1
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Greenwood SN, Kulkarni RS, Mikhail M, Weiser BP. Replication Protein A Enhances Kinetics of Uracil DNA Glycosylase on ssDNA and Across DNA Junctions: Explored with a DNA Repair Complex Produced with SpyCatcher/SpyTag Ligation. Chembiochem 2023; 24:e202200765. [PMID: 36883884 DOI: 10.1002/cbic.202200765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/09/2023]
Abstract
DNA repair proteins participate in extensive protein-protein interactions that promote the formation of DNA repair complexes. To understand how complex formation affects protein function during base excision repair, we tested SpyCatcher/SpyTag ligation to produce a covalent complex between human uracil DNA glycosylase (UNG2) and replication protein A (RPA). Our covalent "RPA-SpyUNG2" complex could identify and excise uracil bases in duplex areas next to ssDNA-dsDNA junctions slightly faster than the wild-type proteins, but this was highly dependent on DNA structure, as the turnover of the RPA-Spy-UNG2 complex slowed at DNA junctions where RPA tightly engaged long ssDNA sections. Conversely, the enzymes preferred uracil sites in ssDNA where RPA strongly enhanced uracil excision by UNG2 regardless of ssDNA length. Finally, RPA was found to promote UNG2 excision of two uracil sites positioned across a ssDNA-dsDNA junction, and dissociation of UNG2 from RPA enhanced this process. Our approach of ligating together RPA and UNG2 to reveal how complex formation affects enzyme function could be applied to examine other assemblies of DNA repair proteins.
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Affiliation(s)
- Sharon N Greenwood
- Rowan University School of Osteopathic Medicine, Molecular Biology, UNITED STATES
| | - Rashmi S Kulkarni
- Rowan University School of Osteopathic Medicine, Molecular Biology, UNITED STATES
| | - Michel Mikhail
- Newark Beth Israel Medical Center, Internal Medicine, UNITED STATES
| | - Brian P Weiser
- Rowan University School of Osteopathic Medicine, Molecular Biology, 307A Science Center, 2 Medical Center Drive, 08084, Stratford, UNITED STATES
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2
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Kulkarni RS, Greenwood SN, Weiser BP. Assay design for analysis of human uracil DNA glycosylase. Methods Enzymol 2022; 679:343-362. [PMID: 36682870 DOI: 10.1016/bs.mie.2022.07.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Human uracil DNA glycosylase (UNG2) is an enzyme whose primary function is to remove uracil bases from genomic DNA. UNG2 activity is critical when uracil bases are elevated in DNA during class switch recombination and somatic hypermutation, and additionally, UNG2 affects the efficacy of thymidylate synthase inhibitors that increase genomic uracil levels. Here, we summarize the enzymatic properties of UNG2 and its mitochondrial analog UNG1. To facilitate studies on the activity of these highly conserved proteins, we discuss three fluorescence-based enzyme assays that have informed much of our understanding on UNG2 function. The assays use synthetic DNA oligonucleotide substrates with uracil bases incorporated in the DNA, and the substrates can be single-stranded, double-stranded, or form other structures such as DNA hairpins or junctions. The fluorescence signal reporting uracil base excision by UNG2 is detected in different ways: (1) Excision of uracil from end-labeled oligonucleotides is measured by visualizing UNG2 reaction products with denaturing PAGE; (2) Uracil excision from dsDNA substrates is detected in solution by base pairing uracil with 2-aminopurine, whose intrinsic fluorescence is enhanced upon uracil excision; or (3) UNG2 excision of uracil from a hairpin molecular beacon substrate changes the structure of the substrate and turns on fluorescence by relieving a fluorescence quench. In addition to their utility in characterizing UNG2 properties, these assays are being adapted to discover inhibitors of the enzyme and to determine how protein-protein interactions affect UNG2 function.
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Affiliation(s)
- Rashmi S Kulkarni
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ, United States
| | - Sharon N Greenwood
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ, United States
| | - Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ, United States.
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3
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Greenwood SN, Belz RG, Weiser BP. A Conserved Mechanism for Hormesis in Molecular Systems. Dose Response 2022; 20:15593258221109335. [PMID: 35936511 PMCID: PMC9350523 DOI: 10.1177/15593258221109335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/06/2022] [Indexed: 11/25/2022]
Abstract
Hormesis refers to dose-response phenomena where low dose treatments elicit a
response that is opposite the response observed at higher doses. Hormetic
dose-response relationships have been observed throughout all of biology, but
the underlying determinants of many reported hormetic dose-responses have not
been identified. In this report, we describe a conserved mechanism for hormesis
on the molecular level where low dose treatments enhance a response that becomes
reduced at higher doses. The hormetic mechanism relies on the ability of protein
homo-multimers to simultaneously interact with a substrate and a competitor on
different subunits at low doses of competitor. In this case, hormesis can be
observed if simultaneous binding of substrate and competitor enhances a response
of the homo-multimer. We characterized this mechanism of hormesis in binding
experiments that analyzed the interaction of homotrimeric proliferating cell
nuclear antigen (PCNA) with uracil DNA glycosylase (UNG2) and a
fluorescein-labeled peptide. Additionally, the basic features of this molecular
mechanism appear to be conserved with at least two enzymes that are stimulated
by low doses of inhibitor: dimeric BRAF and octameric glutamine synthetase 2
(GS2). Identifying such molecular mechanisms of hormesis may help explain
specific hormetic responses of cells and organisms treated with exogenous
compounds.
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Affiliation(s)
- Sharon N Greenwood
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ, USA
| | - Regina G Belz
- University of Hohenheim, Hans-Ruthenberg Institute, Stuttgart, Germany
| | - Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ, USA
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4
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Bao Y, Tong L, Song B, Liu G, Zhu Q, Lu X, Zhang J, Lu YF, Wen H, Tian Y, Sun Y, Zhu WG. UNG2 deacetylation confers cancer cell resistance to hydrogen peroxide-induced cytotoxicity. Free Radic Biol Med 2020; 160:403-417. [PMID: 32649985 DOI: 10.1016/j.freeradbiomed.2020.06.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 05/29/2020] [Accepted: 06/12/2020] [Indexed: 02/06/2023]
Abstract
Cancer therapeutics produce reactive oxygen species (ROS) that damage the cancer genome and lead to cell death. However, cancer cells can resist ROS-induced cytotoxicity and survive. We show that nuclear-localized uracil-DNA N-glycosylase isoform 2 (UNG2) has a critical role in preventing ROS-induced DNA damage and enabling cancer-cell resistance. Under physiological conditions, UNG2 is targeted for rapid degradation via an interaction with the E3 ligase UHRF1. In response to ROS, however, UNG2 protein in cancer cells exhibits a remarkably extended half-life. Upon ROS exposure, UNG2 is deacetylated at lysine 78 by histone deacetylases, which prevents the UNG2-UHRF1 interaction. Accumulated UNG2 protein can thus excise the base damaged by ROS and enable the cell to survive these otherwise toxic conditions. Consequently, combining HDAC inhibitors (to permit UNG2 degradation) with genotoxic agents (to produce cytotoxic cellular levels of ROS) leads to a robust synergistic killing effect in cancer cells in vitro. Altogether, these data support the application of a novel approach to cancer treatment based on promoting UNG2 degradation by altering its acetylation status using an HDAC inhibitor.
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Affiliation(s)
- Yantao Bao
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China; International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Lili Tong
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Boyan Song
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ge Liu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Qian Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Xiaopeng Lu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Jun Zhang
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Ya-Fei Lu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - He Wen
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Yuan Tian
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China
| | - Yujie Sun
- Department of Cell Biology, Nanjing Medical University, Nanjing, 211166, China
| | - Wei-Guo Zhu
- Guangdong Key Laboratory of Genome Instability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Shenzhen University School of Medicine, Shenzhen, 518055, China; International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518055, China; Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China; Shenzhen Bay Laboratory, Shenzhen University School of Medicine, Shenzhen, 518055, China.
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5
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Showler MS, Weiser BP. A possible link to uracil DNA glycosylase in the synergistic action of HDAC inhibitors and thymidylate synthase inhibitors. J Transl Med 2020; 18:377. [PMID: 33028332 PMCID: PMC7539467 DOI: 10.1186/s12967-020-02555-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/27/2020] [Indexed: 11/10/2022] Open
Abstract
It is well established that thymidylate synthase inhibitors can cause cellular toxicity through uracil DNA glycosylase (UNG2)-dependent pathways. Additionally, thymidylate synthase inhibitors and HDAC inhibitors are known to act synergistically in a variety of cancer types. A recent article from J. Transl. Med. links these together by demonstrating widespread depletion of UNG2 levels across a variety of cell lines treated with HDAC inhibitors. Recent findings suggest that UNG2 depletion by HDAC inhibitors would likely be an effective method to sensitize cells to thymidylate synthase inhibitors. This is particularly important for cancer types that are typically resistant to thymidylate synthase inhibitors, such as cells that are deficient in p53 activity.
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Affiliation(s)
| | - Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ, 08084, USA.
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6
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Kara H, Chazal N, Bouaziz S. Is Uracil-DNA Glycosylase UNG2 a New Cellular Weapon Against HIV-1? Curr HIV Res 2020; 17:148-160. [PMID: 31433761 DOI: 10.2174/1570162x17666190821154331] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 08/01/2019] [Accepted: 08/09/2019] [Indexed: 01/12/2023]
Abstract
Uracil-DNA glycosylase-2 (UNG2) is a DNA repair protein that removes uracil from single and double-stranded DNA through a basic excision repair process. UNG2 is packaged into new virions by interaction with integrase (IN) and is needed during the early stages of the replication cycle. UNG2 appears to play both a positive and negative role during HIV-1 replication; UNG2 improves the fidelity of reverse transcription but the nuclear isoform of UNG2 participates in the degradation of cDNA and the persistence of the cellular genome by repairing its uracil mismatches. In addition, UNG2 is neutralized by Vpr, which redirects it to the proteasome for degradation, suggesting that UNG2 may be a new cellular restriction factor. So far, we have not understood why HIV-1 imports UNG2 via its IN and why it causes degradation of endogenous UNG2 by redirecting it to the proteasome via Vpr. In this review, we propose to discuss the ambiguous role of UNG2 during the HIV-1 replication cycle.
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Affiliation(s)
- Hesna Kara
- Cibles Therapeutiques et Conception de Medicaments (CiTCoM), CNRS UMR8038, Faculte des Sciences Pharmaceutiques et Biologiques, Universite Paris Descartes, Paris, France
| | - Nathalie Chazal
- Institut de Recherche en Infectiologie de Montpellier (IRIM), CNRS UMR9004, Universite de Montpellier, Montpellier, France
| | - Serge Bouaziz
- Cibles Therapeutiques et Conception de Medicaments (CiTCoM), CNRS UMR8038, Faculte des Sciences Pharmaceutiques et Biologiques, Universite Paris Descartes, Paris, France
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7
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Iveland TS, Hagen L, Sharma A, Sousa MML, Sarno A, Wollen KL, Liabakk NB, Slupphaug G. HDACi mediate UNG2 depletion, dysregulated genomic uracil and altered expression of oncoproteins and tumor suppressors in B- and T-cell lines. J Transl Med 2020; 18:159. [PMID: 32264925 PMCID: PMC7137348 DOI: 10.1186/s12967-020-02318-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 03/27/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND HDAC inhibitors (HDACi) belong to a new group of chemotherapeutics that are increasingly used in the treatment of lymphocyte-derived malignancies, but their mechanisms of action remain poorly understood. Here we aimed to identify novel protein targets of HDACi in B- and T-lymphoma cell lines and to verify selected candidates across several mammalian cell lines. METHODS Jurkat T- and SUDHL5 B-lymphocytes were treated with the HDACi SAHA (vorinostat) prior to SILAC-based quantitative proteome analysis. Selected differentially expressed proteins were verified by targeted mass spectrometry, RT-PCR and western analysis in multiple mammalian cell lines. Genomic uracil was quantified by LC-MS/MS, cell cycle distribution analyzed by flow cytometry and class switch recombination monitored by FACS in murine CH12F3 cells. RESULTS SAHA treatment resulted in differential expression of 125 and 89 proteins in Jurkat and SUDHL5, respectively, of which 19 were commonly affected. Among these were several oncoproteins and tumor suppressors previously not reported to be affected by HDACi. Several key enzymes determining the cellular dUTP/dTTP ratio were downregulated and in both cell lines we found robust depletion of UNG2, the major glycosylase in genomic uracil sanitation. UNG2 depletion was accompanied by hyperacetylation and mediated by increased proteasomal degradation independent of cell cycle stage. UNG2 degradation appeared to be ubiquitous and was observed across several mammalian cell lines of different origin and with several HDACis. Loss of UNG2 was accompanied by 30-40% increase in genomic uracil in freely cycling HEK cells and reduced immunoglobulin class-switch recombination in murine CH12F3 cells. CONCLUSION We describe several oncoproteins and tumor suppressors previously not reported to be affected by HDACi in previous transcriptome analyses, underscoring the importance of proteome analysis to identify cellular effectors of HDACi treatment. The apparently ubiquitous depletion of UNG2 and PCLAF establishes DNA base excision repair and translesion synthesis as novel pathways affected by HDACi treatment. Dysregulated genomic uracil homeostasis may aid interpretation of HDACi effects in cancer cells and further advance studies on this class of inhibitors in the treatment of APOBEC-expressing tumors, autoimmune disease and HIV-1.
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Affiliation(s)
- Tobias S Iveland
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health, Norwegian University of Science and Technology, 7491, Trondheim, Norway.,Cancer Clinic, St. Olav's Hospital, Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health, Norwegian University of Science and Technology, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim, Norway.,Proteomics and Modomics Experimental Core, PROMEC, at NTNU and the Central Norway Regional Health Authority, Stjørdal, Norway
| | - Animesh Sharma
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health, Norwegian University of Science and Technology, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim, Norway.,Proteomics and Modomics Experimental Core, PROMEC, at NTNU and the Central Norway Regional Health Authority, Stjørdal, Norway
| | - Mirta M L Sousa
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health, Norwegian University of Science and Technology, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim, Norway
| | - Antonio Sarno
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health, Norwegian University of Science and Technology, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim, Norway
| | - Kristian Lied Wollen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Nina Beate Liabakk
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health, Norwegian University of Science and Technology, 7491, Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim, Norway
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health, Norwegian University of Science and Technology, 7491, Trondheim, Norway. .,Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim, Norway. .,Proteomics and Modomics Experimental Core, PROMEC, at NTNU and the Central Norway Regional Health Authority, Stjørdal, Norway.
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8
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Anindya R. Single-stranded DNA damage: Protecting the single-stranded DNA from chemical attack. DNA Repair (Amst) 2020; 87:102804. [PMID: 31981739 DOI: 10.1016/j.dnarep.2020.102804] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 01/18/2020] [Accepted: 01/18/2020] [Indexed: 01/08/2023]
Abstract
Cellular processes, such as DNA replication, recombination and transcription, require DNA strands separation and single-stranded DNA is formation. The single-stranded DNA is promptly wrapped by human single-stranded DNA binding proteins, replication protein A (RPA) complex. RPA binding not only prevent nuclease degradation and annealing, but it also coordinates cell-cycle checkpoint activation and DNA repair. However, RPA binding offers little protection against the chemical modification of DNA bases. This review focuses on the type of DNA base damage that occurs in single-stranded DNA and how the damage is rectified in human cells. The discovery of DNA repair proteins, such as ALKBH3, AGT, UNG2, NEIL3, being able to repair the damaged base in the single-stranded DNA, renewed the interest to study single-stranded DNA repair. These mechanistically different proteins work independently from each other with the overarching goal of increasing fidelity of recombination and promoting error-free replication.
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9
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Weiser BP. Analysis of uracil DNA glycosylase ( UNG2) stimulation by replication protein A (RPA) at ssDNA-dsDNA junctions. Biochim Biophys Acta Proteins Proteom 2019; 1868:140347. [PMID: 31866506 DOI: 10.1016/j.bbapap.2019.140347] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 12/17/2022]
Abstract
Replication Protein A (RPA) is a single-stranded DNA binding protein that interacts with DNA repair proteins including Uracil DNA Glycosylase (UNG2). Here, I report DNA binding and activity assays using purified recombinant RPA and UNG2. Using synthetic DNA substrates, RPA was found to promote UNG2's interaction with ssDNA-dsDNA junctions regardless of the DNA strand polarity surrounding the junction. RPA stimulated UNG2's removal of uracil bases paired with adenine or guanine in DNA as much as 17-fold when the uracil was positioned 21 bps from ssDNA-dsDNA junctions, and the largest degree of UNG2 stimulation occurred when RPA was in molar excess compared to DNA. I found that RPA becomes sequestered on ssDNA regions surrounding junctions which promotes its spatial targeting of UNG2 near the junction. However, when RPA concentration exceeds free ssDNA, RPA promotes UNG2's activity without spatial constraints in dsDNA regions. These effects of RPA on UNG2 were found to be mediated primarily by interactions between RPA's winged-helix domain and UNG2's N-terminal domain, but when the winged-helix domain is unavailable, a secondary interaction between UNG2's N-terminal domain and RPA can occur. This work supports a widespread role for RPA in stimulating uracil base excision repair.
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Affiliation(s)
- Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA.
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10
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Buchinger E, Wiik SÅ, Kusnierczyk A, Rabe R, Aas PA, Kavli B, Slupphaug G, Aachmann FL. Backbone 1H, 13C and 15N chemical shift assignment of full-length human uracil DNA glycosylase UNG2. Biomol NMR Assign 2018; 12:15-22. [PMID: 28879561 DOI: 10.1007/s12104-017-9772-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/28/2017] [Indexed: 06/07/2023]
Abstract
Human uracil N-glycosylase isoform 2-UNG2 consists of an N-terminal intrinsically disordered regulatory domain (UNG2 residues 1-92, 9.3 kDa) and a C-terminal structured catalytic domain (UNG2 residues 93-313, 25.1 kDa). Here, we report the backbone 1H, 13C, and 15N chemical shift assignment as well as secondary structure analysis of the N-and C-terminal domains of UNG2 representing the full-length UNG2 protein.
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Affiliation(s)
- Edith Buchinger
- NOBIPOL, Department of Biotechnology, NTNU-Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Siv Å Wiik
- NOBIPOL, Department of Biotechnology, NTNU-Norwegian University of Science and Technology, 7491, Trondheim, Norway
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, 0317, Oslo, Norway
| | - Anna Kusnierczyk
- Department of Cancer Research and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Renana Rabe
- Department of Cancer Research and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Per A Aas
- Department of Cancer Research and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Bodil Kavli
- Department of Cancer Research and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Geir Slupphaug
- Department of Cancer Research and Molecular Medicine, NTNU - Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Finn L Aachmann
- NOBIPOL, Department of Biotechnology, NTNU-Norwegian University of Science and Technology, 7491, Trondheim, Norway.
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11
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Kara H, Ponchon L, Bouaziz S. Backbone resonance assignment of the human uracil DNA glycosylase-2. Biomol NMR Assign 2018; 12:37-42. [PMID: 28940147 DOI: 10.1007/s12104-017-9776-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 09/13/2017] [Indexed: 06/07/2023]
Abstract
The HIV-1 viral protein R (Vpr) is incorporated into virus particle during budding suggesting that its presence in the mature virion is required in the early steps of the virus life cycle in newly infected cells. Vpr is released into the host cell cytoplasm to participate to the translocation of the preintegration complex (PIC) into the nucleus for integration of the viral DNA into the host genome. Actually, Vpr plays a key role in the activation of the transcription of the HIV-1 long terminal repeat (LTR), mediates cell cycle arrest in G2 to M transition, facilitates apoptosis and controls the fidelity of reverse transcription. Moreover, Vpr drives the repair enzyme uracil DNA glycosylase (UNG2) towards degradation. UNG2 has a major role in "Base excision repair" (BER) whose main function is to maintain genome integrity by controlling DNA uracilation. The interaction of Vpr with the cellular protein UNG2 is a key event in various stages of retroviral replication and its role remains to be defined. We have performed the structural study of UNG2 by NMR and we report its (1HN, 15N, 13Cα, 13Cβ and 13C') chemical shift backbone assignment and its secondary structure in solution as predicted by TALOS-N. We aim to determine with accuracy by NMR, the residues of UNG2 interacting with Vpr, characterize their interaction and use the local structure of UNG2 and its interface with Vpr to propose potential ligands disturbing this interaction.
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Affiliation(s)
- Hesna Kara
- Sorbonne Paris Cité, Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, UMR 8015 CNRS, 4 Av. de l'Observatoire, Paris, France
| | - Luc Ponchon
- Sorbonne Paris Cité, Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, UMR 8015 CNRS, 4 Av. de l'Observatoire, Paris, France
| | - Serge Bouaziz
- Sorbonne Paris Cité, Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, UMR 8015 CNRS, 4 Av. de l'Observatoire, Paris, France.
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12
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Abstract
Pathways that control and modulate DNA methylation patterning in mammalian cells were poorly understood for a long time, although their importance in establishing and maintaining cell type-specific gene expression was well recognized. The discovery of proteins capable of converting 5-methylcytosine (5mC) to putative substrates for DNA repair introduced a novel and exciting conceptual framework for the investigation and ultimate discovery of molecular mechanisms of DNA demethylation. Against the prevailing notion that DNA methylation is a static epigenetic mark, it turned out to be dynamic and distinct mechanisms appear to have evolved to effect global and locus-specific DNA demethylation. There is compelling evidence that DNA repair, in particular base excision repair, contributes significantly to the turnover of 5mC in cells. By actively demethylating DNA, DNA repair supports the developmental establishment as well as the maintenance of DNA methylation landscapes and gene expression patterns. Yet, while the biochemical pathways are relatively well-established and reviewed, the biological context, function and regulation of DNA repair-mediated active DNA demethylation remains uncertain. In this review, we will thus summarize and critically discuss the evidence that associates active DNA demethylation by DNA repair with specific functional contexts including the DNA methylation erasure in the early embryo, the control of pluripotency and cellular differentiation, the maintenance of cell identity, and the nuclear reprogramming.
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Affiliation(s)
- David Schuermann
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland
| | - Alain R Weber
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland
| | - Primo Schär
- Department of Biomedicine, University of Basel, Mattenstrasse 28, CH-4058 Basel, Switzerland.
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Herate C, Vigne C, Guenzel CA, Lambele M, Rouyez MC, Benichou S. Uracil DNA glycosylase interacts with the p32 subunit of the replication protein A complex to modulate HIV-1 reverse transcription for optimal virus dissemination. Retrovirology 2016; 13:26. [PMID: 27068393 PMCID: PMC4828845 DOI: 10.1186/s12977-016-0257-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 03/27/2016] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Through incorporation into virus particles, the HIV-1 Vpr protein participates in the early steps of the virus life cycle by influencing the reverse transcription process. We previously showed that this positive impact on reverse transcription was related to Vpr binding to the uracil DNA glycosylase 2 enzyme (UNG2), leading to enhancement of virus infectivity in established CD4-positive cell lines via a nonenzymatic mechanism. RESULTS We report here that Vpr can form a trimolecular complex with UNG2 and the p32 subunit (RPA32) of the replication protein A (RPA) complex and we explore how these cellular proteins can influence virus replication and dissemination in the primary target cells of HIV-1, which express low levels of both proteins. Virus infectivity and replication in peripheral blood mononuclear cells and monocyte-derived macrophages (MDMs), as well as the efficiency of the viral DNA synthesis, were significantly reduced when viruses were produced from cells depleted of endogenous UNG2 or RPA32. Moreover, viruses produced in macrophages failed to replicate efficiently in UNG2- and RPA32-depleted T lymphocytes. Reciprocally, viruses produced in UNG2-depleted T cells did not replicate efficiently in MDMs confirming the positive role of UNG2 for virus dissemination. CONCLUSIONS Our data show the positive effect of UNG2 and RPA32 on the reverse transcription process leading to optimal virus replication and dissemination between the primary target cells of HIV-1.
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Affiliation(s)
- Cecile Herate
- />Inserm U1016, Institut Cochin, 22 Rue Méchain, 75014 Paris, France
- />CNRS, UMR8104, Paris, France
- />Université Paris-Descartes, Sorbonne Paris-Cité, Paris, France
| | - Clarisse Vigne
- />Inserm U1016, Institut Cochin, 22 Rue Méchain, 75014 Paris, France
- />CNRS, UMR8104, Paris, France
- />Université Paris-Descartes, Sorbonne Paris-Cité, Paris, France
| | - Carolin A. Guenzel
- />Inserm U1016, Institut Cochin, 22 Rue Méchain, 75014 Paris, France
- />CNRS, UMR8104, Paris, France
- />Université Paris-Descartes, Sorbonne Paris-Cité, Paris, France
| | - Marie Lambele
- />Inserm U1016, Institut Cochin, 22 Rue Méchain, 75014 Paris, France
- />CNRS, UMR8104, Paris, France
- />Université Paris-Descartes, Sorbonne Paris-Cité, Paris, France
| | - Marie-Christine Rouyez
- />Inserm U1016, Institut Cochin, 22 Rue Méchain, 75014 Paris, France
- />CNRS, UMR8104, Paris, France
- />Université Paris-Descartes, Sorbonne Paris-Cité, Paris, France
| | - Serge Benichou
- />Inserm U1016, Institut Cochin, 22 Rue Méchain, 75014 Paris, France
- />CNRS, UMR8104, Paris, France
- />Université Paris-Descartes, Sorbonne Paris-Cité, Paris, France
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Xue JH, Xu GF, Gu TP, Chen GD, Han BB, Xu ZM, Bjørås M, Krokan HE, Xu GL, Du YR. Uracil-DNA Glycosylase UNG Promotes Tet-mediated DNA Demethylation. J Biol Chem 2015; 291:731-8. [PMID: 26620559 DOI: 10.1074/jbc.m115.693861] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Indexed: 01/10/2023] Open
Abstract
In mammals, active DNA demethylation involves oxidation of 5-methylcytosine (5mC) into 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) by Tet dioxygenases and excision of these two oxidized bases by thymine DNA glycosylase (TDG). Although TDG is essential for active demethylation in embryonic stem cells and induced pluripotent stem cells, it is hardly expressed in mouse zygotes and dispensable in pronuclear DNA demethylation. To search for other factors that might contribute to demethylation in mammalian cells, we performed a functional genomics screen based on a methylated luciferase reporter assay. UNG2, one of the glycosylases known to excise uracil residues from DNA, was found to reduce DNA methylation, thus activating transcription of a methylation-silenced reporter gene when co-transfected with Tet2 into HEK293T cells. Interestingly, UNG2 could decrease 5caC from the genomic DNA and a reporter plasmid in transfected cells, like TDG. Furthermore, deficiency in Ung partially impaired DNA demethylation in mouse zygotes. Our results suggest that UNG might be involved in Tet-mediated DNA demethylation.
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Affiliation(s)
- Jian-Huang Xue
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Gui-Fang Xu
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China, the School of Life Science, Fudan University, Shanghai 200433, China
| | - Tian-Peng Gu
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guo-Dong Chen
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bin-Bin Han
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhi-Mei Xu
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Magnar Bjørås
- the Department of Microbiology, Clinic for Diagnostics and Intervention, Oslo University Hospital, Rikshospitalet, P. O. Box 4950, Nydalen, N-0424 Oslo, Norway
| | - Hans E Krokan
- the Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway, and
| | - Guo-Liang Xu
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China, the School of Life Science and Technology, ShanghaiTech University, 319 Yue Yang Road, Shanghai 200031, China
| | - Ya-Rui Du
- From the The State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China,
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Liu X, Guo H, Wang H, Markham R, Wei W, Yu XF. HIV-1 Vpr suppresses the cytomegalovirus promoter in a CRL4(DCAF1) E3 ligase independent manner. Biochem Biophys Res Commun 2015; 459:214-9. [PMID: 25704090 DOI: 10.1016/j.bbrc.2015.02.060] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 02/11/2015] [Indexed: 11/21/2022]
Abstract
Although the Vpr protein of human immunodeficiency virus type 1 (HIV-1) has been shown to act as a transcriptional activator of the HIV-1 LTR and certain host genes, the current study demonstrates that it can also function as a potent inhibitor of the cytomegalovirus (CMV) promoter. Previous studies have shown that the cell cycle arrest and apoptotic functions of Vpr required recruitment of the CRL4(DCAF1) E3 ligase, but this complex is shown not to be required for inhibition of the CMV promoter. We identified conserved sites (A30/V31) from diverse Vpr from HIV/SIV that were critical for blocking the CMV promoter activity. Interestingly, the Vpr mutant A30S/V31S protein also impaired the ability of Vpr to down-regulate transcription of the host UNG2 gene. Our findings shed light on the dual functions of Vpr on the transcription of HIV-1, other viruses and host genes which may contribute to viral replication and disease progression in vivo.
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