1
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Tong H, Wang H, Wang X, Liu N, Li G, Wu D, Li Y, Jin M, Li H, Wei Y, Li T, Yuan Y, Shi L, Yao X, Zhou Y, Yang H. Development of deaminase-free T-to-S base editor and C-to-G base editor by engineered human uracil DNA glycosylase. Nat Commun 2024; 15:4897. [PMID: 38851742 PMCID: PMC11162499 DOI: 10.1038/s41467-024-49343-5] [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: 03/18/2024] [Accepted: 05/31/2024] [Indexed: 06/10/2024] Open
Abstract
DNA base editors enable direct editing of adenine (A), cytosine (C), or guanine (G), but there is no base editor for direct thymine (T) editing currently. Here we develop two deaminase-free glycosylase-based base editors for direct T editing (gTBE) and C editing (gCBE) by fusing Cas9 nickase (nCas9) with engineered human uracil DNA glycosylase (UNG) variants. By several rounds of structure-informed rational mutagenesis on UNG in cultured human cells, we obtain gTBE and gCBE with high activity of T-to-S (i.e., T-to-C or T-to-G) and C-to-G conversions, respectively. Furthermore, we conduct parallel comparison of gTBE/gCBE with those recently developed using other protein engineering strategies, and find gTBE/gCBE show the outperformance. Thus, we provide several base editors, gTBEs and gCBEs, with corresponding engineered UNG variants, broadening the targeting scope of base editors.
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Affiliation(s)
- Huawei Tong
- HuidaGene Therapeutics Co., Ltd., Shanghai, China.
| | | | - Xuchen Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Nana Liu
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Guoling Li
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Danni Wu
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Yun Li
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Ming Jin
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Hengbin Li
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Yinghui Wei
- International Joint Agriculture Research Center for Animal Bio-Breeding of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
- School of Future Technology on Bio-Breeding, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Tong Li
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Yuan Yuan
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Linyu Shi
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Xuan Yao
- HuidaGene Therapeutics Co., Ltd., Shanghai, China
| | - Yingsi Zhou
- HuidaGene Therapeutics Co., Ltd., Shanghai, China.
| | - Hui Yang
- HuidaGene Therapeutics Co., Ltd., Shanghai, China.
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Key Laboratory of Primate Neurobiology, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
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2
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Mu Y, Chen Z, Plummer JB, Zelazowska MA, Dong Q, Krug LT, McBride KM. UNG-RPA interaction governs the choice between high-fidelity and mutagenic uracil repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591927. [PMID: 38746347 PMCID: PMC11092621 DOI: 10.1101/2024.04.30.591927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Mammalian Uracil DNA glycosylase (UNG) removes uracils and initiates high-fidelity base excision repair to maintain genomic stability. During B cell development, activation-induced cytidine deaminase (AID) creates uracils that UNG processes in an error-prone fashion to accomplish immunoglobulin (Ig) somatic hypermutation (SHM) or class switch recombination (CSR). The mechanism that governs high-fidelity versus mutagenic uracil repair is not understood. The B cell tropic gammaherpesvirus (GHV) encodes a functional homolog of UNG that can process AID induced genomic uracils. GHVUNG does not support hypermutation, suggesting intrinsic properties of UNG influence repair outcome. Noting the structural divergence between the UNGs, we define the RPA interacting motif as the determinant of mutation outcome. UNG or RPA mutants unable to interact with each other, only support high-fidelity repair. In B cells, transversions at the Ig variable region are abated while CSR is supported. Thus UNG-RPA governs the generation of mutations and has implications for locus specific mutagenesis in B cells and deamination associated mutational signatures in cancer.
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3
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Hayran AB, Liabakk NB, Aas PA, Kusnierczyk A, Vågbø CB, Sarno A, Iveland TS, Chawla K, Zahn A, Di Noia JM, Slupphaug G, Kavli B. RPA guides UNG to uracil in ssDNA to facilitate antibody class switching and repair of mutagenic uracil at the replication fork. Nucleic Acids Res 2024; 52:784-800. [PMID: 38000394 PMCID: PMC10810282 DOI: 10.1093/nar/gkad1115] [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: 03/31/2023] [Revised: 10/27/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
Activation-induced cytidine deaminase (AID) interacts with replication protein A (RPA), the major ssDNA-binding protein, to promote deamination of cytosine to uracil in transcribed immunoglobulin (Ig) genes. Uracil-DNA glycosylase (UNG) acts in concert with AID during Ig diversification. In addition, UNG preserves genome integrity by base-excision repair (BER) in the overall genome. How UNG is regulated to support both mutagenic processing and error-free repair remains unknown. UNG is expressed as two isoforms, UNG1 and UNG2, which both contain an RPA-binding helix that facilitates uracil excision from RPA-coated ssDNA. However, the impact of this interaction in antibody diversification and genome maintenance has not been investigated. Here, we generated B-cell clones with targeted mutations in the UNG RPA-binding motif, and analysed class switch recombination (CSR), mutation frequency (5' Ig Sμ), and genomic uracil in clones representing seven Ung genotypes. We show that the UNG:RPA interaction plays a crucial role in both CSR and repair of AID-induced uracil at the Ig loci. By contrast, the interaction had no significant impact on total genomic uracil levels. Thus, RPA coordinates UNG during CSR and pre-replicative repair of mutagenic uracil in ssDNA but is not essential in post-replicative and canonical BER of uracil in dsDNA.
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Affiliation(s)
- Abdul B Hayran
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Nina B Liabakk
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Per A Aas
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Anna Kusnierczyk
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- PROMEC - Proteomics and Modomics Experimental Core Facility at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Cathrine B Vågbø
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- PROMEC - Proteomics and Modomics Experimental Core Facility at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Antonio Sarno
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Tobias S Iveland
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Cancer Clinic, St. Olav's Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Konika Chawla
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- BioCore - Bioinformatics Core Facility at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Astrid Zahn
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
- Département of Médicine, Université de Montréal H3C 3J7 Montréal, Québec, Canada
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- PROMEC - Proteomics and Modomics Experimental Core Facility at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Bodil Kavli
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
- Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
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4
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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 PMCID: PMC10267839 DOI: 10.1002/cbic.202200765] [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: 12/22/2022] [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 used SpyCatcher/SpyTag ligation to produce a covalent complex between human uracil DNA glycosylase (UNG2) and replication protein A (RPA). Our covalent "RPA-Spy-UNG2" 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
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Rashmi S Kulkarni
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Michel Mikhail
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
- Department of Internal Medicine, Newark Beth Israel Medical Center, Newark, NJ 07112, USA
| | - Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
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5
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Kavli B, Iveland TS, Buchinger E, Hagen L, Liabakk NB, Aas PA, Obermann TS, Aachmann FL, Slupphaug G. RPA2 winged-helix domain facilitates UNG-mediated removal of uracil from ssDNA; implications for repair of mutagenic uracil at the replication fork. Nucleic Acids Res 2021; 49:3948-3966. [PMID: 33784377 PMCID: PMC8053108 DOI: 10.1093/nar/gkab195] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/04/2021] [Accepted: 03/10/2021] [Indexed: 01/14/2023] Open
Abstract
Uracil occurs at replication forks via misincorporation of deoxyuridine monophosphate (dUMP) or via deamination of existing cytosines, which occurs 2-3 orders of magnitude faster in ssDNA than in dsDNA and is 100% miscoding. Tethering of UNG2 to proliferating cell nuclear antigen (PCNA) allows rapid post-replicative removal of misincorporated uracil, but potential 'pre-replicative' removal of deaminated cytosines in ssDNA has been questioned since this could mediate mutagenic translesion synthesis and induction of double-strand breaks. Here, we demonstrate that uracil-DNA glycosylase (UNG), but not SMUG1 efficiently excises uracil from replication protein A (RPA)-coated ssDNA and that this depends on functional interaction between the flexible winged-helix (WH) domain of RPA2 and the N-terminal RPA-binding helix in UNG. This functional interaction is promoted by mono-ubiquitination and diminished by cell-cycle regulated phosphorylations on UNG. Six other human proteins bind the RPA2-WH domain, all of which are involved in DNA repair and replication fork remodelling. Based on this and the recent discovery of the AP site crosslinking protein HMCES, we propose an integrated model in which templated repair of uracil and potentially other mutagenic base lesions in ssDNA at the replication fork, is orchestrated by RPA. The UNG:RPA2-WH interaction may also play a role in adaptive immunity by promoting efficient excision of AID-induced uracils in transcribed immunoglobulin loci.
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Affiliation(s)
- Bodil Kavli
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Tobias S Iveland
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Cancer Clinic, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Edith Buchinger
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N-7034 Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway.,PROMEC Proteomics and Modomics Experimental Core at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
| | - Nina B Liabakk
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Per A Aas
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Tobias S Obermann
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
| | - Finn L Aachmann
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N-7034 Trondheim, Norway
| | - Geir Slupphaug
- Department of Clinical and Molecular Medicine, NTNU Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olavs Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway.,PROMEC Proteomics and Modomics Experimental Core at NTNU and the Central Norway Regional Health Authority, NO-7491 Trondheim, Norway
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6
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Detection of Genomic Uracil Patterns. Int J Mol Sci 2021; 22:ijms22083902. [PMID: 33918885 PMCID: PMC8070346 DOI: 10.3390/ijms22083902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/28/2021] [Accepted: 04/05/2021] [Indexed: 01/06/2023] Open
Abstract
The appearance of uracil in the deoxyuridine moiety of DNA is among the most frequently occurring genomic modifications. Three different routes can result in genomic uracil, two of which do not require specific enzymes: spontaneous cytosine deamination due to the inherent chemical reactivity of living cells, and thymine-replacing incorporation upon nucleotide pool imbalances. There is also an enzymatic pathway of cytosine deamination with multiple DNA (cytosine) deaminases involved in this process. In order to describe potential roles of genomic uracil, it is of key importance to utilize efficient uracil-DNA detection methods. In this review, we provide a comprehensive and critical assessment of currently available uracil detection methods with special focus on genome-wide mapping solutions. Recent developments in PCR-based and in situ detection as well as the quantitation of genomic uracil are also discussed.
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7
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Perkins JL, Zhao L. The N-terminal domain of uracil-DNA glycosylase: Roles for disordered regions. DNA Repair (Amst) 2021; 101:103077. [PMID: 33640758 DOI: 10.1016/j.dnarep.2021.103077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 02/14/2021] [Indexed: 01/10/2023]
Abstract
The presence of uracil in DNA calls for rapid removal facilitated by the uracil-DNA glycosylase superfamily of enzymes, which initiates the base excision repair (BER) pathway. In humans, uracil excision is accomplished primarily by the human uracil-DNA glycosylase (hUNG) enzymes. In addition to BER, hUNG enzymes play a key role in somatic hypermutation to generate antibody diversity. hUNG has several isoforms, with hUNG1 and hUNG2 being the two major isoforms. Both isoforms contain disordered N-terminal domains, which are responsible for a wide range of functions, with minimal direct impact on catalytic efficiency. Subcellular localization of hUNG enzymes is directed by differing N-terminal sequences, with hUNG1 dedicated to mitochondria and hUNG2 dedicated to the nucleus. An alternative isoform of hUNG1 has also been identified to localize to the nucleus in mouse and human cell models. Furthermore, hUNG2 has been observed at replication forks performing both pre- and post-replicative uracil excision to maintain genomic integrity. Replication protein A (RPA) and proliferating cell nuclear antigen (PCNA) are responsible for recruitment to replication forks via protein-protein interactions with the N-terminus of hUNG2. These interactions, along with protein degradation, are regulated by various post-translational modifications within the N-terminal tail, which are primarily cell-cycle dependent. Finally, translocation on DNA is also mediated by interactions between the N-terminus and DNA, which is enhanced under molecular crowding conditions by preventing diffusion events and compacting tail residues. This review summarizes recent research supporting the emerging roles of the N-terminal domain of hUNG.
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Affiliation(s)
- Jacob L Perkins
- Department of Chemistry and Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, CA 92521, United States
| | - Linlin Zhao
- Department of Chemistry and Environmental Toxicology Graduate Program, University of California, Riverside, Riverside, CA 92521, United States.
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8
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Weiser BP. Analysis of uracil DNA glycosylase (UNG2) stimulation by replication protein A (RPA) at ssDNA-dsDNA junctions. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 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] [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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9
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Elango R, Osia B, Harcy V, Malc E, Mieczkowski PA, Roberts SA, Malkova A. Repair of base damage within break-induced replication intermediates promotes kataegis associated with chromosome rearrangements. Nucleic Acids Res 2019; 47:9666-9684. [PMID: 31392335 PMCID: PMC6765108 DOI: 10.1093/nar/gkz651] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/12/2019] [Accepted: 08/02/2019] [Indexed: 02/01/2023] Open
Abstract
Break induced replication (BIR) is a double strand break repair pathway that can promote genetic instabilities similar to those observed in cancer. Instead of a replication fork, BIR is driven by a migration bubble where asynchronous synthesis between leading and lagging strands leads to accumulation of single-stranded DNA (ssDNA) that promotes mutation. However, the details of the mechanism of mutagenesis, including the identity of the participating proteins, remain unknown. Using yeast as a model, we demonstrate that mutagenic ssDNA is formed at multiple positions along the BIR track and that Pol ζ is responsible for the majority of both spontaneous and damage-induced base substitutions during BIR. We also report that BIR creates a potent substrate for APOBEC3A (A3A) cytidine deaminase that can promote formation of mutation clusters along the entire track of BIR. Finally, we demonstrate that uracil glycosylase initiates the bypass of DNA damage induced by A3A in the context of BIR without formation of base substitutions, but instead this pathway frequently leads to chromosomal rearrangements. Together, the expression of A3A during BIR in yeast recapitulates the main features of APOBEC-induced kataegis in human cancers, suggesting that BIR might represent an important source of these hyper-mutagenic events.
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Affiliation(s)
- Rajula Elango
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
| | - Beth Osia
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
| | - Victoria Harcy
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Ewa Malc
- Department of Genetics, Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Piotr A Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center and Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Steven A Roberts
- School of Molecular Biosciences, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Anna Malkova
- Department of Biology, University of Iowa, Iowa City, IA 52245, USA
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10
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Sarno A, Lundbæk M, Liabakk NB, Aas PA, Mjelle R, Hagen L, Sousa MML, Krokan HE, Kavli B. Uracil-DNA glycosylase UNG1 isoform variant supports class switch recombination and repairs nuclear genomic uracil. Nucleic Acids Res 2019; 47:4569-4585. [PMID: 30838409 PMCID: PMC6511853 DOI: 10.1093/nar/gkz145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 01/18/2019] [Accepted: 02/25/2019] [Indexed: 11/23/2022] Open
Abstract
UNG is the major uracil-DNA glycosylase in mammalian cells and is involved in both error-free base excision repair of genomic uracil and mutagenic uracil-processing at the antibody genes. However, the regulation of UNG in these different processes is currently not well understood. The UNG gene encodes two isoforms, UNG1 and UNG2, each possessing unique N-termini that mediate translocation to the mitochondria and the nucleus, respectively. A strict subcellular localization of each isoform has been widely accepted despite a lack of models to study them individually. To determine the roles of each isoform, we generated and characterized several UNG isoform-specific mouse and human cell lines. We identified a distinct UNG1 isoform variant that is targeted to the cell nucleus where it supports antibody class switching and repairs genomic uracil. We propose that the nuclear UNG1 variant, which in contrast to UNG2 lacks a PCNA-binding motif, may be specialized to act on ssDNA through its ability to bind RPA. RPA-coated ssDNA regions include both transcribed antibody genes that are targets for deamination by AID and regions in front of the moving replication forks. Our findings provide new insights into the function of UNG isoforms in adaptive immunity and DNA repair.
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Affiliation(s)
- Antonio Sarno
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics at NTNU and the Central Norway Regional Health Authority
| | - Marie Lundbæk
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Nina Beate Liabakk
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Per Arne Aas
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Robin Mjelle
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics at NTNU and the Central Norway Regional Health Authority
| | - Mirta M L Sousa
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway.,PROMEC Core Facility for Proteomics and Modomics at NTNU and the Central Norway Regional Health Authority
| | - Hans E Krokan
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Bodil Kavli
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.,Clinic of Laboratory Medicine, St. Olav's Hospital, Trondheim University Hospital, NO-7006 Trondheim, Norway
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11
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Weiser BP, Rodriguez G, Cole PA, Stivers JT. N-terminal domain of human uracil DNA glycosylase (hUNG2) promotes targeting to uracil sites adjacent to ssDNA-dsDNA junctions. Nucleic Acids Res 2019; 46:7169-7178. [PMID: 29917162 PMCID: PMC6101581 DOI: 10.1093/nar/gky525] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 05/24/2018] [Indexed: 01/29/2023] Open
Abstract
The N-terminal domain (NTD) of nuclear human uracil DNA glycosylase (hUNG2) assists in targeting hUNG2 to replication forks through specific interactions with replication protein A (RPA). Here, we explored hUNG2 activity in the presence and absence of RPA using substrates with ssDNA–dsDNA junctions that mimic structural features of the replication fork and transcriptional R-loops. We find that when RPA is tightly bound to the ssDNA overhang of junction DNA substrates, base excision by hUNG2 is strongly biased toward uracils located 21 bp or less from the ssDNA–dsDNA junction. In the absence of RPA, hUNG2 still showed an 8-fold excision bias for uracil located <10 bp from the junction, but only when the overhang had a 5′ end. Biased targeting required the NTD and was not observed with the hUNG2 catalytic domain alone. Consistent with this requirement, the isolated NTD was found to bind weakly to ssDNA. These findings indicate that the NTD of hUNG2 targets the enzyme to ssDNA–dsDNA junctions using RPA-dependent and RPA-independent mechanisms. This structure-based specificity may promote efficient removal of uracils that arise from dUTP incorporation during DNA replication, or additionally, uracils that arise from DNA cytidine deamination at transcriptional R-loops during immunoglobulin class-switch recombination.
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Affiliation(s)
- Brian P Weiser
- Department of Molecular Biology, Rowan University School of Osteopathic Medicine, Stratford, NJ 08084, USA
| | - Gaddiel Rodriguez
- Department of Pharmacology & Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Philip A Cole
- Division of Genetics, Department of Medicine and Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA
| | - James T Stivers
- Department of Pharmacology & Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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12
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Weiser BP, Stivers JT, Cole PA. Investigation of N-Terminal Phospho-Regulation of Uracil DNA Glycosylase Using Protein Semisynthesis. Biophys J 2017; 113:393-401. [PMID: 28746850 DOI: 10.1016/j.bpj.2017.06.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 06/09/2017] [Accepted: 06/12/2017] [Indexed: 11/16/2022] Open
Abstract
Uracil DNA Glycosylase (UNG2) is the primary enzyme in humans that prevents the stable incorporation of deoxyuridine monophosphate into DNA in the form of U/A basepairs. During S-phase, UNG2 remains associated with the replication fork through its interactions with two proteins, Proliferating Cell Nuclear Antigen (PCNA) and Replication Protein A (RPA), which are critical for DNA replication and repair. In this work, we used protein semisynthesis and fluorescence anisotropy assays to explore the interactions of UNG2 with PCNA and RPA and to determine the effects of two UNG2 phosphorylation sites (Thr6 and Tyr8) located within its PCNA-interacting motif (PIP-box). In binding assays, we found that phosphorylation of Thr6 or Tyr8 on UNG2 can impede PCNA binding without affecting UNG2 catalytic activity or its RPA interaction. Our data also suggests that unmodified UNG2, PCNA, and RPA can form a ternary protein complex. We propose that the UNG2 N-terminus may serve as a flexible scaffold to tether PCNA and RPA at the replication fork, and that post-translational modifications on the UNG2 N-terminus disrupt formation of the PCNA-UNG2-RPA protein complex.
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Affiliation(s)
- Brian P Weiser
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Philip A Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland.
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13
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D'Errico M, Parlanti E, Pascucci B, Fortini P, Baccarini S, Simonelli V, Dogliotti E. Single nucleotide polymorphisms in DNA glycosylases: From function to disease. Free Radic Biol Med 2017; 107:278-291. [PMID: 27932076 DOI: 10.1016/j.freeradbiomed.2016.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/25/2016] [Accepted: 12/02/2016] [Indexed: 02/08/2023]
Abstract
Oxidative stress is associated with a growing number of diseases that span from cancer to neurodegeneration. Most oxidatively induced DNA base lesions are repaired by the base excision repair (BER) pathway which involves the action of various DNA glycosylases. There are numerous genome wide studies attempting to associate single-nucleotide polymorphisms (SNPs) with predispositions to various types of disease; often, these common variants do not have significant alterations in their biochemical function and do not exhibit a convincing phenotype. Nevertheless several lines of evidence indicate that SNPs in DNA repair genes may modulate DNA repair capacity and contribute to risk of disease. This overview provides a convincing picture that SNPs of DNA glycosylases that remove oxidatively generated DNA lesions are susceptibility factors for a wide disease spectrum that includes besides cancer (particularly lung, breast and gastrointestinal tract), cochlear/ocular disorders, myocardial infarction and neurodegenerative disorders which can be all grouped under the umbrella of oxidative stress-related pathologies.
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Affiliation(s)
- Mariarosaria D'Errico
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
| | - Eleonora Parlanti
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Barbara Pascucci
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Via Salaria, Km 29,300, 00016 Monterotondo Stazione, Rome, Italy
| | - Paola Fortini
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Sara Baccarini
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Valeria Simonelli
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Eugenia Dogliotti
- Department of Environment and Primary Prevention, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy.
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14
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Wu Y, Lu J, Kang T. Human single-stranded DNA binding proteins: guardians of genome stability. Acta Biochim Biophys Sin (Shanghai) 2016; 48:671-7. [PMID: 27217471 DOI: 10.1093/abbs/gmw044] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/15/2016] [Indexed: 01/03/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) are essential for maintaining the integrity of the genome in all organisms. All processes related to DNA, such as replication, excision, repair, and recombination, require the participation of SSBs whose oligonucleotide/oligosaccharide-binding (OB)-fold domain is responsible for the interaction with single-stranded DNA (ssDNA). For a long time, the heterotrimeric replication protein A (RPA) complex was believed to be the only nuclear SSB in eukaryotes to participate in ssDNA processing, while mitochondrial SSBs that are conserved with prokaryotic SSBs were shown to be essential for maintaining genome stability in eukaryotic mitochondria. In recent years, two new proteins, hSSB1 and hSSB2 (human SSBs 1/2), were identified and have better sequence similarity to bacterial and archaeal SSBs than RPA. This review summarizes the current understanding of these human SSBs in DNA damage repair and in cell-cycle checkpoint activation following DNA damage, as well as their relationships with cancer.
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Affiliation(s)
- Yuanzhong Wu
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jinping Lu
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
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15
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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] [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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16
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Marcuzzi A, Vozzi D, Girardelli M, Tricarico PM, Knowles A, Crovella S, Vuch J, Tommasini A, Piscianz E, Bianco AM. Putative modifier genes in mevalonate kinase deficiency. Mol Med Rep 2016; 13:3181-9. [PMID: 26935981 DOI: 10.3892/mmr.2016.4918] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 10/23/2015] [Indexed: 11/06/2022] Open
Abstract
Mevalonate kinase deficiency (MKD) is an autosomal recessive auto‑inflammatory disease, caused by impairment of the mevalonate pathway. Although the molecular mechanism remains to be elucidated, there is clinical evidence suggesting that other regulatory genes may be involved in determining the phenotype. The identification of novel target genes may explain non‑homogeneous genotype‑phenotype correlations, and provide evidence in support of the hypothesis that novel regulatory genes predispose or amplify deregulation of the mevalonate pathway in this orphan disease. In the present study, DNA samples were obtained from five patients with MKD, which were then analyzed using whole exome sequencing. A missense variation in the PEX11γ gene was observed in homozygosis in P2, possibly correlating with visual blurring. The UNG rare gene variant was detected in homozygosis in P5, without correlating with a specific clinical phenotype. A number of other variants were found in the five analyzed DNA samples from the MKD patients, however no correlation with the phenotype was established. The results of the presents study suggested that further analysis, using next generation sequencing approaches, is required on a larger sample size of patients with MKD, who share the same MVK mutations and exhibit 'extreme' clinical phenotypes. As MVK mutations may be associated with MKD, the identification of specific modifier genes may assist in providing an earlier diagnosis.
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Affiliation(s)
- Annalisa Marcuzzi
- Department of Advanced Diagnostic and Clinical Trials, Institute for Maternal and Child Health‑IRCCS 'Burlo Garofolo', Trieste I‑34137, Italy
| | - Diego Vozzi
- Department of Advanced Diagnostic and Clinical Trials, Institute for Maternal and Child Health‑IRCCS 'Burlo Garofolo', Trieste I‑34137, Italy
| | - Martina Girardelli
- Department of Advanced Diagnostic and Clinical Trials, Institute for Maternal and Child Health‑IRCCS 'Burlo Garofolo', Trieste I‑34137, Italy
| | - Paola Maura Tricarico
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste I‑34128, Italy
| | - Alessandra Knowles
- Department of Advanced Diagnostic and Clinical Trials, Institute for Maternal and Child Health‑IRCCS 'Burlo Garofolo', Trieste I‑34137, Italy
| | - Sergio Crovella
- Department of Advanced Diagnostic and Clinical Trials, Institute for Maternal and Child Health‑IRCCS 'Burlo Garofolo', Trieste I‑34137, Italy
| | - Josef Vuch
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste I‑34128, Italy
| | - Alberto Tommasini
- Department of Advanced Diagnostic and Clinical Trials, Institute for Maternal and Child Health‑IRCCS 'Burlo Garofolo', Trieste I‑34137, Italy
| | - Elisa Piscianz
- Department of Advanced Diagnostic and Clinical Trials, Institute for Maternal and Child Health‑IRCCS 'Burlo Garofolo', Trieste I‑34137, Italy
| | - Anna Monica Bianco
- Department of Advanced Diagnostic and Clinical Trials, Institute for Maternal and Child Health‑IRCCS 'Burlo Garofolo', Trieste I‑34137, Italy
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17
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Róna G, Scheer I, Nagy K, Pálinkás HL, Tihanyi G, Borsos M, Békési A, Vértessy BG. Detection of uracil within DNA using a sensitive labeling method for in vitro and cellular applications. Nucleic Acids Res 2016; 44:e28. [PMID: 26429970 PMCID: PMC4756853 DOI: 10.1093/nar/gkv977] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 09/10/2015] [Accepted: 09/15/2015] [Indexed: 11/14/2022] Open
Abstract
The role of uracil in genomic DNA has been recently re-evaluated. It is now widely accepted to be a physiologically important DNA element in diverse systems from specific phages to antibody maturation and Drosophila development. Further relevant investigations would largely benefit from a novel reliable and fast method to gain quantitative and qualitative information on uracil levels in DNA both in vitro and in situ, especially since current techniques does not allow in situ cellular detection. Here, starting from a catalytically inactive uracil-DNA glycosylase protein, we have designed several uracil sensor fusion proteins. The designed constructs can be applied as molecular recognition tools that can be detected with conventional antibodies in dot-blot applications and may also serve as in situ uracil-DNA sensors in cellular techniques. Our method is verified on numerous prokaryotic and eukaryotic cellular systems. The method is easy to use and can be applied in a high-throughput manner. It does not require expensive equipment or complex know-how, facilitating its easy implementation in any basic molecular biology laboratory. Elevated genomic uracil levels from cells of diverse genetic backgrounds and/or treated with different drugs can be demonstrated also in situ, within the cell.
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Affiliation(s)
- Gergely Róna
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, H-1117 Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Szt Gellért Square 4, H-1111 Budapest, Hungary
| | - Ildikó Scheer
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, H-1117 Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Szt Gellért Square 4, H-1111 Budapest, Hungary
| | - Kinga Nagy
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, H-1117 Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Szt Gellért Square 4, H-1111 Budapest, Hungary
| | - Hajnalka L Pálinkás
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, H-1117 Budapest, Hungary Doctoral School of Multidisciplinary Medical Science, University of Szeged, H-6720 Szeged, Hungary
| | - Gergely Tihanyi
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, H-1117 Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Szt Gellért Square 4, H-1111 Budapest, Hungary
| | - Máté Borsos
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, H-1117 Budapest, Hungary
| | - Angéla Békési
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, H-1117 Budapest, Hungary
| | - Beáta G Vértessy
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, H-1117 Budapest, Hungary Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Szt Gellért Square 4, H-1111 Budapest, Hungary
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18
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Xie S, Lu Y, Jakoncic J, Sun H, Xia J, Qian C. Structure of RPA32 bound to the N-terminus of SMARCAL1 redefines the binding interface between RPA32 and its interacting proteins. FEBS J 2014; 281:3382-96. [PMID: 24910198 DOI: 10.1111/febs.12867] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 05/16/2014] [Accepted: 06/05/2014] [Indexed: 11/28/2022]
Abstract
UNLABELLED Replication protein A subunit RPA32 contains a C-terminal domain that interacts with a variety of DNA damage response proteins including SMARCAL1, Tipin, UNG2 and XPA. We have solved the high-resolution crystal structure of RPA32 C-terminal domain (RPA32C) in complex with a 26-amino-acid peptide derived from the N-terminus of SMARCAL1 (SMARCAL1N). The RPA32C-SMARCAL1N structure reveals a 1 : 1 binding stoichiometry and displays a well-ordered binding interface. SMARCAL1N adopts a long α-helical conformation with the highly conserved 11 residues aligned on one face of the α-helix showing extensive interactions with the RPA32C domain. Extensive mutagenesis experiments were performed to corroborate the interactions observed in crystal structure. Moreover, the α1/α2 loop of the RPA32C domain undergoes a conformational rearrangement upon SMARCAL1N binding. NMR study has further confirmed that the RPA32C-SMARCAL1N interaction induces conformational changes in RPA32C. Isothermal titration calorimetry studies have also demonstrated that the conserved α-helical motif defined in the current study is required for sufficient binding of RPA32C. Taken together, our study has provided convincing structural information that redefines the common recognition pattern shared by RPA32C interacting proteins. DATABASE The atomic coordinates of RPA32C in complex with 26-aa SMARCAL1 (SMARCAL1N) peptide have been deposited at the Protein Data Bank with accession code 4MQV. STRUCTURED DIGITAL ABSTRACT RPA32 and SMARCAL1 bind by isothermal titration calorimetry(1, 2, 3, 4, 5, 6, 7, 8, 9) RPA32 and SMARCAL1 bind by molecular sieving (View interaction) RPA32 and SMARCAL1 bind by x-ray crystallography (View interaction) Tipin and RPA32 bind by isothermal titration calorimetry (1, 2) RPA32 and UNG2 bind by isothermal titration calorimetry (1, 2, 3) SMARCAL1 and RPA32 bind by nuclear magnetic resonance (View interaction) UNG2 and RPA32 bind by nuclear magnetic resonance (View interaction) Tipin and RPA32 bind by nuclear magnetic resonance (View interaction).
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Affiliation(s)
- Si Xie
- Department of Biochemistry, the University of Hong Kong, China
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19
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Galashevskaya A, Sarno A, Vågbø CB, Aas PA, Hagen L, Slupphaug G, Krokan HE. A robust, sensitive assay for genomic uracil determination by LC/MS/MS reveals lower levels than previously reported. DNA Repair (Amst) 2013; 12:699-706. [PMID: 23742752 DOI: 10.1016/j.dnarep.2013.05.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 05/06/2013] [Accepted: 05/09/2013] [Indexed: 10/26/2022]
Abstract
Considerable progress has been made in understanding the origins of genomic uracil and its role in genome stability and host defense; however, the main question concerning the basal level of uracil in DNA remains disputed. Results from assays designed to quantify genomic uracil vary by almost three orders of magnitude. To address the issues leading to this inconsistency, we explored possible shortcomings with existing methods and developed a sensitive LC/MS/MS-based method for the absolute quantification of genomic 2'-deoxyuridine (dUrd). To this end, DNA was enzymatically hydrolyzed to 2'-deoxyribonucleosides and dUrd was purified in a preparative HPLC step and analyzed by LC/MS/MS. The standard curve was linear over four orders of magnitude with a quantification limit of 5 fmol dUrd. Control samples demonstrated high inter-experimental accuracy (94.3%) and precision (CV 9.7%). An alternative method that employed UNG2 to excise uracil from DNA for LC/MS/MS analysis gave similar results, but the intra-assay variability was significantly greater. We quantified genomic dUrd in Ung(+/+) and Ung(-/-) mouse embryonic fibroblasts and human lymphoblastoid cell lines carrying UNG mutations. DNA-dUrd is 5-fold higher in Ung(-/-) than in Ung(+/+) fibroblasts and 11-fold higher in UNG2 dysfunctional than in UNG2 functional lymphoblastoid cells. We report approximately 400-600 dUrd per human or murine genome in repair-proficient cells, which is lower than results using other methods and suggests that genomic uracil levels may have previously been overestimated.
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Affiliation(s)
- Anastasia Galashevskaya
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, NO-7489 Trondheim, Norway
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20
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Abstract
Base excision repair (BER) corrects DNA damage from oxidation, deamination and alkylation. Such base lesions cause little distortion to the DNA helix structure. BER is initiated by a DNA glycosylase that recognizes and removes the damaged base, leaving an abasic site that is further processed by short-patch repair or long-patch repair that largely uses different proteins to complete BER. At least 11 distinct mammalian DNA glycosylases are known, each recognizing a few related lesions, frequently with some overlap in specificities. Impressively, the damaged bases are rapidly identified in a vast excess of normal bases, without a supply of energy. BER protects against cancer, aging, and neurodegeneration and takes place both in nuclei and mitochondria. More recently, an important role of uracil-DNA glycosylase UNG2 in adaptive immunity was revealed. Furthermore, other DNA glycosylases may have important roles in epigenetics, thus expanding the repertoire of BER proteins.
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Affiliation(s)
- Hans E Krokan
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, N-7489 Trondheim, Norway.
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