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Wu YC, Lai HX, Li JM, Fung KM, Tseng TS. Discovery of a potent inhibitor, D-132, targeting AsfvPolX, via protein-DNA complex-guided pharmacophore screening and in vitro molecular characterizations. Virus Res 2024; 344:199359. [PMID: 38521505 PMCID: PMC10995865 DOI: 10.1016/j.virusres.2024.199359] [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: 01/15/2024] [Revised: 03/15/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024]
Abstract
The heightened transmissibility and capacity of African swine fever virus (ASFV) induce fatal diseases in domestic pigs and wild boars, posing significant economic repercussions and global threats. Despite extensive research efforts, the development of potent vaccines or treatments for ASFV remains a persistent challenge. Recently, inhibiting the AsfvPolX, a key DNA repair enzyme, emerges as a feasible strategy to disrupt viral replication and control ASFV infections. In this study, a comprehensive approach involving pharmacophore-based inhibitor screening, coupled with biochemical and biophysical analyses, were implemented to identify, characterize, and validate potential inhibitors targeting AsfvPolX. The constructed pharmacophore model, Phar-PolX-S, demonstrated efficacy in identifying a potent inhibitor, D-132 (IC50 = 2.8 ± 0.2 µM), disrupting the formation of the AsfvPolX-DNA complex. Notably, D-132 exhibited strong binding to AsfvPolX (KD = 6.9 ± 2.2 µM) through a slow-on-fast-off binding mechanism. Employing molecular modeling, it was elucidated that D-132 predominantly binds in-between the palm and finger domains of AsfvPolX, with crucial residues (R42, N48, Q98, E100, F102, and F116) identified as hotspots for structure-based inhibitor optimization. Distinctively characterized by a 1,2,5,6-tetrathiocane with modifications at the 3 and 8 positions involving ethanesulfonates, D-132 holds considerable promise as a lead compound for the development of innovative agents to combat ASFV infections.
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Affiliation(s)
- Yi-Chen Wu
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40202, Taiwan
| | - Hui-Xiang Lai
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40202, Taiwan
| | - Ji-Min Li
- Institute of Precision Medicine, College of Medicine, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan; Center of Excellence for Metabolic Associated Fatty Liver Disease, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | - Kit-Man Fung
- Biomedical Translation Research Center (BioTReC), Academia Sinica, Taipei, 11529, Taiwan
| | - Tien-Sheng Tseng
- Institute of Molecular Biology, National Chung Hsing University, Taichung, 40202, Taiwan.
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Lad SB, Upadhyay M, Thorat P, Nair D, Moseley GW, Srivastava S, Pradeepkumar PI, Kondabagil K. Biochemical Reconstitution of the Mimiviral Base Excision Repair Pathway. J Mol Biol 2023; 435:168188. [PMID: 37380013 DOI: 10.1016/j.jmb.2023.168188] [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: 02/05/2023] [Revised: 06/14/2023] [Accepted: 06/20/2023] [Indexed: 06/30/2023]
Abstract
Viruses are believed to be the obligate intracellular parasites that only carry genes essential for infecting and hijacking the host cell machinery. However, a recently discovered group of viruses belonging to the phylum nucleocytovirocota, also known as the nucleo-cytoplasmic large DNA viruses (NCLDVs), possess a number of genes that code for proteins predicted to be involved in metabolism, and DNA replication, and repair. In the present study, first, using proteomics of viral particles, we show that several proteins required for the completion of the DNA base excision repair (BER) pathway are packaged within the virions of Mimivirus as well as related viruses while they are absent from the virions of Marseillevirus and Kurlavirus that are NCLDVs with smaller genomes. We have thoroughly characterized three putative base excision repair enzymes from Mimivirus, a prototype NCLDV and successfully reconstituted the BER pathway using the purified recombinant proteins. The mimiviral uracil-DNA glycosylase (mvUDG) excises uracil from both ssDNA and dsDNA, a novel finding contrary to earlier studies. The putative AP-endonuclease (mvAPE) specifically cleaves at the abasic site created by the glycosylase while also exhibiting the 3'-5' exonuclease activity. The Mimivirus polymerase X protein (mvPolX) can bind to gapped DNA substrates and perform single nucleotide gap-filling followed by downstream strand displacement. Furthermore, we show that when reconstituted in vitro, mvUDG, mvAPE, and mvPolX function cohesively to repair a uracil-containing DNA predominantly by long patch BER and together, may participate in the BER pathway during the early phase of Mimivirus life-cycle.
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Affiliation(s)
- Shailesh B Lad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India. https://twitter.com/shailesh2603
| | - Monica Upadhyay
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India; Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia. https://twitter.com/upadhyaymonica
| | - Pracheta Thorat
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Divya Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Gregory W Moseley
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India. https://twitter.com/sanjeeva_IITB
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India. https://twitter.com/pradeepkumarpi
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India.
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Choi J, Lee H, Cho S, Choi Y, Pham TX, Huynh TTX, Lim YS, Hwang SB. Polygalic acid inhibits african swine fever virus polymerase activity: findings from machine learning and in vitro testing. J Comput Aided Mol Des 2023:10.1007/s10822-023-00520-6. [PMID: 37452977 DOI: 10.1007/s10822-023-00520-6] [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: 05/12/2023] [Accepted: 07/06/2023] [Indexed: 07/18/2023]
Abstract
African swine fever virus (ASFV), an extremely contagious virus with high mortality rates, causes severe hemorrhagic viral disease in both domestic and wild pigs. Fortunately, ASFV cannot be transmitted from pigs to humans. However, ongoing ASFV outbreaks could have severe economic consequences for global food security. Although ASFV was discovered several years ago, no vaccines or treatments are commercially available yet; therefore, the identification of new anti-ASFV drugs is urgently warranted. Using molecular docking and machine learning, we have previously identified pentagastrin, cangrelor, and fostamatinib as potential antiviral drugs against ASFV. Here, using machine learning combined with docking simulations, we identified natural products with a high affinity for AsfvPolX proteins. We selected five natural products (NPs) that are located close in chemical space to the six known natural flavonoids that possess anti-ASFV activity. Polygalic acid markedly reduced AsfvPolX polymerase activity in a dose-dependent manner. We propose an efficient protocol for identifying NPs as potential antiviral drugs by identifying chemical spaces containing high-affinity binders against ASFV in NP databases.
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Affiliation(s)
- Jiwon Choi
- College of Pharmacy, Dongduk Women's University, Seoul, 02748, Republic of Korea.
| | - Hyundo Lee
- College of Pharmacy, Dongduk Women's University, Seoul, 02748, Republic of Korea
| | - Soyoung Cho
- College of Pharmacy, Dongduk Women's University, Seoul, 02748, Republic of Korea
| | - Yorim Choi
- College of Pharmacy, Dongduk Women's University, Seoul, 02748, Republic of Korea
| | - Thuy X Pham
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Trang T X Huynh
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54596, Republic of Korea
| | - Yun-Sook Lim
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54596, Republic of Korea.
| | - Soon B Hwang
- Laboratory of RNA Viral Diseases, Korea Zoonosis Research Institute, Jeonbuk National University, Iksan, 54596, Republic of Korea
- Ilsong Institute of Life Science, Hallym University, Seoul, 07247, Republic of Korea
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Genome Plasticity of African Swine Fever Virus: Implications for Diagnostics and Live-Attenuated Vaccines. Pathogens 2022; 11:pathogens11020145. [PMID: 35215087 PMCID: PMC8875878 DOI: 10.3390/pathogens11020145] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 01/27/2023] Open
Abstract
African swine fever (ASF) is a highly contagious transboundary viral hemorrhagic disease of domestic and wild pigs presenting a significant threat to the global swine industry. Following its introduction in Caucasus, Georgia, in 2007, the genome of the genotype II of African swine fever virus (ASFV) strain Georgia-07 and its derivatives accumulated significant mutations, resulting in the emergence of genetic variants within short epidemiological timescales as it spreads and infects different hosts in diverse ecosystems, causing outbreaks in Europe, South Asia, South East Asia and the Caribbean. This suggests that ASFV, with a comparatively large and complex DNA genome, is susceptible to genetic mutations including deletions and that although the virus is environmentally stable, it is genetically unstable. This has implications for the development of vaccines and diagnostic tests for disease detection and surveillance. Analysis of the ASFV genome revealed recombination hotspots, which in double-stranded DNA (dsDNA) viruses represent key drivers of genetic diversity. The ability of pox virus, a dsDNA virus with a genome complexity similar to ASFV, regaining virulence following the deletion of a virulence gene via gene amplification, coupled with the recent emergence and spread of live-attenuated ASFV vaccine strains causing disease and death in pigs in China, raise legitimate concerns around the use of live-attenuated ASFV vaccines in non-endemic regions to control the potential introduction. Further research into the risk of using live-attenuated ASFV in non-endemic regions is highly needed.
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Prediction of African Swine Fever Virus Inhibitors by Molecular Docking-Driven Machine Learning Models. Molecules 2021; 26:molecules26123592. [PMID: 34208385 PMCID: PMC8231271 DOI: 10.3390/molecules26123592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/23/2021] [Accepted: 06/09/2021] [Indexed: 01/31/2023] Open
Abstract
African swine fever virus (ASFV) causes a highly contagious and severe hemorrhagic viral disease with high mortality in domestic pigs of all ages. Although the virus is harmless to humans, the ongoing ASFV epidemic could have severe economic consequences for global food security. Recent studies have found a few antiviral agents that can inhibit ASFV infections. However, currently, there are no vaccines or antiviral drugs. Hence, there is an urgent need to identify new drugs to treat ASFV. Based on the structural information data on the targets of ASFV, we used molecular docking and machine learning models to identify novel antiviral agents. We confirmed that compounds with high affinity present in the region of interest belonged to subsets in the chemical space using principal component analysis and k-means clustering in molecular docking studies of FDA-approved drugs. These methods predicted pentagastrin as a potential antiviral drug against ASFVs. Finally, it was also observed that the compound had an inhibitory effect on AsfvPolX activity. Results from the present study suggest that molecular docking and machine learning models can play an important role in identifying potential antiviral drugs against ASFVs.
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Chen Y, Chen X, Huang Q, Shao Z, Gao Y, Li Y, Yang C, Liu H, Li J, Wang Q, Ma J, Zhang YZ, Gu Y, Gan J. A unique DNA-binding mode of African swine fever virus AP endonuclease. Cell Discov 2020; 6:13. [PMID: 32194979 PMCID: PMC7076025 DOI: 10.1038/s41421-020-0146-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/13/2020] [Indexed: 12/31/2022] Open
Abstract
African swine fever virus (ASFV) is highly contagious and can cause lethal disease in pigs. ASFV is primarily replicated in the cytoplasm of pig macrophages, which is oxidative and caused constant damage to ASFV genome. ASFV AP endonuclease (AsfvAP) catalyzes DNA cleavage reaction at the abasic site and is a key enzyme of ASFV base excision repair (BER) system. Although it plays an essential role in ASFV survival in host cells, the basis underlying substrate binding and cleavage by AsfvAP remains unclear. Here, we reported the structural and functional studies of AsfvAP, showing that AsfvAP adopts a novel DNA-binding mode distinct from other APs. AsfvAP possesses many unique structural features, including one narrower nucleotide-binding pocket at the active site, the C16-C20 disulfide bond-containing region, and histidine-rich loop. As indicated by our mutagenesis, in vitro binding and cleavage assays, these features are important for AsfvAP to suit the acidic and oxidative environment. Owing to their functional importance, these unique features could serve as targets for designing small molecule inhibitors that could disrupt the repair process of ASFV genome and help fight against this deadly virus in the future.
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Affiliation(s)
- Yiqing Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Xi Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Qi Huang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Zhiwei Shao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Yanqing Gao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Yangyang Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Chun Yang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Hehua Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 200237 Shanghai, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
| | - Yong-Zhen Zhang
- Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, 102206 Beijing, China
| | - Yijun Gu
- National Center for Protein Science Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, 201210 Shanghai, China
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Shanghai Public Health Clinical Center, School of Life Sciences, Fudan University, 200438 Shanghai, China
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Farlow J, Donduashvili M, Kokhreidze M, Kotorashvili A, Vepkhvadze NG, Kotaria N, Gulbani A. Intra-epidemic genome variation in highly pathogenic African swine fever virus (ASFV) from the country of Georgia. Virol J 2018; 15:190. [PMID: 30547827 PMCID: PMC6295034 DOI: 10.1186/s12985-018-1099-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 11/21/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND African swine fever virus (ASFV) causes an acute hemorrhagic infection in suids with a mortality rate of up to 100%. No vaccine is available and the potential for catastrophic disease in Europe remains elevated due to the ongoing ASF epidemic in Russia and Baltic countries. To date, intra-epidemic whole-genome variation for ASFV has not been reported. To provide a more comprehensive baseline for genetic variation early in the ASF outbreak, we sequenced two Georgian ASFV samples, G-2008/1 and G-2008/2, derived from domestic porcine blood collected in 2008. METHODS Genomic DNA was extracted directly from low-volume ASFV PCR-positive porcine blood samples and subjected to next generation sequencing on the Illumina Miseq platform. De novo and mapped sequence assemblies were performed using CLCBio software. Genomic illustrations, sequence alignments and assembly figures were generated using Geneious v10.2.4. Sequence repeat architecture was analyzed using DNASTAR GeneQuest 14.1.0. RESULTS The G-2008/1 and G-2008/2 genomes were distinguished from each other by coding changes in seven genes, including MGF 110-1 L, X69R, MGF 505-10R, EP364R, H233R, E199L, and MGF 360-21R in addition to eight homopolymer tract variations. The 2008/2 genome possessed a novel allele state at a previously undescribed intergenic repeat locus between genes C315R and C147L. The C315R/C147L locus represents the earliest observed variable repeat sequence polymorphism reported among isolates from this epidemic. No sequence variation was observed in conventional ASFV subtyping markers. The two genomes exhibited complete collinearity and identical gene content with the Georgia 2007/1 reference genome. Approximately 56 unique homopolymer A/T-tract variations were identified that were unique to the Georgia 2007/1 genome. In both 2008 genomes, within-sample sequence read heterogeneity was evident at six homopolymeric G/C-tracts confined to the known hypervariable ~ 7 kb region in the left terminal region of the genome. CONCLUSIONS This is the first intra-epidemic comparative genomic analysis reported for ASFV and provides insight into the intra-epidemic microevolution of ASFV. The genomes reported here, in addition to the G-2007/1 genome, provide an early baseline for future genome-level comparisons and epidemiological tracing efforts.
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Affiliation(s)
- Jason Farlow
- Farlow Scientific Consulting Company, LLC, Lewiston, UT 84320 USA
| | | | | | - Adam Kotorashvili
- Richard G. Lugar Center for Public Health Research at the National Center for Disease Control (NCDC), Tbilisi, Georgia
| | | | - Nato Kotaria
- Richard G. Lugar Center for Public Health Research at the National Center for Disease Control (NCDC), Tbilisi, Georgia
| | - Ana Gulbani
- Laboratory of the Ministry of Agriculture, Tbilisi, Georgia
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Chen Y, Zhang J, Liu H, Gao Y, Li X, Zheng L, Cui R, Yao Q, Rong L, Li J, Huang Z, Ma J, Gan J. Unique 5'-P recognition and basis for dG:dGTP misincorporation of ASFV DNA polymerase X. PLoS Biol 2017; 15:e1002599. [PMID: 28245220 PMCID: PMC5330486 DOI: 10.1371/journal.pbio.1002599] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 01/20/2017] [Indexed: 12/22/2022] Open
Abstract
African swine fever virus (ASFV) can cause highly lethal disease in pigs and is becoming a global threat. ASFV DNA Polymerase X (AsfvPolX) is the most distinctive DNA polymerase identified to date; it lacks two DNA-binding domains (the thumb domain and 8-KD domain) conserved in the homologous proteins. AsfvPolX catalyzes the gap-filling reaction during the DNA repair process of the ASFV virus genome; it is highly error prone and plays an important role during the strategic mutagenesis of the viral genome. The structural basis underlying the natural substrate binding and the most frequent dG:dGTP misincorporation of AsfvPolX remain poorly understood. Here, we report eight AsfvPolX complex structures; our structures demonstrate that AsfvPolX has one unique 5′-phosphate (5′-P) binding pocket, which can favor the productive catalytic complex assembly and enhance the dGTP misincorporation efficiency. In combination with mutagenesis and in vitro catalytic assays, our study also reveals the functional roles of the platform His115-Arg127 and the hydrophobic residues Val120 and Leu123 in dG:dGTP misincorporation and can provide information for rational drug design to help combat ASFV in the future. The African swine fever virus genome encodes the most distinctive DNA polymerase known, AsfvPolX. A structural and functional study reveals the basis for its strategic error-prone misincorporation of dGTP opposite a dG residue. African swine fever virus (ASFV) is highly contagious and can cause lethal disease in pigs. AsfvPolX catalyzes the gap-filling reaction during the DNA repair process of the virus genome; it is highly error prone and plays an important role in the strategic mutagenesis of the virus genome. Unlike the homologous proteins, AsfvPolX has several unique structural features, including a 5′-P binding pocket, a His115-Arg127 platform, and hydrophobic residues Val120 and Leu123, which can all affect the catalytic efficiency (especially during dG:dGTP misincorporation) of AsfvPolX. These properties, especially the 5′-P binding pocket, provide an ideal structural basis for designing of small molecules, which can specifically inhibit the activity of AsfvPolX and disrupt the DNA repair process of the ASFV genome.
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Affiliation(s)
- Yiqing Chen
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Hehua Liu
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Yanqing Gao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Xuhang Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Lina Zheng
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Ruixue Cui
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Qingqing Yao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Liang Rong
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
| | - Jixi Li
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhen Huang
- Department of Chemistry, Georgia State University, Atlanta, Georgia, United States of America
- College of Life Sciences, Sichuan University, Chengdu, China
- * E-mail: (ZH); (JBM); (JHG)
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China
- * E-mail: (ZH); (JBM); (JHG)
| | - Jianhua Gan
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
- * E-mail: (ZH); (JBM); (JHG)
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Redrejo-Rodríguez M, Salas ML. Repair of base damage and genome maintenance in the nucleo-cytoplasmic large DNA viruses. Virus Res 2013; 179:12-25. [PMID: 24184318 DOI: 10.1016/j.virusres.2013.10.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 10/21/2013] [Accepted: 10/21/2013] [Indexed: 11/27/2022]
Abstract
Among the DNA viruses, the so-called nucleo-cytoplasmic large DNA viruses (NCLDV) constitute a monophyletic group that currently consists of seven families of viruses infecting a very broad variety of eukaryotes, from unicellular marine protists to humans. Many recent papers have analyzed the sequence and structure of NCLDV genomes and their phylogeny, providing detailed analysis about their genomic structure and evolutionary history and proposing their inclusion in a new viral order named Megavirales that, according to some authors, should be considered as a fourth domain of life, aside from Bacteria, Archaea and Eukarya. The maintenance of genetic information protected from environmental attacks and mutations is essential not only for the survival of cellular organisms but also viruses. In cellular organisms, damaged DNA bases are removed in two major repair pathways: base excision repair (BER) and nucleotide incision repair (NIR) that constitute the major pathways responsible for repairing most endogenous base lesions and abnormal bases in the genome by precise repair procedures. Like cells, many NCLDV encode proteins that might constitute viral DNA repair pathways that would remove damages through BER/NIR pathways. However, the molecular mechanisms and, specially, the biological roles of those viral repair pathways have not been deeply addressed in the literature so far. In this paper, we review viral-encoded BER proteins and the genetic and biochemical data available about them. We propose and discuss probable viral-encoded DNA repair mechanisms and pathways, as compared with the functional and molecular features of known homologs proteins.
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Affiliation(s)
- Modesto Redrejo-Rodríguez
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - María L Salas
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas-Universidad Autónoma de Madrid, 28049 Madrid, Spain
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Involvement of the reparative DNA polymerase Pol X of African swine fever virus in the maintenance of viral genome stability in vivo. J Virol 2013; 87:9780-7. [PMID: 23824796 DOI: 10.1128/jvi.01173-13] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The function of the African swine fever virus (ASFV) reparative DNA polymerase, Pol X, was investigated in the context of virus infection. Pol X is a late structural protein that localizes at cytoplasmic viral factories during DNA replication. Using an ASFV deletion mutant lacking the Pol X gene, we have shown that Pol X is not required for virus growth in Vero cells or swine macrophages under one-step growth conditions. However, at a low multiplicity of infection, when multiple rounds of replication occur, the growth of the mutant virus is impaired in swine macrophages but not in Vero cells, suggesting that Pol X is needed to repair the accumulated DNA damage. The replication of the mutant virus in Vero cells presents sensitivity to oxidative damage, and mutational analysis of viral DNA shows that deletion of Pol X results in an increase in the mutation frequency in macrophages. Therefore, our data reveal a biological role for ASFV Pol X in the context of the infected cell in the preservation of viral genetic information.
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Dixon LK, Chapman DAG, Netherton CL, Upton C. African swine fever virus replication and genomics. Virus Res 2012; 173:3-14. [PMID: 23142553 DOI: 10.1016/j.virusres.2012.10.020] [Citation(s) in RCA: 418] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Revised: 10/19/2012] [Accepted: 10/19/2012] [Indexed: 01/03/2023]
Abstract
African swine fever virus (ASFV) is a large icosahedral DNA virus which replicates predominantly in the cytoplasm of infected cells. The ASFV double-stranded DNA genome varies in length from about 170 to 193 kbp depending on the isolate and contains between 150 and 167 open reading frames. These are closely spaced and read from both DNA strands. The virus genome termini are covalently closed by imperfectly base-paired hairpin loops that are present in two forms that are complimentary and inverted with respect to each other. Adjacent to the termini are inverted arrays of different tandem repeats. Head to head concatemeric genome replication intermediates have been described. A similar mechanism of replication to Poxviruses has been proposed for ASFV. Virus genome transcription occurs independently of the host RNA polymerase II and virus particles contain all of the enzymes and factors required for early gene transcription. DNA replication begins in perinuclear factory areas about 6h post-infection although an earlier stage of nuclear DNA synthesis has been reported. The virus genome encodes enzymes required for transcription and replication of the virus genome and virion structural proteins. Enzymes that are involved in a base excision repair pathway may be an adaptation to enable virus replication in the oxidative environment of the macrophage cytoplasm. Other ASFV genes encode factors involved in evading host defence systems and modulating host cell function. Variation between the genomes of different ASFV isolates is most commonly due to gain or loss of members of multigene families, MGFs 100, 110, 300, 360, 505/530 and family p22. These are located within the left terminal 40kbp and right terminal 20kbp. ASFV is the only member of the Asfarviridae, which is one of the families within the nucleocytoplasmic large DNA virus superfamily.
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Affiliation(s)
- Linda K Dixon
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United Kingdom.
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Redrejo-Rodríguez M, Ishchenko AA, Saparbaev MK, Salas ML, Salas J. African swine fever virus AP endonuclease is a redox-sensitive enzyme that repairs alkylating and oxidative damage to DNA. Virology 2009; 390:102-9. [PMID: 19464038 PMCID: PMC2958311 DOI: 10.1016/j.virol.2009.04.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2009] [Revised: 04/10/2009] [Accepted: 04/29/2009] [Indexed: 11/26/2022]
Abstract
African swine fever virus (ASFV) encodes an AP endonuclease (pE296R) which is essential for virus growth in swine macrophages. We show here that the DNA repair functions of pE296R (AP endonucleolytic, 3′ → 5′ exonuclease, 3′-diesterase and nucleotide incision repair (NIR) activities) and DNA binding are inhibited by reducing agents. Protein pE296R contains one intramolecular disulfide bond, whose disruption by reducing agents might perturb the interaction of the viral AP endonuclease with the DNA substrate. The characterization of the 3′ → 5′ exonuclease and 3′-repair diesterase activities of pE296R indicates that it has strong preference for mispaired and oxidative base lesions at the 3′-termini of single-strand breaks. Finally, the viral protein protects against DNA damaging agents in both prokaryotic and eukaryotic cells, emphasizing its importance in vivo. The biochemical and genetic properties of ASFV AP endonuclease are consistent with the repair of DNA damage generated by the genotoxic intracellular environment of the host macrophage.
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Affiliation(s)
- Modesto Redrejo-Rodríguez
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas/Universidad Autónoma de Madrid), Universidad Autónoma de Madrid, C/Nicolás Cabrera 1, 28049 Madrid, Spain
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13
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Abstract
African swine fever virus (ASFV) is a large, intracytoplasmically-replicating DNA arbovirus and the sole member of the family Asfarviridae. It is the etiologic agent of a highly lethal hemorrhagic disease of domestic swine and therefore extensively studied to elucidate the structures, genes, and mechanisms affecting viral replication in the host, virus-host interactions, and viral virulence. Increasingly apparent is the complexity with which ASFV replicates and interacts with the host cell during infection. ASFV encodes novel genes involved in host immune response modulation, viral virulence for domestic swine, and in the ability of ASFV to replicate and spread in its tick vector. The unique nature of ASFV has contributed to a broader understanding of DNA virus/host interactions.
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Affiliation(s)
- E R Tulman
- Department of Pathobiology and Veterinary Science, Center of Excellence for Vaccine Research, University of Connecticut, Storrs 06269, USA.
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Sampoli Benítez BA, Arora K, Balistreri L, Schlick T. Mismatched base-pair simulations for ASFV Pol X/DNA complexes help interpret frequent G*G misincorporation. J Mol Biol 2008; 384:1086-97. [PMID: 18955064 DOI: 10.1016/j.jmb.2008.10.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2008] [Revised: 10/02/2008] [Accepted: 10/06/2008] [Indexed: 10/21/2022]
Abstract
DNA polymerase X (pol X) from the African swine fever virus is a 174-amino-acid repair polymerase that likely participates in a viral base excision repair mechanism, characterized by low fidelity. Surprisingly, pol X's insertion rate of the G*G mispair is comparable to that of the four Watson-Crick base pairs. This behavior is in contrast with another X-family polymerase, DNA polymerase beta (pol beta), which inserts G*G mismatches poorly, and has higher DNA repair fidelity. Using molecular dynamics simulations, we previously provided support for an induced-fit mechanism for pol X in the presence of the correct incoming nucleotide. Here, we perform molecular dynamics simulations of pol X/DNA complexes with different incoming incorrect nucleotides in various orientations [C*C, A*G, and G*G (anti) and A*G and G*G (syn)] and compare the results to available kinetic data and prior modeling. Intriguingly, the simulations reveal that the G*G mispair with the incoming nucleotide in the syn configuration undergoes large-scale conformational changes similar to that observed in the presence of correct base pair (G*C). The base pairing in the G*G mispair is achieved via Hoogsteen hydrogen bonding with an overall geometry that is well poised for catalysis. Simulations for other mismatched base pairs show that an intermediate closed state is achieved for the A*G and G*G mispair with the incoming dGTP in anti conformation, while the protein remains near the open conformation for the C*C and the A*G syn mismatches. In addition, catalytic site geometry and base pairing at the nascent template-incoming nucleotide interaction reveal distortions and misalignments that range from moderate for A*G anti to worst for the C*C complex. These results agree well with kinetic data for pol X and provide a structural/dynamic basis to explain, at atomic level, the fidelity of this polymerase compared with other members of the X family. In particular, the more open and pliant active site of pol X, compared to pol beta, allows pol X to accommodate bulkier mismatches such as guanine opposite guanine, while the more structured and organized pol beta active site imposes higher discrimination, which results in higher fidelity. The possibility of syn conformers resonates with other low-fidelity enzymes such as Dpo4 (from the Y family), which readily accommodate oxidative lesions.
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Affiliation(s)
- Benedetta A Sampoli Benítez
- Department of Natural Sciences and Mathematics, Marymount Manhattan College, 221 East 71st Street, New York, NY 10021, USA
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Bandaru V, Zhao X, Newton MR, Burrows CJ, Wallace SS. Human endonuclease VIII-like (NEIL) proteins in the giant DNA Mimivirus. DNA Repair (Amst) 2007; 6:1629-41. [PMID: 17627905 PMCID: PMC2096709 DOI: 10.1016/j.dnarep.2007.05.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2007] [Revised: 05/24/2007] [Accepted: 05/25/2007] [Indexed: 11/28/2022]
Abstract
Endonuclease VIII (Nei), which recognizes and repairs oxidized pyrimidines in the base excision repair (BER) pathway, is sparsely distributed among both the prokaryotes and eukaryotes. Recently, we and others identified three homologs of Escherichia coli endonuclease VIII-like (NEIL) proteins in humans. Here, we report identification of human NEIL homologs in Mimivirus, a giant DNA virus that infects Acanthamoeba. Characterization of the two mimiviral homologs, MvNei1 and MvNei2, showed that they share not only sequence homology but also substrate specificity with the human NEIL proteins, that is, they recognize oxidized pyrimidines in duplex DNA and in bubble substrates and as well show 5'2-deoxyribose-5-phosphate lyase (dRP lyase) activity. However, unlike MvNei1 and the human NEIL proteins, MvNei2 preferentially cleaves oxidized pyrimidines in single stranded DNA forming products with a different end chemistry. Interestingly, opposite base specificity of MvNei1 resembles human NEIL proteins for pyrimidine base damages whereas it resembles E. coli formamidopyrimidine DNA glycosylase (Fpg) for guanidinohydantoin (Gh), an oxidation product of 8-oxoguanine. Finally, a conserved arginine residue in the "zincless finger" motif, previously identified in human NEIL1, is required for the DNA glycosylase activity of MvNei1. Thus, Mimivirus represents the first example of a virus to carry oxidative DNA glycosylases with substrate specificities that resemble human NEIL proteins. Based on the sequence homology to the human NEIL homologs and novel bacterial NEIL homologs identified here, we predict that Mimivirus may have acquired the DNA glycosylases through the host-mediated lateral transfer from either a bacterium or from vertebrates.
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Affiliation(s)
- Viswanath Bandaru
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, Vermont 05405-0068
| | - Xiaobei Zhao
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt lake City, Utah 84112-0850
| | - Michael R. Newton
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt lake City, Utah 84112-0850
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt lake City, Utah 84112-0850
| | - Susan S. Wallace
- Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, Vermont 05405-0068
- Address correspondence to: Susan S. Wallace, Department of Microbiology and Molecular Genetics, The Markey Center for Molecular Genetics, The University of Vermont, Stafford Hall, 95 Carrigan Drive, Burlington, Vermont 05405-0068, Tel. (802) 656-2164; Fax: (802) 656-8749; E-mail:
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Kumar S, Lamarche BJ, Tsai MD. Use of damaged DNA and dNTP substrates by the error-prone DNA polymerase X from African swine fever virus. Biochemistry 2007; 46:3814-25. [PMID: 17335287 DOI: 10.1021/bi061501l] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structural specificity that translesion DNA polymerases often show for a particular class of lesions suggests that the predominant criterion of selection during their evolution has been the capacity for lesion tolerance and that the error-proneness they display when copying undamaged templates may simply be a byproduct of this adaptation. Regardless of selection criteria/evolutionary history, at present both of these properties coexist in these enzymes, and both properties confer a fitness advantage. The repair polymerase, Pol X, encoded by the African swine fever virus (ASFV) is one of the most error-prone polymerases known, leading us to previously hypothesize that it may work in tandem with the exceptionally error-tolerant ASFV DNA ligase to effect viral mutagenesis. Here, for the first time, we test whether the error-proneness of Pol X is coupled with a capacity for lesion tolerance by examining its ability to utilize the types of damaged DNA and dNTP substrates that are expected to be relevant to ASFV. We (i) test Pol X's ability to both incorporate opposite to and extend from ubiquitous oxidative purine (7,8-dihydro-8-oxoguanine), oxidative pyrimidine (5,6-dihydroxy-5,6-dihydrothymine), and noncoding (AP site) lesions, in addition to 5,6-dihydrothymine, (ii) determine the catalytic efficiency and dNTP specificity of Pol X when catalyzing incorporation opposite to, and when extending from, 7,8-dihydro-8-oxoguanine in a template/primer context, and (iii) quantitate Pol X-catalyzed incorporation of the damaged nucleotide 8-oxo-dGTP opposite to undamaged templates in the context of both template/primer and a single-nucleotide gap. Our findings are discussed in light of ASFV biology and the mutagenic DNA repair hypothesis described above.
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Affiliation(s)
- Sandeep Kumar
- Department of Chemistry, The Biophysics Program, The Ohio State University, Columbus, Ohio 43210, USA
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Lamarche BJ, Kumar S, Tsai MD. ASFV DNA polymerse X is extremely error-prone under diverse assay conditions and within multiple DNA sequence contexts. Biochemistry 2007; 45:14826-33. [PMID: 17144676 PMCID: PMC2584803 DOI: 10.1021/bi0613325] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We previously demonstrated that the DNA repair system encoded by the African swine fever virus (ASFV) is both extremely error-prone during the single-nucleotide gap-filling step (catalyzed by ASFV DNA polymerase X) and extremely error-tolerant during the nick-sealing step (catalyzed by ASFV DNA ligase). On the basis of these findings we have suggested that at least some of the diversity known to exist among ASFV isolates may be a consequence of mutagenic DNA repair, wherein damaged nucleotides are replaced with undamaged but incorrect nucleotides by Pol X and the resultant mismatched nicks are sealed by ASFV DNA ligase. Recently, this hypothesis appeared to be discredited by Salas and co-workers [(2003) J. Mol. Biol. 326, 1403-1412], who reported the fidelity of Pol X to be, on average, 2 orders of magnitude higher than what we previously published. In an effort to address this discrepancy and provide a definitive conclusion about the fidelity of Pol X, herein we examine the fidelity of Pol X-catalyzed single-nucleotide gap-filling in both the steady state and the pre-steady state under a diverse array of assay conditions (varying pH and ionic strength) and within different DNA sequence contexts. These studies corroborate our previously published data (demonstrating the low fidelity of Pol X to be independent of assay condition/sequence context), do not reproduce the data of Salas et al., and therefore confirm Pol X to be one of the most error-prone polymerases known. These results are discussed in light of ASFV biology and the mutagenic DNA repair hypothesis described above.
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Affiliation(s)
| | | | - Ming-Daw Tsai
- To whom correspondence should be addressed at the Department of Chemistry [phone: (614) 292-3080; fax: (614) 292-1532; ]
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