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Diatlova EA, Mechetin GV, Yudkina AV, Zharkov VD, Torgasheva NA, Endutkin AV, Shulenina OV, Konevega AL, Gileva IP, Shchelkunov SN, Zharkov DO. Correlated Target Search by Vaccinia Virus Uracil-DNA Glycosylase, a DNA Repair Enzyme and a Processivity Factor of Viral Replication Machinery. Int J Mol Sci 2023; 24:ijms24119113. [PMID: 37298065 DOI: 10.3390/ijms24119113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/13/2023] [Accepted: 05/21/2023] [Indexed: 06/12/2023] Open
Abstract
The protein encoded by the vaccinia virus D4R gene has base excision repair uracil-DNA N-glycosylase (vvUNG) activity and also acts as a processivity factor in the viral replication complex. The use of a protein unlike PolN/PCNA sliding clamps is a unique feature of orthopoxviral replication, providing an attractive target for drug design. However, the intrinsic processivity of vvUNG has never been estimated, leaving open the question whether it is sufficient to impart processivity to the viral polymerase. Here, we use the correlated cleavage assay to characterize the translocation of vvUNG along DNA between two uracil residues. The salt dependence of the correlated cleavage, together with the similar affinity of vvUNG for damaged and undamaged DNA, support the one-dimensional diffusion mechanism of lesion search. Unlike short gaps, covalent adducts partly block vvUNG translocation. Kinetic experiments show that once a lesion is found it is excised with a probability ~0.76. Varying the distance between two uracils, we use a random walk model to estimate the mean number of steps per association with DNA at ~4200, which is consistent with vvUNG playing a role as a processivity factor. Finally, we show that inhibitors carrying a tetrahydro-2,4,6-trioxopyrimidinylidene moiety can suppress the processivity of vvUNG.
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Affiliation(s)
- Evgeniia A Diatlova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Grigory V Mechetin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Anna V Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Vasily D Zharkov
- Biology Department, Tomsk State University, 634050 Tomsk, Russia
| | - Natalia A Torgasheva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Olga V Shulenina
- NRC "Kurchatov Institute"-B. P. Konstantinov Petersburg Nuclear Physics Institute, Leningrad Region, 188300 Gatchina, Russia
| | - Andrey L Konevega
- NRC "Kurchatov Institute"-B. P. Konstantinov Petersburg Nuclear Physics Institute, Leningrad Region, 188300 Gatchina, Russia
| | - Irina P Gileva
- State Research Center of Virology and Biotechnology Vector, Novosibirsk Region, 630559 Koltsovo, Russia
| | - Sergei N Shchelkunov
- State Research Center of Virology and Biotechnology Vector, Novosibirsk Region, 630559 Koltsovo, Russia
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
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2
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Diatlova EA, Mechetin GV, Zharkov DO. Distinct Mechanisms of Target Search by Endonuclease VIII-like DNA Glycosylases. Cells 2022; 11:cells11203192. [PMID: 36291061 PMCID: PMC9600533 DOI: 10.3390/cells11203192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/08/2022] [Accepted: 10/09/2022] [Indexed: 12/02/2022] Open
Abstract
Proteins that recognize specific DNA sequences or structural elements often find their cognate DNA lesions in a processive mode, in which an enzyme binds DNA non-specifically and then slides along the DNA contour by one-dimensional diffusion. Opposite to the processive mechanism is distributive search, when an enzyme binds, samples and releases DNA without significant lateral movement. Many DNA glycosylases, the repair enzymes that excise damaged bases from DNA, use processive search to find their cognate lesions. Here, using a method based on correlated cleavage of multiply damaged oligonucleotide substrates we investigate the mechanism of lesion search by three structurally related DNA glycosylases—bacterial endonuclease VIII (Nei) and its mammalian homologs NEIL1 and NEIL2. Similarly to another homologous enzyme, bacterial formamidopyrimidine–DNA glycosylase, NEIL1 seems to use a processive mode to locate its targets. However, the processivity of Nei was notably lower, and NEIL2 exhibited almost fully distributive action on all types of substrates. Although one-dimensional diffusion is often regarded as a universal search mechanism, our results indicate that even proteins sharing a common fold may be quite different in the ways they locate their targets in DNA.
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Affiliation(s)
- Evgeniia A. Diatlova
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Grigory V. Mechetin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Dmitry O. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Correspondence:
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3
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Wang L, Song K, Yu J, Da LT. Computational investigations on target-site searching and recognition mechanisms by thymine DNA glycosylase during DNA repair process. Acta Biochim Biophys Sin (Shanghai) 2022; 54:796-806. [PMID: 35593467 PMCID: PMC9828053 DOI: 10.3724/abbs.2022050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
DNA glycosylase, as one member of DNA repair machineries, plays an essential role in correcting mismatched/damaged DNA nucleotides by cleaving the N-glycosidic bond between the sugar and target nucleobase through the base excision repair (BER) pathways. Efficient corrections of these DNA lesions are critical for maintaining genome integrity and preventing premature aging and cancers. The target-site searching/recognition mechanisms and the subsequent conformational dynamics of DNA glycosylase, however, remain challenging to be characterized using experimental techniques. In this review, we summarize our recent studies of sequential structural changes of thymine DNA glycosylase (TDG) during the DNA repair process, achieved mostly by molecular dynamics (MD) simulations. Computational simulations allow us to reveal atomic-level structural dynamics of TDG as it approaches the target-site, and pinpoint the key structural elements responsible for regulating the translocation of TDG along DNA. Subsequently, upon locating the lesions, TDG adopts a base-flipping mechanism to extrude the mispaired nucleobase into the enzyme active-site. The constructed kinetic network model elucidates six metastable states during the base-extrusion process and suggests an active role of TDG in flipping the intrahelical nucleobase. Finally, the molecular mechanism of product release dynamics after catalysis is also summarized. Taken together, we highlight to what extent the computational simulations advance our knowledge and understanding of the molecular mechanism underlying the conformational dynamics of TDG, as well as the limitations of current theoretical work.
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Affiliation(s)
- Lingyan Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Kaiyuan Song
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghai200240China
| | - Jin Yu
- Department of Physics and AstronomyDepartment of ChemistryNSF-Simons Center for Multiscale Cell Fate ResearchUniversity of CaliforniaIrvineCA92697USA
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education)Shanghai Center for Systems BiomedicineShanghai Jiao Tong UniversityShanghai200240China,Correspondence address. Tel: +86-21-34207348; E-mail:
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4
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Westwood MN, Ljunggren KD, Boyd B, Becker J, Dwyer TJ, Meints GA. Single-Base Lesions and Mismatches Alter the Backbone Conformational Dynamics in DNA. Biochemistry 2021; 60:873-885. [PMID: 33689312 DOI: 10.1021/acs.biochem.0c00784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA damage has been implicated in numerous human diseases, particularly cancer, and the aging process. Single-base lesions and mismatches in DNA can be cytotoxic or mutagenic and are recognized by a DNA glycosylase during the process of base excision repair. Altered local dynamics and conformational properties in damaged DNAs have previously been suggested to assist in recognition and specificity. Herein, we use solution nuclear magnetic resonance to quantify changes in BI-BII backbone conformational dynamics due to the presence of single-base lesions in DNA, including uracil, dihydrouracil, 1,N6-ethenoadenine, and T:G mismatches. Stepwise changes to the %BII and ΔG of the BI-BII dynamic equilibrium compared to those of unmodified sequences were observed. Additionally, the equilibrium skews toward endothermicity for the phosphates nearest the lesion/mismatched base pair. Finally, the phosphates with the greatest alterations correlate with those most relevant to the repair of enzyme binding. All of these results suggest local conformational rearrangement of the DNA backbone may play a role in lesion recognition by repair enzymes.
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Affiliation(s)
- M N Westwood
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
| | - K D Ljunggren
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
| | - Benjamin Boyd
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
| | - Jaclyn Becker
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
| | - Tammy J Dwyer
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, United States
| | - Gary A Meints
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
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5
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Tian J, Wang L, Da LT. Atomic resolution of short-range sliding dynamics of thymine DNA glycosylase along DNA minor-groove for lesion recognition. Nucleic Acids Res 2021; 49:1278-1293. [PMID: 33469643 PMCID: PMC7897493 DOI: 10.1093/nar/gkaa1252] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/10/2020] [Accepted: 12/15/2020] [Indexed: 02/06/2023] Open
Abstract
Thymine DNA glycosylase (TDG), as a repair enzyme, plays essential roles in maintaining the genome integrity by correcting several mismatched/damaged nucleobases. TDG acquires an efficient strategy to search for the lesions among a vast number of cognate base pairs. Currently, atomic-level details of how TDG translocates along DNA as it approaches the lesion site and the molecular mechanisms of the interplay between TDG and DNA are still elusive. Here, by constructing the Markov state model based on hundreds of molecular dynamics simulations with an integrated simulation time of ∼25 μs, we reveal the rotation-coupled sliding dynamics of TDG along a 9 bp DNA segment containing one G·T mispair. We find that TDG translocates along DNA at a relatively faster rate when distant from the lesion site, but slows down as it approaches the target, accompanied by deeply penetrating into the minor-groove, opening up the mismatched base pair and significantly sculpturing the DNA shape. Moreover, the electrostatic interactions between TDG and DNA are found to be critical for mediating the TDG translocation. Notably, several uncharacterized TDG residues are identified to take part in regulating the conformational switches of TDG occurred in the site-transfer process, which warrants further experimental validations.
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Affiliation(s)
- Jiaqi Tian
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lingyan Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Lin-Tai Da
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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6
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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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7
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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] [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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8
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Dey P, Bhattacherjee A. Structural Basis of Enhanced Facilitated Diffusion of DNA-Binding Protein in Crowded Cellular Milieu. Biophys J 2020; 118:505-517. [PMID: 31862109 PMCID: PMC6976804 DOI: 10.1016/j.bpj.2019.11.3388] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 11/03/2019] [Accepted: 11/18/2019] [Indexed: 02/06/2023] Open
Abstract
Although the fast association between DNA-binding proteins (DBPs) and DNA is explained by a facilitated diffusion mechanism, in which DBPs adopt a weighted combination of three-dimensional diffusion and one-dimensional (1D) sliding and hopping modes of transportation, the role of cellular environment that contains many nonspecifically interacting proteins and other biomolecules is mostly overlooked. By performing large-scale computational simulations with an appropriately tuned model of protein and DNA in the presence of nonspecifically interacting bulk and DNA-bound crowders (genomic crowders), we demonstrate the structural basis of the enhanced facilitated diffusion of DBPs inside a crowded cellular milieu through, to our knowledge, novel 1D scanning mechanisms. In this one-dimensional scanning mode, the protein can float along the DNA under the influence of nonspecific interactions of bulk crowder molecules. The search mode is distinctly different compared to usual 1D sliding and hopping dynamics in which protein diffusion is regulated by the DNA electrostatics. In contrast, the presence of genomic crowders expedites the target search process by transporting the protein over DNA segments through the formation of a transient protein-crowder bridged complex. By analyzing the ruggedness of the associated potential energy landscape, we underpin the molecular origin of the kinetic advantages of these search modes and show that they successfully explain the experimentally observed acceleration of facilitated diffusion of DBPs by molecular crowding agents and crowder-concentration-dependent enzymatic activity of transcription factors. Our findings provide crucial insights into gene regulation kinetics inside the crowded cellular milieu.
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Affiliation(s)
- Pinki Dey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India.
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9
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Dey P, Bhattacherjee A. Mechanism of Facilitated Diffusion of DNA Repair Proteins in Crowded Environment: Case Study with Human Uracil DNA Glycosylase. J Phys Chem B 2019; 123:10354-10364. [DOI: 10.1021/acs.jpcb.9b07342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Pinki Dey
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India 110067
| | - Arnab Bhattacherjee
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India 110067
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10
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Abstract
Comprehensive data about the composition and structure of cellular components have enabled the construction of quantitative whole-cell models. While kinetic network-type models have been established, it is also becoming possible to build physical, molecular-level models of cellular environments. This review outlines challenges in constructing and simulating such models and discusses near- and long-term opportunities for developing physical whole-cell models that can connect molecular structure with biological function.
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Affiliation(s)
- Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA;
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
| | - Yuji Sugita
- Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047, Japan
- Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan
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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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Vestergaard CL, Blainey PC, Flyvbjerg H. Single-particle trajectories reveal two-state diffusion-kinetics of hOGG1 proteins on DNA. Nucleic Acids Res 2019; 46:2446-2458. [PMID: 29361033 PMCID: PMC5861423 DOI: 10.1093/nar/gky004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 01/05/2018] [Indexed: 12/28/2022] Open
Abstract
We reanalyze trajectories of hOGG1 repair proteins diffusing on DNA. A previous analysis of these trajectories with the popular mean-squared-displacement approach revealed only simple diffusion. Here, a new optimal estimator of diffusion coefficients reveals two-state kinetics of the protein. A simple, solvable model, in which the protein randomly switches between a loosely bound, highly mobile state and a tightly bound, less mobile state is the simplest possible dynamic model consistent with the data. It yields accurate estimates of hOGG1’s (i) diffusivity in each state, uncorrupted by experimental errors arising from shot noise, motion blur and thermal fluctuations of the DNA; (ii) rates of switching between states and (iii) rate of detachment from the DNA. The protein spends roughly equal time in each state. It detaches only from the loosely bound state, with a rate that depends on pH and the salt concentration in solution, while its rates for switching between states are insensitive to both. The diffusivity in the loosely bound state depends primarily on pH and is three to ten times higher than in the tightly bound state. We propose and discuss some new experiments that take full advantage of the new tools of analysis presented here.
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Affiliation(s)
- Christian L Vestergaard
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark.,Decision and Bayesian Computation, Pasteur Institute, CNRS UMR 3571, 25-28 rue du Dr Roux, 75015 Paris, France.,Bioinformatics and Biostatistics Hub, C3BI, Pasteur Institute, CNRS USR 3756, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Paul C Blainey
- MIT Department of Biological Engineering and Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
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13
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Abstract
Genomic DNA is susceptible to endogenous and environmental stresses that modify DNA structure and its coding potential. Correspondingly, cells have evolved intricate DNA repair systems to deter changes to their genetic material. Base excision DNA repair involves a number of enzymes and protein cofactors that hasten repair of damaged DNA bases. Recent advances have identified macromolecular complexes that assemble at the DNA lesion and mediate repair. The repair of base lesions generally requires five enzymatic activities: glycosylase, endonuclease, lyase, polymerase, and ligase. The protein cofactors and mechanisms for coordinating the sequential enzymatic steps of repair are being revealed through a range of experimental approaches. We discuss the enzymes and protein cofactors involved in eukaryotic base excision repair, emphasizing the challenge of integrating findings from multiple methodologies. The results provide an opportunity to assimilate biochemical findings with cell-based assays to uncover new insights into this deceptively complex repair pathway.
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Affiliation(s)
- William A Beard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA;
| | - Julie K Horton
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA;
| | - Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA;
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA;
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14
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Esadze A, Stivers JT. Facilitated Diffusion Mechanisms in DNA Base Excision Repair and Transcriptional Activation. Chem Rev 2018; 118:11298-11323. [PMID: 30379068 DOI: 10.1021/acs.chemrev.8b00513] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Preservation of the coding potential of the genome and highly regulated gene expression over the life span of a human are two fundamental requirements of life. These processes require the action of repair enzymes or transcription factors that efficiently recognize specific sites of DNA damage or transcriptional regulation within a restricted time frame of the cell cycle or metabolism. A failure of these systems to act results in accumulated mutations, metabolic dysfunction, and disease. Despite the multifactorial complexity of cellular DNA repair and transcriptional regulation, both processes share a fundamental physical requirement that the proteins must rapidly diffuse to their specific DNA-binding sites that are embedded within the context of a vastly greater number of nonspecific DNA-binding sites. Superimposed on the needle-in-the-haystack problem is the complex nature of the cellular environment, which contains such high concentrations of macromolecules that the time frame for diffusion is expected to be severely extended as compared to dilute solution. Here we critically review the mechanisms for how these proteins solve the needle-in-the-haystack problem and how the effects of cellular macromolecular crowding can enhance facilitated diffusion processes. We restrict the review to human proteins that use stochastic, thermally driven site-recognition mechanisms, and we specifically exclude systems involving energy cofactors or circular DNA clamps. Our scope includes ensemble and single-molecule studies of the past decade or so, with an emphasis on connecting experimental observations to biological function.
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Affiliation(s)
- Alexandre Esadze
- Department of Pharmacology and Molecular Sciences , Johns Hopkins University School of Medicine , 725 North Wolfe Street , WBSB 314, Baltimore , Maryland 21205 , United States
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences , Johns Hopkins University School of Medicine , 725 North Wolfe Street , WBSB 314, Baltimore , Maryland 21205 , United States
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15
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Taylor EL, Kesavan PM, Wolfe AE, O'Brien PJ. Distinguishing Specific and Nonspecific Complexes of Alkyladenine DNA Glycosylase. Biochemistry 2018; 57:4440-4454. [PMID: 29940097 DOI: 10.1021/acs.biochem.8b00531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Human alkyladenine DNA glycosylase (AAG) recognizes many alkylated and deaminated purine lesions and excises them to initiate the base excision DNA repair pathway. AAG employs facilitated diffusion to rapidly scan nonspecific sites and locate rare sites of damage. Nonspecific DNA binding interactions are critical to the efficiency of this search for damage, but little is known about the binding footprint or the affinity of AAG for nonspecific sites. We used biochemical and biophysical approaches to characterize the binding of AAG to both undamaged and damaged DNA. Although fluorescence anisotropy is routinely used to study DNA binding, we found unexpected complexities in the data for binding of AAG to DNA. Systematic comparison of different fluorescent labels and different lengths of DNA allowed binding models to be distinguished and demonstrated that AAG can bind with high affinity and high density to nonspecific DNA. Fluorescein-labeled DNA gave the most complex behavior but also showed the greatest potential to distinguish specific and nonspecific binding modes. We suggest a unified model that is expected to apply to many DNA binding proteins that exhibit affinity for nonspecific DNA. Although AAG strongly prefers to excise lesions from duplex DNA, nonspecific binding is comparable for single- and double-stranded nonspecific sites. The electrostatically driven binding of AAG to small DNA sites (∼5 nucleotides of single-stranded and ∼6 base pairs of duplex) facilitates the search for DNA damage in chromosomal DNA, which is bound by nucleosomes and other proteins.
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Affiliation(s)
- Erin L Taylor
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Preethi M Kesavan
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Abigail E Wolfe
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Patrick J O'Brien
- Department of Biological Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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16
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Rodriguez G, Esadze A, Weiser BP, Schonhoft JD, Cole PA, Stivers JT. Disordered N-Terminal Domain of Human Uracil DNA Glycosylase (hUNG2) Enhances DNA Translocation. ACS Chem Biol 2017; 12:2260-2263. [PMID: 28787572 DOI: 10.1021/acschembio.7b00521] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Nuclear human uracil-DNA glycosylase (hUNG2) initiates base excision repair (BER) of genomic uracils generated through misincorporation of dUMP or through deamination of cytosines. Like many human DNA glycosylases, hUNG2 contains an unstructured N-terminal domain that encodes a nuclear localization signal, protein binding motifs, and sites for post-translational modifications. Although the N-terminal domain has minimal effects on DNA binding and uracil excision kinetics, we report that this domain enhances the ability of hUNG2 to translocate on DNA chains as compared to the catalytic domain alone. The enhancement is most pronounced when physiological ion concentrations and macromolecular crowding agents are used. These data suggest that crowded conditions in the human cell nucleus promote the interaction of the N-terminus with duplex DNA during translocation. The increased contact time with the DNA chain likely contributes to the ability of hUNG2 to locate densely spaced uracils that arise during somatic hypermutation and during fluoropyrimidine chemotherapy.
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Affiliation(s)
- Gaddiel Rodriguez
- Department of Pharmacology
and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205−2185, United States
| | - Alexandre Esadze
- Department of Pharmacology
and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205−2185, United States
| | - Brian P. Weiser
- Department of Pharmacology
and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205−2185, United States
| | - Joseph D. Schonhoft
- Department of Pharmacology
and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205−2185, United States
| | - Philip A. Cole
- Department of Pharmacology
and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205−2185, United States
| | - James T. Stivers
- Department of Pharmacology
and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, Maryland 21205−2185, United States
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17
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Woodcock CB, Yakubov AB, Reich NO. Caulobacter crescentus Cell Cycle-Regulated DNA Methyltransferase Uses a Novel Mechanism for Substrate Recognition. Biochemistry 2017; 56:3913-3922. [PMID: 28661661 DOI: 10.1021/acs.biochem.7b00378] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Caulobacter crescentus relies on DNA methylation by the cell cycle-regulated methyltransferase (CcrM) in addition to key transcription factors to control the cell cycle and direct cellular differentiation. CcrM is shown here to efficiently methylate its cognate recognition site 5'-GANTC-3' in single-stranded and hemimethylated double-stranded DNA. We report the Km, kcat, kmethylation, and Kd for single-stranded and hemimethylated substrates, revealing discrimination of 107-fold for noncognate sequences. The enzyme also shows a similar discrimination against single-stranded RNA. Two independent assays clearly show that CcrM is highly processive with single-stranded and hemimethylated DNA. Collectively, the data provide evidence that CcrM and other DNA-modifying enzymes may use a new mechanism to recognize DNA in a key epigenetic process.
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Affiliation(s)
- Clayton B Woodcock
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
| | - Aziz B Yakubov
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
| | - Norbert O Reich
- Department of Chemistry and Biochemistry, University of California , Santa Barbara, California 93106, United States
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18
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Coey CT, Drohat AC. Kinetic Methods for Studying DNA Glycosylases Functioning in Base Excision Repair. Methods Enzymol 2017; 592:357-376. [PMID: 28668127 DOI: 10.1016/bs.mie.2017.03.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Base excision repair (BER) is a conserved and ubiquitous pathway that is initiated by DNA glycosylases, which recognize and remove damaged or mismatched nucleobases, setting the stage for restoration of the correct DNA sequence by follow-on BER enzymes. DNA glycosylases employ a nucleotide-flipping step prior to cleavage of the N-glycosyl bond, and most exhibit slow release of the abasic DNA product and/or strong product inhibition. As such, studying the catalytic mechanism of these enzymes requires care in the design, execution, and interpretation of single- and multiple-turnover kinetics experiments, which is the topic of this chapter.
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Affiliation(s)
| | - Alexander C Drohat
- University of Maryland School of Medicine, Baltimore, MD, United States; Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD, United States.
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19
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Feng W, Chakraborty A. Fragility Extraordinaire: Unsolved Mysteries of Chromosome Fragile Sites. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1042:489-526. [PMID: 29357071 DOI: 10.1007/978-981-10-6955-0_21] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Chromosome fragile sites are a fascinating cytogenetic phenomenon now widely implicated in a slew of human diseases ranging from neurological disorders to cancer. Yet, the paths leading to these revelations were far from direct, and the number of fragile sites that have been molecularly cloned with known disease-associated genes remains modest. Moreover, as more fragile sites were being discovered, research interests in some of the earliest discovered fragile sites ebbed away, leaving a number of unsolved mysteries in chromosome biology. In this review we attempt to recount some of the early discoveries of fragile sites and highlight those phenomena that have eluded intense scrutiny but remain extremely relevant in our understanding of the mechanisms of chromosome fragility. We then survey the literature for disease association for a comprehensive list of fragile sites. We also review recent studies addressing the underlying cause of chromosome fragility while highlighting some ongoing debates. We report an observed enrichment for R-loop forming sequences in fragile site-associated genes than genomic average. Finally, we will leave the reader with some lingering questions to provoke discussion and inspire further scientific inquiries.
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Affiliation(s)
- Wenyi Feng
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA.
| | - Arijita Chakraborty
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY, USA
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20
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Mechetin GV, Dyatlova EA, Sinyakov AN, Ryabinin VA, Vorobjev PE, Zharkov DO. Correlated target search by uracil-DNA glycosylase in the presence of bulky adducts and DNA-binding ligands. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2017. [DOI: 10.1134/s106816201606008x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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21
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Trasviña-Arenas CH, Lopez-Castillo LM, Sanchez-Sandoval E, Brieba LG. Dispensability of the [4Fe-4S] cluster in novel homologues of adenine glycosylase MutY. FEBS J 2016; 283:521-40. [PMID: 26613369 DOI: 10.1111/febs.13608] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Revised: 11/15/2015] [Accepted: 11/24/2015] [Indexed: 01/31/2023]
Abstract
7,8-Dihydro-8-deoxyguanine (8oG) is one of the most common oxidative lesions in DNA. DNA polymerases misincorporate an adenine across from this lesion. Thus, 8oG is a highly mutagenic lesion responsible for G:C→T:A transversions. MutY is an adenine glycosylase, part of the base excision repair pathway that removes adenines, when mispaired with 8oG or guanine. Its catalytic domain includes a [4Fe-4S] cluster motif coordinated by cysteinyl ligands. When this cluster is absent, MutY activity is depleted and several studies concluded that the [4Fe-4S] cluster motif is an indispensable component for DNA binding, substrate recognition and enzymatic activity. In the present study, we identified 46 MutY homologues that lack the canonical cysteinyl ligands, suggesting an absence of the [4Fe-4S] cluster. A phylogenetic analysis groups these novel MutYs into two different clades. One clade is exclusive of the order Lactobacillales and another clade has a mixed composition of anaerobic and microaerophilic bacteria and species from the protozoan genus Entamoeba. Structural modeling and sequence analysis suggests that the loss of the [4Fe-4S] cluster is compensated by a convergent solution in which bulky amino acids substitute the [4Fe-4S] cluster. We functionally characterized MutYs from Lactobacillus brevis and Entamoeba histolytica as representative members from each clade and found that both enzymes are active adenine glycosylases. Furthermore, chimeric glycosylases, in which the [4Fe-4S] cluster of Escherichia coli MutY is replaced by the corresponding amino acids of LbY and EhY, are also active. Our data indicates that the [4Fe-4S] cluster plays a structural role in MutYs and evidences the existence of alternative functional solutions in nature.
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Affiliation(s)
- Carlos H Trasviña-Arenas
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Laura M Lopez-Castillo
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Eugenia Sanchez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
| | - Luis G Brieba
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Irapuato, Guanajuato, México
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22
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Burmeister WP, Tarbouriech N, Fender P, Contesto-Richefeu C, Peyrefitte CN, Iseni F. Crystal Structure of the Vaccinia Virus Uracil-DNA Glycosylase in Complex with DNA. J Biol Chem 2015; 290:17923-17934. [PMID: 26045555 DOI: 10.1074/jbc.m115.648352] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Indexed: 11/06/2022] Open
Abstract
Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase catalytic subunit E9 associated with its heterodimeric co-factor A20·D4 required for processive genome synthesis. Although A20 has no known enzymatic activity, D4 is an active uracil-DNA glycosylase (UNG). The presence of a repair enzyme as a component of the viral replication machinery suggests that, for poxviruses, DNA synthesis and base excision repair is coupled. We present the 2.7 Å crystal structure of the complex formed by D4 and the first 50 amino acids of A20 (D4·A201-50) bound to a 10-mer DNA duplex containing an abasic site resulting from the cleavage of a uracil base. Comparison of the viral complex with its human counterpart revealed major divergences in the contacts between protein and DNA and in the enzyme orientation on the DNA. However, the conformation of the dsDNA within both structures is very similar, suggesting a dominant role of the DNA conformation for UNG function. In contrast to human UNG, D4 appears rigid, and we do not observe a conformational change upon DNA binding. We also studied the interaction of D4·A201-50 with different DNA oligomers by surface plasmon resonance. D4 binds weakly to nonspecific DNA and to uracil-containing substrates but binds abasic sites with a Kd of <1.4 μm. This second DNA complex structure of a family I UNG gives new insight into the role of D4 as a co-factor of vaccinia virus DNA polymerase and allows a better understanding of the structural determinants required for UNG action.
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Affiliation(s)
- Wim P Burmeister
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions (UVHCI), F-38000 Grenoble, France; CNRS, UVHCI, F-38000 Grenoble, France.
| | - Nicolas Tarbouriech
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions (UVHCI), F-38000 Grenoble, France; CNRS, UVHCI, F-38000 Grenoble, France
| | - Pascal Fender
- Université Grenoble Alpes, Unit of Virus Host Cell Interactions (UVHCI), F-38000 Grenoble, France; CNRS, UVHCI, F-38000 Grenoble, France
| | - Céline Contesto-Richefeu
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, F-91223 Brétigny-sur-Orge cedex, France
| | - Christophe N Peyrefitte
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, F-91223 Brétigny-sur-Orge cedex, France; Emerging Pathogens Laboratory, Fondation Mérieux, F-69007 Lyon, France
| | - Frédéric Iseni
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, F-91223 Brétigny-sur-Orge cedex, France.
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23
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Schormann N, Banerjee S, Ricciardi R, Chattopadhyay D. Binding of undamaged double stranded DNA to vaccinia virus uracil-DNA Glycosylase. BMC STRUCTURAL BIOLOGY 2015; 15:10. [PMID: 26031450 PMCID: PMC4450493 DOI: 10.1186/s12900-015-0037-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/21/2015] [Indexed: 01/10/2023]
Abstract
BACKGROUND Uracil-DNA glycosylases are evolutionarily conserved DNA repair enzymes. However, vaccinia virus uracil-DNA glycosylase (known as D4), also serves as an intrinsic and essential component of the processive DNA polymerase complex during DNA replication. In this complex D4 binds to a unique poxvirus specific protein A20 which tethers it to the DNA polymerase. At the replication fork the DNA scanning and repair function of D4 is coupled with DNA replication. So far, DNA-binding to D4 has not been structurally characterized. RESULTS This manuscript describes the first structure of a DNA-complex of a uracil-DNA glycosylase from the poxvirus family. This also represents the first structure of a uracil DNA glycosylase in complex with an undamaged DNA. In the asymmetric unit two D4 subunits bind simultaneously to complementary strands of the DNA double helix. Each D4 subunit interacts mainly with the central region of one strand. DNA binds to the opposite side of the A20-binding surface on D4. Comparison of the present structure with the structure of uracil-containing DNA-bound human uracil-DNA glycosylase suggests that for DNA binding and uracil removal D4 employs a unique set of residues and motifs that are highly conserved within the poxvirus family but different in other organisms. CONCLUSION The first structure of D4 bound to a truly non-specific undamaged double-stranded DNA suggests that initial binding of DNA may involve multiple non-specific interactions between the protein and the phosphate backbone.
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Affiliation(s)
- Norbert Schormann
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
| | - Surajit Banerjee
- Northeastern Collaborative Access Team and Department of Chemistry and Chemical Biology, Cornell University, Argonne, Chicago, IL, 60439, USA.
| | - Robert Ricciardi
- Department of Microbiology, School of Dental Medicine, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Debasish Chattopadhyay
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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24
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Cravens SL, Schonhoft JD, Rowland MM, Rodriguez AA, Anderson BG, Stivers JT. Molecular crowding enhances facilitated diffusion of two human DNA glycosylases. Nucleic Acids Res 2015; 43:4087-97. [PMID: 25845592 PMCID: PMC4417188 DOI: 10.1093/nar/gkv301] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 03/27/2015] [Indexed: 12/22/2022] Open
Abstract
Intracellular space is at a premium due to the high concentrations of biomolecules and is expected to have a fundamental effect on how large macromolecules move in the cell. Here, we report that crowded solutions promote intramolecular DNA translocation by two human DNA repair glycosylases. The crowding effect increases both the efficiency and average distance of DNA chain translocation by hindering escape of the enzymes to bulk solution. The increased contact time with the DNA chain provides for redundant damage patrolling within individual DNA chains at the expense of slowing the overall rate of damaged base removal from a population of molecules. The significant biological implication is that a crowded cellular environment could influence the mechanism of damage recognition as much as any property of the enzyme or DNA.
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Affiliation(s)
- Shannen L Cravens
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - Joseph D Schonhoft
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - Meng M Rowland
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - Alyssa A Rodriguez
- Department of Chemistry and Biochemistry, The University of San Diego, 5998 Alcalá Park, San Diego, CA 92110, USA
| | - Breeana G Anderson
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA
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25
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Mechetin GV, Zharkov DO. Mechanisms of diffusional search for specific targets by DNA-dependent proteins. BIOCHEMISTRY (MOSCOW) 2015; 79:496-505. [PMID: 25100007 DOI: 10.1134/s0006297914060029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
To perform their functions, many DNA-dependent proteins have to quickly locate specific targets against the vast excess of nonspecific DNA. Although this problem was first formulated over 40 years ago, the mechanism of such search remains one of the unsolved fundamental problems in the field of protein-DNA interactions. Several complementary mechanisms have been suggested: sliding, based on one-dimensional random diffusion along the DNA contour; hopping, in which the protein "jumps" between the closely located DNA fragments; macroscopic association-dissociation of the protein-DNA complex; and intersegmental transfer. This review covers the modern state of the problem of target DNA search, theoretical descriptions, and methods of research at the macroscopic (molecule ensembles) and microscopic (individual molecules) levels. Almost all studied DNA-dependent proteins search for specific targets by combined three-dimensional diffusion and one-dimensional diffusion along the DNA contour.
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Affiliation(s)
- G V Mechetin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
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26
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Taylor EL, O'Brien PJ. Kinetic mechanism for the flipping and excision of 1,N(6)-ethenoadenine by AlkA. Biochemistry 2015; 54:898-908. [PMID: 25537480 PMCID: PMC4310629 DOI: 10.1021/bi501356x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
Escherichia coli 3-methyladenine DNA glycosylase
II (AlkA), an adaptive response glycosylase with a broad substrate
range, initiates base excision repair by flipping a lesion out of
the DNA duplex and hydrolyzing the N-glycosidic bond. We used transient
and steady state kinetics to determine the minimal mechanism for recognition
and excision of 1,N6-ethenoadenine (εA)
by AlkA. The natural fluorescence of this endogenously produced lesion
allowed us to directly monitor the nucleotide flipping step. We found
that AlkA rapidly and reversibly binds and flips out εA prior
to N-glycosidic bond hydrolysis, which is the rate-limiting step of
the reaction. The binding affinity of AlkA for the εA-DNA lesion
is only 40-fold tighter than for a nonspecific site and 20-fold weaker
than for the abasic DNA site. The mechanism of AlkA-catalyzed excision
of εA was compared to that of the human alkyladenine DNA glycosylase
(AAG), an independently evolved glycosylase that recognizes many of
the same substrates. AlkA and AAG both catalyze N-glycosidic bond
hydrolysis to release εA, and their overall rates of reaction
are within 2-fold of each other. Nevertheless, we find dramatic differences
in the kinetics and thermodynamics for binding to εA-DNA. AlkA
catalyzes nucleotide flipping an order of magnitude faster than AAG;
however, the equilibrium for flipping is almost 3 orders of magnitude
more favorable for AAG than for AlkA. These results illustrate how
enzymes that perform the same chemistry can use different substrate
recognition strategies to effectively repair DNA damage.
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Affiliation(s)
- Erin L Taylor
- Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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27
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Hedglin M, Zhang Y, O'Brien PJ. Probing the DNA structural requirements for facilitated diffusion. Biochemistry 2014; 54:557-66. [PMID: 25495964 PMCID: PMC4303293 DOI: 10.1021/bi5013707] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
DNA glycosylases perform a genome-wide
search to locate damaged
nucleotides among a great excess of undamaged nucleotides. Many glycosylases
are capable of facilitated diffusion, whereby multiple sites along
the DNA are sampled during a single binding encounter. Electrostatic
interactions between positively charged amino acids and the negatively
charged phosphate backbone are crucial for facilitated diffusion,
but the extent to which diffusing proteins rely on the double-helical
structure DNA is not known. Kinetic assays were used to probe the
DNA searching mechanism of human alkyladenine DNA glycosylase (AAG)
and to test the extent to which diffusion requires B-form duplex DNA.
Although AAG excises εA lesions from single-stranded DNA, it
is not processive on single-stranded DNA because dissociation is faster
than N-glycosidic bond cleavage. However, the AAG complex with single-stranded
DNA is sufficiently stable to allow for DNA annealing when a complementary
strand is added. This observation provides evidence of nonspecific
association of AAG with single-stranded DNA. Single-strand gaps, bubbles,
and bent structures do not impede the search by AAG. Instead, these
flexible or bent structures lead to the capture of a nearby site of
damage that is more efficient than that of a continuous B-form duplex.
The ability of AAG to negotiate these helix discontinuities is inconsistent
with a sliding mode of diffusion but can be readily explained by a
hopping mode that involves microscopic dissociation and reassociation.
These experiments provide evidence of relatively long-range hops that
allow a searching protein to navigate around DNA binding proteins
that would serve as obstacles to a sliding protein.
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Affiliation(s)
- Mark Hedglin
- Chemical Biology Program and ‡Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109-5606, United States
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28
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Cravens SL, Hobson M, Stivers JT. Electrostatic properties of complexes along a DNA glycosylase damage search pathway. Biochemistry 2014; 53:7680-92. [PMID: 25408964 PMCID: PMC4263432 DOI: 10.1021/bi501011m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Human uracil DNA glycosylase (hUNG) follows an extended reaction coordinate for locating rare uracil bases in genomic DNA. This process begins with diffusion-controlled engagement of undamaged DNA, followed by a damage search step in which the enzyme remains loosely associated with the DNA chain (translocation), and finally, a recognition step that allows the enzyme to efficiently bind and excise uracil when it is encountered. At each step along this coordinate, the enzyme must form DNA interactions that are highly specialized for either rapid damage searching or catalysis. Here we make extensive measurements of hUNG activity as a function of salt concentration to dissect the thermodynamic, kinetic, and electrostatic properties of key enzyme states along this reaction coordinate. We find that the interaction of hUNG with undamaged DNA is electrostatically driven at a physiological concentration of potassium ions (ΔGelect = -3.5 ± 0.5 kcal mol(-1)), with only a small nonelectrostatic contribution (ΔGnon = -2.0 ± 0.2 kcal mol(-1)). In contrast, the interaction with damaged DNA is dominated by the nonelectrostatic free energy term (ΔGnon = -7.2 ± 0.1 kcal mol(-1)), yet retains the nonspecific electrostatic contribution (ΔGelect = -2.3 ± 0.2 kcal mol(-1)). Stopped-flow kinetic experiments established that the salt sensitivity of damaged DNA binding originates from a reduction of kon, while koff is weakly dependent on salt. Similar findings were obtained from the salt dependences of the steady-state kinetic parameters, where the diffusion-controlled kcat/Km showed a salt dependence similar to kon, while kcat (limited by product release) was weakly dependent on salt. Finally, the salt dependence of translocation between two uracil sites separated by 20 bp in the same DNA chain was indistinguishable from that of kon. This result suggests that the transition-state for translocation over this spacing resembles that for DNA association from bulk solution and that hUNG escapes the DNA ion cloud during translocation. These findings provide key insights into how the ionic environment in cells influences the DNA damage search pathway.
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Affiliation(s)
- Shannen L Cravens
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine , 725 North Wolfe Street, Baltimore, Maryland 21205-2185, United States
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Rowland MM, Schonhoft JD, McKibbin PL, David SS, Stivers JT. Microscopic mechanism of DNA damage searching by hOGG1. Nucleic Acids Res 2014; 42:9295-303. [PMID: 25016526 PMCID: PMC4132736 DOI: 10.1093/nar/gku621] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 06/25/2014] [Accepted: 06/26/2014] [Indexed: 01/25/2023] Open
Abstract
The DNA backbone is often considered a track that allows long-range sliding of DNA repair enzymes in their search for rare damage sites in DNA. A proposed exemplar of DNA sliding is human 8-oxoguanine ((o)G) DNA glycosylase 1 (hOGG1), which repairs mutagenic (o)G lesions in DNA. Here we use our high-resolution molecular clock method to show that macroscopic 1D DNA sliding of hOGG1 occurs by microscopic 2D and 3D steps that masquerade as sliding in resolution-limited single-molecule images. Strand sliding was limited to distances shorter than seven phosphate linkages because attaching a covalent chemical road block to a single DNA phosphate located between two closely spaced damage sites had little effect on transfers. The microscopic parameters describing the DNA search of hOGG1 were derived from numerical simulations constrained by the experimental data. These findings support a general mechanism where DNA glycosylases use highly dynamic multidimensional diffusion paths to scan DNA.
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Affiliation(s)
- Meng M Rowland
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Joseph D Schonhoft
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
| | - Paige L McKibbin
- Department of Chemistry, University of California at Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Sheila S David
- Department of Chemistry, University of California at Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - James T Stivers
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205, USA
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Contesto-Richefeu C, Tarbouriech N, Brazzolotto X, Betzi S, Morelli X, Burmeister WP, Iseni F. Crystal structure of the vaccinia virus DNA polymerase holoenzyme subunit D4 in complex with the A20 N-terminal domain. PLoS Pathog 2014; 10:e1003978. [PMID: 24603707 PMCID: PMC3946371 DOI: 10.1371/journal.ppat.1003978] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/21/2014] [Indexed: 12/21/2022] Open
Abstract
Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase E9, the uracil-DNA glycosylase D4 and A20, a protein with no known enzymatic activity. The D4/A20 heterodimer is the DNA polymerase co-factor whose function is essential for processive DNA synthesis. Genetic and biochemical data have established that residues located in the N-terminus of A20 are critical for binding to D4. However, no information regarding the residues of D4 involved in A20 binding is yet available. We expressed and purified the complex formed by D4 and the first 50 amino acids of A20 (D4/A20₁₋₅₀). We showed that whereas D4 forms homodimers in solution when expressed alone, D4/A20₁₋₅₀ clearly behaves as a heterodimer. The crystal structure of D4/A20₁₋₅₀ solved at 1.85 Å resolution reveals that the D4/A20 interface (including residues 167 to 180 and 191 to 206 of D4) partially overlaps the previously described D4/D4 dimer interface. A20₁₋₅₀ binding to D4 is mediated by an α-helical domain with important leucine residues located at the very N-terminal end of A20 and a second stretch of residues containing Trp43 involved in stacking interactions with Arg167 and Pro173 of D4. Point mutations of the latter residues disturb D4/A20₁₋₅₀ formation and reduce significantly thermal stability of the complex. Interestingly, small molecule docking with anti-poxvirus inhibitors selected to interfere with D4/A20 binding could reproduce several key features of the D4/A20₁₋₅₀ interaction. Finally, we propose a model of D4/A20₁₋₅₀ in complex with DNA and discuss a number of mutants described in the literature, which affect DNA synthesis. Overall, our data give new insights into the assembly of the poxvirus DNA polymerase cofactor and may be useful for the design and rational improvement of antivirals targeting the D4/A20 interface.
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Affiliation(s)
| | - Nicolas Tarbouriech
- Université Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
- Unit for Virus Host-Cell Interactions, UMI 3265, Université Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Xavier Brazzolotto
- Département de Toxicologie et Risque Chimique, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
| | - Stéphane Betzi
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes & Aix-Marseille Universités, Marseille, France
| | - Xavier Morelli
- Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes & Aix-Marseille Universités, Marseille, France
| | - Wim P. Burmeister
- Université Grenoble Alpes, UVHCI, Grenoble, France
- CNRS, UVHCI, Grenoble, France
- Unit for Virus Host-Cell Interactions, UMI 3265, Université Grenoble Alpes-EMBL-CNRS, Grenoble, France
| | - Frédéric Iseni
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
- * E-mail:
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