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Wan L, Toland S, Robinson-McCarthy LR, Lee N, Schaich MA, Hengel SR, Li X, Bernstein KA, Van Houten B, Chang Y, Moore PS. Unlicensed origin DNA melting by MCV and SV40 polyomavirus LT proteins is independent of ATP-dependent helicase activity. Proc Natl Acad Sci U S A 2023; 120:e2308010120. [PMID: 37459531 PMCID: PMC10372695 DOI: 10.1073/pnas.2308010120] [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: 05/17/2023] [Accepted: 06/21/2023] [Indexed: 07/20/2023] Open
Abstract
Cellular eukaryotic replication initiation helicases are first loaded as head-to-head double hexamers on double-stranded (ds) DNA origins and then initiate S-phase DNA melting during licensed (once per cell cycle) replication. Merkel cell polyomavirus (MCV) large T (LT) helicase oncoprotein similarly binds and melts its own 98-bp origin but replicates multiple times in a single cell cycle. To examine the actions of this unlicensed viral helicase, we quantitated multimerization of MCV LT molecules as they assembled on MCV DNA origins using real-time single-molecule microscopy. MCV LT formed highly stable double hexamers having 17-fold longer mean lifetime (τ, >1,500 s) on DNA than single hexamers. Unexpectedly, partial MCV LT assembly without double-hexamer formation was sufficient to melt origin dsDNA as measured by RAD51, RPA70, or S1 nuclease cobinding. DNA melting also occurred with truncated MCV LT proteins lacking the helicase domain, but was lost from a protein without the multimerization domain that could bind only as a monomer to DNA. SV40 polyomavirus LT also multimerized to the MCV origin without forming a functional hexamer but still melted origin DNA. MCV origin melting did not require ATP hydrolysis and occurred for both MCV and SV40 LT proteins using the nonhydrolyzable ATP analog, adenylyl-imidodiphosphate (AMP-PNP). LT double hexamers formed in AMP-PNP, and melted DNA, consistent with direct LT hexamer assembly around single-stranded (ss) DNA without the energy-dependent dsDNA-to-ssDNA melting and remodeling steps used by cellular helicases. These results indicate that LT multimerization rather than helicase activity is required for origin DNA melting during unlicensed virus replication.
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Affiliation(s)
- Li Wan
- Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA15213
| | - Sabrina Toland
- Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA15213
| | | | - Nara Lee
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA15219
| | - Matthew A. Schaich
- Genome Stability Program, Hillman Cancer Center, Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA15232
| | - Sarah R. Hengel
- Department of Pharmacology, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA15232
| | - Xiaochen Li
- Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA15213
- School of Medicine, Tsinghua University, Beijing100084, China
| | - Kara A. Bernstein
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Bennett Van Houten
- Genome Stability Program, Hillman Cancer Center, Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA15232
| | - Yuan Chang
- Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA15213
| | - Patrick S. Moore
- Cancer Virology Program, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA15213
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2
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Kose HB, Xie S, Cameron G, Strycharska MS, Yardimci H. Duplex DNA engagement and RPA oppositely regulate the DNA-unwinding rate of CMG helicase. Nat Commun 2020; 11:3713. [PMID: 32709841 PMCID: PMC7382467 DOI: 10.1038/s41467-020-17443-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 07/01/2020] [Indexed: 01/09/2023] Open
Abstract
A ring-shaped helicase unwinds DNA during chromosome replication in all organisms. Replicative helicases generally unwind duplex DNA an order of magnitude slower compared to their in vivo replication fork rates. However, the origin of slow DNA unwinding rates by replicative helicases and the mechanism by which other replication components increase helicase speed are unclear. Here, we demonstrate that engagement of the eukaryotic CMG helicase with template DNA at the replication fork impairs its helicase activity, which is alleviated by binding of the single-stranded DNA binding protein, RPA, to the excluded DNA strand. Intriguingly, we found that, when stalled due to interaction with the parental duplex, DNA rezipping-induced helicase backtracking reestablishes productive helicase-fork engagement, underscoring the significance of plasticity in helicase action. Our work provides a mechanistic basis for relatively slow duplex unwinding by replicative helicases and explains how replisome components that interact with the excluded DNA strand stimulate fork rates.
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Affiliation(s)
- Hazal B Kose
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Sherry Xie
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - George Cameron
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Melania S Strycharska
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Hasan Yardimci
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, NW1 1AT, London, UK.
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3
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Joo S, Chung BH, Lee M, Ha TH. Ring-shaped replicative helicase encircles double-stranded DNA during unwinding. Nucleic Acids Res 2020; 47:11344-11354. [PMID: 31665506 PMCID: PMC6868380 DOI: 10.1093/nar/gkz893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/29/2019] [Accepted: 10/23/2019] [Indexed: 11/14/2022] Open
Abstract
Ring-shaped replicative helicases are hexameric and play a key role in cellular DNA replication. Despite their importance, our understanding of the unwinding mechanism of replicative helicases is far from perfect. Bovine papillomavirus E1 is one of the best-known model systems for replicative helicases. E1 is a multifunctional initiator that senses and melts the viral origin and unwinds DNA. Here, we study the unwinding mechanism of E1 at the single-molecule level using magnetic tweezers. The result reveals that E1 as a single hexamer is a poorly processive helicase with a low unwinding rate. Tension on the DNA strands impedes unwinding, indicating that the helicase interacts strongly with both DNA strands at the junction. While investigating the interaction at a high force (26–30 pN), we discovered that E1 encircles dsDNA. By comparing with the E1 construct without a DNA binding domain, we propose two possible encircling modes of E1 during active unwinding.
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Affiliation(s)
- Sihwa Joo
- BioNanoTechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.,Department of Nanobiotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Bong H Chung
- BioNanoTechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.,Department of Nanobiotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea.,BioNano Health Guard Research Center, Daejeon 34141, Republic of Korea
| | - Mina Lee
- Center for Nano-Bio Measurement, Korea Research Institute of Standards and Science, Daejeon 34113, Republic of Korea
| | - Tai H Ha
- BioNanoTechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea.,Department of Nanobiotechnology, University of Science and Technology (UST), Daejeon 34113, Republic of Korea
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4
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The Ubiquitin-Specific Protease Usp7, a Novel Merkel Cell Polyomavirus Large T-Antigen Interaction Partner, Modulates Viral DNA Replication. J Virol 2020; 94:JVI.01638-19. [PMID: 31801860 DOI: 10.1128/jvi.01638-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/01/2019] [Indexed: 02/06/2023] Open
Abstract
Merkel cell polyomavirus (MCPyV) is the major cause for Merkel cell carcinoma (MCC), a rare but highly aggressive skin cancer predominantly found in elderly and immunosuppressed patients. The early viral gene products large T-antigen (LT) and small T-antigen (sT) are important for efficient viral DNA replication, and both contribute to transformation processes. These functions are executed mainly through interactions with host factors. Here, we identify the cellular ubiquitin-specific processing protease 7 (Usp7) as a new interaction partner of the MCPyV LT. Using glutathione S-transferase pulldown experiments, we show that MCPyV LT directly binds to Usp7 and that N- as well as C-terminal regions of LT bind to the TRAF (tumor necrosis factor receptor-associated) domain of Usp7. We demonstrate that endogenous Usp7 coprecipitates with MCPyV T-antigens and relocalizes to viral DNA replication centers in cells actively replicating MCPyV genomes. We show that Usp7 does not alter ubiquitination levels of the T-antigens; however, Usp7 binding increases the binding affinity of LT to the origin of replication, thereby negatively regulating viral DNA replication. Together, these data identify Usp7 as a restriction factor of MCPyV replication. In contrast to other DNA viruses, Usp7 does not affect MCPyV gene expression via its ubiquitination activity but influences MCPyV DNA replication solely via a novel mechanism that modulates binding of LT to viral DNA.IMPORTANCE MCPyV is the only human polyomavirus that is associated with cancer; the majority of Merkel cell cancers have a viral etiology. While much emphasis was placed on investigations to understand the transformation process by MCPyV oncoproteins and cellular factors, we have only limited knowledge of cellular factors participating in the MCPyV life cycle. Here, we describe Usp7, a cellular deubiquitination enzyme, as a new factor involved in MCPyV replication. Usp7 is known in the context of large DNA tumor viruses, Epstein-Barr virus (EBV) and Kaposi's sarcoma herpesvirus, to restrict viral replication. Similar to EBV, where Usp7 binding to EBNA1 increases EBNA1 binding affinity to viral DNA, we find MCPyV LT binding to the origin of replication to be increased in the presence of Usp7, resulting in restriction of viral DNA replication. However, Usp7-induced restriction of MCPyV replication is independent of its enzymatic activity, thereby constituting a novel mechanism of Usp7-induced restriction of viral replication.
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5
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On KF, Jaremko M, Stillman B, Joshua-Tor L. A structural view of the initiators for chromosome replication. Curr Opin Struct Biol 2018; 53:131-139. [PMID: 30218786 DOI: 10.1016/j.sbi.2018.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/07/2018] [Indexed: 11/18/2022]
Affiliation(s)
- Kin Fan On
- W.M. Keck Structural Biology Laboratory, United States; Howard Hughes Medical Institute, United States; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Matt Jaremko
- W.M. Keck Structural Biology Laboratory, United States; Howard Hughes Medical Institute, United States; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States.
| | - Leemor Joshua-Tor
- W.M. Keck Structural Biology Laboratory, United States; Howard Hughes Medical Institute, United States; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States.
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6
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DeCaprio JA. Merkel cell polyomavirus and Merkel cell carcinoma. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0276. [PMID: 28893943 DOI: 10.1098/rstb.2016.0276] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2017] [Indexed: 12/27/2022] Open
Abstract
Merkel cell polyomavirus (MCPyV) causes the highly aggressive and relatively rare skin cancer known as Merkel cell carcinoma (MCC). MCPyV also causes a lifelong yet relatively innocuous infection and is one of 14 distinct human polyomaviruses species. Although polyomaviruses typically do not cause illness in healthy individuals, several can cause catastrophic diseases in immunocompromised hosts. MCPyV is the only polyomavirus clearly associated with human cancer. How MCPyV causes MCC and what oncogenic events must transpire to enable this virus to cause MCC is the focus of this essay.This article is part of the themed issue 'Human oncogenic viruses'.
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Affiliation(s)
- James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA .,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, 450 Brookline Avenue, Boston, MA 02215, USA
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7
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The ring-shaped hexameric helicases that function at DNA replication forks. Nat Struct Mol Biol 2018; 25:122-130. [PMID: 29379175 DOI: 10.1038/s41594-018-0024-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/27/2017] [Indexed: 11/08/2022]
Abstract
DNA replication requires separation of genomic duplex DNA strands, an operation that is performed by a hexameric ring-shaped helicase in all domains of life. The structures and chemomechanical actions of these fascinating machines are coming into sharper focus. Although there is no evolutionary relationship between the hexameric helicases of bacteria and those of archaea and eukaryotes, they share many fundamental features. Here we review recent studies of these two groups of hexameric helicases and the unexpected distinctions they have also unveiled.
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Abid Ali F, Douglas ME, Locke J, Pye VE, Nans A, Diffley JFX, Costa A. Cryo-EM structure of a licensed DNA replication origin. Nat Commun 2017; 8:2241. [PMID: 29269875 PMCID: PMC5740162 DOI: 10.1038/s41467-017-02389-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 11/24/2017] [Indexed: 11/08/2022] Open
Abstract
Eukaryotic origins of replication are licensed upon loading of the MCM helicase motor onto DNA. ATP hydrolysis by MCM is required for loading and the post-catalytic MCM is an inactive double hexamer that encircles duplex DNA. Origin firing depends on MCM engagement of Cdc45 and GINS to form the CMG holo-helicase. CMG assembly requires several steps including MCM phosphorylation by DDK. To understand origin activation, here we have determined the cryo-EM structures of DNA-bound MCM, either unmodified or phosphorylated, and visualize a phospho-dependent MCM element likely important for Cdc45 recruitment. MCM pore loops touch both the Watson and Crick strands, constraining duplex DNA in a bent configuration. By comparing our new MCM-DNA structure with the structure of CMG-DNA, we suggest how the conformational transition from the loaded, post-catalytic MCM to CMG might promote DNA untwisting and melting at the onset of replication.
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Affiliation(s)
- Ferdos Abid Ali
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Max E Douglas
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Julia Locke
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Andrea Nans
- Structural Biology of Cells and Viruses, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - John F X Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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9
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Cryo-EM structure of Mcm2-7 double hexamer on DNA suggests a lagging-strand DNA extrusion model. Proc Natl Acad Sci U S A 2017; 114:E9529-E9538. [PMID: 29078375 PMCID: PMC5692578 DOI: 10.1073/pnas.1712537114] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During replication initiation, the core component of the helicase-the Mcm2-7 hexamer-is loaded on origin DNA as a double hexamer (DH). The two ring-shaped hexamers are staggered, leading to a kinked axial channel. How the origin DNA interacts with the axial channel is not understood, but the interaction could provide key insights into Mcm2-7 function and regulation. Here, we report the cryo-EM structure of the Mcm2-7 DH on dsDNA and show that the DNA is zigzagged inside the central channel. Several of the Mcm subunit DNA-binding loops, such as the oligosaccharide-oligonucleotide loops, helix 2 insertion loops, and presensor 1 (PS1) loops, are well defined, and many of them interact extensively with the DNA. The PS1 loops of Mcm 3, 4, 6, and 7, but not 2 and 5, engage the lagging strand with an approximate step size of one base per subunit. Staggered coupling of the two opposing hexamers positions the DNA right in front of the two Mcm2-Mcm5 gates, with each strand being pressed against one gate. The architecture suggests that lagging-strand extrusion initiates in the middle of the DH that is composed of the zinc finger domains of both hexamers. To convert the Mcm2-7 DH structure into the Mcm2-7 hexamer structure found in the active helicase, the N-tier ring of the Mcm2-7 hexamer in the DH-dsDNA needs to tilt and shift laterally. We suggest that these N-tier ring movements cause the DNA strand separation and lagging-strand extrusion.
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10
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Replication of JC Virus DNA in the G144 Oligodendrocyte Cell Line Is Dependent Upon Akt. J Virol 2017; 91:JVI.00735-17. [PMID: 28768870 DOI: 10.1128/jvi.00735-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 07/26/2017] [Indexed: 12/24/2022] Open
Abstract
Progressive multifocal leukoencephalopathy (PML) is an often-fatal demyelinating disease of the central nervous system. PML results when oligodendrocytes within immunocompromised individuals are infected with the human JC virus (JCV). We have identified an oligodendrocyte precursor cell line, termed G144, that supports robust levels of JCV DNA replication, a central part of the JCV life cycle. In addition, we have determined that JC virus readily infects G144 cells. Furthermore, we have determined that JCV DNA replication in G144 cells is stimulated by myristoylated (i.e., constitutively active) Akt and reduced by the Akt-specific inhibitor MK2206. Thus, this oligodendrocyte-based model system will be useful for a number of purposes, such as studies of JCV infection, establishing key pathways needed for the regulation of JCV DNA replication, and identifying inhibitors of this process.IMPORTANCE The disease progressive multifocal leukoencephalopathy (PML) is caused by the infection of particular brain cells, termed oligodendrocytes, by the JC virus. Studies of PML, however, have been hampered by the lack of an immortalized human cell line derived from oligodendrocytes. Here, we report that the G144 oligodendrocyte cell line supports both infection by JC virus and robust levels of JCV DNA replication. Moreover, we have established that the Akt pathway regulates JCV DNA replication and that JCV DNA replication can be inhibited by MK2206, a compound that is specific for Akt. These and related findings suggest that we have established a powerful oligodendrocyte-based model system for studies of JCV-dependent PML.
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Chang CW, Lee S, Tsai FTF. Structural Elements Regulating AAA+ Protein Quality Control Machines. Front Mol Biosci 2017; 4:27. [PMID: 28523272 PMCID: PMC5415569 DOI: 10.3389/fmolb.2017.00027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 04/13/2017] [Indexed: 11/13/2022] Open
Abstract
Members of the ATPases Associated with various cellular Activities (AAA+) superfamily participate in essential and diverse cellular pathways in all kingdoms of life by harnessing the energy of ATP binding and hydrolysis to drive their biological functions. Although most AAA+ proteins share a ring-shaped architecture, AAA+ proteins have evolved distinct structural elements that are fine-tuned to their specific functions. A central question in the field is how ATP binding and hydrolysis are coupled to substrate translocation through the central channel of ring-forming AAA+ proteins. In this mini-review, we will discuss structural elements present in AAA+ proteins involved in protein quality control, drawing similarities to their known role in substrate interaction by AAA+ proteins involved in DNA translocation. Elements to be discussed include the pore loop-1, the Inter-Subunit Signaling (ISS) motif, and the Pre-Sensor I insert (PS-I) motif. Lastly, we will summarize our current understanding on the inter-relationship of those structural elements and propose a model how ATP binding and hydrolysis might be coupled to polypeptide translocation in protein quality control machines.
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Affiliation(s)
- Chiung-Wen Chang
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHouston, TX, USA
| | - Sukyeong Lee
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHouston, TX, USA
| | - Francis T F Tsai
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of MedicineHouston, TX, USA.,Departments of Molecular and Cellular Biology, and Molecular Virology and Microbiology, Baylor College of MedicineHouston, TX, USA
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12
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Wang D, Álvarez-Cabrera AL, Chen XS. Study of SV40 large T antigen nucleotide specificity for DNA unwinding. Virol J 2017; 14:79. [PMID: 28410592 PMCID: PMC5391581 DOI: 10.1186/s12985-017-0733-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/19/2017] [Indexed: 02/02/2023] Open
Abstract
Background Simian Virus 40 (SV40) Large Tumor Antigen (LT) is an essential enzyme that plays a vital role in viral DNA replication in mammalian cells. As a replicative helicase and initiator, LT assembles as a double-hexamer at the SV40 origin to initiate genomic replication. In this process, LT converts the chemical energy from ATP binding and hydrolysis into the mechanical work required for unwinding replication forks. It has been demonstrated that even though LT primarily utilizes ATP to unwind DNA, other NTPs can also support low DNA helicase activity. Despite previous studies on specific LT residues involved in ATP hydrolysis, no systematic study has been done to elucidate the residues participating in the selective usage of different nucleotides by LT. In this study, we performed a systematic mutational analysis around the nucleotide pocket and identified residues regulating the specificity for ATP, TTP and UTP in LT DNA unwinding. Methods We performed site-directed mutagenesis to generate 16 LT nucleotide pocket mutants and characterized each mutant’s ability to unwind double-stranded DNA, oligomerize, and bind different nucleotides using helicase assays, size-exclusion chromatography, and isothermal titration calorimetry, respectively. Results We identified four residues in the nucleotide pocket of LT, cS430, tK419, cW393 and cL557 that selectively displayed more profound impact on using certain nucleotides for LT DNA helicase activity. Conclusion Little is known regarding the mechanisms of nucleotide specificity in SV40 LT DNA unwinding despite the abundance of information available for understanding LT nucleotide hydrolysis. The systematic residue analysis performed in this report provides significant insight into the selective usage of different nucleotides in LT helicase activity, increasing our understanding of how LT may structurally prefer different energy sources for its various targeted cellular activities.
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Affiliation(s)
- Damian Wang
- Genetic, Molecular, and Cellular Biology Program, Keck School of Medicine, University of Southern California, Los Angeles, 90033, CA, USA
| | - Ana Lucia Álvarez-Cabrera
- Molecular and Computational Biology Program, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, 90089, CA, USA
| | - Xiaojiang S Chen
- Molecular and Computational Biology Program, Departments of Biological Sciences and Chemistry, University of Southern California, Los Angeles, 90089, CA, USA. .,Center of Excellence in NanoBiophysics, University of Southern California, Los Angeles, 90089, CA, USA. .,Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, 90089, CA, USA.
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