentic proteins containing post-translational modifications similar to those of the native protein. The development of expression systems for mammalian cells has been ongoing for several years, resulting in a wide variety of effective expression vectors. The aim of this review is to highlight episomal expression vectors. Such episomal plasmids are usually based on sequences from DNA viruses, such as BK virus, bovine papilloma virus 1 and Epstein-Barr virus. In this review we will mainly focus on the improvements made towards the usefulness of these systems for gene expression studies and gene therapy.
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Weisshart K, Förster H, Kremmer E, Schlott B, Grosse F, Nasheuer HP. Protein-protein interactions of the primase subunits p58 and p48 with simian virus 40 T antigen are required for efficient primer synthesis in a cell-free system. J Biol Chem 2000; 275:17328-37. [PMID: 10747950 DOI: 10.1074/jbc.m000717200] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA polymerase alpha-primase (pol-prim, consisting of p180-p68-p58-p48), and primase p58-p48 (prim(2)) synthesize short RNA primers on single-stranded DNA. In the SV40 DNA replication system, only pol-prim is able to start leading strand DNA replication that needs unwinding of double-stranded (ds) DNA prior to primer synthesis. At high concentrations, pol-prim and prim(2) indistinguishably reduce the unwinding of dsDNA by SV40 T antigen (Tag). RNA primer synthesis on ssDNA in the presence of replication protein A (RPA) and Tag has served as a model system to study the initiation of Okazaki fragments on the lagging strand in vitro. On ssDNA, Tag stimulates whereas RPA inhibits the initiation reaction of both enzymes. Tag reverses and even overcompensates the inhibition of primase by RPA. Physical binding of Tag to the primase subunits and RPA, respectively, is required for these activities. Each subunit of the primase complex, p58 and p48, performs physical contacts with Tag and RPA independently of p180 and p68. Using surface plasmon resonance, the dissociation constants of the Tag/pol-prim and Tag/primase interactions were 1.2 x 10(-8) m and 1.3 x 10(-8) m, respectively.
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Affiliation(s)
- K Weisshart
- Institut für Molekulare Biotechnologie e.V., Abteilung Biochemie, Beutenbergstrasse 11, D-07745 Jena, Germany
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Abstract
Human aging is a complex process that leads to the gradual deterioration of body functions with time. Various models to approach the study of aging have been launched over the years such as the genetic analysis of life span in the yeast S. cerevisiae, the worm C. elegans, the fruitfly, and mouse, among others. In human models, there have been extensive efforts using replicative senescence, the study of centenerians, comparisons of young versus old at the organismal, cellular, and molecular levels, and the study of premature aging syndromes to understand the mechanisms leading to aging. One good model for studying human aging is a rare autosomal recessive disorder known as the Werner syndrome (WS), which is characterized by accelerated aging in vivo and in vitro. A genetic defect implicated in WS was mapped to the WRN locus. Mutations in this gene are believed to be associated, early in adulthood, with clinical symptoms normally found in old individuals. WRN functions as a DNA helicase, and recent evidence, summarized in this review, suggests specific biochemical roles for this multifaceted protein. The interaction of WRN protein with RPA (replication protein A) and p53 will undoubtedly direct efforts to further dissect the genetic pathway(s) in which WRN protein functions in DNA metabolism and will help to unravel its contribution to the human aging process.
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Affiliation(s)
- J O Nehlin
- Laboratory of Molecular Gerontology and Dermatology, Copenhagen University Hospital, Denmark.
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