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Burmeister WP, Boutin L, Balestra AC, Gröger H, Ballandras-Colas A, Hutin S, Kraft C, Grimm C, Böttcher B, Fischer U, Tarbouriech N, Iseni F. Structure and flexibility of the DNA polymerase holoenzyme of vaccinia virus. PLoS Pathog 2024; 20:e1011652. [PMID: 38768256 DOI: 10.1371/journal.ppat.1011652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 04/15/2024] [Indexed: 05/22/2024] Open
Abstract
The year 2022 was marked by the mpox outbreak caused by the human monkeypox virus (MPXV), which is approximately 98% identical to the vaccinia virus (VACV) at the sequence level with regard to the proteins involved in DNA replication. We present the production in the baculovirus-insect cell system of the VACV DNA polymerase holoenzyme, which consists of the E9 polymerase in combination with its co-factor, the A20-D4 heterodimer. This led to the 3.8 Å cryo-electron microscopy (cryo-EM) structure of the DNA-free form of the holoenzyme. The model of the holoenzyme was constructed from high-resolution structures of the components of the complex and the A20 structure predicted by AlphaFold 2. The structures do not change in the context of the holoenzyme compared to the previously determined crystal and NMR structures, but the E9 thumb domain became disordered. The E9-A20-D4 structure shows the same compact arrangement with D4 folded back on E9 as observed for the recently solved MPXV holoenzyme structures in the presence and the absence of bound DNA. A conserved interface between E9 and D4 is formed by a cluster of hydrophobic residues. Small-angle X-ray scattering data show that other, more open conformations of E9-A20-D4 without the E9-D4 contact exist in solution using the flexibility of two hinge regions in A20. Biolayer interferometry (BLI) showed that the E9-D4 interaction is indeed weak and transient in the absence of DNA although it is very important, as it has not been possible to obtain viable viruses carrying mutations of key residues within the E9-D4 interface.
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Affiliation(s)
- Wim P Burmeister
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes (UGA), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Grenoble, France
| | - Laetitia Boutin
- Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
| | - Aurelia C Balestra
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes (UGA), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Grenoble, France
| | - Henri Gröger
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes (UGA), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Grenoble, France
| | - Allison Ballandras-Colas
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes (UGA), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Grenoble, France
| | - Stephanie Hutin
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes (UGA), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Grenoble, France
| | | | | | | | - Utz Fischer
- Biozentrum, Universität Würzburg, Würzburg, Germany
| | - Nicolas Tarbouriech
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes (UGA), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Centre National de la Recherche Scientifique (CNRS), Grenoble, France
| | - Frédéric Iseni
- Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
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2
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Shen Y, Li Y, Yan R. Structural basis for the inhibition mechanism of the DNA polymerase holoenzyme from mpox virus. Structure 2024:S0969-2126(24)00086-8. [PMID: 38579705 DOI: 10.1016/j.str.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 01/31/2024] [Accepted: 03/11/2024] [Indexed: 04/07/2024]
Abstract
There are three key components at the core of the mpox virus (MPXV) DNA polymerase holoenzyme: DNA polymerase F8, processivity factors A22, and the Uracil-DNA glycosylase E4. The holoenzyme is recognized as a vital antiviral target because MPXV replicates in the cytoplasm of host cells. Nucleotide analogs such as cidofovir and cytarabine (Ara-C) have shown potential in curbing MPXV replication and they also display promise against other poxviruses. However, the mechanism behind their inhibitory effects remains unclear. Here, we present the cryo-EM structure of the DNA polymerase holoenzyme F8/A22/E4 bound with its competitive inhibitor Ara-C-derived cytarabine triphosphate (Ara-CTP) at an overall resolution of 3.0 Å and reveal its inhibition mechanism. Ara-CTP functions as a direct chain terminator in proximity to the deoxycytidine triphosphate (dCTP)-binding site. The extra hydrogen bond formed with Asn665 makes it more potent in binding than dCTP. Asn665 is conserved among eukaryotic B-family polymerases.
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Affiliation(s)
- Yaping Shen
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China
| | - Yaning Li
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Renhong Yan
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong Province, China.
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3
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Li Y, Zhu J, Guo Y, Yan R. Structural insight into the assembly and working mechanism of helicase-primase D5 from Mpox virus. Nat Struct Mol Biol 2024; 31:68-81. [PMID: 38177671 DOI: 10.1038/s41594-023-01142-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 09/27/2023] [Indexed: 01/06/2024]
Abstract
The Mpox pandemic, caused by the Mpox virus (or monkeypox virus, MPXV), has gained global attention. The D5 protein, a putative helicase-primase found in MPXV, plays a vital role in viral replication and genome uncoating. Here we determined multiple cryo-EM structures of full-length hexameric D5 in diverse states. These states were captured during ATP hydrolysis while moving along the single-stranded DNA (ssDNA) track. Through comprehensive structural analysis combined with the helicase activity system, we revealed that when the primase domain is truncated or the interaction between the primase and helicase domains is disrupted, the double-stranded DNA (dsDNA) unwinds into ssDNA, suggesting a critical regulatory role of the primase domain. Two transition states bound with ssDNA substrate during unwinding reveals that two ATP molecules were consumed to drive DNA moving forward two nucleotides. Collectively, our findings shed light on the molecular mechanism that links ATP hydrolysis to the DNA unwinding in poxviruses.
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Affiliation(s)
- Yaning Li
- Department of Biochemistry, School of Medicine, Key University Laboratory of Metabolism and Health of Guangdong, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jing Zhu
- Department of Biochemistry, School of Medicine, Key University Laboratory of Metabolism and Health of Guangdong, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China
| | - Yingying Guo
- Department of Biochemistry, School of Medicine, Key University Laboratory of Metabolism and Health of Guangdong, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China.
| | - Renhong Yan
- Department of Biochemistry, School of Medicine, Key University Laboratory of Metabolism and Health of Guangdong, Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, China.
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4
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Wang X, Ma L, Li N, Gao N. Structural insights into the assembly and mechanism of mpox virus DNA polymerase complex F8-A22-E4-H5. Mol Cell 2023; 83:4398-4412.e4. [PMID: 37995690 DOI: 10.1016/j.molcel.2023.10.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 08/21/2023] [Accepted: 09/25/2023] [Indexed: 11/25/2023]
Abstract
The DNA replication of mpox virus is performed by the viral polymerase F8 and also requires other viral factors, including processivity factor A22, uracil DNA glycosylase E4, and phosphoprotein H5. However, the molecular roles of these viral factors remain unclear. Here, we characterize the structures of F8-A22-E4 and F8-A22-E4-H5 complexes in the presence of different primer-template DNA substrates. E4 is located upstream of F8 on the template single-stranded DNA (ssDNA) and is catalytically active, highlighting a functional coupling between DNA base-excision repair and DNA synthesis. Moreover, H5, in the form of tetramer, binds to the double-stranded DNA (dsDNA) region downstream of F8 in a similar position as PCNA (proliferating cell nuclear antigen) does in eukaryotic polymerase complexes. Omission of H5 or disruption of its DNA interaction showed a reduced synthesis of full-length DNA products. These structures provide snapshots for the working cycle of the polymerase and generate insights into the mechanisms of these essential factors in viral DNA replication.
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Affiliation(s)
- Xiaohan Wang
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China
| | - Liangwen Ma
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China
| | - Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China; National Biomedical Imaging Center, Peking University, Beijing 100871, China.
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5
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Li Y, Shen Y, Hu Z, Yan R. Structural basis for the assembly of the DNA polymerase holoenzyme from a monkeypox virus variant. SCIENCE ADVANCES 2023; 9:eadg2331. [PMID: 37075110 PMCID: PMC10115419 DOI: 10.1126/sciadv.adg2331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The ongoing global pandemic caused by a variant of the monkeypox (or mpox) virus (MPXV) has prompted widespread concern. The MPXV DNA polymerase holoenzyme, consisting of F8, A22, and E4, is vital for replicating the viral genome and represents a crucial target for the development of antiviral drugs. However, the assembly and working mechanism for the DNA polymerase holoenzyme of MPXV remains elusive. Here, we present the cryo-electron microscopy (cryo-EM) structure of the DNA polymerase holoenzyme at an overall resolution of 3.5 Å. Unexpectedly, the holoenzyme is assembled as a dimer of heterotrimers, of which the extra interface between the thumb domain of F8 and A22 shows a clash between A22 and substrate DNA, suggesting an autoinhibition state. Addition of exogenous double-stranded DNA shifts the hexamer into trimer exposing DNA binding sites, potentially representing a more active state. Our findings provide crucial steps toward developing targeted antiviral therapies for MPXV and related viruses.
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Affiliation(s)
- Yaning Li
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yaping Shen
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province 310024, China
| | - Ziwei Hu
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
| | - Renhong Yan
- Department of Biochemistry, Key University Laboratory of Metabolism and Health of Guangdong, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province 518055, China
- Corresponding author.
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6
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Wang J, Shahed-Ai-Mahmud M, Chen A, Li K, Tan H, Joyce R. An Overview of Antivirals against Monkeypox Virus and Other Orthopoxviruses. J Med Chem 2023; 66:4468-4490. [PMID: 36961984 DOI: 10.1021/acs.jmedchem.3c00069] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
The current monkeypox outbreaks during the COVID-19 pandemic have reignited interest in orthopoxvirus antivirals. Monkeypox belongs to the Orthopoxvirus genus of the Poxviridae family, which also includes the variola virus, vaccinia virus, and cowpox virus. Two orally bioavailable drugs, tecovirimat and brincidofovir, have been approved for treating smallpox infections. Given their human safety profiles and in vivo antiviral efficacy in animal models, both drugs have also been recommended to treat monkeypox infection. To facilitate the development of additional orthopoxvirus antivirals, we summarize the antiviral activity, mechanism of action, and mechanism of resistance of orthopoxvirus antivirals. This perspective covers both direct-acting and host-targeting antivirals with an emphasis on drug candidates showing in vivo antiviral efficacy in animal models. We hope to speed the orthopoxvirus antiviral drug discovery by providing medicinal chemists with insights into prioritizing proper drug targets and hits for further development.
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Affiliation(s)
- Jun Wang
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Md Shahed-Ai-Mahmud
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Angelo Chen
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Kan Li
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Haozhou Tan
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Ryan Joyce
- Department of Medicinal Chemistry, Ernest Mario School of Pharmacy, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, United States
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7
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Guan H, Nuth M, Isaacs SN, Xiao Y, Scott RW, Parker MH, Strobel ED, Kulp JL, Bailey TR, Reitz AB, Ricciardi RP. A small molecule that targets the processivity factor of molluscum contagiosum virus has therapeutic potential. Antiviral Res 2023; 211:105520. [PMID: 36603771 PMCID: PMC10209390 DOI: 10.1016/j.antiviral.2022.105520] [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: 06/16/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023]
Abstract
Molluscum contagiosum (MC) is an infectious disease that occurs only in humans with a tropism that is narrowly restricted to the outermost epidermal layer of the skin. Molluscum contagiosum virus (MCV) is the causative agent of MC which produces skin lesions that can persist for months to several years. MCV is efficiently transmitted by direct physical contact or by indirect contact with fomites. MC is most prevalent in children and immune compromised patients. The failure to develop a drug that targets MCV replication has been hampered for decades by the inability to propagate MCV in cell culture. To address this dilemma, we recently engineered a surrogate poxvirus expressing the MCV processivity factor (mD4) as the drug target. The mD4 protein is essential for viral replication by keeping the viral polymerase tethered to the DNA template. In this study we have designed and synthesized a lead compound (7269) that is able to prevent mD4 dependent processive DNA synthesis in vitro (IC50 = 6.8 μM) and effectively inhibit propagation of the mD4-VV surrogate virus in BSC-1 cells (EC50 = 13.2 μM) with negligible cytotoxicity. In human liver microsomes, 7269 was shown to be stable for almost 2 h. When tested for penetration into human cadaver skin in a formulated gel, the level of 7269 in the epidermal layer was nearly 100 times the concentration (EC50) needed to inhibit propagation of the mD4-VV surrogate virus in BSC-1 cells. The gel formulated 7269 was scored as a non-irritant on skin and shown to have a shelf-life that was completely stable after several months. In summary, 7269 is a potential Lead for becoming the first MCV anti-viral compound to treat MC and thereby, addresses this unmet medical need that has persisted for many decades.
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Affiliation(s)
- Hancheng Guan
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, USA
| | - Manunya Nuth
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, USA
| | - Stuart N Isaacs
- Perelman School of Medicine, University of Pennsylvania, USA
| | - Yuhong Xiao
- Perelman School of Medicine, University of Pennsylvania, USA
| | | | | | | | - John L Kulp
- Conifer Point Pharmaceuticals, Doylestown, PA, USA
| | | | | | - Robert P Ricciardi
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, USA; Abramson Cancer Center, School of Medicine, University of Pennsylvania, USA.
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8
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Peng Q, Xie Y, Kuai L, Wang H, Qi J, Gao GF, Shi Y. Structure of monkeypox virus DNA polymerase holoenzyme. Science 2023; 379:100-105. [PMID: 36520947 DOI: 10.1126/science.ade6360] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The World Health Organization declared mpox (or monkeypox) a public health emergency of international concern in July 2022, and prophylactic and therapeutic measures are in urgent need. The monkeypox virus (MPXV) has its own DNA polymerase F8, together with the processive cofactors A22 and E4, constituting the polymerase holoenzyme for genome replication. Here, we determined the holoenzyme structure in complex with DNA using cryo-electron microscopy at the global resolution of ~2.8 angstroms. The holoenzyme possesses an architecture that suggests a "forward sliding clamp" processivity mechanism for viral DNA replication. MPXV polymerase has a DNA binding mode similar to that of other B-family DNA polymerases from different species. These findings reveal the mechanism of the MPXV genome replication and may guide the development of anti-poxvirus drugs.
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Affiliation(s)
- Qi Peng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yufeng Xie
- Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Lu Kuai
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Han Wang
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,College of Future Technology, Peking University, Beijing 100871, China
| | - Jianxun Qi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - George F Gao
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.,Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.,Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing 100101, China.,Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
| | - Yi Shi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,Center for Influenza Research and Early-warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Disease (CEEID), Chinese Academy of Sciences, Beijing 100101, China.,Research Unit of Adaptive Evolution and Control of Emerging Viruses, Chinese Academy of Medical Sciences, Beijing 100052, China
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9
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Kannan SR, Sachdev S, Reddy AS, Kandasamy SL, Byrareddy SN, Lorson CL, Singh K. Mutations in the monkeypox virus replication complex: Potential contributing factors to the 2022 outbreak. J Autoimmun 2022; 133:102928. [PMID: 36252459 PMCID: PMC9562781 DOI: 10.1016/j.jaut.2022.102928] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/01/2022] [Accepted: 10/07/2022] [Indexed: 11/05/2022]
Abstract
Attributes contributing to the current monkeypox virus (MPXV) outbreak remain unknown. It has been established that mutations in viral proteins may alter phenotype and pathogenicity. To assess if mutations in the MPXV DNA replication complex (RC) contribute to the outbreak, we conducted a temporal analysis of available MPXV sequences to identify mutations, generated a DNA replication complex (RC) using structures of related viral and eukaryotic proteins, and structure prediction method AlphaFold. Ten mutations within the RC were identified and mapped onto the RC to infer role of mutations. Two mutations in F8L (RC catalytic subunit), and two in G9R (a processivity factor) were ∼100% prevalent in the 2022 sequences. F8L mutation L108F emerged in 2022, whereas W411L emerged in 2018, and persisted in 2022. L108 is topologically located to enhance DNA binding affinity of F8L. Therefore, mutation L108F can change the fidelity, sensitivity to nucleoside inhibitors, and processivity of F8L. Surface exposed W411L likely affects the binding of regulatory factor(s). G9R mutations S30L and D88 N in G9R emerged in 2022, and may impact the interaction of G9R with E4R (uracil DNA glycosylase). The remaining six mutations that appeared in 2001, reverted to the first (1965 Rotterdam) isolate. Two nucleoside inhibitors brincidofovir and cidofovir have been approved for MPXV treatment. Cidofovir resistance in vaccinia virus is achieved by A314T and A684V mutations. Both A314 and A684 are conserved in MPXV. Therefore, resistance to these drugs in MPXV may arise through similar mechanisms.
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Affiliation(s)
| | - Shrikesh Sachdev
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Athreya S. Reddy
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | | | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE, 68198, USA,Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, USA,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, 68198, USA,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Christian L. Lorson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA,Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, USA,Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden,Corresponding author. 471g, Bond Life Sciences Center, 1201 E Rollins Street, Columbia, MO, 65211, USA
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10
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Abstract
Poxviruses, of which vaccinia virus is the prototype, are a large family of double-stranded DNA viruses that replicate exclusively in the cytoplasm of infected cells. This physical and genetic autonomy from the host cell nucleus necessitates that these viruses encode most, if not all, of the proteins required for replication in the cytoplasm. In this review, we follow the life of the viral genome through space and time to address some of the unique challenges that arise from replicating a 195-kb DNA genome in the cytoplasm. We focus on how the genome is released from the incoming virion and deposited into the cytoplasm; how the endoplasmic reticulum is reorganized to form a replication factory, thereby compartmentalizing and helping to protect the replicating genome from immune sensors; how the cellular milieu is tailored to support high-fidelity replication of the genome; and finally, how newly synthesized genomes are faithfully and specifically encapsidated into new virions. Expected final online publication date for the Annual Review of Virology, Volume 9 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Matthew D Greseth
- Department of Biochemistry and Molecular Biology, The Medical University of South Carolina, Charleston, South Carolina, USA;
| | - Paula Traktman
- Department of Biochemistry and Molecular Biology, The Medical University of South Carolina, Charleston, South Carolina, USA; .,Department of Microbiology and Immunology, The Medical University of South Carolina, Charleston, South Carolina, USA
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11
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Bersch B, Tarbouriech N, Burmeister WP, Iseni F. Solution Structure of the C-terminal Domain of A20, the Missing Brick for the Characterization of the Interface between Vaccinia Virus DNA Polymerase and its Processivity Factor. J Mol Biol 2021; 433:167009. [PMID: 33901538 DOI: 10.1016/j.jmb.2021.167009] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 11/26/2022]
Abstract
Poxviruses are enveloped viruses with a linear, double-stranded DNA genome. Viral DNA synthesis is achieved by a functional DNA polymerase holoenzyme composed of three essential proteins. For vaccinia virus (VACV) these are E9, the catalytic subunit, a family B DNA polymerase, and the heterodimeric processivity factor formed by D4 and A20. The A20 protein links D4 to the catalytic subunit. High-resolution structures have been obtained for the VACV D4 protein in complex with an N-terminal fragment of A20 as well as for E9. In addition, biochemical studies provided evidence that a poxvirus-specific insertion (insert 3) in E9 interacts with the C-terminal residues of A20. Here, we provide solution structures of two different VACV A20 C-terminal constructs containing residues 304-426, fused at their C-terminus to either a BAP (Biotin Acceptor Peptide)-tag or a short peptide containing the helix of E9 insert 3. Together with results from titration studies, these structures shed light on the molecular interface between the catalytic subunit and the processivity factor component A20. The interface comprises hydrophobic residues conserved within the Chordopoxvirinae subfamily. Finally, we constructed a HADDOCK model of the VACV A20304-426-E9 complex, which is in excellent accordance with previous experimental data.
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Affiliation(s)
- Beate Bersch
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France.
| | - Nicolas Tarbouriech
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Wim P Burmeister
- Institut de Biologie Structurale, Univ. Grenoble Alpes, CNRS, CEA, IBS, F-38000 Grenoble, France
| | - Frédéric Iseni
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, BP73, F-91223 Brétigny-sur-Orge Cedex, France
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12
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Mechetin GV, Endutkin AV, Diatlova EA, Zharkov DO. Inhibitors of DNA Glycosylases as Prospective Drugs. Int J Mol Sci 2020; 21:ijms21093118. [PMID: 32354123 PMCID: PMC7247160 DOI: 10.3390/ijms21093118] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 12/22/2022] Open
Abstract
DNA glycosylases are enzymes that initiate the base excision repair pathway, a major biochemical process that protects the genomes of all living organisms from intrinsically and environmentally inflicted damage. Recently, base excision repair inhibition proved to be a viable strategy for the therapy of tumors that have lost alternative repair pathways, such as BRCA-deficient cancers sensitive to poly(ADP-ribose)polymerase inhibition. However, drugs targeting DNA glycosylases are still in development and so far have not advanced to clinical trials. In this review, we cover the attempts to validate DNA glycosylases as suitable targets for inhibition in the pharmacological treatment of cancer, neurodegenerative diseases, chronic inflammation, bacterial and viral infections. We discuss the glycosylase inhibitors described so far and survey the advances in the assays for DNA glycosylase reactions that may be used to screen pharmacological libraries for new active compounds.
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Affiliation(s)
- Grigory V. Mechetin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
| | - Anton V. Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
| | - Evgeniia A. Diatlova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
| | - Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia; (G.V.M.); (A.V.E.); (E.A.D.)
- Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Correspondence: ; Tel.: +7-383-363-5187
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13
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Punctuated Evolution of Myxoma Virus: Rapid and Disjunct Evolution of a Recent Viral Lineage in Australia. J Virol 2019; 93:JVI.01994-18. [PMID: 30728252 DOI: 10.1128/jvi.01994-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 01/23/2019] [Indexed: 11/20/2022] Open
Abstract
Myxoma virus (MYXV) has been evolving in a novel host species-European rabbits-in Australia since 1950. Previous studies of viruses sampled from 1950 to 1999 revealed a remarkably clock-like evolutionary process across all Australian lineages of MYXV. Through an analysis of 49 newly generated MYXV genome sequences isolated in Australia between 2008 and 2017, we show that MYXV evolution in Australia can be characterized by three lineages, one of which exhibited a greatly elevated rate of evolutionary change and a dramatic breakdown of temporal structure. Phylogenetic analysis revealed that this apparently punctuated evolutionary event occurred between 1996 and 2012. The branch leading to the rapidly evolving lineage contained a relatively high number of nonsynonymous substitutions, and viruses in this lineage reversed a mutation found in the progenitor standard laboratory strain (SLS) and all previous sequences that disrupts the reading frame of the M005L/R gene. Analysis of genes encoding proteins involved in DNA synthesis or RNA transcription did not reveal any mutations likely to cause rapid evolution. Although there was some evidence for recombination across the MYXV phylogeny, this was not associated with the increase in the evolutionary rate. The period from 1996 to 2012 saw significant declines in wild rabbit numbers, due to the introduction of rabbit hemorrhagic disease and prolonged drought in southeastern Australia, followed by the partial recovery of populations. It is therefore possible that a rapidly changing environment for virus transmission changed the selection pressures faced by MYXV, altering the course and pace of virus evolution.IMPORTANCE The coevolution of myxoma virus (MYXV) and European rabbits in Australia is one of the most important natural experiments in evolutionary biology, providing insights into virus adaptation to new hosts and the evolution of virulence. Previous studies of MYXV evolution have also shown that the virus evolves both relatively rapidly and in a strongly clock-like manner. Using newly acquired MYXV genome sequences from Australia, we show that the virus has experienced a dramatic change in evolutionary behavior over the last 20 years, with a breakdown in clock-like structure, the appearance of a rapidly evolving virus lineage, and the accumulation of multiple nonsynonymous and indel mutations. We suggest that this punctuated evolutionary event may reflect a change in selection pressures as rabbit numbers declined following the introduction of rabbit hemorrhagic disease virus and drought in the geographic regions inhabited by rabbits.
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14
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Endutkin AV, Yudkina AV, Sidorenko VS, Zharkov DO. Transient protein-protein complexes in base excision repair. J Biomol Struct Dyn 2018; 37:4407-4418. [PMID: 30488779 DOI: 10.1080/07391102.2018.1553741] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Transient protein-protein complexes are of great importance for organizing multiple enzymatic reactions into productive reaction pathways. Base excision repair (BER), a process of critical importance for maintaining genome stability against a plethora of DNA-damaging factors, involves several enzymes, including DNA glycosylases, AP endonucleases, DNA polymerases, DNA ligases and accessory proteins acting sequentially on the same damaged site in DNA. Rather than being assembled into one stable multisubunit complex, these enzymes pass the repair intermediates between them in a highly coordinated manner. In this review, we discuss the nature and the role of transient complexes arising during BER as deduced from structural and kinetic data. Almost all of the transient complexes are DNA-mediated, although some may also exist in solution and strengthen under specific conditions. The best-studied example, the interactions between DNA glycosylases and AP endonucleases, is discussed in more detail to provide a framework for distinguishing between stable and transient complexes based on the kinetic data. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anton V Endutkin
- SB RAS Institute of Chemical Biology and Fundamental Medicine , Novosibirsk , Russia.,Novosibirsk State University , Novosibirsk , Russia.,Podalirius Ltd. , Novosibirsk , Russia
| | - Anna V Yudkina
- SB RAS Institute of Chemical Biology and Fundamental Medicine , Novosibirsk , Russia.,Novosibirsk State University , Novosibirsk , Russia
| | - Viktoriya S Sidorenko
- Department of Pharmacological Sciences, Stony Brook University , Stony Brook , NY , USA
| | - Dmitry O Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine , Novosibirsk , Russia.,Novosibirsk State University , Novosibirsk , Russia
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15
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Delaune D, Iseni F, Ferrier-Rembert A, Peyrefitte CN, Ferraris O. The French Armed Forces Virology Unit: A Chronological Record of Ongoing Research on Orthopoxvirus. Viruses 2017; 10:E3. [PMID: 29295488 PMCID: PMC5795416 DOI: 10.3390/v10010003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/20/2017] [Accepted: 12/21/2017] [Indexed: 01/04/2023] Open
Abstract
Since the official declaration of smallpox eradication in 1980, the general population vaccination has ceased worldwide. Therefore, people under 40 year old are generally not vaccinated against smallpox and have no cross protection against orthopoxvirus infections. This naïve population may be exposed to natural or intentional orthopoxvirus emergences. The virology unit of the Institut de Recherche Biomédicale des Armées (France) has developed research programs on orthopoxviruses since 2000. Its missions were conceived to improve the diagnosis capabilities, to foster vaccine development, and to develop antivirals targeting specific viral proteins. The role of the virology unit was asserted in 2012 when the responsibility of the National Reference Center for the Orthopoxviruses was given to the unit. This article presents the evolution of the unit activity since 2000, and the past and current research focusing on orthopoxviruses.
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Affiliation(s)
- Déborah Delaune
- Unité de virologie, Centre National de Référence-Laboratoire Expert Orthopoxvirus, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France.
| | - Frédéric Iseni
- Unité de virologie, Centre National de Référence-Laboratoire Expert Orthopoxvirus, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France.
| | - Audrey Ferrier-Rembert
- Unité de virologie, Centre National de Référence-Laboratoire Expert Orthopoxvirus, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France.
| | - Christophe N Peyrefitte
- Unité de virologie, Centre National de Référence-Laboratoire Expert Orthopoxvirus, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France.
| | - Olivier Ferraris
- Unité de virologie, Centre National de Référence-Laboratoire Expert Orthopoxvirus, Institut de Recherche Biomédicale des Armées, 91220 Brétigny-sur-Orge, France.
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16
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Tarbouriech N, Ducournau C, Hutin S, Mas PJ, Man P, Forest E, Hart DJ, Peyrefitte CN, Burmeister WP, Iseni F. The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding. Nat Commun 2017; 8:1455. [PMID: 29129932 PMCID: PMC5682278 DOI: 10.1038/s41467-017-01542-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 09/26/2017] [Indexed: 11/12/2022] Open
Abstract
Vaccinia virus (VACV), the prototype member of the Poxviridae, replicates in the cytoplasm of an infected cell. The catalytic subunit of the DNA polymerase E9 binds the heterodimeric processivity factor A20/D4 to form the functional polymerase holoenzyme. Here we present the crystal structure of full-length E9 at 2.7 Å resolution that permits identification of important poxvirus-specific structural insertions. One insertion in the palm domain interacts with C-terminal residues of A20 and thus serves as the processivity factor-binding site. This is in strong contrast to all other family B polymerases that bind their co-factors at the C terminus of the thumb domain. The VACV E9 structure also permits rationalization of polymerase inhibitor resistance mutations when compared with the closely related eukaryotic polymerase delta–DNA complex. The catalytic subunit E9 of the vaccinia virus DNA polymerase forms a functional polymerase holoenzyme by interacting with the heterodimeric processivity factor A20/D4. Here the authors present the structure of full-length E9 and show that an insertion within its palm domain binds A20, in a mode different from other family B polymerases.
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Affiliation(s)
- Nicolas Tarbouriech
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Corinne Ducournau
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, BP 73, 91223, Brétigny-sur-Orge Cedex, France
| | - Stephanie Hutin
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Philippe J Mas
- Integrated Structural Biology Grenoble (ISBG) CNRS, CEA, Université Grenoble Alpes, EMBL, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Petr Man
- BioCeV-Institute of Microbiology, Czech Academy of Sciences, Prumyslova 595, 252 50, Vestec, Czech Republic.,Faculty of Science, Charles University, Hlavova 8, 128 43, Prague 2, Czech Republic
| | - Eric Forest
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Darren J Hart
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Christophe N Peyrefitte
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, BP 73, 91223, Brétigny-sur-Orge Cedex, France.,Emerging Pathogens Laboratory, Fondation Mérieux, 21 Avenue Tony Garnier, 69007, Lyon, France
| | - Wim P Burmeister
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CNRS, CEA, 71 Avenue des Martyrs, 38042, Grenoble, France
| | - Frédéric Iseni
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, BP 73, 91223, Brétigny-sur-Orge Cedex, France.
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17
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Czarnecki MW, Traktman P. The vaccinia virus DNA polymerase and its processivity factor. Virus Res 2017; 234:193-206. [PMID: 28159613 DOI: 10.1016/j.virusres.2017.01.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 01/29/2017] [Indexed: 10/20/2022]
Abstract
Vaccinia virus is the prototypic poxvirus. The 192 kilobase double-stranded DNA viral genome encodes most if not all of the viral replication machinery. The vaccinia virus DNA polymerase is encoded by the E9L gene. Sequence analysis indicates that E9 is a member of the B family of replicative polymerases. The enzyme has both polymerase and 3'-5' exonuclease activities, both of which are essential to support viral replication. Genetic analysis of E9 has identified residues and motifs whose alteration can confer temperature-sensitivity, drug resistance (phosphonoacetic acid, aphidicolin, cytosine arabinsode, cidofovir) or altered fidelity. The polymerase is involved both in DNA replication and in recombination. Although inherently distributive, E9 gains processivity by interacting in a 1:1 stoichiometry with a heterodimer of the A20 and D4 proteins. A20 binds to both E9 and D4 and serves as a bridge within the holoenzyme. The A20/D4 heterodimer has been purified and can confer processivity on purified E9. The interaction of A20 with D4 is mediated by the N'-terminus of A20. The D4 protein is an enzymatically active uracil DNA glycosylase. The DNA-scanning activity of D4 is proposed to keep the holoenzyme tethered to the DNA template but allow polymerase translocation. The crystal structure of D4, alone and in complex with A201-50 and/or DNA has been solved. Screens for low molecular weight compounds that interrupt the A201-50/D4 interface have yielded hits that disrupt processive DNA synthesis in vitro and/or inhibit plaque formation. The observation that an active DNA repair enzyme is an integral part of the holoenzyme suggests that DNA replication and repair may be coupled.
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Affiliation(s)
- Maciej W Czarnecki
- Departments of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, United States; Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI 53226, United States
| | - Paula Traktman
- Departments of Biochemistry & Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, United States; Departments of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC 29425, United States; Departments of the Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425, United States; Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI 53226, United States.
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18
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Nuth M, Guan H, Ricciardi RP. A Conserved Tripeptide Sequence at the C Terminus of the Poxvirus DNA Processivity Factor D4 Is Essential for Protein Integrity and Function. J Biol Chem 2016; 291:27087-27097. [PMID: 27836975 DOI: 10.1074/jbc.m116.761908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/11/2016] [Indexed: 12/27/2022] Open
Abstract
Vaccinia virus (VACV) is a poxvirus, and the VACV D4 protein serves both as a uracil-DNA glycosylase and as an essential component required for processive DNA synthesis. The VACV A20 protein has no known catalytic function itself but associates with D4 to form the D4-A20 heterodimer that functions as the poxvirus DNA processivity factor. The heterodimer enables the DNA polymerase to efficiently synthesize extended strands of DNA. Upon characterizing the interaction between D4 and A20, we observed that the C terminus of D4 is susceptible to perturbation. Further analysis demonstrated that a conserved hexapeptide stretch at the extreme C terminus of D4 is essential for maintaining protein integrity, as assessed by its requirement for the production of soluble recombinant protein that is functional in processive DNA synthesis. From the known crystal structures of D4, the C-terminal hexapeptide is shown to make intramolecular contact with residues spanning the inner core of the protein. Our mutational analysis revealed that a tripeptide motif (215GFI217) within the hexapeptide comprises apparent residues necessary for the contact. Prediction of protein disorder identified the hexapeptide and several regions upstream of Gly215 that comprise residues of the interface surfaces of the D4-A20 heterodimer. Our study suggests that 215GFI217 anchors these potentially dynamic upstream regions of the protein to maintain protein integrity. Unlike uracil-DNA glycosylases from diverse sources, where the C termini are disordered and do not form comparable intramolecular contacts, this feature may be unique to orthopoxviruses.
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Affiliation(s)
- Manunya Nuth
- From the Department of Microbiology, School of Dental Medicine and
| | - Hancheng Guan
- From the Department of Microbiology, School of Dental Medicine and
| | - Robert P Ricciardi
- From the Department of Microbiology, School of Dental Medicine and .,the Abramson Cancer Center, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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19
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Schormann N, Zhukovskaya N, Bedwell G, Nuth M, Gillilan R, Prevelige PE, Ricciardi RP, Banerjee S, Chattopadhyay D. Poxvirus uracil-DNA glycosylase-An unusual member of the family I uracil-DNA glycosylases. Protein Sci 2016; 25:2113-2131. [PMID: 27684934 DOI: 10.1002/pro.3058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 11/07/2022]
Abstract
Uracil-DNA glycosylases are ubiquitous enzymes, which play a key role repairing damages in DNA and in maintaining genomic integrity by catalyzing the first step in the base excision repair pathway. Within the superfamily of uracil-DNA glycosylases family I enzymes or UNGs are specific for recognizing and removing uracil from DNA. These enzymes feature conserved structural folds, active site residues and use common motifs for DNA binding, uracil recognition and catalysis. Within this family the enzymes of poxviruses are unique and most remarkable in terms of amino acid sequences, characteristic motifs and more importantly for their novel non-enzymatic function in DNA replication. UNG of vaccinia virus, also known as D4, is the most extensively characterized UNG of the poxvirus family. D4 forms an unusual heterodimeric processivity factor by attaching to a poxvirus-specific protein A20, which also binds to the DNA polymerase E9 and recruits other proteins necessary for replication. D4 is thus integrated in the DNA polymerase complex, and its DNA-binding and DNA scanning abilities couple DNA processivity and DNA base excision repair at the replication fork. The adaptations necessary for taking on the new function are reflected in the amino acid sequence and the three-dimensional structure of D4. An overview of the current state of the knowledge on the structure-function relationship of D4 is provided here.
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Affiliation(s)
- Norbert Schormann
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Natalia Zhukovskaya
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Gregory Bedwell
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Manunya Nuth
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Richard Gillilan
- MacCHESS (Macromolecular Diffraction Facility at CHESS) Cornell University, Ithaca, New York, 14853
| | - Peter E Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294
| | - Robert P Ricciardi
- Department of Microbiology, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104.,Abramson Cancer Center, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, 19104
| | - Surajit Banerjee
- Department of Chemistry and Chemical Biology, Cornell University, and NE-CAT, Argonne, Illinois, 60439
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20
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Contesto-Richefeu C, Tarbouriech N, Brazzolotto X, Burmeister WP, Peyrefitte CN, Iseni F. Structural analysis of point mutations at the Vaccinia virus A20/D4 interface. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2016; 72:687-91. [PMID: 27599859 DOI: 10.1107/s2053230x16011778] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/19/2016] [Indexed: 01/10/2023]
Abstract
The Vaccinia virus polymerase holoenzyme is composed of three subunits: E9, the catalytic DNA polymerase subunit; D4, a uracil-DNA glycosylase; and A20, a protein with no known enzymatic activity. The D4/A20 heterodimer is the DNA polymerase cofactor, the function of which is essential for processive DNA synthesis. The recent crystal structure of D4 bound to the first 50 amino acids of A20 (D4/A201-50) revealed the importance of three residues, forming a cation-π interaction at the dimerization interface, for complex formation. These are Arg167 and Pro173 of D4 and Trp43 of A20. Here, the crystal structures of the three mutants D4-R167A/A201-50, D4-P173G/A201-50 and D4/A201-50-W43A are presented. The D4/A20 interface of the three structures has been analysed for atomic solvation parameters and cation-π interactions. This study confirms previous biochemical data and also points out the importance for stability of the restrained conformational space of Pro173. Moreover, these new structures will be useful for the design and rational improvement of known molecules targeting the D4/A20 interface.
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Affiliation(s)
- Céline Contesto-Richefeu
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, BP 73, 91223 Brétigny-sur-Orge CEDEX, France
| | - Nicolas Tarbouriech
- Institut de Biologie Structurale, CEA, CNRS, Université Grenoble Alpes, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Xavier Brazzolotto
- Département de Toxicologie et Risques Chimiques, Institut de Recherche Biomédicale des Armées, BP 73, 91223 Brétigny-sur-Orge CEDEX, France
| | - Wim P Burmeister
- Institut de Biologie Structurale, CEA, CNRS, Université Grenoble Alpes, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Christophe N Peyrefitte
- Emerging Pathogens Laboratory, Fondation Mérieux, 21 Avenue Tony Garnier, 69007 Lyon, France
| | - Frédéric Iseni
- Unité de Virologie, Institut de Recherche Biomédicale des Armées, BP 73, 91223 Brétigny-sur-Orge CEDEX, France
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21
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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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22
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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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Schormann N, Ricciardi R, Chattopadhyay D. Uracil-DNA glycosylases-structural and functional perspectives on an essential family of DNA repair enzymes. Protein Sci 2014; 23:1667-85. [PMID: 25252105 DOI: 10.1002/pro.2554] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 09/16/2014] [Indexed: 12/26/2022]
Abstract
Uracil-DNA glycosylases (UDGs) are evolutionarily conserved DNA repair enzymes that initiate the base excision repair pathway and remove uracil from DNA. The UDG superfamily is classified into six families based on their substrate specificity. This review focuses on the family I enzymes since these are the most extensively studied members of the superfamily. The structural basis for substrate specificity and base recognition as well as for DNA binding, nucleotide flipping and catalytic mechanism is discussed in detail. Other topics include the mechanism of lesion search and molecular mimicry through interaction with uracil-DNA glycosylase inhibitors. The latest studies and findings detailing structure and function in the UDG superfamily are presented.
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Affiliation(s)
- N Schormann
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, 35294
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A novel target and approach for identifying antivirals against molluscum contagiosum virus. Antimicrob Agents Chemother 2014; 58:7383-9. [PMID: 25267668 DOI: 10.1128/aac.03660-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The dermatological disease molluscum contagiosum (MC) presents as lesions restricted solely to the skin. The poxvirus molluscum contagiosum virus (MCV) is responsible for this skin disease that is easily transmitted through casual contact among all populations, with greater frequency in children and immunosuppressed individuals. In addition, sexual transmission of MCV in adolescents and adults is a health concern. Although the skin lesions ultimately resolve in immunocompetent individuals, they can persist for extended periods, be painful, and result in scarring. Treatment is problematic, and there is no drug that specifically targets MCV. The inability of MCV to propagate in cell culture has impeded drug development. To overcome these barriers, we integrated three new developments. First, we identified a new MCV drug target (mD4) that is essential for processive DNA synthesis in vitro. Second, we discovered a small chemical compound that binds to mD4 and prevents DNA synthesis in vitro. Third, and most significant, we engineered a hybrid vaccinia virus (mD4-VV) in which the natural vaccinia D4 (vD4) gene is replaced by the mD4 target gene. This hybrid virus is dependent on mD4 for viral growth in culture and is inhibited by the small compound. This target system provides, for the first time, a platform and approach for the discovery and evaluation of new therapeutics that can be used to treat MC.
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